committees - cirpeb - Università degli Studi di Napoli Federico II

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Committees
Scientific Committee
Carlo Mealli
ICCOM-CNR, Firenze (AIC president)
Michele Saviano
IBB-CNR, Napoli (Chair)
Luca Bindi
Università degli Studi di Firenze
Giovanni Luca Cascarano
IC-CNR, Bari
Ferdinando Costantino
Università degli Studi di Perugia
Claudio De Rosa
Università degli Studi di Napoli “Federico II”
Marco Milanesio
Università degli Studi del Piemonte Orientale “A.
Avogadro”
Organizing Committee
Attilio Immirzi
Università degli Studi di Salerno (Chair)
Gaetano Guerra
Università degli Studi di Salerno (Co-Chair)
Consiglia Tedesco
Università degli Studi di Salerno (Secretariat)
Ettore Benedetti
Rita Berisio
IBB-CNR, Napoli
Giuseppina De Simone
IBB-CNR, Napoli
Luciana Esposito
IBB-CNR, Napoli
Massimo Moret
Carlo A. Mattia
Università degli Studi di Milano Bicocca
Università degli Studi di Salerno
Paola Paoli
Lelio Mazzarella
Università degli Studi di Firenze
Adrina Zagari
Paola Rizzo
Carlo Pedone
Vincenzo Venditto
Luigi Vitagliano
IBB-CNR, Napoli
Sponsoring and Supporting Institutions
Sponsors and exhibitors
Program
PROGRAM-AT-A-GLANCE
Associazione Italiana di Cristallografia
S unday 20 th S eptember
15:00-16:30
Registration
16:30-17:00
Opening ceremony
17:00-18:00
PL1 The Impact of Synchrotron radiation on the future challenges in
crystallography
Sine Larsen
18:00-18:30
Nardelli Prize Probing molecular conformation and configuration at high pressure
Nicola Casati
18:30-19:20
PL2 - Mammi Prize Il Milione: past and future
Giovanni Luca Cascarano
19:20-19:30
Best Thesis Prize - Award Ceremony
Ilio Miccoli
19:30
Welcome party
21:30
Concert
M onday 21 st S eptember
9:00-10:00
4
PL3 Reconstruction of polar surfaces in crystals. The boundary conditions
imposed by the symmetry of crystal bulk
Marco Rubbo
10:00-10:30
Parallel sessions MS1/MS2
MS1 Weak interactions: the supramolecular chemist's tool kit
MS2 Minerals as a treasure trove for advanced materials
10:30-11:00
Coffee break
11:00-13:00
MS1: Weak interactions: the supramolecular chemist's tool kit
MS2: Minerals as a treasure trove for advanced materials
13:00-14:00
Lunch
14:00-14:30
Commercial Presentations
14:00-15:30
Poster Session
15:00-15:30
Coffee break
15:30-18:00
MS3 Crystal growth: a bridge across many disciplines
MS4 Structure and properties of semicrystalline polymers
18:00-19:00
PL4 Crystallography and polymers
Finizia Auriemma
XXXVIII Congresso Nazionale
PROGRAM-AT-A-GLANCE
T uesday 22 nd S eptember
9:00-10:00
PL5 A roadmap to nanocrystallography
Jan Pieter Abrahams
10:00-10:30
MS5 Biocrystallography for human health
MS6 New advances of powder diffraction in the material sciences
10:30-11:00
Coffee break
11:00-13:00
MS5 Biocrystallography for human health
MS6 New advances of powder diffraction in the material sciences
13:00-14:00
Lunch
14:00-14:30
Commercial Presentations
14:00-15:30
Poster Session
15:00-15:30
Coffee break
15:30-18:00
MS7 Methods and crystallography
18:00-20:00General Assembly
21:00
Social Dinner
W ednesday 23 rd S eptember
9:00-10:00
PL6 Ligand-stabilized metal nanoparticles at the borderline of molecular and
colloidal chemistry
Giuliano Longoni
10:30-11:00
Coffee break
11:00-13:00
MS8 Structure/Properties Relationships in complex molecular systems: the
multi-technique approach
Closing ceremony
5
MICROSYMPOSIA AGENDA
Monday 21st September
MS1: Weak interactions: the supramolecular chemist’s tool kit
Chair P.Paoli
10:00-10:30
KN1 Molecular Electron Density Displacement [MEDD] for Intermolecular
Interactions Investigation
Franco Ugozzoli
11:00-11:30
KN2 Dynamic porous properties of supramolecular networks inspired by halogen
bonding
Pierangelo Metrangolo
11:30-11:50
MS1-OR1 Supramolecular design of functional materials based on metallorganic
wheel-and-axle systems
Alessia Bacchi
11:50-12:10
MS1-OR2 Acetylene adsorption in a calixarene based organic microporouscrystal
12:10-12:30
MS1-OR3 Supramolecular Interactions in Solid State: Tubes, Stripes and Waves in
Inorganic Organic Hybrids with Diphosphinates and Bipyridines
12:30-12:50 MS1-OR4 Cyclen derivative sensors for multiple applications in solution and solid
state
Loredana Erra
Andrea Ienco
Eleonora Macedi
12:50-13:00
Conclusion Remarks
MS2: Minerals as a treasure trove for advanced materials
Chair L. Bindi
10:00-10:30
KN3 Melting of cooperative Jahn-Teller effect in MgxCu1-xCr2O4
11:00-11:30 KN4 HT X-ray diffraction and spectroscopic study of sideronatrite and its relationships
with some analogues
Serena Tarantino
Gennaro Ventruti
11:30-11:50 MS2-OR1 Structural relaxation around Cr3+ in YAlO3-YCrO3 perovskites from electron
absorption spectra
Matteo Ardit
11:50-12:10
MS2-OR2 Compressibility of the Ca2Sb2O7 weberite-like compound: In situ highpressure single-crystal X-ray diffraction study
12:10-12:30 MS2-OR3 Phase transitions induced by solid-solution: the BCa – BMg substitution in
richteritic amphiboles
Laura Chelazzi
Gianluca Iezzi
12:30-12:50
MS2-OR4 Compressibility of serpentine: the case of antigorite
12:50-13:00
Conclusion Remarks
6
Fabrizio Nestola
MS3: Crystal growth: a bridge across many disciplines
Chair M. Moret
15:30-16:00
KN5 Growth of Minerals in Biological Systems
16:00-16:30
KN6 Crystalline organic heterostructures: growth, properties, and perspectives
16:30-16:50
MS3-OR1 On the growth rates, shape and composition of AlGaAs nanowires by Aucatalyzed MOVPE
Giuseppe Falini
Adele Sassella
Paola Prete
16:50-17:10
MS3-OR2 NaCl anomalous mixed crystals grown from water-formamide solutions.
Adsorption-absorption and growth morphology.
Linda Pastero
17:10-17:30 MS3-OR3 Crystallization of soluble proteins suitable for single crystal X-ray
diffraction: the difficult cases
Stefano Mangani
17:30-17:50
MS3-OR4 On the theoretical equilibrium morphology of gypsum (CaSO4.2H2O)
17:50-18:00 Conclusion Remarks
Dino Aquilano
MS4: Structure and properties of semicrystalline polymers
Chair C. De Rosa
15:30-16:00
KN7 Small Angle X-ray Scattering on polymers and nanocomposites: a quantitative
approach
Antonio Marigo
16:00-16:30
KN8 Strategies for crystal structure solution of polymers: examples and some
comments
16:30-16:50
MS4-OR1 Polymeric films with three different orientations of s-PS helical crystalline
phases
Stefano Valdo Meille
Alexandra R. Albunia
16:50-17:10
MS4-OR2 Long range order and self-assembly driven by epitaxial crystallization in
block copolymers
Rocco Di Girolamo
17:10-17:30
MS4-OR3 Strategies for the control of crystallinity in PANI/nanodiamond composites
17:30-17:50
MS4-OR4 Clathrates of syndiotactic polystyrene with guest molecules imprisoned in
channels: structure of the co-crystal with p-nitroaniline
Valeria Guglielmotti
Maria Maddalena Schiavone
17:50-18:00
Conclusion Remarks
7
Tuesday 22nd September
MS5: Biocrystallography for human health
Chair A. Zagari
10:00-10:30 KN9 The interplay between electron microscopy and protein crystallography: structural
studies of DNA replication
Silvia Onesti
11:00-11:30
KN10 Structural studies of type 1 pili from uropathogenic Escherichia coli.
11:30-11:50 MS5-OR1 Mechanism of CDK9 auto-regulation and of its inhibition by flavopiridol
revealed by crystal structures of the CDK9/CycT1 complex
Guido Capitani
Graziano Lolli
11:50-12:10 MS5-OR2 The crystal structure of intact Human Complement Factor I
12:10-12:30 MS5-OR3 Present challenges in Biocrystallography data collection and related
instrumentation
Pietro Roversi
Michele Cianci
12:30-12:50 MS5-OR4 Structural basis of Serine/Threonine Phosphatase inhibition by the
archetypal cantharidin ligands
Vito Calderone
12:50-13:00
Conclusion Remarks
MS6: New advances of powder diffraction in the material sciences
Chair: F. Costantino
10:00-10:30
KN11 In situ powder diffraction studies of as-synthesised inorganic hydrates to access
potential porosity
Thierry Bataille
11:00-11:30 KN12 Structure/microstructure analysis of nanocrystalline materials
11:30-11:50
MS6-OR1 Turning the Debye-Function into an Efficient Total-Scattering Approach for
Nanocrystalline Materials
Matteo Leoni
Antonella Guagliardi
11:50-12:10 MS6-OR2 Polymorphism in drugs
12:10-12:30
MS6-OR3 Direct space methods in EXPO2009
12:30-12:50
MS6-OR4 Insights on qualification of materials via "On site XRD"
12:50-13:00
Conclusion Remarks
8
Norberto Masciocchi
Corrado Cuocci
Giovanni Berti
MS7: Methods and crystallography
Chair G. L. Cascarano
15:30-16:00
KN13 Use of internal coordinates in the study of fibrous polymer
16:00-16:30
KN14 The ab-initio structure solution from polycrystalline compounds in EXPO2009:
new strategies
Attilio Immirzi
Rosanna Rizzi
16:30-16:50 MS7-OR1 MAD techniques applied to the structure solution from powder data: a new
probabilistic approach.
Maria Cristina Burla
16:50-17:10
MS7-OR2 New computing strategies for protein structure determination by X-ray
crystallography
Rocco Caliandro
17:10-17:30 MS7-OR3 Electron diffractive imaging of transition-metal oxide nanocrystals at 70 pm
resolution
Liberato De Caro
17:30-17:50
MS7-OR4 Detection, validation, and use of correlations between peptide geometry and
conformation in oligopeptides and proteins
Luciana Esposito
17:50-18:00
Conclusion Remarks
Wednesday 23rd September
MS8: S tructure / properties relationships in complex
molecular systems : the multi - technique approach
Chair M. Milanesio
10:00-10:30
KN15 Crystalline Porous Materials containing nanochannels: a combined XRD and
NMR approach
Angiolina Comotti
11:00-11:30 KN16 A multidisciplinary study of the structure of sulfonamide antibiotics adsorbed in
HY faujasite zeolite: X-Ray, spectroscopic, resonance and theoretical investigations
Maurizio Cossi
11:30-11:50
MS8-OR1 Structural investigations on tricyclic sulfonamides
11:50-12:10
MS8-OR2 Competitive H bonding synthons in organic hydrazides
12:10-12:30
MS8-OR3 Keto/Enol Solid-State Polymorphs of 2-Thiobarbituric
12:30-12:50
MS8-OR4 Novel zirconium phosphonates based upon chiral building blocks
12:50-13:00 Conclusion Remarks
Patrizia Rossi
Roberto Centore
Lucia Maini
Marco Taddei
9
PLENARY LECTURES
PL2
Il Milione: past and future
G.L. Cascarano
CNR- Istituto di Cristallografia, 70126 – Bari
During the last 30 years the crystallographic computing has achieved results more and more important.
Having Multan80[1] as a referring program, our research group, leaded by Carmelo Giacovazzo, has
developed innovative theories and created new algorithms to solve the phase problem.
From the seed of the early versions of Sir, software for the the crystal structure solution from powder
diffraction data[2] and for the solution of macromolecules[3] has been produced.
More than 4000 licence agreements have been signed by scientific leaders of research groups in the world
to obtain our software; some of our these programs have been adopted by producers of diffractometers
as default tool for the structure solution stage. Nowadays Expo is the the most used program in the world
for powders and Il Milione[4] is one of the most powerful package aiming at crystal structure solution
using single crystal data. It makes possible to solve small structures (by means of Sir2008, integrated in
the package) as well as proteins using a variety of techniques (ab initio, MAD/SAD, MIR/SIR, MIRAS/
SIRAS, Molecular Replacement). X ray data as well as electron diffraction data and neutron data may be
used. The most recent algorithms developed by our research group (e.g., revisited Patterson techniques,
structure factor extrapolation) allow the protein crystal structure solution even at non-atomic resolution.
An iterative algorithm based on Electron Density Modification (DEDM-EDM), connected with an external
program for the Automated Model Building (AMB), is often able to produce in automatic way an almost
complete model of the protein (the DEA procedure).
Figure 1. The DEA procedure
Starting from Sir88 punched on cards and running on mainframes to solve small molecules, up to Il
Milione solving proteins on net-books: a short story of our research group will be illustrated together with
the perspectives and the new challenges.
References
1. P. Main, S. J. Fiske, S. E. Hull, L. Lessinger, G. Germain, J.P. Declercq, M.M. Woolfson, (1980) Universities of York,
England, and Louvain, Belgium.
2. A. Altomare, G. Cascarano, C. Giacovazzo, A. Guagliardi, M.C. Burla, G. Polidori, M. Camalli - J. Appl. Crystallogr. (2007),
27, 435-436.
3. C. Giacovazzo & D. Siliqi – Acta Cryst. (1997), A53,789-798.
4. M.C.Burla, R. Caliandro, M. Camalli, B. Carrozzini, G.L. Cascarano, L. De Caro, C. Giacovazzo, G. Polidori D. Siliqi, R.
Spagna - J. Appl. Crystallogr. (2007), 40, 609-613.
12
PL1
The impact of synchrotron radiation on
the future challenges in crystallography
S. Larsen
European Synchrotron Radiation Facility, 38043 Grenoble, France
University of Copenhagen, DK-2100 Copenhagen, Denmark
The unique properties of synchrotron radiation from third generation storage rings, e.g. the brilliance,
coherence and time structure explain the increasing demand to use this intense radiation for experiments
in a broad range of scientific areas. A result of these needs is the many new synchrotron facilities have
been created all over the world during the last decade. New exciting possibilities for radiation based
research will also be offered by the X-ray free electron lasers that are to become operational in the near
future. Another important aspect is that synchrotron facilities give access to beamlines with advanced
instrumentation. In addition to automation of repetitive measurements, the instrumentation developments
enable experiments with very advanced sample environments making it possible to perform the experiments
under different thermodynamic conditions (high pressure, high/low temperatures, magnetic fields etc), to
use complementary methods to study the sample during the experiments.
Synchrotron radiation has a great impact on crystallography, understood as the broad scientific areas that
are represented by the International Union of Crystallography. Taking structural biology as an example
the impact is so large that it is stated that synchrotron radiation has revolutionised structural biology and
is responsible for the exponential growth of known protein structures. About 80 % of all structures that
are deposited to-day in the Protein Data Bank are based on diffraction data measured with synchrotron
radiation. The developments of the highly automated beamlines for macromolecular crystallography are
of general benefit for other experiments performed at a synchrotron. The scientific challenges in the future
are in the study of more and more complex systems which brings structural biology closer to the studies
of soft condensed matter. There is also an increasing interest to complement the diffraction studies with
complementary methods like small angle scattering and imaging. The need for submicron sized X-ray
beams for the experiments is another noteworthy development of the use of synchrotron radiation. The
nanometer sized beams open possibilities for an unprecedented spatial resolution that open new scientific
possibilities in materials science, soft matter chemistry and in the characterization of complex chemical
systems. One can also observe an increase in the exploitation of the coherence of the synchrotron radiation in
X-ray imaging and in employing the time structure of synchrotron radiation in studies of suitable chemical
reactions. How the largest European synchrotron, ESRF plans to meet the future scientific challenges
is described in its Science and Technology programme 2008-2017[1]. The trends described above in the
application of synchrotron radiation in crystallographic science now and in the future will be illustrated
by scientific examples.
References
1. http://www.esrf.eu/Upgrade/documentation/purple-book
Plenary Lectures
13
PL3
Reconstruction of polar surfaces in crystals.
The boundary conditions imposed by the symmetry of crystal bulk
M. Rubbo
Dipartimento di Scienze Mineralogiche e Petrologiche – Università degli Studi di Torino, Torino
Surface polarity can occur either in polar crystals or on peculiar faces of non-polar crystals. To the first
class belong, as an example, crystals such as ZnS – wurtzite (P63mc) or ZnS – sphalerite (F43m) whilst
to the second class belong the centro-symmetric NaCl-like lattices that show a non-intrinsic polarity on
their {111} forms induced by the alternating ideal layers of positive and negative electric charges. In both
cases and when the surface is infinite (at atomic scale) the polarity induces the electrical instability on
the crystal surface, since the infinite 2D array of surface dipole moments makes infinite the value of the
electrical field in the surface sites.
Then, to explain the presence of such unstable surfaces on the real crystals, one has to invoke a modification
at the atomic level induced by adsorption of foreign substances and/or a reconstruction of the surfaces to
cancel out the dipole arrays on the polar surfaces.
Dealing with crystal in a vacuum, at 0 K, the usual “golden recipe” found in literature consists in removing
one half of the atomic population from the outermost hkl ideal surface layer and in relocating it on the
opposite h k l crystal plane. As a rule it is not stated where the hole are placed. Actually, this reconstruction
fulfils both condition of electro-neutrality and dipole annihilation on the surface, regardless of the
topological criterion followed for the atoms removal. Nevertheless, from the absence of such a criterion,
a serious drawback ensues as far as concerns the evaluation of the specific free energy (γhkl) of the
reconstructed surfaces. As a matter of fact, there is a number of different ways to remove one half surface
ions and to each is associated a value of γhkl. In other words, the “50%” model of reconstruction is not
self-consistent.
A peculiar reconstruction of the {111} form of the NaCl-like structures was proposed by Lacmann. He
imagined a NaCl-like crystal built by a 3D array of “octopoles”, each containing four NaCl couples,
neutral and non-polar. In this way the resulting {111} surfaces are reconstructed: the outermost layer is
made by 25% of the ions while the underneath one contains 75% of the ions of opposite charge. Further,
this kind of surface fulfils the symmetry imposed by the crystal bulk as the <111> directions coincide with
the A3 axes.
In this work we summarize the investigations we performed on the reconstruction of polar surfaces
of different kind of crystals (CaCO3 – calcite, NaCl, UO2– uraninite ). We aimed at finding a general
relationship between the reconstruction model, the 2D symmetry of a given (hkl) surface and the
corresponding specific surface energy γhkl value. The surfaces we examined are: i) - the {0112}
rhombohedron of calcite, crossed by a glide c plane; ii) - the {0001} pinacoid of calcite , compatible with
0001
111
a 3axis and three c planes around it; iii) - the {111} NaCl – octahedron, compatible with a A3 axis and
three m planes around it; iv) - the {001}cube of the (Fm3m) UO2 . From all these cases it ensues that: the
“50%” reconstruction corresponding to the absolute minimum of γ calcite is only that which respects the
12
U
O γ2calcite and
symmetry c plane; by applying the octopolar model one obtains the01 absolute
minima for both
γ
001
NaCl
γ
; from the reconstruction respecting the A4 axis the absolute minimum is obtained for
. Then,
the “golden rule” for reconstructing a polar surface prescribes the electro-neutrality, the dipole annihilation
on the surface and the fulfilment of the boundary conditions imposed by the surface symmetry. These are
the necessary and sufficient constraints.
14
PL4
Crystallinity and polymers
F. Auriemma, C. De Rosa
Dipartimento di Chimica “Paolo Corradini”, Università di Napoli “Federico II”, Napoli,
The concept that in polymers crystallinity may be present with the concomitant occurrence of a large
amount of structural disorder and in the absence of true three-dimensional long-range order is illustrated[1].
Application of this concept in the study of material properties allows a fine understanding of their physical
and mechanical behavior in terms of the structural organization of the polymer chains in the crystals,
polymorphism and molecular architecture.
Some results recently obtained in the course of our extensive studies on stereoregular polyolefins prepared
using metallorganic catalysts are illustrated, aimed at building correlations between the chain microstructure
(type and concentration of stereo- and regio-defects, and nature of comonomeric units in copolymers), the
crystal structure and physical and mechanical properties of a given polymeric material.[2,3] First we show
results which are directly related to the field of basic polymer crystallography, namely the crystal structure
of the trigonal form of isotactic polypropylene, isomorphous to isotactic poly(1-butene) form I, as an
example of density driven polymer structure,[4] the crystal structure of alternating ethylene-norbornene
copolymers, the first case of plastic crystals from macromolecules,[5] and the crystal structure of a novel
polymer stereocomplex where the two pure enantiomers are unable to crystallize. Novel advances in the
field of polymer science are also discussed related to the deformation behavior of semicrystalline polymeric
materials, in relation to the crystal structure and stress-induced polymorphic transformations.[6] It is shown
that the comprehension of the factors that determine the different kinds and amounts of disorder in the
crystals of polymers, through the methods and the language of structural analysis, may be very useful to
interpret the physical and mechanical behavior of polymeric materials.
References
1. P. Corradini in The Stereochemistry of Macromolecules. Ketley A. D. (eds). Marcel Dekker, New York, 1968, vol. 3, p.1;
C. De Rosa in Materials Chirality, Topics in Stereochemistry 24, 71 John Wiley and Sons, Haboken, New Jersey, 2003; P.
Corradini, F. Auriemma, C. De Rosa J. Acc. Chem. Res. (2006), 39, 314.
2. C. De Rosa, F. Auriemma Prog. Polym. Sci. (2006), 31, 145.
3. C. De Rosa, F. Auriemma in Progress in Understanding of Polymer Crystallization, Lecture Notes in Physics (2007), 714, 345.
4. C. De Rosa, F. Auriemma, P. Corradini, O. Tarallo, S. Dello Iacono, E. Ciaccia, L. Resconi J. Am. Chem. Soc. (2006), 128,
80; C. De Rosa, S. Dello Iacono, F. Auriemma, E. Ciaccia, L. Resconi, Macromolecules (2006), 39, 6098; C. De Rosa, F.
Auriemma, G. Talarico, O. Ruiz de Ballesteros, Macromolecules (2007), 40, 8531.
5. C. De Rosa, A. Buono, F. Auriemma, A. Grassi Macromolecules (2004), 37 2004; C. De Rosa, P: Corradini, A. Buono, F.
Auriemma, A. Grassi, P. Altamura Macromolecules (2003), 36, 3789.
6. C. De Rosa, F. Auriemma, O. Ruiz de Ballesteros, S. Dello Iacono, D. De Luca, L. Resconi Cryst. Growth & Design (2009),
9, 165; C. De Rosa, F. Auriemma, M. Corradi, L. Caliano, G. Talarico Macromolecules (2008), 41, 8712; C. De Rosa, F.
Auriemma, O. Ruiz de Ballesteros,L. Resconi, I. Camurati Chem. Mat. (2007), 19, 5122.
Plenary Lectures
15
PL5
A roadmap to nanocrystallography
J. P. Abrahams
Department of Biophysical Structural Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden
University, 2300 RA Leiden, The Netherlands.
If protein crystals have multiple layers, but are smaller than 1 micron, they are currently beyond the reach
of crystallographic structure determination, whether by X-rays or electrons. For structure determination
of 3D protein crystals that are smaller than about 0.5 micron, it can be shown that electrons are more
suited for structure determination than X-rays, as they are less damaging by several orders of magnitude
when normalised to the amount of elastically scattered quanta. Indeed, if only two-dimensional, singlelayer crystals of proteins are available, electron diffraction already is the method of choice for structure
determination. However, if such crystals have multiple layers, practical problems include the data
acquisition, the lack of software to process such data and the absence of successful pilot studies. These
drawbacks currently prompt most protein crystallographers to put their efforts into growing larger crystals
that diffract X-rays, and make them abandon projects if only nanocrystals can be obtained.
In this lecture, the implications of the fundamental differences between electron refraction and X-ray
diffraction of 3D crystals will be discussed and potential solutions to many of the practical problems in
electron 3D nanocrystallography will be evaluated. These include sample preparation and handling
routines, data collection strategies, the use of quantum area detectors, data processing software and the
potential of novel approaches towards phasing the diffraction data.
16
PL6
Ligand-stabilized metal nanoparticles at the borderline
of molecular and colloidal chemistry
G. Longoni
Dipartimento di Chimica Fisica ed Inorganica, Alma Mater Studiorum Università di Bologna, 40136 Bologna
The size of highest-nuclearity molecular metal clusters is comparable to that of colloidal gold nanoparticles
stabilized by thiols (or thiolates), as well as phosphine ligands. Consider, for instance, the giant carbonylsubstituted low-valent (e.g. Pd145(CO)60(PEt3)30 [1] and Pd165-xPtx(CO)72(PPh3)20 [2]) or the thiolate high-valent
clusters (e.g. Ag320S130(SBut)60(dppp)12 and Ag490S188(SC5H11)114),[3] in comparison with the nanosized quasi
mono-dispersed Au147(SC12)59 gold colloid,[4] for which structural details are yet lacking.
The known homoleptic carbonyl metal cluster anions (MCC) are yet far from the above nuclearities;
nevertheless, their size may trespass from the bottom in the nano-world.[5] As an advantage, MCC are
obtained in macroscopic amounts as collection of particles all identical in size, composition and structure.
A few emerging properties of MCC will be presented. First of all, it will be demonstrated that their metal
kernels undergo a progressive insulator-to-metal transition as a function of nuclearity, which trigger
nanocapacitor behaviour. The metallization as a function of size occurs much earlier in MCC than in
gold-thiolate colloidal particles. The possible reasons of the delayed metallization of gold-thiolates were
investigated on model compounds and became straightforward after the recent structural characterization
of Au102(SR)40.[6]
As a possible consequence of metallization, ascertainment of NMR signals of MCC becomes problematic
beyond a nuclearity of ca. 20. That might be due to insurgence of magnetic behaviour. Several even-electron
MCC have been reported in the past to display temperature-dependent paramagnetism (TDP). However,
the TDP of MCC has been disputed by early DFT calculations and in two cases has unambiguously been
demonstrated to arise from contamination by odd-electron species. The question has recently been reopened by undisputable examples of magnetic even-electron MCC.
A possible alternative explanation of vanishing NMR signals could be anisotropy of their solutions,
triggered by the great aptitude of high-nuclearity MCC to self-assemble in giant nanoparticles (10-200
nm) by formation of covalent bonds or ionic interactions. A few examples of self-assembly in solid state
via formation of covalent bonds will be reported.
References
1. N.T. Tran,D.R. Powell,L.F. Dahl Angew. Chem. Int. Ed. (2000), 112, 4287.
2. E.G. Mednikov, M.C. Jewell,L.F. Dahl J. Am. Chem. Soc. (2007), 129, 11619.
3. C.E. Anson, A. Eichhofer,I. Issac,D. Fenske,O. Fuhr,P. Sevillano,C. Persau, D. Stalke,J. Zhang Angew. Chem. Int. Ed.
(2008), 47, 1326.
4. N.K. Chaki,Y. Negishi,H. Tsunoyama,Y. Shichibu,T. Tsukuda J. Am. Chem. Soc. (2008), 130, 8608.
5. C. Femoni,M.C. Iapalucci,F. Kaswalder,G. Longoni,S. Zacchini Coord. Chem. Rev. (2006), 250, 1580.
6. P.D. Jadzinsky,G. Calero,C.J. Ackerson,D.A. Bushnell,R.D. Kornberg Science (2007), 318, 430.
Plenary Lectures
17
Nardelli Prize
Probing molecular conformation and configuration at high pressure
N. Casati1, P. Macchi2, A. Sironi1
1. Università degli studi di Milano, DCSSI, 20133 - Milano
2. University of Bern, Departement für Chemie und BioChemie, CH 3012 - Bern
Structural characterization of molecular crystals at high pressure (HP) is a growing field as rather large
modifications are induced by moderate pressures of a few GPa. Volume decreases in excess of 20% are
rather common and permit the observation of many different phenomena. Intermolecular distances are
particularly affected by pressure, as well as soft intramolecular modes such as torsions, angles, and soft
bonds (metal-metal or metal-ligand). The compression of metal carbonyl dimers, for example,[1] shows that
conformations not stable in ambient conditions are more suitable for reduced molecular volumes and may
lead to the unexpected elongation of a metal-metal bond. In strongly hydrogen-bonded systems, on the
other hand, HP experiment may permit to observe the reaction of the system to the decrease of the donoracceptor distance. In particular, in oxalic acid dihydrate this leads to the continuous proton migration from
the oxalic acid to the water, thus creating an ionic couple after a solid state acid/base reaction.[2]
Figure 1. The effect of pressure on oxalic acid dihydrate.
Large structural modifications may be directly visible just by looking at the crystals and are mirrored by
the change in properties of these materials. The variation of molecular torsions in organic chromophores,
for example, seems to be responsible of the large variations in their NLO response.[3]
HP structural characterization proves to be a particularly powerful tool to experimentally probe molecular
conformations and configurations at high pressure.
References
1. N. Casati, P. Macchi, A. Sironi Chemistry a European Journal, (2009), 15(17), 4446.
2. N. Casati, P. Macchi, A. Sironi Chemm. Comm. (2009), 19, 2679.
3. N. Casati, P. Macchi, E. Marelli, A. Sironi (2009) to be published
18
Key Notes Lectures
KN1
Molecular electron density displacement (MEDD)
for intermolecular interactions investigation.
F. Ugozzoli
University of Parma, Dipartimento di Chimica Generale ed Inorganica, Chimica Analitica, Chimica Fisica,
43100 Parma, Italy.
The electron density displacement, defined as the difference between the electron density of a complex and
the electron densities of the isolated molecular (or ionic) species, gives the electron redistribution upon
complex formation and can be used to interpret the mechanism of the molecular interactions occouring
under complexation. So far, the analysis of the electron density displacement has been only limited to
define atomic charges and local dipole moments on atoms rather than to the investigation of intermolecular
interactions[1],[2],[3].
In this work, the electron density displacement, determined by the electron densities calculated at the
MP2/6-311++G** and MP2/aug-cc-PVDZ levels for 38 complexes with H bonds, CH···π, halogen bond,
cation···π, anion···π, and dispersion interactions, have been studied to characterize the electron density
displacement as “fingerprints” for each kind of interaction.
For each complex the amount of charge shifted under complexation (Qe) have been calculated and
correlated to binding energy of the complex.
For both the basis sets a linear correlation have been found for all the complexes with H bonds, CH···π,
halogen bond, and dispersion interactions suggesting a new point of view for molecular recognition when
the “best” receptor has to be designed for a molecular or ionic substrate.
References
1. F.L. Hirshfeld, Theor. Chim. Acta (1977), 44, 129.
2. E.R. Davidson, S.Chakravorty, Theor. Chim. Acta (1992), 83, 319.
3. J.F. Harrison, J. Chem. Phys. (2003), 119, 8763.
22
KN2
Dynamic porous properties of supramolecular
networks inspired by halogen bonding
P. Metrangolo1, Y. Carcenac1, M. Lahtinen2, T. Pilati3, K. Rissanen2, A. Vij4 and G. Resnati1,3
1.
2.
3.
4.
Politecnico di Milano, D.C.M.I.C. “Giulio Natta”, I–20131 – Milano
University of Jyväskylä, Department of Chemistry, FI–40014 – Jyväskylä
CNR, ISTM, I–20133 – Milano
Air Force Research Laboratory, CA 93524–USA – Edwards
Halogen bonding[1,2] has increasingly facilitated assembly of diverse host-guest solids.[3,4] Here we show that
a well-known class of organic salts, bis(trimethylammonium) alkane diiodides 1, can reversibly encapsulate
α,ω-diiodoperfluoroalkanes (DIPFAs) 2 through intermolecular interactions between the host’s I- anions
and guest’s terminal iodine substituents.[5] The process is highly selective for the fluorocarbon that forms
an I-∙∙∙I(CF2)mI∙∙∙I- superanion matched in length to the chosen dication. DIPFAs two to twelve carbons in
length – common industrial intermediates – can thereby be isolated from mixtures by crystallization from
solution on addition of the dissolved size-matched ionic salt. Remarkably, the solid state salts can also
selectively capture the DIPFAs from the vapor phase, yielding the same product formed from solution
despite a lack of porosity of the starting lattice structure. Heating liberates the DIPFAs and regenerates the
original salt lattice, highlighting practical potential for the system in separation applications.[6]
References
1.
2.
3.
4.
5.
6.
P. Metrangolo, G. Resnati Science (2008), 321, 918.
P. Metrangolo, T. Pilati, G. Resnati CrystEngComm (2006), 8, 946.
P. Metrangolo, H. Neukirch, T. Pilati, G. Resnati Acc. Chem. Res. (2005), 38, 386.
P. Metrangolo, F. Meyer, T. Pilati, G. Resnati, G. Terraneo Angew. Chem. Int. Ed. (2008), 47, 6114.
P. Metrangolo, T. Pilati, G. Terraneo, S. Biella, G. Resnati CrystEngComm (2009), DOI: 10.1039/b821300c.
P. Metrangolo, Y. Carcenac, M. Lahtinen, T. Pilati, K. Rissanen, A. Vij, G. Resnati Science (2009), 323, 1461.
Key Notes Lectures
23
KN3
Melting of cooperative Jahn-Teller distortion
in MgxCu1-xCr2O4 solid solution
S.C. Tarantino1,2, M. Zema 1,2, P. Ghigna 3 and M. Giannini1
1. Dipartimento di Scienze della Terra, Università di Pavia, 27100 - Pavia
2. CNR-IGG, UoS Pavia, 27100 - Pavia
3. Dipartimento di Chimics Fisica “Mario Rolla”, Università di Pavia, 27100 - Pavia
A large number of compounds of general formula AB2X4 adopt structures related to that of the mineral
spinel MgAl2O4. Spinels are one of the most extensive series of related chemical compounds known and
have a remarkable record of applicability being used in numerous areas, including magnetic devices,
electronics, catalysis, and batteries.[1] Chromium-rich spinels MCr2O4 are part of a group of exciting and
challenging materials that have attracted much research interest in recent years due to complex magnetic
ground states resulting from high geometrical frustration.[2]
CuCr2O4 is a tetragonally distorted spinel with c/a < 1. The structure distortion is due to a cooperative
Jahn-Teller (cJT) effect which is also associated, as recently proposed,[3] with orbital ordering. CuCr2O4
undergoes a first-order structural transition from I41/amd to the archetype cubic spinel structure (Fd-3m)
at 853 K.[4] The temperature and composition dependence of the I41/amd - Fd-3m phase transition, due to
the melting of the cJT distortion, in MgxCu1-xCr2O4 solid solution has been studied by means of in situ HT
X-ray diffraction. Black octahedral crystals of MgxCu1-xCr2O4 (with x = 0, 0.2, 0.45, 0.50, 0.8, 1), typically
twinned and with a maximum size of 1×1×1 mm3, have been prepared by flux decomposition method.
Single-crystal diffraction data have been collected in situ from RT up to 900°C. Crystals with composition
up to x = 0.5 have been refined in I41/amd, whereas crystals with higher Mg content have cubic symmetry.
The progressive substitution of the Jahn-Teller and d9 Cu(II) cation with the spherical and closed-shell
Mg(II) cation has a dramatic effect on the crystal structure. The tetragonal distortion, as measured by
the tetrahedral angle variance and by the deviation of the c/a ratio from one, decreases with increasing
Mg content. The Mg ions, distributed on the tetrahedral sites, dilute the nearest neighbour interactions of
the Cu ions, thus reducing the efficiency of the cooperative distortion. The tetragonal-to-cubic transition
temperature in the Cu-rich members decreases with increasing Mg content. Indeed, the strength of the
Cu-Cu interaction can be modulated by varying the Cu/Mg ratio. Structure refinements of diffraction
data collected at different temperatures revealed that heating induces a gradual reduction in the CuO4
tetrahedron compression, which however remains significant until near the transition temperature.
References
1.
2.
3.
4.
24
N.W. Grimes Phys. Technol. (1975), 6, 22.
P. G. Radaelli New J. Phys. (2005), 7, 53.
B.J. Kennedy and Q. Zhou J. Solid State Chem. (2008), 181, 2227.
Z.G. Yé, O. Crottaz, F. Vaudano, F. Kubel, P. Tissot, H. Schmid Ferroelectrics (1994), 162, 103.
KN4
HT X-ray diffraction and spectroscopic study of
sideronatrite and its relationships with some analogues
G. Ventruti
Dipartimento Geomineralogico, Università di Bari - 70125 - Bari
Sulfate minerals are found in a variety of geological settings, including volcanic, hydrothermal, evaporitic,
and chemical-weathering environments. Secondary sulfate minerals, resulting from oxidation of preexisting sulfides, are currently recognized as sensitive environmental indicators and play an important
role in the acid drainage mobilization of metals and in the monitoring of water quality. The present study
is focused on a particular iron hydrated secondary sulfate, sideronatrite, a weathering product of oxidized
iron sulfides under acidic conditions which frequently forms in paragenesis with other hydrated sulfates.
The presence of sideronatrite in geochemical samples provides evidence that sampling sites are strongly
acidic.
The OD character of sideronatrite hampered to date a complete structural determination of this mineral.
Sideronatrite belongs to a family of OD structures of category I characterized by equivalent layers with
P21/m symmetry. Only two MDO structures are feasible for sideronatrite: (1) MDO1 orthorhombic
polytype, solved and refined in this study, with space group P212121 and cell parameters: a = 7.265(2), b
= 20.522 (6), c = 7.120 (2) Å; (2) MDO2 monoclinic polytype, calculated through the application of the
OD theory, with space group P21/c, and lattice parameters a = 7.265, b = 7.120, c = 20.828 Å, α = 99.84°.
The structure of sideronatrite is based on parallel chains having [Fe3+(SO4)2(OH)]2- composition and ∼ 7 Å
repeat distance. These chains are cross-linked by columns of edge-sharing Na distorted octahedra to form
layers. Adjacent layers are hydrogen-bonded through water molecules. When heated to temperatures close
to 35°C or slightly higher, sideronatrite transforms quickly to metasideronatrite. In a damp atmosphere
metasideronatrite reverts to sideronatrite. The structure of metasideronatrite, solved here for the first time, is
also based on the same 7 Å chains of sideronatrite, but differs from the parent structure for the arrangement
of the Na atoms and the hydrogen bonds configuration. The Na-centred octahedra alternatively share one
face and one edge, and provide both inter-chain linkage and interlayer connection formerly present in
sideronatrite. The weak hydrogen bonds and the ease of releasing and re-trapping the water molecules
seem to be the main factors affecting the stability of the sideronatrite and its quick and reversible transition
from an OD structure (sideronatrite), to an ordered one (metasideronatrite). The structural changes across
the sideronatrite ↔ metasideronatrite transition were also followed by in-situ HT-FTIR spectroscopy
to monitor the hydrogen bonding system in the H2O stretching (4000-3000 cm-1) and bending (∼ 1600
cm-1) regions. The IR spectra collected up to 600 °C are characterized by the evolution of the complex
system of SO42- and H2O internal modes. In particular the not-linear behaviour of the H2O band intensity
with temperature is consistent with a succession of structural phase transitions in agreement with hightemperature X-ray powder diffraction results and mass loss steps from thermogravimetry.
Key Notes Lectures
25
KN5
Growth of minerals in biological systems
Patrizia Vergni, Giuseppe Falini, Simona Fermani
Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum University of Bologna Italy
The growth of crystals in biological systems generally occurs in a controlled manner within a preformed
organic structural framework (the organic matrix). This is a basic mode of skeletal formation adopted by
many different organisms.[1] Protein self-assembly into ordered structures is a critical step towards the
control of mineral deposition in biomineralizing systems such as bone, teeth, corals and mollusc shells. In
this presentation three examples of structural organization of the organic matrix are presented: the solubleinsoluble macromolecules assembly in fish otoliths, the gelling biopolymeric environment in corals and
the transient proteins superstructure that guides the enamel formation.[2-4]
Otoliths of teleost fishes are made of vaterite and aragonite, two calcium carbonate polymorphs, located
in different sacs and never mixed together. Experimental evidences from calcium carbonate overgrowth
on the surface of otoliths and in vitro crystallization on the chitin-silk fibroin assembly organic matrix
suggest that the intracrystalline macromolecules associated to the otolith influence the aragonite-vaterite
polymorphism.[2]
Scleractinian corals from Mediterranean are made mainly of aragonite. In them the deposition of calcium
carbonate occurs in a biological confined environment. However, it is still a theme of discussion at which
level the calcification occurs under biological and environmental control. The researches have shown
that the organic matrix components make a gelling environment which influences the calcium carbonate
precipitation and that this effect is enhanced by their co-presence.[3]
Mammalian tooth enamel is the hardest tissue in the vertebrate body and is a secretory product of cells
of epithelial origin called ameloblasts. Enamel mineralization is a dynamic process that includes protein
secretion, matrix assembly and initiation and growth of the crystals within an amelogenin-rich matrix.
The assembly of the mineralized enamel matrix continues through the transition stage during which
ameloblast activity is drastically reduced and the bulk of the protein matrix is eventually processed during
the maturation stage, concomitant with the rapid growth and maturation of the mineral.[4]
References
1. G. Falini, S. Fermani, N. Roveri “Calcium Carbonate Polymorphism in Biominerlization. From in vivo knowledge to in vitro
application” Current Topics in Crystal Growth Research (2004) 7, 24-342.
2. G. Falini, S. Fermani, M. Maritic, S. Vanzo, G. Zaffino “Influence on aragonite or varerite formation by otolith
macromolecules” European Journal of Inorganic Chemistry, (2005) 1, 162-167
3. P. Vergni, E. Caroselli, S. Fermani, S. Goffredo, G,e Falini “Mediterranean coral organic matrix influence on CaCO3
precipitation” Composite Materials, (2009) in press
4. C. Du, , J. Moradian-Oldak, G. Falini “On the formation of amelogenin micro-ribbons” EurJOralSci. (2006), 114, 289-296.
26
KN6
Incommensurate epitaxial organic heterostructures
A. Sassella1, M. Campione2, M. Moret1, and L. Raimondo1
2
1 Università di Milano Bicocca, Dipartimento di Scienza dei Materiali, 20125 Milano
Università di Milano Bicocca, Dipartimento di Scienze Geologiche e Geotecnologie, 20126 Milano
Organic-organic epitaxy is a recent approach for growing highly oriented and crystalline hetero-junctions of
organic semiconductors. Contrarily to inorganic systems where lattice commensurism plays a crucial role
on deciding the substrate/overlayer epitaxial relationships, for molecular systems such as organic crystalline
solids the final outcome of Organic Molecular Beam Epitaxy is dictated by weak van der Waals interactions
at the organic-organic interface of generally incommensurate lattices. Overlayers with crystalline order over
macroscopic areas and with well defined textural orientations can be obtained producing organic-organic
heterostructures. For the deposit/substrate pairs rubrene/tetracene(001), quaterthiophene/tetracene(001),
and quaterthiophene/rubrene(100), high resolution atomic force microscopy imaging evidenced clear
preferences for azimuthal orientations of overlayers with respect to substrate. Such azimuthal orientations
are related to maximization of adhesion energies, as also demonstrated by empirical force field simulations.
Optimization of adhesive interactions arises from coincidence of molecular corrugations of substrate and
overlayer crystal surfaces, which occurs only for specific azimuthal orientations, giving rise to line-on-line
epitaxy. Therefore, the driving force during growth of the overlayer atop the substrate is ruled effectively
by the weak interactions even in absence of lattice commensurism.
Figure 1. Model of the rubrene/tetracene(001) heteroepitaxial structure.
Key Notes Lectures
27
KN7
Small Angle X-ray Scattering on polymers and
nanocomposites: a quantitative approach
A. Marigo
Università degli Studi di Padova , Dipartimento di Scienze Chimiche, 35131 - Padova
Small Angle X-ray Scattering can play a major role in the structural characterization of multilayers and it
is applied to polymers because they usually show electron density variations with correlation length within
the range covered by this technique and, moreover, because their lamellar structures may be adequately
described by assuming the electron density variation to occur in one coordinate direction only.
The interpretation of SAXS data is usually very much dependent on the cooperation with other techniques
of investigation as Transmission Electron Microscopy and Wide Angle X-ray Scattering.
For example methods involving the use of the One Dimensional Correlation Function allow to evaluate the
lamellar thickness, but only by using the degree of crystallinity previously determined by WAXS.
An original SAXS analysis will be described, based on a fitting method of experimental SAXS patterns
with calculated ones[1,2]. The patterns are calculated from theoretical models of lamellar stackings and
parameters such as the thicknesses of the crystalline lamellae and amorphous layers, the degree of
crystallinity and the lamellar dimension distributions are evaluated independently from other techniques.
It will be shown that the data of SAXS fitting from some polymers and the results obtained from the
analysis of TEM images on the same samples are in good agreement[3] and other examples of application
of the method will be presented.
The same method was successfully applied to the analysis of the multilayer structures of clays in polymeric
nanocomposites in order to investigate the possible interactions between clay and polymer[4,5].
References
1.
2.
3.
4.
5.
28
C. Marega, A. Marigo, G. Cingano, R. Zannetti, G. Paganetto Polymer (1996), 37, 5549.
C. Marega, A. Marigo, V. Causin J Appl Polym Sci (2003), 90, 2400.
A. Marigo, C. Marega, R. Zannetti, P. Sgarzi Eur. Polym. J. (1998), 34, 597.
V. Causin, C. Marega, A. Marigo, G. Ferrara Polymer (2005), 46, 9533.
V. Causin, C. Marega, A. Marigo, G. Ferrara Polymer (2006), 47, 4773.
kn8
Strategies for crystal structure solution of polymers:
examples and some comments
Stefano Valdo Meille
Dipartimento di Chimica, Materiali ed Ingegneria Chimica del Politecnico di Milano, I-20131 - Milano (Italy)
Notwithstanding the advances in both computational facilities and experimental equipment, which
in the past 40 years have dramatically improved the effectiveness both small-molecules and protein
crystallography, the solution and refinement of polymer crystal structures remains rather a craft than
an automatic procedure. This fact relates in general to the poor quality of polymer crystals and to the
related very limited resolution of diffraction patterns that can be obtained from polymer samples, where
disordered crystalline phases coexist with substantial amounts of amorphous phases.
The determination of polymer crystal structures relies on fibre diffraction techniques for organic or
biological polymers with large asymmetric units. Modern 2-D detectors have increased the efficiency
in the acquisition of intensity data, although the task remains tedious due to the shape irregularity of
polymer diffraction maxima. On the other hand, for synthetic polymers with relatively simple monomer
units, powder diffraction approaches have proven increasingly effective in the past two decades, because
quantitative data are obtained readily also for phases which give poor fibre data.
In polymer powder diffraction patterns, the breadth of maxima cause extensive reflection overlapping,
making automatic indexing procedures ineffective. As a consequence, also space group determination,
which generally proves to be the key step in the polymer crystal structure solution process, is often not
straightforward.
Along with experimental methods which help resolve ambiguities, rational approaches relying on analysis
of the polymer chain symmetry and of the packing effectiveness of different symmetry elements for given
structures, can greatly aid the determination of the space group and the crystal solution process. Rather
than invoking unspecified disorder, renouncing in fact crystal structure solution in favour of “cartoons”,
the definition of simple “limited ordered” models, updating Corradini’s traditional approach, is often a
more effective and informative route. Thereafter a thoughtful selection of initial model permutations and
constrained least-squares procedures in combination with modern molecular mechanics and dynamics
procedures, usually lead to reliable crystal structure models, which often also afford insights in the disorder
features of the system.
Selected examples in the field of synthetic polymers, from both the author’s experience, and from the
literature will be discussed.
References
1. S. Brückner, S.V. Meille. Nature, (1989) 340, 455
2. E.Corradi, A. Farina, M.C.Gallazzi, S.Brückner, S.V.Meille. Polymer, (1999), 40, 4473.
3. P. Arosio, A. Famulari, M. Catellani, S. Luzzati, L. Torsi, S. V. Meille. Macromolecules, (2007) 40, 3.
Key Notes Lectures
29
kn9
The interplay between protein crystallography and electron
microscopy: what did we learn about the structure
and function of the replicative MCM helicase
S. Onesti
Sincrotrone Trieste S.C.p.A., 34149 Basovizza, Trieste Italy
The eukaryotic MCM2-7 complex is recruited onto origins of replication during the G1 phase of the cell
cycle and acts as the main helicase at the replication fork during the S phase. The MCM proteins are
present only in proliferating cells and are highly expressed in malignant human cancers cells and precancerous cells undergoing malignant transformation, whereas they are not expressed in differentiated
somatic cells that have been withdrawn from the cell cycle. Therefore, these proteins are ideal diagnostic
markers for cancer and possibly targets for anti-cancer drug development
Using electron microscopy we have obtained over the years a number of low resolution structures that
corresponds to a variety of functional states, therefore providing snapshots of the helicase reaction. By
combining the electron microscopy structure with the chemical models derived from protein crystallography
we elucidate the possible conformational changes and dynamic behaviour of MCM helicase during the
processes of DNA melting and unwinding.
30
kn10
Structural studies of type 1 pili from
uropathogenic Escherichia coli
G. Capitani1, M.A. Schaerer1, O. Eidam2, M.G. Grütter2, O. Ignatov3, C. Puorger3, R. Glockshuber3
1. Paul Scherrer Institut, Biomolecular Research, CH-5232 Villigen
2. University of Zurich, Institute of Biochemistry, CH-8057 Zurich
3. ETH Zurich, Institute of Molecular Biology and Biophysics, CH-8093 Zurich
Type 1 pili are proteinaceous organelles that are anchored to the outer membrane of uropathogenic
Escherichia coli (UPEC) and enable the bacterium to attach to the bladder epithelium of the host. This way,
type 1 pili mediate the first critical step of bladder infection by UPEC, leading to cystitis. It is estimated
that more than 80% of urinary tract infections, including cystitis, are caused by UPEC[1].
Pilus biogenesis takes place via the so-called “chaperone-usher” pathway[2], the understanding of which
has greatly advanced in the recent years, thanks mainly to structural and kinetic studies[3, 4].
The focus of the talk will be on recent structural studies of pilus proteins and complexes thereof, carried
out using a combination of crystallography, bioinformatics[5] and biochemical techniques.
References
1.
2.
3.
4.
5.
A. Ronald Am J Med. (2002), 113, 14S.
F.G. Sauer et al. Curr Opin Struct Biol. (2000), 10, 548.
R. Fronzes et al. EMBO J. (2008), 27, 2271.
G. Capitani et al. Microbes Infect. (2006), 8, 2284.
G. Capitani et al. Proteins (2006), 65, 816.
Key Notes Lectures
31
kn11
In situ powder diffraction studies of as-synthesised
inorganic hydrates to access potential porosity
T. Bataille1, W. Rekik1,2, H. Naïli2, F. Costantino3 and S. Midollini4
1.
2.
3.
4.
Sciences Chimiques de Rennes, CNRS - Université de Rennes 1, F-35042 – Rennes, France
Laboratoire de l’Etat Solide, Faculté des Sciences de Sfax, 3018 – Sfax, Tunisia
Laboratorio di Chimica Inorganica, Dipartimento di Chimica, 06123 – Perugia
ICCOM CNR, 50019 – Florence
Porous materials are usually prepared as crystalline products from liquid media, for subsequent structural
characterisation from X-ray diffraction. As a consequence, many of them exhibit voids that are filled with
solvent molecules, so that they cannot be used as-is for industrial applications. Structural modifications
arising from desolvation stages may result in alteration of the awaited efficient porosity. In situ powder
diffraction is then an efficient tool to follow the structural behaviour of the precursors during the first stages
of the desolvation reactions.
Here we show a few examples of thermal dehydration of inorganic compounds that lead to unexpected
structures and/or properties at higher temperatures. Most of the studies are based on temperature-dependent
X-ray diffraction experiments, carried out with laboratory powder X-ray diffractometers, while structural
studies might involve specific sample environment or less usual techniques:
1. Anomalous diffraction allows locating both Na+ and Ca2+ cations within a LTA zeolite framework
after calcination.[1]
2. For copper diphenylenediphosphinate compounds, the reversibility of the dehydration, as well
as the relative stability of the phases, are fully explained by in situ powder diffraction.[2]
3. Supramolecular metal amine sulfates are good candidates to open-framework materials when
partly or fully dehydrated.[3]
Figure 1. Reversible transformation from 1D to 3D structures of (C4H14N2)[Mn2(SO4)3(H2O)6]
References
1. C. Pichon, B. Rebours, H. Paoli, T. Bataille, J. Lynch Mater. Sci. Forum (2004), 443-444, 315-318.
2. T. Bataille, F. Costantino, A. Ienco, A. Guerri, F. Marmottini, S. Midollini Chem. Commun. (2008), 6381-6383.
3. W. Rekik, H. Naïli, T. Mhiri, T. Bataille Solid State Sci. (2009), 11, 614-621.
32
kn12
Structure/microstructure analysis of nanocrystalline materials
M. Leoni1
University of Trento, Department of Materials Engineering and Industrial Technologies, 38123 - Trento
Odd profile shapes, deeply anisotropic line-profile broadening, unexpected features are sometimes observed
in X-ray powder diffraction patterns. Even apparently well-behaving data lead sometimes to questionable
refinement results (e.g. apparent polymorphism in transformations, unrealistic thermal parameters) in which
materials’ physics contrasts with the hypotheses on which the analysis method is based (e.g. 3D-periodic
lattice). Complementary information is usually needed in those cases, together with new analysis tools
able to cope with the real physical environment in which the problem is re-framed. A couple of such tools
are the Whole Powder Pattern Method[1] that can provide microstructure information in simple cases, and
the DIFFaX+[2] approach, able to deal with traditional, layered and modular structures showing a local
or global reduction of the lattice symmetry due to the presence of defects. Basics and examples of both
methods will be shown and commented.
References
1. P. Scardi, M.Leoni Acta. Crystallogr. (2002), A58, 190.
2. M. Leoni, A. Gualtieri, N. Roveri J. Appl. Crystallogr. (2004), 37, 166.
Key Notes Lectures
33
kn13
Use of internal coordinates in the study of fibrous polymers
A. Immirzi, C. Tedesco
Dipartimento di Chimica, Università di Salerno, 84084 Fisciano (SA), Italy
The basic principles for the study of fibrous polymer by diffraction methods do not differ from the general
ones. However, there are difficulties which make the study exacting and risky: i) the polycrystalline nature
of the samples, ii) the limited crystallinity, the impurity of phases, and the steric impurity of chains; iii)
the uncertain unit-cell and Bragg indices; iv) the poor quality of the measurements, v) the low data-toparameters ratio.
While the diffusion of automated instruments and computers did improve substantially the quality of
single-crystal studies, polymer crystallography continued for long with the photographic techniques and
the trial-and-error method. The quality remained modest, the certainty of results too. Structure refinement
was rarely attempted. Only after 1980 the introduction of the “image-plate” raised substantially the quality
of intensity measurements.
The low data-to-parameters ratio makes necessary the use of “constrained models” with fixed bondlengths and maybe fixed bond-angles. This approach was followed de facto even by the first polymer
crystallographers, disregarding however a point that only recently has been considered with due attention:
the independency (non redundancy) of the internal coordinates used. The mathematic methods were those
established by Lagrange when he devised the generalized coordinates (1794), the basis of Lagrangian
mechanics and Hamiltonian mechanics.
In order to perform structural refinement with a constrained model, it is necessary to follow a precise
building protocol: first to build the chain, then to direct its axis parallel to the c edge. Two special points
must be well considered: i) only an orientation angle must be used rather than three; ii) the “chain
continuity” must me obeyed: the chain is continue when, extending it by repeating orderly chain bondlengths, bond-angles, and torsion angles, any segment of three consecutive (non coplanar) atoms overlaps
with the segment itself repeated by translation. These requirements are owned by the computer program
TRY (entirely based on internal coordinates) which allows both structure modelling and structure
refinement. Chain continuity is ensured and maintained during refinement using Lagrange’s multipliers.[1]
Three recently studied problems will be illustrated: a) the syndiotactic 1, 2-poly(4-methyl-1, 3-pentadiene) a
triclinic polymer with 36 C atoms in the asymmetric unit);[2] b) the polyisobutene;[3] c) the natural rubber.[4]
References
1.
2.
3.
4.
34
A. Immirzi J. Appl. Crystallogr. (2007), 40, 1044.
A. Immirzi, C. Tedesco, S. V. Meille, A. Famulari, S. van Smaalen Macromolecules (2003), 40, 3666.
A. Immirzi, D. Alfano, C. Tedesco J. Appl. Crystallogr. (2007), 40, 10.
A. Immirzi, C. Tedesco, G. Monaco, A. E. Tonelli Macromolecules (2005), 38, 1223.
kn14
The ab-initio structure solution from polycrystalline
compounds in EXPO2009: new strategies
R. Rizzi1, A. Altromare1, C. Cuocci1, C. Giacovazzo1,2 and A. Moliterni1
2
1 CNR- Istituto di Cristallografia, 70126 – Bari
Universita’ degli Studi di Bari, Dip. Geomineralogico, 70125 – Bari
In the last twenty years the interest for the ab initio crystal structure solution by powder diffraction data
has been considerably increased. Great efforts in the experimental and theoretical fields have been made
to overcome the typical problems of peak overlapping, background and preferred orientation. The high
quality of data, obtained by modern diffractometers and, particularly, synchrotrons, combined with new
computing procedure, has made possible the solution of a large number of complex structures.
The following steps are necessary to perform a crystal structure solution from powder data: a) unit cell
indexation; b) space group determination; c) crystal structure solution; d) crystal structure refinement.
The package EXPO2009 nowadays includes new routines aiming at making more straightforward the full
pathway for the ab initio crystal structure solution. They concern:
1. The unit cell indexation. A new indexing procedure, optimized for the triclinic system with a
new global figure of merit for recognizing the correct unit cell, has been introduced. The procedure
is also able to automatically estimate the most probable extinction group.
2. Space group determination. The statistical analysis of integrated intensities estimated performing
the full pattern decomposition according to the Laue group.
3. Crystal structure determination. In EXPO2009 has been introduced a recent theory aiming at
reducing the effects of the limited resolution in the electron density maps.
4. MAD technique. The method of joint probability distribution function, has been applied to
powder data to find the anomalous scatterer substructure.
To manage organic crystal structures, particularly resistant to Direct Methods, a new strategy in direct
space, combining Direct Methods and Simulated Annealing approaches, has been implemented.
Key Notes Lectures
35
kn15
Crystalline porous materials and gas absorption properties
A. Comotti, S. Bracco, P. Sozzani
Department of Materials Science, University of Milano Bicocca, I-20125 Milano, Italy
The presentation will be focused on the study of nanoporous materials containing channels of different
cross-sections from 4 to 40 Å for storage and selective absorption of gases such as carbon dioxide, methane
and hydrogen. The confined gases and the recognition of the host-guest interactions were revealed by
a multi-technique approach ranging from synchrotron radiation X-ray diffraction to spectroscopic
methods. The host materials include dipeptide crystals and molecular zeolites[1] as well as metal-organic
frameworks and crystalline hybrid organosilicas.[2] High capacity of gas absorption could be reached in the
largest nanochannels as demonstrated by adsorption isotherms and synchrotron X-ray diffraction whilst
high selectivity (e.g. CO2 vs CH4), especially at low pressure was obtained in the narrow channels of
dipeptides. The dipeptide crystals allow to fabricate hydrophobic nanochannels with a remarkable affinity
for molecular hydrogen, suggesting new strategies for the use of biological building blocks in the field of
materials for gas storage.
The open pore structure and the easy accessibility of the nanochannels to the gas phase was demonstrated
by hyperpolarized (HP) Xenon NMR. This technique revealed an unprecedented description of the
nanochannel space and the internal surfaces as well as the orientation of the aligned nanochannels in
single crystals (the selective absorption of xenon into the cavities with cross-section larger than 3 Ǻ).
Gases such as carbon dioxide and methane were observed directly by 13C and 1H NMR after their diffusion
into the channels lined with aromatic rings. The upfield chemical shift caused by the host ring currents
onto the guest molecules at the van der Waals contacts provided an unconventional tool to measure the
intermolecular distances and determine the CH...π interactions. In hydrogen-bonded assisted molecular
crystals a combined approach of X-ray diffraction and solid state NMR could highlight the dual properties
of identical guest molecules confined in two amphipathic nanospaces with very distinct geometries and
polarities.
A recent discovery in nanoporous hybrid materials revealed the high molecular mobility of aromatic
elements in the crystalline pore walls.[3] This creates extended arrays of molecular rotors that decorate the
surfaces of the nanochannels and are easily accessible to the diffusing gases.
References
1. a) A. Comotti, S. Bracco, G. Distefano, P. Sozzani Chem. Commun. (2009), 284. b) P. Sozzani, S. Bracco, A. Comotti,
L. Ferretti, R. Simonutti Angew. Chem. Int. Ed. (2005), 44, 1816 . c) A. Comotti, S. Bracco, L. Ferretti, M. Mauri, R.
Simonutti, P. Sozzani Chem. Commun. (2007), 350. d) A. Comotti,P. Sozzani, S. Bracco, S. Hawxwell, M. D. Ward Cryst.
Growth Des. (2009), ASAP.
2. a) A. Comotti, S. Bracco, S. Horike, R. Matsuda, M. Takata, S. Kitagawa J. Am. Chem. Soc. (2008), 130, 13664. b) A.
Comotti, S. Bracco, P. Valsesia, L. Ferretti, P. Sozzani J. Am. Chem. Soc. 2007, 129, 8566.
3. S. Bracco, A. Comotti, P. Valsesia, B. F. Chmelka, P. Sozzani Chem. Commun. 2008, 4798
36
kn16
A multidisciplinary study of sulfonamide antibiotics
adsorbed in HY faujasite zeolite: X-Ray, spectroscopic,
resonance and theoretical investigations
M. Cossi1, I. Braschi1,2, A. Martucci3, G. Gatti1, G. Paul1, C. E. Gessa2, A. Alberti3, L. Marchese1
1. Università del Piemonte Orientale, Dip. di Scienze e Tecnologie Avanzate - DISTA, 15100 - Alessandria
2. Università di Bologna, Dip. di Scienze e Tecnologie Agroambientali, 40127 - Bologna
3. Università di Ferrara, Dip. di Scienze della Terra, 44100 - Ferrara
Sulfonamide antibiotics, widely used for the treatment of bacterial, protozoal and fungal infections
in human therapy, livestock production and aquaculture, may cause severe pollution of water bodies.
Recently, some of the authors have proposed an effective technique to remove such pollutants from water
bodies using cheap and safe materials as zeolites.
We report on experimental and computational studies of the interaction of three sulfonamides into a
highly dealuminated HY zeolite. The host/guest antibiotics and zeolite interactions are elucidated by a
multidisciplinary approach including XRPD, SS-NMR, FTIR and Raman spectroscopy, along with high
level ab initio computational modelling.
The comparison between experimental and theoretical results allow us to propose a structure for the
sulfonamides embedded into zeolite cages and to evaluate the key factors driving the adsorption process.
Figure 1. The DFT optimized structure of sulfachloropyridazine molecule embedded in a zeolite cage.
Key Notes Lectures
37
orals communications
MS1-OR2
Acetylene adsorption in a calixarene
based organic microporous crystal
L.Erra1, C. Tedesco1, M. Brunelli2, V. Cipolletti1, C. Gaeta1,
J. L. Atwood3, A. N. Fitch2, P.Neri1, A. Immirzi1
1. Dipartimento di Chimica, Università di Salerno, 84084 Fisciano (SA), Italy
2. ESRF European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
3. Departement of Chemistry, University of Missouri-Columbia, USA
At the Dept. of Chemistry of the University of Salerno we prepared and characterized a crystalline solid based
on p-But-calix[4]dihydroquinone 1 revealing an high BET surface area (230 m2 g-1) and the simultaneous
existence of interconnected water channels and very large hydrophobic cavities (988 Å3). Interestingly the
supramolecular framework is preserved also after the removal of channel water molecules.[1,2]
Combining two different experimental techniques and theoretical calculations it has been possible to study
the adsorption of acetylene in the porous structure.
Volumetric adsorption measurements were performed using an home-made volumetric system[3] at 3
different temperatures (298 K, 278 K and 203 K) and at initial pressures between 0.1 and 0.5 atm. In
most favourable conditions for adsorption (the higher pressure and the lower temperature) the efficiency
of 1 for acetylene adsorption is 2.41 wt% while, in the same condition, for methane molecules, the value
resulted 1.22 wt%. The ratio between gas molecules and calixarene molecules and is 1:2, which means
an approximate number of 24 acetylene molecules per unit cell. High resolution XRPD data have been
collected at ESRF beam line ID31 at 298, 213 and 173 K and 0.5 atm pressure with the aim to understand
the temperature effect on the sorption process in the host structure and to locate the acetylene molecules.
For this purpose the simulated annealing procedure, as implemented in the program TOPAS[4] has been
used. It resulted that the host structure does not show any significant alteration with respect to the previous
model[1] confirming that the material behaves as a supramolecular zeolite; nevertheless the cell parameter
is affected by the sorption and, in particular, it increases as the temperature decreases. The guest molecules
are located inside the channels and they do not show any specific contacts with the host framework.
Interesting interactions can be detected among the acetylene molecules: the ethyne group may work as
a hydrogen bond donor as well as an acceptor[5], in this way we can distinguish 24 pair of acetylene
molecules joined by this CH/π (C≡C) bond.
References
1.
2.
3.
4.
5.
40
C. Tedesco, I. Immediata, L. Gregoli, L. Vitagliano, A. Immirzi, P. Neri, CrystEngComm (2005), 7, 449.
P.K. Thallapally, B. P. McGrail, J.L. Atwood, C. Gaeta, C. Tedesco, P. Neri, Chem. Mater. (2007), 19, 3355.
J. L. Atwood, L.J. Barbour, P.K. Thallapally, T.B. Wirsig, Chem. Comm. (2005), 51.
A. A. Coelho, J. Appl. Cryst. (2000), 33, 899.
M. Nishio, CrystEngComm (2004), 6, 130.
MS1-OR1
Supramolecular design of functional materials based
on metallorganic wheel-and-axle systems
A. Bacchi, G. Cantoni, M. Carcelli, P. Pelagatti, M. Zecchini
Università di Parma, Dipartimento di Chimica GIAF, 43124 - Parma
This work is focused on inclusion propensity of hybrid organic-inorganic systems designed to have a wheeland-axle shape, which has shown to be favourable to inclusion of small guest in the solid state. Molecular
shape has a key role in orienting and modulating crystal packing efficiency, and it is consequently also
crucial in determining host-guest properties of solid state materials. It has been suggested that when the
shape of the molecule is too complex to allow efficient self-recognition, host-guest inclusion compounds
are preferentially formed, since the potential voids are filled by guests. Dumb-bell molecules, also called
wheel-and-axle possess a shape that make them good candidates for hosting small guests in the crystal
lattice. Recently we have been particularly interested in the realization of organic-inorganic systems
able to capture and to release reversibly small guests, and we have shown that the size and shape of the
organic ligands are crucial in determining the inclusion propensity of these materials.[1] These systems
generally assemble in soft dynamic frameworks that can create pores on demand to accommodate small
guest molecules, by switching between two similarly stable states, the apohost sustained by host---host
contacts, and the solvate form, sustained by host---guest interactions.
Figure 1. Typical host-guest arrangement for metallorganic wheel-and-axle systems
Here we investigate the influence on inclusion properties of shape modifications induced by changing
the metal stereochemistry and the wheel hindrance, and we present new metal-organic wheel-and-axle
(waamo) systems based on ruthenium half-sandwich units, designed in order to favour the creation of
bistable flexible networks.
References
1. A. Bacchi, M. Carcelli, T. Chiodo, F. Mezzadri, CrystEngComm (2008) 10, 1916
Orals Communications
41
ms1-or3
Supramolecular interactions in solid state: tubes, stripes and waves
in inorganic organic hybrids with diphosphinates and bipyridines
A. Ienco1, F. Costantino2, A. Guerri3, S. Midollini1
1. ICCOM-CNR, 50019 Sesto Fiorentino (Firenze), Italy
2. Dipartimento di Chimica e CEMIN , Università di Perugia, 06123 Perugia, Italy
3. Dipartimento di Chimica, Università degli Studi di Firenze, 50019 Sesto Fiorentino (Firenze), Italy
Phosphonic and phosphinic acids play an important role in engineering coordination polymers.[1] The linker
P,P’-diphenylmethylenediphosphinato (pcp) (see Scheme 1) has been recently found capable to assembly
divalent metal ions to give a number of hybrids materials with a various architectures.[2]
Scheme 1
In this comunication, we compare the structures of a series of metal hybrids isolated using bipositive metal
ions and pcp together with different bipyridine linker. The dramatic effect produced by the change of the
aliphatic chain connecting the pyridine is discussed looking at the supramolecular forces involved in the
building of the three-dimensional structures in the solid state.
Figure 1. From the left to the right the polymers [[Cu(pcp)(4,4’bipy)0.5] 2.5H2O]n, [[Cu(pcp)(bpye)] 2H2O]n and
[[Cu(pcp)(bpyp)0.5] H2O]n form respectively in 1D tubes, 1D stripes and 2D waves.
References
1. A. Vioux, J. Le Bideau, P.H. Mutin, D. Leclerq Top Curr. Chem. (2004), 232, 143.
2. J. Beckmann, F. Costantino, D. Daknernieks, A. Orlandini, A. Duthie, A. Ienco, S. Midollini, C. Mitchell, A. Orlandini, L.
Storace Inorg. Chem. (2005) 44, 9416; S. Midollini, P. Lorenzo-Luis, A. Orlandini Inorg. Chim. Acta (2006), 359, 3275 and
references therein.
42
ms1-or4
Cyclen derivative sensors for multiple applications
in solution and solid state
G. Ambrosi1, S. Ciattini2, M. Formica1, V. Fusi1, L. Giorgi1,
E. Macedi1, M. Micheloni1, M. A. Varrese1
1. Institute of Chemical Sciences, University of Urbino, I-61029 Urbino, Italy
2. CRIST, University of Florence, I-50019 Sesto F.no, Firenze, Italy
In the recent years, many efforts have been devoted to the design of receptors capable of selectively
recognize cations, anions and substrates of biological interest, signalling the interaction by chromatic
change or fluorescence enhancement. To this aim, a suitable building-block is the cyclen moiety due to
its ability in binding several guests and to its easy functionalization, the latter allowing to obtain versatile
receptors of different topologies.
The linkage of a fluorophore to the cyclen moiety is a strategy to switch on or off the fluorescence upon the
coordination of a guest, as for the new NBD-polyaza-macrocycle sensor L, that becomes fluorescent, with
different emission wavelengths, when the Cu(II) and Zn(II) cations are coordinated in acetonitrile, thus L
shows to be an effective metal ion sensor.
The crystalline L-Cu(II) complex shows solid state fluorescence.
Figure 1. (a) Linkage of a sensor to the cyclen unit; (b) ORTEP drawing of the complex [CuLCl]+
43
ms2-or1
Structural relaxation around Cr3+ in YAlO3-YCrO3
perovskites from electron absorption spectra
M. Ardit1, G. Cruciani1, M. Dondi2, F. Matteucci2, M. Blosi2,3, M. C. Dalconi4, S. Albonetti3
1.
2.
3.
4.
University of Ferrara, Department of Earth Sciences, 44100 Ferrara
Institute of Science and Technology for Ceramics (ISTEC-CNR), 48018 Faenza
University of Bologna, Department of Industrial Chemistry and Materials, 40136 Bologna
University of Padova, Department of Geosciences, 35137 Padova
The structural relaxation around Cr3+ in YAl1-xCrxO3 perovskites (Pnma space group) was investigated and
compared with analogous Cr-Al joins (corundum, spinel, garnet). Eight compositions (xCr3+=0, 0.035, 0.075,
0.135, 0.25, 0.5, 0.75, 1.0) were prepared by sol-gel combustion and analyzed by a combined X-ray diffraction
(XRD) and electron absorption spectroscopy (EAS) approach. At variance to what observed in the series of
(REEs,Y)AlO3 perovskites, the unit cell parameters and the XRD averaged octahedral (Cr,Al)-O and [VIII]Y-O
bond distances scale linearly with the chromium fraction, in apparent agreement with the Vegard’s law.[1] In
reality, the octahedral volume expansion due to Cr-Al substitution is not directly transferred to the whole unit
cell, but it is partially compensated by tilting phenomena and through a significant change of the effective
coordination number of Y in the A site below xCr3+~0.4. The optical parameters show an expected decrease
of crystal field strength (10Dq) as well as an increase of covalency (B35) and polarizability (B55) towards
YCrO3, but non linear trends outline some excess 10Dq, with constant B35 and B55, below xCr3+~0.4. The local
Cr-O bond lengths, as calculated from EAS, indicate a compression from 1.98Å (xCr3+=1.0) down to 1.95Å
(xCr3+=0.035), so that the relaxation coefficient is ε=0.54, implying a remarkably low structural relaxation in
comparison with garnet (ε=0.74)[2], spinel (ε=0.68)[3] and corundum (ε=0.58)[4]. This ranking is likely due to a
progressive decrease of polyhedral network flexibility, but the lowest relaxation degree of perovskite appears
to be somewhat in contrast with its structural features. The enhanced covalent character of the Cr3+-O-Cr3+ bond
in the one-dimensional arrangement of corner-sharing octahedra can be invoked as a factor limiting to some
extent the perovskite network flexibility. The comparably lowest ε v alue of Y(Al,Cr)O3 perovskites found in
this study can be also understood by considering an additional contribution to 10Dq due to the electrostatic
potential of the rest of lattice ions upon the localized electrons of the CrO6 octahedron.[5] Such an “excess” 10Dq
increases when the point symmetry of the Cr site is low, as in perovskite, and would be non-linearly affected
by the change of yttrium effective coordination number observed by XRD for xCr3+ below ~0.4. The above
interpretation would justify the systematic underestimation of local Cr-O bond distances, as inferred from
EAS, compared to what derived from XAS studies, implying a stronger degree of relaxation around Cr3+ of all
the structures considered (ε~1 for garnet,[6] 0.83 for spinel,[7] 0.76 for corundum,[8] ~0.8 for perovskites). These
results support the hypothesis that crystal field strength from EAS contains more information than previously
retained, particularly an additional contribution from the next nearest neighbouring ions. Furthermore this
insight into the interdependence of colour on crystal structure is a key to understand in depth the colour
mechanism and design new and more efficient pigments, exploiting the different chromatic spectra from the
chromium end-member (green) to the Cr-doped aluminium end-member (red).
References
1.
2.
3.
4.
5.
G. Cruciani, F. Matteucci, M. Dondi, G. Baldi, A. Barzanti Z. Kristallogr. (2005), 220, 930.
K. Langer, A.N. Platonov, S.S. Matsyuk Z. Kristallogr. (2004), 219, 272 - M. Andrut, M. Wildner Am. Mineral. (2001), 86, 1219.
D. Reinen Structure and Bonding (1969), 6, 30.
C.P. Poole, J.F. Itzel J. Chem. Phys. (1963), 39, 3445 - D. Reinen Structure and Bonding (1969), 6, 30.
J.M. Garcia-Lastra, J.A. Aramburu, M.T. Barriuso, M. Moreno Phys. Rev. B (2006), 74, 115118 - J.M. Garcia-Lastra, J.Y. Buzaré,
M.T. Barriuso, J.A. Aramburu, M. Moreno Phys. Rev. B (2007), 75, 155101.
6. A. Juhin, G. Calas, D. Cabaret, L. Galoisy, J.-L. Hazemann Am. Mineral. (2008), 93, 800.
7. A. Juhin, G. Calas, D. Cabaret, L. Galoisy, J.-L. Hazemann Phys. Rev. B (2007), 76, 054105.
8. É. Gaudry, A. Kiratisin, Ph. Sainctavit, Ch. Brouder, F. Mauri, A. Ramos, A. Rogalev, J. Goulon Phys. Rev. B (2003), 67, 094108.
44
ms2-or2
Compressibility of the Ca2Sb2O7 weberite-like compound:
In situ high-pressure single-crystal X-ray diffraction study
L. Chelazzi1, T. Boffa Ballaran2, F. Nestola3, L. Bindi4 P. Bonazzi1
1.
2.
3.
4.
Dipartimento di Scienze della Terra, Univ. Firenze, 50121, Firenze
Bayerisches Geoinstitut, Universität Bayreuth, 95440, Bayreuth, Germany
Dipartimento di Mineralogia e Petrologia, Univ. Padova, 35137, Padova
Museo di Storia Naturale, Sezione di Mineralogia, Univ. Firenze, 50121, Firenze
The weberite-like minerals and compounds have a broad range of chemical and physical properties and
great technological potential. In particular, the A2Sb2O7 (A = Ca2+, Pb2+ and Sr2+) are among the most studied
weberites owing to their ferroelectric properties. Therefore, investigation of their thermodynamic properties
(e.g. thermal expansion and compressibility) is crucial in determining their stability field. Nonetheless,
no data on compressibility of antimoniates have been reported in literature so far, except for the natural
ingersonite, MnCa3Sb4O14[1], which adopts a weberite-3T structure. In this work we have investigated the
synthetic compound Ca2Sb2O7 having a weberite-2O structure by means of in situ single-crystal X-ray
diffraction at high-pressure using a diamond anvil cell. In both polytypes, the octahedrally coordinated
Sb5+ and the larger A (Mn2+ and/or Ca) cations form a packing which deviates only slightly from the ideal
ccp array of the pyrochlore structure. Aim of the work was to determine the high-pressure behaviour and to
compare the obtained results with those previously obtained for ingersonite. The high-pressure data were
collected at room temperature up to Pmax = 9.2 GPa on a crystal of Ca2Sb2O7. Unit-cell data were measured
at 16 different pressures. No phase-transition was observed in the range of pressure investigated. The P-V
data, as suggested by the relative FE-fE plot, were fitted using a second-order Birch-Murnaghan Equation
of State (EoS). The refined EoS coefficients are: V0= 555.8(1) Å3 and K0 = 155(1) GPa. The value of the
bulk modulus obtained for Ca2Sb2O7 appears to be identical to that reported for ingersonite [154(2) GPa
[1]
]. Although the bulk moduli of the two weberite compounds are simila, their respective high-pressure
behaviour seems to be significantly different with respect to their axial compressibility. Indeed, ingersonite
compresses almost isotropically whereas Ca2Sb2O7 shows a marked anisotropic compression. On the whole
range, the increase of pressure leads to smaller distortion of the Ca2Sb2 pseudocubic array.
References
1. P. F. Zanazzi, L. Chelazzi, P. Bonazzi, L. Bindi Am. Min. (2009), 94, 352.
45
ms2-or3
Phase transitions induced by solid-solution:
The BCa – BMg substitution in richteritic amphiboles
G. Iezzi1,2, G. Della Ventura3, M. Tribaudino4, P. Nemeth5,
I. Margiolaki6, A. Cavallo2, F. Gaillard7, H. Behrens8
1.
2.
3.
4.
5.
6.
7.
8.
Dipartimento DIGAT, Università G. d’Annunzio, Chieti, Italy
INGV, Roma, Italy;
Dipartimento di Scienze Geologiche, Università di Roma Tre, Roma, Italy
Dipartimento di Scienze della Terra, Università di Parma, Italy
Department of Surface Modifications and Nanostructures, Budapest, Hungary
European Synchrotron Radiation Facility (ESRF), Grenoble, France
ISTO, Université d’Orleans, Orléans, France
Institut of Mineralogy, University of Hannover, Hannover, Germany
Eleven compositions along the join Na(NaMg)Mg5Si8O22(OH)2 (“magnesiorichterite”) - Na(NaCa)
Mg5Si8O22(OH)2 (richterite) have been synthesized at T = 800-850°C and PH2O = 0.35-0.5 GPa. The runproducts have been characterized by electron probe micro-analysis (EPMA), synchrotron and conventional
X-ray powder diffraction (XRPD), Fourier transformed infrared (FTIR) spectroscopy and selected area
electron diffraction (SAED-TEM). Nominally, the chemical variation along the join can be expressed
as BMgx BCa1-x with 0 ≤ x ≤ 1. A combination of EPMA and FTIR data in the OH stretching region show
that a complete solid-solution is obtained under the used conditions. Nevertheless, a slight deviation from
the nominal compositions involving a limited loss of Na at A- and B-sites, balanced by an increase of Ca
at the B-site, is present. Several indications of a displacive and coelastic P21/m → C2/m transformation
induced by the Ca-Mg chemical substitution are observed. The phase transition occurs (Xc) at a B-site
composition close to B(Na1Mg0.7Ca0.3). A significant strain tail is observed behind this stoichiometry and
is correlated to local compositional inhomogeneities; the residual strain disappears as the amount of BCa
significantly increases respect to that of BMg. The transformation behavior observed here mirrors that of
pyroxenes along the join diopside (CaMgSi2O6) - enstatite (Mg2Si2O6). The cell parameters of amphiboles
with CMg5, TSi8 and W(OH)2 and variable A- and B-site populations follow almost linear and continuous
trends, indicative of small amount of spontaneous strain accompanying these monoclinic phase transitions
and the absence of miscibility gaps at high-temperature among different amphibole groups.
46
ms2-or4
Compressibility of serpentine: the case of antigorite
F. Nestola1, R.J. Angel2, J. Zhao2, C.J. Garrido3, V. López
Sánchez-Vizcaíno4, G. Capitani5, M. Mellini6
1.
2.
3.
4.
5.
6.
Dipartimento di Geoscienze, Università di Padova, 35137-Padova
Crystallography Laboratory, Virginia Tech, VA 24061-Blacksburg
Instituto Andaluz de Ciencias de la Tierra, CSIC and UGR, 18002-Granada
Departamento de Geología, Universidad de Jaén, Escuela Polítecnica Superior, 23700-Linares
Dipartimento di Scienze Geologiche e Geotecnologiche, Università di Milano Bicocca, 20126-Milano
Dipartimento di Scienze della Terra, Università di Siena, Siena
Serpentine minerals attracted much attention in the last 20 years not only due to their importance as
major rock forming minerals but also because one of serpentine form (chrysotile) is inserted in the list
of asbestos minerals. Therefore, determining their thermodynamic properties (e.g. compressibility and
thermal expansion) is crucial to define serpentine stability field and chemical-physical properties. Only
recently, one of the serpentine form, antigorite, has been discovered for the first time as a well crystallized
sample. Such discover not only allowed to refine the crystal structure for the first time[1,2] but also in
this study allowed us to determine the compressibility and in general the high-pressure behaviour of
antigorite by single-crystal X-ray diffraction with greater accuracy than previous investigation performed
on polycrystalline material[3]. The sample was studied in situ using a diamond anvil-cell up to about 9
GPa. Between 6 and 6.5 GPa a significant anomaly, marked by a volume softening, was found and never
reported before. The volume softening is a consequence of the anomalous behaviour of the c axis and β
angle. Due to the softening it was not possible to fit the pressure – volume data using a single equation
of state but a 3rd –order Birch-Murnaghan equation was used to fit the data only to 5.8 GPa giving the
following coefficients: V0 = 2914.07(23) Å3, KT0 = 62.9(4) GPa, K′ = 6.1(2). The volume compressibility,
βV, can be calculated as -1/KT0 resulting in βV=0.015898 GPa-1.
Figure 1. The pressure – volume data in this study (filled squares) fitted by a 3rd-order BM3 EoS: the data at pressures greater than 7
GPa could not be fitted indicating an anomalous volume softening. For purpose of comparison previous data were reported.
References
1. G. Capitani, M. Mellini Am. Min. (2004), 89, 147.
2. G. Capitani, M. Mellini Am. Min. (2006), 91, 394.
3. N. Hilairet, I. Daniel, B. Reynard Geophys. Res. Lett. (2006), 33, L02302.
47
ms3-or1
On the growth rates, shape and composition of
AlGaAs nanowires by Au-catalyzed MOVPE
P. Paiano1, P. Prete2, E. Speiser,3 B. Buick,3 N. Lovergine,1 and W. Richter3
1. Università del Salento, Dipartimento di Ingegneria dell’Innovazione, 73100 - Lecce
2. IMM-CNR, Unità di Lecce, 73100 - Lecce
3. Dipartimento di Fisica, Università di Roma Tor Vergata, 00133 - Roma
We report on the growth of AlGaAs nanowires by Au-catalyzed MOVPE and on their morphological
and compositional characterization. Colloidal Au nanoparticles in aqueous solution with average diameter
around 60-70 nm were used as catalyst and deposited on (111)B-GaAs substrates. AlGaAs nanowires were
grown using trimethylgallium, trimethylaluminum (TMAl), and tertiarybutylarsine (TBAs). Growth runs
were performed between 450°C and 575°C under a H2 flow of 7.0 l/min and 50 mbar reactor pressure. Fieldemission SEM observations showed that nanowires grown under an Al fraction in the vapour xv=0.50 are
kink-free with their axis along the [111]B substrate direction and a tapered morphology. Nanowires grown
under xv=0.68 are more kinked, possibly a result of Al-induced instabilities at the Au-catalyst/nanowire
interface. The phonon spectra of AlGaAs nanowires still on their original substrate were measured by
Raman scattering with micrometer spatial resolution by means of a scanning confocal microscope system.
In order to determine the nanowire stoichiometry we exploited the fact that the phonon frequencies in mixed
crystals depend on composition[1]. Quantitative analyses of the Raman spectra indicated that nanowires
grown below 475°C are made of GaAs; these nanowires are n-type doped, an effect ascribed to residual
Si contamination in TMAl[2]. Spectra of samples grown above 475°C revealed instead several GaAs- and
AlAs-like LO phonon modes, indicating the presence of different Al compositions. By displacing the
microscope focal plane in the vertical (i.e., along the nanowire [111] axial) direction the composition in
different parts of single AlGaAs nanowires was investigated. Present experimental results are consistent
with the AlGaAs nanowires having a core–shell structure, with a higher Al composition in the nanowire
core than in the shell: for xv=0.50, both core and shell compositions increase monotonically with the growth
temperature up to 550°C, the core reaching a maximum xAlcore=0.60, with the shell composition remaining
below about xAlshell=0.20. The nanowire axial growth rate above 475°C increases with temperature and
stays well above that of GaAs nanowires (i.e., without TMAl)[3], while no substantial differences with
respect to the GaAs case are observed for growth along the sidewalls. However, their section gradually
changes from hexagonal- (as for GaAs nanowires [7]) to triangular-shaped with increasing the Al content,
a result ascribed to different AlGaAs growth rates along the nanowire [211]A and [211]B directions.
References
1. O.K. Kim, and W.G. Spitzer, J. Appl. Phys. 50 (1979) 4362.
2. P. Prete et al., J. Cryst. Growth 310 (2008) 5114.
3. P. Paiano et al., J. Appl. Phys. 100 (2006) 094305.
48
ms3-or2
NaCl anomalous mixed crystals grown from water-formamide
solutions. Adsorption-absorption and growth morphology.
L. Pastero, D. Aquilano
Università degli Studi di Torino, Dip. di Scienze Mineralogiche e Petrologiche, 10125 – Torino
Formamide (H-CO-NH2) is a well known habit modifier of NaCl crystals, since the pioneering work by
Boistelle et al. [1] , who showed that the {111} octahedron becomes dominant at the expense of the cube,
when going from pure aqueous to formamide-doped solutions. However, no explanation has been done, up
to now, on its surface adsorption mechanism.
Here, we will deal with the crystallization of sodium chloride either from aqueous solutions, in the presence
of 20% formamide, or from pure formamide, as limiting case.
Figure 1. Left side: {111} octahedron dominating the {100} cube of NaCl crystals grown from aqueous solution in
the presence of formamide (20% wt). Right side: Thermo Gravimetric Analysis carried out on the as grown crystals
(shown on the left side). The weight loss with temperature shows six steps, each of them corresponding to different
bond energies between absorbed formamide layers and different NaCl lattice planes, within the growing crystal.
It will be demonstrated that:
1. Formamide is 2D-epitaxially adsorbed, through its {101} form, on the {111} NaCl octahedron
that competes with the cube, according to the formamide percentage in solution
2. After the adsorption, formamide is buried into the growing crystal, owing to the strong
compatibility between the thickness of the respective growing steps (d111(NaCl) = 3.25Å while
d101(formamide) = 3.05Å). Then, the absorption induces the formation of anomalous mixed crystals,
according to the original definition by Seifert [2] and Neuhaus [3].
3. The absorption does not generate homogeneous crystals, as it is proved by X-ray patterns and
especially by TGA diagrams showing a sharp stepped behaviour of the weight loss.
References
1. M. Bienfait, R. Boistelle, R. Kern « Adsorption et Croissance Cristalline » Ed. CNRS vol. 152 (1965), 577.
2. H. Seifert Fortschr. Miner. (1935), 19, 103.
3. A. Neuhaus Z. Krist. (1937), 97, 28.
49
ms3-or3
Crystallization of soluble proteins suitable for
single crystal X-ray diffraction: the difficult cases
S. Mangani1,2, M. Benvenuti1
1. Dipartimento di Chimica, Universita` di Siena, Siena 53100, Italy.
2. CERM, Università di Firenze, Firenze 50019, Italy.
The preparation of protein single crystals represents one of the major obstacles in obtaining the detailed
3D structure of a biological macromolecule. The complete automation of the crystallization procedures
requires large investments in terms of money and labor, which are available only to large dedicated
infrastructures and is mostly suited for genomic-scale projects. Furthermore, the systematic screening of
the multiparametric crystallization space is practically unfeasible.
On the other hand, many research projects from departmental laboratories are devoted to the study of
few specific proteins. In our experience and to the best of our knowledge, understanding the chemistry
of the protein under study by investigating it by a variety of tools, provides essential information for the
success of crystallization and even if it lengthens the initial steps of the process, it might represent the
only approach to achieve crystallization. Such approach has been successful even for proteins that are
characterized by a molten-globule-like state in solution[1,2]. Here, we provide clues based on our experience
and a series of examples for the crystallization of soluble proteins, with emphasis on the difficult cases.
References
1. M. Benvenuti, S. Mangani Nat. Protocols (2007), 2, 1633
2. L. Banci, I. Bertini, V. Calderone, F. Cramaro, R. R. Del Conte, A. Fantoni, S. Mangani, A. Quattrone, M.S. Viezzoli Proc.
Natl. Acad. Sci. U S A. (2005), 102, 7541.
50
ms3-or4
On the theoretical equilibrium morphology
of gypsum (CaSO4·2H2O)
D. Aquilano
Università degli Studi di Torino, Dip. di Scienze Mineralogiche e Petrologiche, 10125 Torino, Italy
The theoretical equilibrium morphology of gypsum (CaSO4·2H2O) has been reassessed, starting from
the historical papers by Simon and Bienfait (1965)[1] and by Heijnen and Hartman (1991)[2]. The surface
profiles of the most recurrent crystal forms have been determined following two ways: in the first one we
used the Hartman-Perdok method (the PBC analysis, based on the interaction between first neighbouring
growth units) while in the second one the profile of each face was obtained using the GDIS program[3].
In both cases, the calculation of the specific surface energy has been made using the GULP code[4]. From
the synthesis of the two methods a new and much more isotropic equilibrium shape is calculated, for both
unrelaxed and relaxed surfaces. Further, and for the first time, beyond the well known and singular {010},
{120}, {0-11} and {-111} F-forms, two stepped, {100} and {-122}, and one kinked form, {-102}, are
found to build the equilibrium shape of gypsum.
The evolution of the theoretical equilibrium shape of gypsum: from the pioneering works by Simon and
Heijnen & Hartman (left side) to the present prediction which consider both the PBC theory and the way
codified in the GDIS programme (right side).
References
1.
2.
3.
4.
B.Simon, M. Bienfait Acta Cryst. 1965, 19, 750.
P.Hartman , W.M.M. Heijnen, J. Crystal Growth 1983, 63, 261.
S. Fleming, A. Rohl, Z. Krist. 2005, 220, 580.
J.D .Gale, J. Chem. Soc. Faraday Trans. 1997, 93(4), 629.
51
ms4-or1
Polymeric films with three different orientations
of s-PS helical crystalline phases
A. R. Albunia1, P. Rizzo1, O. Tarallo2, V. Petraccone2 and G. Guerra1
1. Dipartimento di Chimica and INSTM Research Unit, Università degli Studi di Salerno, 84084, Fisciano, Italy
2. Dipartimento di Chimica “Paolo Corradini”, Università di Napoli “Federico II”, 80126 Napoli, Italy
Polymer crystals, although generally much smaller than inorganic and organic crystals, present the
advantage of easy orientation, also at macroscopic scale. In fact, for all semicrystalline polymers it is easy
to get axial orientation of the crystalline phases. Moreover, as for s-PS films, exhibiting co-crystalline
phases with low-molecular-mass molecules,1 it is possible to achieve the unprecedented formation of three
different kinds of uniplanar orientations.2
The three uniplanar orientations achieved for s-PS co-crystalline phases can be maintained after guest
extraction leading to the nanoporous δ phase, as well as after annealing leading to the dense helical γ phase.
Then, by chloroform treatment, the nanoporous ε phase is obtained, thus getting three different orientations
of the crystalline nanochannels with respect to the surface of also macroscopic films.3
Figure 1. Representation of the limit ordered uniplanar orientations for the nanoporous δ (A-C) and ε (D-F) crystalline
phases. The symbols ⊥ and // indicate crystal axes being perpendicular and parallel to the film surface, respectively.
Suitable procedures allow the transformation from the δ orientations sketched in A-C into the ε orientations sketched in
D-F, respectively. The red lines indicate the possible preferential direction of interchannel guest diffusion for the ε phase.
The availability of s-PS films with three different kinds of uniplanar orientation allows establishing fine
structural features, e.g., experimental evaluation of the orientation of transition moment vectors of host and
guest vibrational modes. It also allows active guest orientation and guest diffusivity control.
References
1. O. Tarallo, V. Petraccone,V. Venditto, G. Guerra Polymer (2006), 47, 2402.
2. A.R. Albunia, P. Rizzo, O. Tarallo, V. Petraccone, G. Guerra Macromolecules (2008), 41, 8632.
3. A.R. Albunia, P. Rizzo, G. Guerra Chemistry of Materials DOI: 10.1021/cm900968c.
52
ms4-or2
Long range order and self-assembly driven by
epitaxial crystallization in block copolymers
Claudio De Rosa, Finizia Auriemma, Giovanni Talarico, Rocco Di Girolamo, and Rossella Aprea
Dipartimento di Chimica “Paolo Corradini”, Università di Napoli “Federico II”, Napoli, (Italy)
Epitaxy is defined as the oriented growth of a crystal on the surface of a crystal of another substance (the
substrate). The growth of the crystals occurs in one or more strictly defined crystallographic orientations
defined by the crystal lattice of the crystalline substrate.[1] The resulting mutual orientation is due to a twodimensional or, less frequently, a monodimensional structural analogy, the lattice matching, in the plane
of contact of the two species.[1,2]
The crystallization of polymers induced by epitaxy on specific substrates is a powerful means to induce
crystallization of various polymorphic forms of polymers and obtain high and specific orientation of
crystals that cannot be obtained generally with the classic methods of crystallization of single crystals or
bulk material.[2,3]
Recently, it has been demonstrated that epitaxy may be used to control the morphology of semicrystalline
block copolymers and to obtain ordered nanostructure, in particular nanopatterns on the surface of thin
films.[4]
In this communication we have used epitaxy for the crystallization of a diblock copolymer, constituted
by crystallizable syndiotactic polypropylene (sPP) block covalently linked to an amorphous ethylene/
propylene random copolymer (EP) block (sPP-EP), on the surface of crystals of p-terphenyl (3Ph). The
epitaxial crystallization has produced “edge on” orientation of sPP lamellar single crystals onto the
substrate surface, and a high orientation of the lamellar microdomains made of alternating amorphous EP
and crystalline sPP layers. The crystalline layers are parallel sPP lamellae oriented edge-on on the substrate
surface with the b axis of sPP parallel to the b axis of 3Ph crystals.
This ordered nanostructure has been used as host for the selective inclusion of gold nanoparticles by simple
evaporation and deposition obtaining innovative nanocomposites where the positioning of the nanoparticles
is ordered and guided by the order produced in the polymer matrix by epitaxy. This procedure provides a
simple method for the obtainment of block-copolymer based hybrid nanocomposites ordered over large
area, useful for many applications in thin films technology.
References
1.
2.
3.
4.
5.
L. Royer Bull Soc Fr Mineral Crystallogr (1928), 51, 7.
GS. Swei GS, JB.Lando JB, SE. Rickert SE, KA.Mauritz Encyclopedia Polym. Sci. Eng. (1986), 6, 209.
J.C. Wittmann, B. Lotz Prog Polym Sci (1990), 15, 909.
C. De Rosa, C. Park, E. L. Thomas, B. Lotz Nature (2000), 405, 433.
W. Stocker, M. Schumacher, S. Graff, J. Laug, J.C. Wittmann, A.J. Lovinger, B. Lotz, Macromolecules (1994), 27, 6948.
53
ms4-or3
Strategies for the control of crystallinity in
PANI/nanodiamond composites
V. Guglielmotti1, E. Tamburri1, V. Giacani1, M. L. Terranova1, S. Orlanducci1 and M. Rossi2
1. Università degli Studi di Roma ‘Tor Vergata’, Dipartimento di Scienze e Tecnologie Chimiche, 00133 - Roma
2. Università degli Studi di Roma ‘Sapienza’, Dipartimento di Energetica, 00100 – Roma
Polyaniline (PANI) is one of the most interesting conducting polymers, intensively investigated over the
past decades due to the striking electronic and optical properties of a material easy to synthesize and
environmentally stable. PANI has been also proposed as matrix for the preparation of nanocomposites,
using as fillers metal and metal oxide nanoparticles, carbon nanotube, fullerene and clays. The insertion
of nanosized fillers was found to enable the assembling of architectures with a high-degree of control over
the polymer crystallinity.
In this work, for the first time, innovative composites based on PANI and nanodiamond particles were
prepared. In particular, ultra disperse diamond (UDD) nanocrystals with average size of 4-5 nm were
added during the oxidative polymerization of ANI.
Morphological and structural characterization of the nanocomposites have been performed by Scanning
Electron Microscopy, Raman Spectroscopy and X-Ray Diffraction. The effects produced on the crystalline
structure of PANI by the UDD insertion was clearly evidenced by the analysis of the diffraction data.
The nanodiamond particles behave as critical nuclei around which nucleation of the polymer proceeds.
Moreover the presence of UDD in the solution accelerates the polymerization process indicating a catalytic
effect.
Applications being explored for these structured nanodiamond/polymer systems include electrochromic
displays, batteries, artificial muscles, microelectronics, bionic interfaces and sensors.
54
ms4-or4
Clathrates of syndiotactic polystyrene with guest
molecules imprisoned in channels: structure
of the co-crystal with p-nitroaniline
M. M. Schiavone, O. Tarallo, V. Petraccone
Università degli Studi di Napoli Federico II, Dipartimento di Chimica “P. Corradini”, 80126 - Napoli
Syndiotactic polystyrene (s-PS) is able to form different kinds of co-crystalline phases with a large number
of guest molecules. All of these exhibit a s(2/1)2 helical polymer conformation, with a repetition period
of nearly 0.79 nm. Most s-PS co-crystals can be obtained by guest sorption in the nanoporous δ phase
of s-PS and are characterized, as the δ form, by the presence of ac layers of close-packed alternated
enantiomorphous helices. These δ type co-crystals can be divided in two classes. In the first one guest
molecules are imprisoned into isolated cavities cooperatively generated by two enantiomorphous helices
of two adjacent ac layers. These clathrates have been defined as δ clathrates and are generally characterized
by a guest/monomer-unit molar ratio ¼.[1] The second class of s-PS co-crystals, defined as intercalates, is
characterized by the same ac layers of helices. In these co-crystals, guests are not isolated but contiguous
inside layers intercalated with the ac polymer layers. These structures generally present a guest/monomerunit molar ratio of ½.[1] Finally, a third class of s-PS co-crystals, with a definitely different structure,
has been obtained by guest sorption in the recently discovered nanoporous ε phase of s-PS.[2] In this
class, guest molecules are imprisoned into channels passing the unit cell from side to side along the c
direction. This new class of s-PS co-crystals has been defined as ε clathrates. For s-PS co-crystals, the 3-D
orientational order of the guest molecules can be also extended to macroscopic level being possible the
obtainment of co-crystalline and nanoporous films exhibiting three different kinds of uniplanar orientations
of the crystalline phases. This gives the unique opportunity of controlling, also at a macroscopic scale,
the orientation of active guest molecules, by choosing the orientation of the polymeric host phases. For
example, δ and ε co-crystalline phases can be easily obtained with molecules of very high polarity (like
p-nitroaniline, µ≈6.2D) allowing the preparation of s-PS co-crystals that, by appropriately controlling
the dipole orientation are suitable for electrical poling processes, possibly leading to non-linear optical,
ferro-electric and piezo-electric properties.[2a,3] This contribution presents, for the first time, the detailed
description of the crystalline structure of the ε clathrate form of s-PS with p-nitroaniline. This structure
presents guests arranged in the channels of the ε form with their main molecular plane parallel to the bc
plane and their dipole almost parallel to the chain axis. In each channel guests are stacked with the same
relative dipole orientation and are not uniformly distributed but arranged in “couples” in which subsequent
molecules are linked by hydrogen bonds analogously to what has been found for the crystal structure
p-nitroaniline.[4]
References
1. O. Tarallo, V. Petraccone, V. Venditto, G. Guerra Polymer (2006), 47, 2402 and references therein.
2. (a) P. Rizzo, C. Daniel, A. De Girolamo Del Mauro, G. Guerra Chem.Mater. (2007), 19, 3864. (b)V. Petraccone, O. Ruiz de
Ballesteros, O. Tarallo, P. Rizzo, G. Guerra Chem.Mater. (2008), 20, 3663.
3. O. Tarallo, V. Petraccone, C. Daniel, G.Guerra Cryst. Eng. Comm. (2009), in press.
4. K. N. Trueblood, E. Goldish, J. Donohue Acta Cryst (1961), 14, 1009.
55
ms5-or1
Mechanism of CDK9 auto-regulation and of its
inhibition by flavopiridol revealed by crystal
structures of the CDK9/CycT1 complex
G. Lolli1,2,3, S. Baumli1, L.N. Johnson1
1. University of Oxford, Laboratory of Molecular Biophysics, OX1 3QU – Oxford
2. Venetian Institute of Molecular Medicine, 35129 – Padova
3. Universita’ di Padova, Dipartimento di Scienze Chimiche, 35131 - Padova
Cyclin Dependent Kinases (CDKs) regulate the cell division cycle, apoptosis, transcription and
differentiation in addition to functions in the nervous system. Their deregulation is involved in different
diseases ranging from several types of cancer to AIDS. The positive transcription elongation factor b
(P-TEFb) (CDK9/cyclin T (CycT)) promotes mRNA transcriptional elongation through phosphorylation
of elongation repressors and RNA polymerase II. To understand the regulation of a transcriptional CDK
by its cognate cyclin, we have determined the structure of the CDK9/CycT1 complex [1]. There are
distinct differences between CDK9/CycT1 and the cell cycle CDK CDK2/CycA manifested by a relative
rotation of 26 degrees of CycT1 with respect to the CDK, showing for the first time plasticity in CDK
cyclin interactions. The CDK9/CycT1 interface is relatively sparse but retains some core CDK-cyclin
interactions. Flavopiridol, an anticancer drug in phase II clinical trials, binds to the ATP site of CDK9
inducing unanticipated structural changes that bury the inhibitor. CDK9 activity and recognition of
regulatory proteins are governed by autophosphorylation. We show that CDK9/CycT1 autophosphorylates
on Thr186 in the activation segment and three C-terminal phosphorylation sites. Autophosphorylation on
all sites occurs in cis.
References
1. S. Baumli, G. Lolli. E.D. Lowe, S. Troiani, L. Rusconi, A.N. Bullock, J.E. Debreczeni, S. Knapp, L.N. Johnson EMBO J.
(2008), 27, 1907-18.
56
ms5-or2
The crystal structure of intact Human Complement Factor I
Pietro Roversi1, Steven Johnson1, Stefanos Tsiftosglou2, Ling ChiauChow2, Tony Willis2, Alister Dodds2, Bob Sim2,3 and Susan Lea1
1. Sir William Dunn School of Pathology, Oxford University, Oxford OX1 3RE, England, UK
2. Department of Biochemistry, Oxford University, Oxford OX1 3QU, England, UK
3. Department of Pharmacology, Oxford University, OX1 3QT, Oxford, England, UK
The determination of the crystal structure of Human Complement Factor I will be discussed. The intact,
fully glycosylated protein has been isolated from blood-bank human plasma by monoclonal antibody
affinity chromatography, purified by size exclusion chromatography and cleaned of residual contaminants
by further affinity chromatography. Diffraction data from two crystal forms were used to determine the
structure. Initial phases were obtained by molecular replacement using models for 4 of the 5 domains and
the structure was completed by iterative model building and refinement, guided by multi-crystal fourfoldaveraged density-modified structure amplitudes and phases. The crystal structure elucidates many aspects
of the biochemistry and physiological functions of factor I, its known disease-associated human mutations,
and constitutes a major step towards a molecular characterisation of its interactions with C3b, C4b and
cofactors. The structure will provide a basis for the development of structure-based Factor I specific
inhibitors, distinct from known cross-reacting thrombin inhibitors, which may find application in renal
disease and transplantation.
57
ms5-or3
Present challenges in Biocrystallography data
collection and related instrumentation
M.Cianci1, G.Bourenkov1, S.Fiedler1, M.Roessle1, and T.R.Schneider1
EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
In the recent years new trends and challenges have appeared in biocrystallography. With the limited success
of expression with recombinant technologies, mammalian proteins are increasingly purified directly from
natural sources, with consequent heavy atom derivatization for phasing having a second golden age.
One example is the homodimeric mammalian fatty acid synthase (FAS), a 270-kilodalton cellular
multienzyme complex, which was purified from porcine mammary gland, and phased to 4.5 Å resolution
with MIRAS with U and Pt[1]. In another case the molecular organization of cypovirus polyhedra, purified
from insect cells, was elucidated with the 2Å crystal structure of both recombinant and infectious silkworm
cypovirus polyhedra determined using crystals of 5–12 microns in diameter. The structure was phased
using Au, Ag, Se and I derivatives[2].
At synchrotrons such projects require the provision of automation, microbeams, radiation damage issues
and new strategies for data collections.
Moreover, low-resolution structures may also be further investigated by complementing crystallographic
information with in-crystallo spectroscopy. In fact by combining polarized EXAFS and x-ray diffraction
data on PSII single crystals, the photosystem II (PSII) Mn4Ca cluster, which catalyzes oxidation of water
to dioxygen, was constrained in geometry and placed within PSII at resolution of 3.5 Å[3].
At PETRA III, the new 3rd generation synchrotron at DESY in Hamburg, the European Molecular Biology
Laboratory (EMBL) is building state-of-art beam lines devoted to macromolecular crystallography.
MX1 monochromator will be tunable over the energy range 5(4) to 17 keV to allow crystallographic
data acquisition on a broad range of elemental absorption edges for experimental phase determination.
In addition it will offer Si (311) for narrow band pass for new developments in phasing and in-crystallo
spectroscopy. This beam line will also provide a very low beam divergence (0.2 mrad (H) x 0.15 mrad (V))
and variable focus size (20 to 100 microns) to adapt to challenging biological projects. We will discuss
the challenges of modern biocrystallography data collection and how ideas and perspectives have been
transferred into the design of MX1 beam line in particular.
References
1. T. Mayer et al., Science 311, 1258 (2006);
2. F. Coulibaly et al., Nature 446, 97 (2007);
3. J. Yano et al., Science 314, 821 (2006).
58
ms5-or4
Structural basis of Serine/Threonine Phosphatase
inhibition by the archetypal cantharidin ligands
I. Bertini, V. Calderone, M. Fragai, C. Luchinat and E. Talluri
The inhibition of human Ser/Thr Protein Phosphatase activity is responsible for the citotoxicity of
cantharidin and norcantharidin against tumor cells. It is shown that the anhydride rings of cantharidin
and norcantharidin are hydrolized when bound to the catalytic domain of the human isoform 5 (PP5c),
and the high-resolution crystal structures of PP5c complexed with the corresponding dicarboxylic acid
derivatives of the two molecules are reported. Norcantharidin shows a unique binding conformation with
the catalytically active Mn2PP5c, while cantharidin is characterized by a double conformation in its binding
mode to the protein. Different binding modes of norcantharidin are observed depending on whether the
starting ligand is in the anhydride or in the dicarboxylic acid form. All these structures will provide the
basis for the rational design of new cantharidin-based drugs.
59
ms6-or1
Turning the debye-function into an efficient totalscattering approach for nanocrystalline materials
A. Guagliardi 1, A. Cervellino2 and C. Giannini 3
1. Istituto di Cristallografia, IC-CNR 70126 - Bari
2. SLS-PSI, CH-5232 – Villigen, Switzerland
3. Istituto di Cristallografia, IC-CNR 70126 - Bari
The synthesis of materials at the nanoscale (metals, oxides, semiconductors and more complex objects,
such as Hybrid NCs) has registered a continuous progress in the last decades along with the control of their
properties as a function of atomic structure, size and shape distributions of the nanocrystalline domains.
In most cases, synthesis aims at obtaining: i) a narrow size and shape distribution, ii) protection against
aggregation and chemical stability over the time, and iii) a wide range of chemical compositions. Each
of these features can play an important role in producing unique physical-chemical properties of relevant
interest in a countless number of applications: catalysis, data storage, magnetic resonance imaging, optics,
opto-electronics, biotechnology, medicine, industrial and environmental applications, etc. Despite the
importance of a full structural and microstructural characterization of small NCs (<10 nm) for a deeper
understanding of properties and for tailoring functional materials towards optimized features, Diffraction
Methods traditionally available for the structural analysis of materials have not caught up with the fast
advances of synthesis procedures and the complexity of the problem. NCs are materials with a shortrange order that, in the diffraction space, turns into a diffuse scattering between the Bragg peaks. Only
Total Scattering approaches, such as the Pair Distribution Function (PDF) and the Debye Function (DF)
methods, can simultaneously account for both Bragg and diffuse intensities, deal with ordered as well as
disordered materials, and use the entire information content of the experimental diffraction pattern. The
DF method relies on the distribution of the interatomic distances within the sample, which are computed
from atomistic models of NCs, but suffers from very long computational time. A project has been set
off in the last years to optimize the computational efficiency of DF approach in order to quantitatively
extract structure, size, size-dependent strain and shape distributions from the powder diffraction pattern of
nanocrystalline materials1-3. Applications to spherical-like NCs will be presented. The work is in progress
to match the complex problem of modeling variable shapes (rods and platelets) and layered structures and
some preliminary results will be also shown.
References
1. A. Cervellino, C. Giannini, A. Guagliardi - J. Appl. Crystallogr. (2003), 36, 1148.
2. A. Cervellino, C. Giannini, A. Guagliardi, M. Ladisa - Phys. Rev. B (2005), 72, 035412-(1-9).
3. A. Cervellino, C. Giannini, A. Guagliardi - J. Comp. Chem. (2006), 27, 995.
60
ms6-or2
Polymorphism in drugs
N, Masciocchi1, E. Maccaroni1, L. Malpezzi2
1. Università dell’Insubria, Dipartimento di Scienze Chimiche e Ambientali, 22100 Como, Italy
2. Politecnico di Milano, Dipartimento di Chimica, 20131 Milano, Italy
In recent years, pharmaceutical companies often required the complete and exact determination
of the solid-state structure of Active Pharmaceutical Ingredients (API’s)[1], since the same API, in
the different crystal forms, may show different activity, solubility, bioavailability, permeability
and adsorption from the tissues or biological membranes, thus heavily influencing the efficiency
(and toxicity) of the pharmaceutical formulation[1]. Accordingly, we have recently started a project,
in collaboration with some Italian Pharmaceutical Industries, on the structural characterization of
API’s[2]. Following our experience in solving structures from polycrystalline samples, we shifted our
interests to the rich crystal chemistry of marketed drugs, discovering new polymorphs and solvates.
In-situ thermodiffractometry, solid state 13C CP-MAS NMR and simultaneous TG/DSC analyses helped in
assigning the correct stoichiometry, space group symmetry and solid-state reaction and phase transformation
processes.
Figure 1. The last born: Bupropione hydrochloride
References
1. R. Hilfiker. Polymorphism in the Pharmaceutical Industry, Wiley-VCH, 2006.
2. To mention a few: G. Fantin, M. Fogagnolo, O. Bortolini, N. Masciocchi, S. Galli, A. Sironi. New J. Chem. 27 (2003)
1794; L. Malpezzi, G.A. Magnone, N. Masciocchi, A. Sironi. J. Pharm. Sci. 94 (2005) 1067-1078; E. Maccaroni, E. Alberti,
L. Malpezzi, N. Masciocchi, C. Vladiskovic. Int. J. Pharm. 351 (2008) 144-151; E. Maccaroni, E. Alberti, L. Malpezzi, N.
Masciocchi, C. Pellegatta. J. Pharm. Sci. 97 (2008) 5229-5239; E. Maccaroni, G.B. Giovenzana, G. Palmisano, D. Botta, P.
Volante, N. Masciocchi. Steroids. 74 (2009) 102-111.
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Direct space methods in EXPO2009
C. Cuocci1, A. Altomare1, C. Giacovazzo1,2, A. Moliterni1 and R. Rizzi1
1. Istituto di Cristallografia (IC-CNR), 70126 – Bari
2. Dipartimento Geomineralogico, Università di Bari, 70126 - Bari
Direct space methods for crystal structure determination from powder diffraction data have become widely
available and popular in recent years and have successfully been applied to solve the structures of organic,
inorganic and organometallic materials. Different but similar procedures can be realized: grid search,
Monte Carlo, simulated annealing (SA), parallel tempering, genetic algorithm. Each method involves the
generation of a random sequence of trial structures starting from an appropriate 3D model and moving
it until to find a good match between the calculated and the observed pattern. The information about
chemical knowledge of molecules is actively used to reduce the number of parameters to be varied: bond
distances and angles are usually known and kept fixed while only the torsion angles are varied during the
procedure. Several commercial and public software implementing this techniques are now available: FOX,
DASH, TOPAS, PowderSolve, ESPOIR, Endeavour.[1] EXPO2009, the last version of EXPO[2] program,
a widely used software able to solve powder crystal structure by Direct Methods (DM), includes also a
SA direct space strategy. Respect to other programs EXPO2009 provides the capability of combining
and comparing the results from DM and SA so increasing the reliability of the structure solution.[3] The
direct space procedure is not oriented only towards organic molecules. Also non-molecular compound can
be solved by using the dynamical occupancy correction for atoms lying on special positions and atoms
sharing the same position in the crystal structure. Graphical interface can be used to import the starting
model in different formats (mol, mol2, z-matrix, cif), to modify the default options of SA algorithm (type
of cost function, starting temperature, cooling rate, number of moves, number of SA runs, random number
seed, powder pattern resolution), to decide which parameters are fixed or refined, to explore the solutions
at the end of SA. The progress of the structure solution can be monitored by: 1) the visualization of the
best model, 2) the visual comparison between the observed and calculated pattern, 3) the graph of cost
function value against number of moves. Numerous tests demonstrate that using direct space approach in
EXPO2009 is possible to solve routinely structures up to about 15 degrees of freedom with diffraction data
of reasonable quality but more complex structures can be solved with appropriate chemical knowledge and
excellent data.
References
1. L.M.D. Cranswick Powder Diffraction Theory and Practice RCS Publishing, Cambridge (2008), 494.
2. A. Altomare, R. Caliandro, M. Camalli, C. Cuocci, C. Giacovazzo, A. Guagliardi, A.G.G. Moliterni R. Rizzi J. Appl. Crystallogr.
(2004), 37, 1025.
3. A. Altomare, R. Caliandro, C. Cuocci, C. Giacovazzo, A.G.G. Moliterni, R. Rizzi, C. Platteau J. Appl. Crystallogr. (2007), 41,56.
62
ms6-or4
Insights on qualification of materials via “On site XRD”
G. Berti1, F. De Marco2
1. Diaprtimento di Scienze della Terra – Università di Pisa, 56126 - Pisa
2. XRD-Tools, 56124 – Pisa
Recent advances on x-ray Diffraction (XRD) extend concepts, methods and technologies to give solutions
to some still standing problems. Among these problems the qualification of materials for their intended
uses identifies the XRD method as the excellent one. The excellence stems from the recently achieved
availability of the following functionalities complying with many of the several needs and requirements
of the qualification:
■■ Non destructive testing approach
■■ Collection of data on the site where the manufacture is located, possibly without any contact
or manipulation of the specimen and even from a variable distances from the surface under
investigation
■■ Adaptability of the instrument to the orientation of the surface and to the lattice orientation of
the materials
■■ Robotic functionalities and remote controllability
In order to obtain a non destructive application of x-ray diffraction in the most restrictive sense the first
step has been obtained by the implementation of a new diffractometer (DifRob® US patent n.726,178).
DifRob is a fine positioning and pointing system actuated through a controllable and interactive feedback
for auto-focusing before starting the x-ray diffraction measurements. Besides the functionalities of the
new technological development there are also new concepts evolving from the traditional in lab. x-ray
diffraction to the “on site NDT x-ray diffraction”. These new concepts involves:
■■ the alignment verification of the x-ray optics that is no longer intrinsic to the instrument but
involves also the orientation of the surface under investigation; the surface is kept fixed and distant
from the instrument;
■■ the calibration involves not only the intrinsic performances of the instrumental devices but
includes the environment conditions.
The consequence is that the traditional characterization of materials (e.g. crystallographic structure,
mineralogical composition of compounds, etc.) assumes a sort of static and ideal meaning. It is no longer
useful to qualify the material for its intended uses. The qualification of the material for the intended use
shall consider the interfaces and the interaction of its implant on the manufacture; the qualification is the
calculation of the convolution of several models describing the material (according to the characteristic
parameters), the instrument and the environment (with the expected variations). This convolution of
models shall comply with the data collected from monitoring the manufactures on site. Even the reference
materials shall selected according to the purposed they are used. So the distinction between the calibration
specimen shall be considered when the specimens is used either to calibrate the instrument performances
(i.e to calculate the residual and not removable systematic contributions) or to identify the benchmarks of
the properties under investigation. These benchmarks represent the origin of the scale where measuring
the variations of the properties in relation to the variation of the environment, the ageing, degradation and
the time. The paper reports some example of experiments performed to identify the appropriate specimen
to the investigate properties.
63
ms7-or1
MAD techniques applied to the structure solution
from powder data: a new probabilistic approach
Maria Cristina Burla1, Angela Altomare2, Corrado Cuocci2, Carmelo Giacovazzo2,3,
Fabia Gozzo4, Anna Moliterni2, Giampiero Polidori1, Rosanna Rizzi2
1.
2.
3.
4.
Dip. Scienze della Terra Università di Perugia, Perugia, 06100, Italy,
IC, CNR, Bari, 70126, Italy,
Dipartimento Geomineralogico Università di Bari, 70125, Bari, Italy
Paul Scherrer Institute, Swiss Light Source,Villingen PSI, 5232, Switzerland
Phase determination via multiple-wavelength anomalous dispersion (MAD) techniques, owing to the
tunability of the wavelength of the synchroton radiation, is one of the most popular approaches for the
solution of the phase problem in protein crystallography. The classical MAD technique is essentially
a three-step procedure: a) the estimation of the structure factor moduli of the anomalous scatterer
substructure; b) the location of the anomalous scatterers via Patterson or Direct Methods; c) the protein
phase estimation. MAD techniques were not very beneficial for powder crystallography owing to the
unavoidable peak overlapping in powder patterns. Indeed: a) the reflections F+ and F- systematically
overlap: consequently, anomalous differences |F+|2 - |F-|2 cannot be measured, and only the intensities Ih
= |F+|2 + |F-|2 are experimentally available; b) dispersive differences between (|F2+|2 + |F2-|2) and (|F1+|2
+ |F1-|2) may be estimated from the experiment, however the estimates may be heavily affected by
the casual and/or by the systematic overlapping present in the diffraction patterns. The evident minor
experimental information provided by a powder diffraction experiment discouraged the use of MAD
and its applications up to now. This new approach combines the joint probability distribution function
method with MAD techniques to solve the phase problem from powder data. The probabilistic bases
of the method were established and the distributions are calculated by assuming the prior knowledge
of the scattering intensities Ih collected at two wavelengths, the first close to the absorption edge of the
anomalous scatterer and the second far away from it. The method is able to derive from these quantities
the formulas providing estimates of the substructure structure factor moduli |Foa| which allow to retrieve
the anomalous scatterer positions by means of Patterson deconvolution or Direct Methods [1]. Given the
anomalous scatterer substructure the method leads to formulas estimating the full structure phases and
their reliability [2]. The related procedure was implemented into a modified version of EXPO2004 [3].
Applications to synchrotron data will be shown.
References
1. Altomare et al. (2009) J.Appl.Cryst. 42, 30-35.
2. Altomare et al. (2009) Acta Cryst. A65, 291-299
3. Altomare et al. (2004) J.Appl.Cryst. 37, 1025-1028.
64
ms7-or2
New computing strategies for protein structure
determination by X-ray crystallography
R. Caliandro1, B. Carrozzini1, G. L. Cascarano1, C. Giacovazzo1,2, A. Mazzone1 and D. Siliqi1
1. CNR, Istituto di Cristallografia, 70126 - Bari
2. Università degli Studi di Bari, Dipartimento Geomineralogico, 70126 – Bari
New algorithms developed by our team allow pushing forward the limits of crystallographic methods for
protein structure determination and reducing as much as possible the manual efforts in all the steps of the
phasing process. Modern crystallography uses several tools for extending and improving phases: electron
density modification (EDM), difference Fourier synthesis and automatic procedures to build and refine
structural models starting from approximated electron density maps (AMB).
The difference Fourier synthesis tool, routinely used for model completion, has been recently revised[1],
and, as a result, peculiar features have emerged. They have been exploited by developing a new phase
refinement tool: the Difference Electron Density Modification (DEDM). It showed to improve phase
values in a complementary way with respect to the standard EDM tool, therefore a novel procedure, called
EDM-DEDM has been devised, which increases the potentialities of the two separate tools[2]. Furthermore,
the EDM, DEDM and AMB tools have been combined into a single, iterative procedure, called DEA, to
perform both the phase refinement and the model building steps in a fully automatic way[3]. It has been
tested by starting from very approximated models and/or electron density maps, considering both known
and unkown protein structures. It proved to be more effective in obtaining the protein solution, by greatly
reducing the manual efforts to reach it. In particular, it has been shown that DEA succeeds where different
combinations of the single programs fail and that it greatly increases the efficiency of the structure solution
process. From the point of view of the execution time, DEA shows a supplementary practical advantage.
Since most of the computing time is spent by the AMB programs, the use of the DEDM- EDM cycles
reduces the number of AMB applications, and thus dramatically reduces the total computing time.
The new algorithms have been included into the package IL MILIONE[4], provided with a user-friendly
graphic interface, and available under licence agreement. It may be integrated by external AMB programs
via suitable scripts.
References
1.
2.
3.
4.
R. Caliandro, B. Carrozzini, G.L. Cascarano, L. De Caro, C. Giacovazzo, D. Siliqi Acta Cryst. (2008), A64, 519.
R. Caliandro, B. Carrozzini, G.L. Cascarano, C. Giacovazzo, A. Mazzone, D. Siliqi Acta Cryst. (2009), D65, 249.
R. Caliandro, B. Carrozzini, G.L. Cascarano, C. Giacovazzo, A. Mazzone, D. Siliqi Acta Cryst. (2009), D65, 477.
M.C. Burla, R. Caliandro, M. Camalli, B. Carrozzini, G.L. Cascarano, L. De Caro, C. Giacovazzo, G. Polidori, D. Siliqi, R.
Spagna J. Appl. Cryst. (2007), 40, 609.
65
ms7-or3
Electron diffractive imaging of transition-metal
oxide nanocrystals at 70 pm resolution
Liberato De Caro1, Elvio Carlino2, Gianvito Caputo3,4,
Pantaleo Davide Cozzoli3,4, Cinzia Giannini1
1.
2.
3.
4.
Istituto di Cristallografia (IC-CNR), 70126 Bari, Italy
TASC-INFM National Laboratory, Area Science Park - Basovizza, 34012 Trieste, Italy
Scuola Superiore ISUFI, Università del Salento, Distretto Tecnologico, 73100 Lecce, Italy
National Nanotechnology Laboratory (NNL) of CNR-INFM, Unità di Ricerca IIT, 73100 Lecce, Italy
Diffractive imaging has recently proved to be a powerful method to study the structure of nano-matter,
since the synergic use of measured diffraction patterns and phase-retrieval techniques is able to bypass the
need for imaging lenses, avoiding the resolution limits associated to their aberrations. As the resolution, in
principle, is limited only by the amount of high-angle scattering[1,2], diffractive imaging has the potential
to achieve atomic resolution for hard X-rays or other short-wavelength particles. Indeed, by electron
diffractive imaging (EDI), the projected potential of well-aligned atomic columns of individual nanoobjects has been reconstructed with a sub-ångström resolution. Presently, shape and internal structure
of Au[3] and CdS[4] nanocrystals of few nm diameters have been already achieved, reaching a spatial
resolution of about 80 pm. We here phase-retrieved electron diffractive HRTEM images of individual
TiO2 nanocrystals at 70 pm resolution, even exposing the specimen to a low electron dose.[5] For the first
time, while retrieving the detailed crystal structure of the oxide nanomaterial, O atomic columns were
visualized in the coupled EDI-HRTEM experiment without the need for any lens aberration corrector.[6]
In addition, our approach allowed us to reveal subtle deviation of the nanocrystal unit cell structure from
the bulk counterpart. These highlighting results demonstrate EDI-HRTEM as a unique tool to study the
actual atomic structure of nanomaterials with an unprecedented level of accuracy and sensitivity to light
atomic elements.
References
1. Miao, J., Charalambous, P., Kirz, J. & Sayre, D. Extending the methodology of X-ray crystallography to allow imaging of
micrometre-sized non-crystalline specimens. Nature 400, 342-344 (1999).
2. Abbey, B. et al. Keyhole coherent diffractive imaging. Nat. Phys. 4, 394 (2008).
3. Huang, W. J. et al. Coordination-dependent surface atomic contraction in nanocrystals revealed by coherent diffraction. Nat.
Mater. 7, 308-313 (2008).
4. Huang, W. J., Zuo, J. M., Jiang, B., Kwon, K. W. & Shim, M. Sub-ångström-resolution diffractive imaging of single
nanocrystals. Nat. Phys. 5, 129-133 (2009).
5. De Caro L., Carlino E., Caputo G., Cozzoli P.D., Giannini C., Resolving oxygen atoms at sub-ångström resolution in
transition-metal oxide nanocrystals by diffractive imaging in a transmission electron microscope, unpublished.
6. Urban, K. W. Studying Atomic Structures by Aberration-Corrected Transmission Electron Microscopy. Science 321, 506-510
(2008).
66
ms7-or4
Detection, validation, and use of correlations between peptide
geometry and conformation in oligopeptides and proteins
R. Improta1, L. Vitagliano1, and L. Esposito1
Istituto di Biostrutture e Bioimmagini, CNR, I-80134 Napoli
Over the last decade, the number of high- or ultra-high-resolution protein crystal structures has increased
dramatically[1,2]. Statistical analyses of geometric and conformational parameters of residues in this
extended and very accurate structural database are revealing fine details[3-5]. Deviations of peptide bonds
from planarity have been extensively investigated, but the identification of clear trends for the distortion
derived from experimental data has been controversial[6,7]. We have previously analysed the planarity of
the peptide group by surveying a dataset of atomic resolution protein structures[3,4,7]. We demonstrated that
the values of the ω dihedral angle are strictly correlated to the values of the ψ adjacent angle[7]. In order to
propose an explanation for this experimental trend as well as to investigate the influence of local effects, we
have carried out quantum-mechanics (QM) calculations on different peptide model systems. Calculations
have been performed by density functional theory methods either in gas phase or in solvent, modeled by
using the PCM model. In particular, optimizations of ω angle and geometry have been performed while
setting (φ,ψ) dihedral angles to fixed values which cover the most populated regions of the Ramachandran
map.
Our computations on small model systems are able to reproduce the conformational dependence of θC and
∆ω planarity deviations emerged from experimental data. In addition, the examination of bond distances
and angles involving main-chain atoms reveals a number of previously undetected correlations. Results
of the searching of both the small molecule CSD database and the ultrahigh-resolution protein structure
dataset indicate good agreement with the computational findings.
In conclusion, QM calculations, corroborated by statistical analysis of very accurate protein/peptide
structures, provide a new comprehensive model for the peptide bond plasticity observed in protein and
peptide structures. The unveiled intricate interplay of peptide bond geometrical parameters may represent
a challenging benchmark for force fields developed for crystallographic refinements, molecular mechanics
and molecular dynamics investigations. In addition, the detected correlations may be used as a validation
tool for ultra-high resolution protein structures.
References
1.
2.
3.
4.
5.
6.
7.
C. Lecomte, B. Guillot, N. Muzet, V. Pichon-Pesme, C. Jelsch Cell. Mol. Life Sci. (2004), 61, 774.
L. Esposito, L. Vitagliano, L. Mazzarella Protein and Peptide Letters (2002), 9, 95.
L. Esposito, L. Vitagliano, A. Zagari, L. Mazzarella Protein Eng. (2000), 13, 825.
L. Esposito, L. Vitagliano, A. Zagari, L. Mazzarella Protein Sci. (2000), 9, 2038.
M. Jaskolski, M. Gilski, Z. Dauter, A. Wlodawer Acta Crystallogr. D Biol. Crystallogr. (2007), 63, 611.
M.W. MacArthur, J.M. Thornton J. Mol. Biol. (1996), 264, 1180.
L. Esposito, A. De Simone, A. Zagari, L. Vitagliano J. Mol. Biol. (2005), 347, 483.
67
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Structural investigations on tricyclic sulfonamides
P. Rossi, 1 M. Altamura,2 V. Fedi,2 D. Giannotti,2 P. Paoli1
1. Dip. di Energetica “S. Stecco”, Univ. di Firenze, 50136 Firenze
2. Menarini Ricerche S.p.A., 50131 Firenze
Amongst the molecular moieties recognized as being able to provide high affinity ligands for many types
of receptors, tricycles play an important role both in the field of the drugs for central nervous system
and in other very different applications as reported recently.[1] Amongst these structures we have focused
our attention on those whose skeleton contains an amide (A) or a sulfonamide function (B).[2] It is worth
nothing that the sulfonamide skeletons possess some peculiar properties in terms of both chemical and
pharmacological versatility since they contain positions which are functionalizable in different conditions
rendering these molecules an ideal platform for new derivatives.
Figure 1. Left: examples of tricyclic structures featuring amide and sulfonamide groups; Middle and right: Newmann
projections highlighting different conformations in the solid state structures of the studied species
In the present work we describe a structural investigation both experimental (by single crystal X-ray
diffraction) and theoretical (by quantum chemical calculations) of type B molecules. In particular attention
has been focused on the conformation of the sulfonamide moiety and the present experimental data and
what is considered the standard conformation in sulfonamides are compared and discussed. In fact, given
that several biologically important compounds feature this functional group, the comprehension of the
conformational behaviour of this functionality is one of the key steps in order to clarify the way these
species act at the molecular level.
References
1. V. Fedi, A. Guidi and M. Altamura, Mini-Reviews in Medicinal Chemistry, (2008), 8, 1464.
2. M. Altamura, P. Dapporto, A. Guidi, N. J. S. Harmat, L. Jierry, E. Libralesso, P. Paoli and P. Rossi. New J. Chem., (2008),
32, 1617 and references herein.
68
ms8-or2
Competitive H bonding synthons in organic hydrazides
Roberto Centore1, Angela Tuzi1, Amedeo Capobianco2, Andrea Peluso2
1. Department of Chemistry ”Paolo Corradini”, University of Naples ”Federico II”, 80126 Naples, Italy.
2. Department of Chemistry, University of Salerno, 84084 Fisciano, Italy.
A theoretical, statistical and crystallographic analysis of the H bonding patterns in organic monohydrazides
is presented. The theoretical analysis has shown that the conformation of the hydrazido group with the two
amino H atoms staggered with respect to the amide bond is energetically more favoured. Assuming this
conformation, four intermolecular H bonding patterns can be reasonably foreseen, two forming chains,
C(4) and C22(8), and two forming rings, R22(10) or R22(6).
The frequency of occurrence of the four patterns in the set of crystal structures of hydrazides retrieved
from CSD was evaluated. In particular, it was found that the four motifs are present in 79 % of the total of
the crystal structures of hydrazides found in CSD and that ring motif (III) is the most probable. Finally, the
crystal structures of four new benzohydrazides having additional H bonding donor or acceptor groups in
para position are presented and discussed with reference to the H bonding patterns.
69
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Keto/Enol solid-state polymorphs of 2-thiobarbituric
L. Maini1, D. Braga1, M. R. Chierotti2 L. Pellegrino2, N. Garino2, L. Ferrero2, R. Gobetto2
1. Dipartimento di Chimica G. Ciamician, Università di Bologna, 40126 Bologna, Italy
2. Dipartimento di Chimica I.F.M., Università di Torino, 10121 Torino, Italy
Four new different polymorphs and one hydrate forms of the 2-thiobarbituric acid have been isolated in
the solid state. Form I and the hydrate have enol structure, form II and IV possess keto structure while
form III shows a hybrid structure with a keto and an enol molecule in the asymmetric unit cell. All the
new forms have been characterized by means of single crystal X-ray diffractions, 1D and 2D (1H, 13C
and 15N) solid-state NMR experiments, DSC and Raman spectroscopy. By means of mechanochemical
methods it has been possible to induce keto-enol conversions of the forms. The role of hydrogen bond
interactions in determining the relative stability of the polymorphs and as driving force in the conversions
has been ascertained. This system represents one of the few examples of tautomeric polymorphism
reported in literature leading to the opportunity of facing questions concerning the definition of the term
polymorphism.
70
ms8-or4
Novel zirconium phosphonates based upon chiral building blocks
M. Taddei1, R. Vivani1, F. Costantino1, V. Manuali1, M. Milanesio2
1
Università di Perugia, Dipartimento di Chimica, 06100 - Perugia
2 Università del Piemonte Orientale, 15100 - Alessandria
The research field of zirconium aminomethylenephosphonates is a topic of great interest in the last years
for the large variety of structures, with different dimensionality and reactivity, that can be obtained by
changing the nature of the phosphonate building blocks[1,2,3].
The use of phosphonate groups containing α-aminoacidic moieties gives the chance to obtain microcrystalline
samples with bulk chirality and free carboxylic groups, which could be useful for applications in catalysis,
intercalation of active species and separation of racemic mixtures.
N-phopshonomethyl-L-proline has been synthesized by means of the Moedritzer-Irani method starting
from L-proline. Reacting this building block with zirconium, two different zirconium phosphonates phases
were obtained by changing the synthesis conditions. They had a sufficient crystallinity degree to allow us
ab initio structural investigations.
One of the two phases resulted to be monoclinic and its structure was solved by synchrotron data. It has a
one-dimensional structure made of inorganic fibers with pending organic moieties. This phase undergoes
a transition at 240°C and the solved structure suggests that the inorganic framework is retained, while the
organic five-membered rings rotate.
The second phase is ortorhombic and its structure is still unsolved. It includes water molecules, that are
lost at 100°C, leading to a different structural arrangement. This phase is metastable because when the
synthesis time is increased it converts into the monoclinic phase.
These materials have also been analyzed by IR and Raman spectroscopy, performing either room
temperature and high temperature analysis, thus collecting further data in order to have a better description
of the behavior of the systems.
Work is still in progress to combine spectroscopic and XRPD data.
References
1. U. Costantino, R. Vivani, M. Nocchetti, J. Am. Chem. Soc., 124 (2002) 8428
2. B. Zhang, D. M. Poojary, A. Clearfield, G.Z. Peng, Chem. Mater., 1996, 8, 1333
3. R. Vivani, U. Costantino and M. Nocchetti, J. Mater. Chem., 2002, 12, 3254
71
commercial presentations
cp1
An introduction to the modern Rigaku solutions
Joseph D. Ferrara1, Akira Kishi2, Hideo Toraya2, Paul Ulrich Pennartz3
1. Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, TX, USA 77381
2. Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo, Japan, 196-8666
3. Rigaku European Headquarters, Groß-Berliner-Damm 151, 12487 Berlin, Germany
With hundreds of innovations to its credit, Rigaku is world leader in the fields of protein and small
molecule X-ray crystallography, general X-ray diffraction, X-ray spectrometry, semiconductor metrology,
automation, cryogenics and X-ray optics. We are supplying tools to better semiconductor chips, enabling
drug discovery, improving production line quality or exploring the new frontier of nanotechnology, Rigaku
products and services lead with innovation.
During our presentation we will show latest results from our developments in the world of XRD-powder
diffraction. Here the XRD-DSC, a combination of a powder diffraction system with a complete DSC
(Differential Scanning Calorimetry) attachment is opening new frontiers in the time- and temperature
resolved powder diffraction experiments. Application from general chemistry reactions to applications
from the field of pharmaceutical products will be shown. An example is shown in picture 1
Also our latest developments for a high resolution K-alpha1 Ultima IV/SmartLab system will be presented.
We will show latest application on this innovative solution for high resolution powder diffraction.
In addition, we will also focus on the latest developments in Single Crystal (small molecule) structure
solution. Rigaku’s broad portfolio of detectors (Imaging plate to different CCD detectors), x-ray sources
and goniometers has the ability to fit to scientists needs and budgets.
Figure 1: Phase Transition of Potassium Nitrate simultaneous XRD and DSC measurements
74
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Size distribution and specific surface area determination
of nanosized particles and/or pores by mean of
small-angle X ray scattering (SAXS)
E. Casini1, J. Bolze2, D. Becker2, V. Kogan2,3
1. PANalytical B.V., 20035 – Lissone, Italy
2. PANalytical B.V., 7602 – EA Almelo, The Netherlands
3. DANNALAB, Dipartimento, Enschede, The Netherlands
The use of nanoscaled materials is becoming more and more important in various applications such
as coatings, paints, cosmetics, ceramics, polymers, catalysis and drug delivery. Even at relatively low
concentrations such additives may result in a significant improvement in the desired field of applications.
The properties and performance characteristics of nanoparticles are strongly related to both their size
distribution and specific surface area. Here we present a few examples of the SAXS analysis for the
investigation of crystalline and amorphous materials on a length scale ranging from ca. 1 – 100nm. We will
focus on the characterization with respect to the particle size distribution, specific surface area and pore
size distribution of a few samples such as dry powders, dispersions of inorganic and organic nanoparticles,
porous material. We will show that SAXS analysis results in a fast analytical method where, compared to
BET, TEM and light scattering techniques, no specific sample preparation procedure is requested and at
the same time a good precision is as well guaranteed. In this picture it will be demonstrated that such type
of analysis are possible on a multi-purpose X-ray diffractometer.
Figure 1. Left – SAXS data collected on a 1:1 mixture of two titania nanopowder samples containing particles of
different sizes. Right- Bimodal size distribution by volume as determined from the SAXS data.
75
cp3
Exploiting the potential potential of structural biology
through NMR and associated technologies
L. Vitagliano1, M. Saviano1, E. Vianello1, C. Pedone1
DFM scarl, I-80134 Napoli
EPISIDE is a project funded by the EC in the FP7 program framework. EPISODE’s goal is to maximize the
regional benefits of Structural Biology Research Infrastructures in NMR and associated technologies for
the economic development of the pharma/biotech industries in Tuscany, Berlin-Brandenburg and European
Convergence Regions, including Campania. As traditional Structural Biology research moves towards
new horizons, a major goal has become a systemic view of Life, implying a change of focus from single
molecules and interactions to an integrated view of networks of interactions at varying levels of biological
organization. NMR, X-ray crystallography and other associated technologies are an integral part of such
research, and their importance has recently been reflected in the ESFRI Roadmap’s INSTRUCT Integrated
Structural Biology Infrastructure. While this emerging paradigm presents myriad new opportunities for the
R&D programs of the pharma/biotech sectors, the technologies and their associated research infrastructures
have not yet been fully exploited, a situation that must urgently be understood and rectified. Regions
involved in the project are uniquely poised to meet this challenge, in part through the presence of strong
research infrastructures. EPISODE encourages cooperation and collaboration among regional research
institutions, business and areas agencies to couple research with revenue, through the following actions:
(i) research-driven clusters will be expanded and stimulated interregionally and transnationally; (ii) current
regional capabilities in terms of research potential and exploitation will be studied; (iii) a Joint Action
Plan will be developed to define how to drive future economic development. Dissemination and outreach
efforts, the encouragement of collaborations, support measures for SMEs and spin-offs, and the mentoring
of less-developed regions are given special attention throughout the project. EPISODE will positively
impact research potential and economic potential, with corresponding effects on the health and welfare
of regional, European and global populations. Within the project DFM leads the mentoring activities that
are based on the needs of developing areas to stimulate formation of new research-driven clusters in EU
convergence regions. Updated information on the events organized within the project is available at the
web site : http://www.episodeproject.net/
76
poster communications
MS1-P1
Exploring cyclopeptoids as useful building blocks
G. Cerasuolo, C. Tedesco, C. De Cola, D. Comegna, I. Izzo, F. De Riccardis, A. Immirzi
Dipartimento di Chimica, Università di Salerno, 84084 Fisciano (SA), Italy
The development of self-assembled solid-state supramolecular architectures with nanodimensioned pores
or cavities is an intensively active research area, aiming at the preparation of new materials with potential
applications in nanotechnology such as molecular sieves, sensors, and gas-storage devices.
Taubert and co-workers[1] recently reported on bioinspired metal-peptide frameworks (MPF). In particular
MPF-9 shows a porous network structure, wich is stable up to 250°C. They also point out the limited use
of peptides or peptidomimetics as connectors in realizing metal-organic frameworks.
A new class of promising building blocks could be represented by cyclopeptoids, an archetypal example
of bioinspired peptidomimetics with unique structural and physical properties.
Peptoids differ from peptides in the side chains, which are shifted by one position along the peptide
backbone to the nitrogen atom to give N-substituted oligoglycine. These compounds offer a great variability
in functional groups by simple chemical synthesis.
At the Department of Chemistry of the University of Salerno cyclic tri-, tetra-, and hexa-Nbenzyloxyethylglycines were prepared and their structure and complexing properties were investigated by
means of computational, spectroscopic, and X-ray crystallographic studies.[2]
Figure 1. Tri-, tetra-, and hexa-N-benzyloxyethylglycines (1-3)
References
1. A Mantion, L. Massüger, P. Rabu, C. Palivan, L. B. McCusker, A. Taubert J. Am. Chem. Soc. (2008), 130, 2517.
2. N. Maulucci, I. Izzo, G. Bifulco, A. Aliberti, C. De Cola, D. Comegna, C. Gaeta, A. Napolitano, C. Pizza, C. Tedesco, D.
Flot, F. De Riccardis Chem. Comm. (2008), 3927.
80
ms1-p2
Functionalized of nanoporous crystals of
calixarene/porphyrin complex by ion diffusion
De Zorzi R., Guidolin N., Randaccio L., Geremia S.
Centro di Eccellenza in Biocristallografia, Dipartimento di Scienze Chimiche, Università di Trieste, 34127 Trieste
The high concentration and high degree of order provided by the crystalline state potentially imply high
activity of reactions associated with high stereocontrol. However, among the forms of matter, the solid
state is the least reactive, as reactions in the bulk are generally difficult to promote because of the close
packing. For this reason, microporous frameworks having voids and channels of various aperture sizes
and shapes are important for a wide range of technological applications, such as selective guest storage
and molecular sieving as well as use as nanoreactors[1]. Among the noncovalent frameworks, several
hydrogen-bonded open networks have been designed and realized, exploiting the directional property of
the hydrogen bond[2]. Noncovalent design and synthesis, which are based on nondirectional interactions,
are less accessible because of the inherent difficulty of avoiding a close-packed solid by controlling only
these weak interactions. Among the molecular building blocks, porphyrins appear as very promising
systems for light harvesting with optical properties that can be easily tuned through metallation and
functionalization[3,4]. A negatively charged calixarene[5,6] has been used to form star shaped supramolecular
complexes[7] in presence of four-fold symmetric cationic porphyrin units.
A highly flexible nanoporous material has been obtained by synergistic non-covalent interactions of
calixarene and porphyrin building blocks and characterized by X-ray diffraction on single crystal. This
supramolecular zeolite-like structure has been easily functionalized by diffusion and coordination of metal
ions[8]. Moreover, crystallization experiments conducted in similar conditions using a copper-porphyrin
yield a isomorphous structure, that have been subsequently functionalised by diffusion of metal ions,
obtaining crystals containing two different metal centres. The new bi-functionalized porous material
described here contains a porphyrinic pigment together with a potential catalytic metal centre.
References
1.
2.
3.
4.
5.
6.
7.
8.
Koblenz, T. S., et al., Chem. Soc. Rev. (2008), 37, 247-62.
Desiraju, G. R., Angew. Chem. Int. Ed. (2007), 46, 8342-56.
Scandola, F., et al., Coord. Chem. Rev. (2006), 250(11-12), 1471-96.
Prodi, A., et al., J. Am. Chem. Soc. (2005), 127(5), 1454-62.
Gulino, F.G., et al., Chem. Eur. J. (2006), 12(10), 2722-9.
Di Costanzo, L., et al., Angew. Chem. Int. Ed. (2001), 40(22), 4245-7.
De Zorzi, R., et al., J. Org. Chem. (2007), 72(12), 4528-31.
De Zorzi, R., et al., J. Am. Chem. Soc. (2009), 131(7), 2487-9.
Poster Communications
81
ms1-p3
Anion binding through second sphere coordination
Valeria Ferretti1, Valerio Bertolasi1, Ajnesh Singh2, Raj Pal Sharma2
1. Università di Ferrara, Dipartimento di Chimica and Centro di Strutturistica Diffrattometrica, 44100- Ferrara
2. Panjab University, Department of Chemistry, Chandigarh-160014, India
Anion recognition plays very crucial role in chemistry and many biological processes. Despite their
importance, little has been done in the field of design and synthesis of supramolecular anion receptors
as compared to that of cations. In most of the anion receptor molecules, the basic approach utilized is to
develop an organic framework with the suitable functionalities to bind the anion with the help of hydrogen
bonding interactions. An alternate approach which may be employed is to utilize the second sphere
interactions around the metal centre for the binding of anions, mainly utilizing the directional nature of the
hydrogen bonds and charge transfer electrostatic interactions. In this regard we have undertaken[1] extensive
research program to explore cationic cobalt(III) metal complexes as anion receptors; in particular, we have
focused our attention on complex salts of [Co(phen)3]3+ (phen = 1,10-phenantroline) with a series of anions
differing in size, charge and nature (organic or inorganic).
Figure 1. ORTEPIII view of [Co(phen)3]3+ cation, anions: 2.4-dinitrophenolate; isothiocyanate; [Cd2Br7]3-;
[Cd2Cl7]3-; [V4O12]4-; [S2O8]2-; [Cr2O7]2-
In this communication we report the crystal structures of the above listed salts and a detailed analysis
of their packing modes, with particular reference to those weak intermolecular interactions that, besides
electrostatic forces, contribute to stabilize the crystalline architecture. Understanding of such network
interactions would be rewarding as it can provide means of constructing intricate and novel molecular
entities based on second sphere coordination.
References
1. R.P.Sharma, A. Singh, P. Venugopalan,V. Ferretti, J. Mol. Struct. (2009), 918, 123; R. P. Sharma, A. Singh, I. K. Bharaj, P.
Venugopalan, V. Ferretti, J. Mol. Struct., in press.
82
ms1-p4
Amino-benzodifurane derivatives. Structure and properties
G. Roviello1, A. Carella1, A. Tuzi1 and G. N. Roviello2
1. Università degli Studi di Napoli “Federico II”, Dipartimento di Chimica “P. Corradini”, 80126 Napoli, Italy
2. Istituto di Biostrutture e Bioimmagini-CNR, 80134, Napoli, Italy
Recently, we have elucidated[1] the synthesis and the reactivity of 2,6-diamino,benzo[1,2-b:4,5-b’]difuran3,7-dicarboxylic acid, dialkyl ester and their N,N’-disubstituted derivatives. Single crystal X ray analysis
was performed on some of the prepared compounds thus obtaining informations on the extent of electronic
conjugation.
Figure 1. Amino benzodifurane derivatives Cn (n = 2, 4, 8); R1, R2 = H, COMe, COPh
This feature makes benzodifuranes and their derivatives very interesting for potential applications as
building blocks for optoelectronic devices, as efficient organic dyes for solar cells and as hole-transporting
material in multilayered organic light-emitting diodes (OLEDs).[2] Moreover, this family of compounds
show relevant application in the bioorganic and medical field,[3] i.e. as antiviral drugs. Aiming to contribute
to the last field of application, we have synthesized and characterized benzodifuranes Cn with n= odd, to
obtain more soluble terms suitable for biological applications. In fact, it is well-known that alkyl chains
with odd number of C atoms, influence the crystal packing and then the solubility of the compounds. Cn
with n = 3, 5, 7 were prepared and characterized, also through X-Ray diffraction analysis. The correlation
between the crystal packing and the parity of the alkyl chains will be discussed. Furthermore, X-Ray
molecular structure of oxazinones, obtained by cyclization reaction of the N,N’-benzoyl amide with the
adjacent ester group, showing interesting conductivity properties in the solid state, will be also reported.
References
1. U. Caruso, B. Panunzi, G. N. Roviello, G. Roviello, M. Tingoli, A. Tuzi C. R. Chimie (2009), 12, 622.
2. a) M. Abdul-Aziz, J. V. Auping, M. A. Meador, J. Org. Chem. 60 (1995) 1303; b) J. Daub, M. Beck, A. Knorr, H. Spreitzer,
Pure Appl. Chem. 68 (1996) 1399; c) I. Jung, J. K. Lee, K. Song, S. O. Kang, J. Ko, J. Org. Chem. 72 (2007) 3652; d) H.
Tsuji, C. Mitsui, L. Ilies, Y. Sato, E. Nakamura, J. Am. Chem. Soc. 129 (2007) 11902.
3. a) Z. Feng, S. Mohapatra, P. G. Klimko, M. R. Hellberg, J. A. May, C. Kelly, G. Williams, M. A. McLaughlin, N. A. Sharif,
Bioorg. Med. Chem. Lett. 17 (2007) 2998; b) J. J. Chambers, D. H. Kurrasch-Orbaugh, M. A. Parker, D. E. Nichols, J. Med.
Chem. 44 (2001) 1003.
83
ms2-p1
Characterization of sodalite from sanidinite
rocks of Somma-Vesuvius (Italy)
G. Balassone1, C. Biagioni2, G. Fameli3, A. Mormone1, M. Pasero2, C. Petti4
1.
2.
3.
4.
Università “Federico II”, Dipartimento di Scienze della Terra, I-80134 Napoli
Università di Pisa, Dipartimento di Scienze della Terra, I-56126 Pisa
ENEA, Località Granatello, I-80055 Portici
Centro Museale “Musei Scienze Naturali” Università “Federico II, I-80134 Napoli
Great attention of Earth Science and Material Science researches is devoted to meso- (pores less 20 Å) and
microporous (3-20 Å pores) compounds, that can act as molecular sieves and are distinct from zeolites s.s..
Some examples are framework silicates of the cancrinite-sodalite group, which reveal high flexibility and
versatility in hosting other tetrahedral cations in the lattice and variable channels/cavities components [1,2,3].
Sodalite group minerals show a tetrahedral framework structure (“sodalite-cages”) with general formula
M7-8(T12O24)X1.5-2. The extra-tetrahedral site M contains mainly Na and Ca (less K, Mg, Fe2+, Mn), Si and
Al (Fe3+, Be) occupy the tetrahedral site T, and the X site can contain Cl, So4, CO3, OH, H2O and (S2-)
e (S3-) groups in the lazurites. The extra-tetrahedral molecules in these minerals can play a fundamental
role in the technological applications. Sodalite occurs in numerous Somma-Vesuvius samples, related to
different chemical-physical environments covering a wide range of temperatures (i.e. from those magmatic
to post-magmatic) [4]. Euhedral sodalite crystals can be found in vesuvian ejected rocks, mostly in carbonate
metamorphosed and sanidinite ejecta. Recently, a vesuvian sodalite showing an unusual stoichiometry was
investigated; it shows a content in SO3 (5.7% in weight) more then Cl (3.1% in weight) and about 1.2% in
weight in CO2 [5]. This study concerns a chemical and structural examination of sodalites from sanidinite
ejecta of the private collection of Prof. Enrico Franco, to whom this research is dedicated. We report new
data on compositive features, obtained by SEM-EDS and microprobe study; interesting features have
been pointed out, such as significant amounts of sulphur (up to 7.0 wt% SO3) and mobybdenum (up to 1.2
wt MoO3). The presence of (MoO4)2- as “guest anions” can be pointed out in some synthetic sodalites[6].
Moreover, preliminary powder and single crystal XRD results are presented, together with those from
FTIR and Raman analyses.
References
1.
2.
3.
4.
5.
6.
84
G. Ferraris, S. Merlino Micro- and Meoporous mineral phases Rev. Min. Geoch. MSA (2005), 57, 448 pp.
Krivovichev S. Minerals as advanvced materials Springer (2008), 254 pp.
Z. Zheng, V.V. Guliants, S. Misture J. Porous Mat. (2008), 16, 343-347
M.Russo, I. Punzo I minerali del Somma-vesuvio AMI (2004), 317 pp.
P. Ballirano, A. Maras (2005) Eur. J. Mineral., 17, 805-812.
W. Depmeier, W. Büher Acta Crystall. (1991), B47, 197-206.
ms2-p2
Sr-rich cerussite at Yanque (Peru)
G. Balassone, N. Mondillo and M. Boni
Università “Federico II” Dipartimento di Scienze della Terra, I-80134 – Napoli
The mobility of Pb in the alteration zone of ore deposit is governed largerly by the formation of secondary
minerals such as lead carbonates, sulfates, chlorides, etc. A knowledge of the crystal chemistry of these
Pb-minerals is important for understanding many processes, like transport and re-deposition of Pb during
weathering. Besides their geological importance, formation of Pb-carbonate and oxide and hydroxide
carbonates (e.g. hydrocerussite) is important for lead acid batteries because their presence in battery
plates increases the resistivity of the electrolyte [1]. During the last years low-temperature minerals, like
carbonates, have received considerable attention because of their importance to the environment. Such
phases are important for the transport of heavy metals from ore bodies as well as mine sites and mill tailings
to the biosphere [2]. Cerussite (PbCO3) is an orthorhombic lead carbonate containing up to stoichiometric
78 wt% Pb. For this reason it has an economic relevance as lead metal source. It mainly occurs in oxidation
deposits called “Nonsulfides zinc - lead” ores, to be distinguished from the classical sulphide (sphalerite
– ZnS, and galena - PbS) ore deposits. This study is focused on a crystal chemical characterization of
cerussite from the Yanque Ore Deposit (Peru), which shows very peculiar characteristics because it is
anomalously rich in strontium (up to ~ 15 wt% SrO, average 5 wt% SrO). The Yanque prospect is a
Pb sulfide/carbonate and Zn nonsulfide stratabound deposit, located at the Jurassic-Cretaceous boundary
between slates-limestones of Yura Group (southeastern Cordillera of Peru) [3]. Yanque is considered
primarily as a Carbonate Replacement Deposit. Secondary oxidation, which upgraded the deposit to
an economic value, has re-precipitated zinc to Zn-carbonates, silicates, and hydroxides/oxides. Most of
primary galena (PbS) has been reprecipitated as cerussite. Because even small differences in dissolution
rates may have strong implications for the metallurgical requirements, a thorough understanding of the
mineralogy, crystallography and geochemistry of the different minerals is a “must” in feasibility studies
of nonsulfide deposits. This work reports a very detailed SEM-EDS and microprobe (WDS) study of a
number of Sr-rich samples. Moreover, new FTIR, Raman and XRD data are also presented.
Figure 1. Backscattered-electron image of Sr-rich cerussite from Yanque oxidation zone: dark grey areas contain over
15 wt% SrO, while light grey areas show values below 2 %wt SrO.
References
1. I.M. Steel, Pluth J.J., A. Livingstone Mineral. Mag. (1998), 451-459
2. S. V. Krivovichev, P.C. Burns Mineral. Mag. (2000), 1063-1068
3. M. Boni, G. Balassone, V. Arsenau, P. Schmidt Econ. Geol. (2009), 267-289
85
ms2-p3
Synthesis and structure of a palygorskite/methyl red pigment
R. Giustetto1,2, O. Wahyudi1, G. Ricchiardi2,3, D. Levy1 and P. Benna1
1. Department of Mineralogical and Petrologic Sciences – University of Turin, 10125 – Turin (Italy).
2. Nanostructured Interfaces and Surfaces (NIS) – Centre of Excellence – 10125 – Turin (Italy).
3. Department of IFM Chemistry – University of Turin, 10125 – Turin (Italy).
Palygorskite [(Mg,Al)4Si8O20(OH)2(OH2)4•4H2O] is a fibrous clay mineral whose structure can be described
as a framework of chessboard connected TOT ribbons[1], crossed by z-axis elongated nano-tunnels (6.4x3.7
Å wide) filled by zeolitic water. When mixed and heated with the indigo dye it forms Maya Blue, a pigment
used in Pre-Columbian America whose remarkable stability is due to specific clay/dye interactions, the
nature of which is still disputed (whether inside the nano-tunnels[2] or on the fibres surface[3]). The sorption
properties of palygorskite were exploited to synthesize new nanostructured compounds, based on the
fixation in the clay framework of different dyes with the aim to create a new palette of pigments, granted
by limited toxicity and low production expenses.
Figure 1. a) methyl red; b) insertion within a palygorskite channel. Figure 2. Synchrotron XRPD patterns (vertical line is calcite)
A stable, brilliant, purple/red pigment was obtained by mixing palygorskite with 2wt% methyl red
(C15H15N3O2) in acidic solution (20% HCl) and gradually heating up to 140°C for 22h. The pigment was
purified through Soxhlet extraction under ethanol and its chemical stability tested through prolonged (24h)
acid and alkali attack (HNO3, H2SO4, NaOH and aqua regia). In spite of methyl red drastic chromatic
changes with pH variations (<4.4: red; 4.4–6.2: orange; >6.2: yellow), the powders maintained their
reddish/purple hue after any treatment, with only negligible fading: the fixation of methyl red dye on the
palygorskite framework causes therefore its colour to become stable.
The nature of the interaction between the clay and the dye was studied by means of graphic and modelling
techniques. Methyl red molecule can theoretically diffuse inside the nano-tunnels, once the zeolitic water
has been expelled as a result of the heating. Synchrotron powder diffraction patterns of both palygorskite
and palygorskite+methyl red (2wt%) pigment were collected (ESRF, ID31 beamline, Grenoble, France)
to perform a full-structural analysis with the Rietveld method. The comparison of the two profiles does
not account for strong differences in the observed intensities, implying that the clay/dye interaction might
occur – at least in part – on the clay surface. Further experiences using spectroscopic techniques (UVvisible, FTIR, Raman, NMR) are hoped to shed light on this aspect.
References
1. G. Ferraris, E. Makovicky, S. Merlino. Crystallography of Modular Materials (2004), IUCr/Oxford Univ. Press.
2. R. Giustetto, G. Chiari. Eur. J. Mineral. (2006), 18, 629-640.
3. L. Polette-Niewold, S. Manciu, B. Torres, M. Alvarado Jr., R. Chianelli. J. Inorg. Bioch. (2007), 101, 1958-1973.
86
ms2-p4
Light-induced reversible transition in HgI2.As4S4:
evidence by single-crystal X-ray diffraction
P. Bonazzi1, L. Bindi2 , A. Pfitzner3
1. Università di Firenze, Dipartimento di Scienze della Terra, I-50121 Firenze, Italy
2. Università di Firenze, Museo di Storia Naturale, I-50121 Firenze, Italy
3. Universität Regensburg, Institut für Anorganische Chemie, D-93040, Regensburg, Germany
Synthetic and natural arsenic sulfides, as well as bulk glasses and thin films in the As-S system, are of interest
to physicists and material scientists for their potential or actual application in optics and optoelectronics,
mainly because of photoinduced changes of their physico-chemical properties. In particular, the effects
of the exposure to visible light of realgar, α-As4S4, and its high-temperature polymorph, β-As4S4, were
recently studied by several authors. Both of these polymorphs, indeed, undergo an alteration when exposed
to visible light, the final product of the photoinduced transition being pararealgar, As4S4, in both cases.
Realgar and β-As4S4 are based on the same cage-like molecule whereas pararealgar, is based on a different
As4S4 molecular group, so that the transition from a realgar- to a pararealgar-type molecule implies the
displacement of one As-As and one As-S covalent bond. Although the As4S4 molecules in both realgar and
β-As4S4 structures are quite identical, they transform to pararealgar upon exposure to light following different
mechanisms which have to be ascribed to the different molecular packing. Therefore, it is interesting to
investigate the behavior of the As4S4 molecule within different crystal-chemical environments. Here we
report the study of light-induced changes on the structure of the adduct of mercury iodide and molecular
arsenic sulfide, which consists of a packing of nearly linear HgI2 molecules and As4S4 cage-molecules. HgI2.
As4S4 was obtained by heating HgI2, gray arsenic and sulfur in the molar ratio 1:4:4 in evacuated quartz
ampoules. The reactants were molten at 400°C and then annealed at 200°C for two weeks. A transparent
crystal, orange in color, was selected and mounted on a Mach3 single-crystal diffractometer. Before any
exposure to light the unit-cell dimensions in the P21/n setting were: a= 9.421(1), b=14.982(3), c=9.476(1)
Å, β=104.32(2)°, V= 1295.9(4) Å3. The crystal was then exposed to filtered polychromatic light (550 nm
long-wavelength pass filter). After each light exposure, the unit-cell parameters were determined until it
was still possible to center the same set of reflections. After a total light-exposure time of 2760 minutes the
increase in the unit-cell volume was 3.0 %. Structure refinements performed after different exposure times
indicated evidence of the formation of an increasing fraction of pararealgar- replacing the realgar-type
molecule. The crystal was kept in the dark for several days and the unit-cell parameters were measured at
selected times. Surprisingly, the unit-cell volume continuously decreased down to 1293 Å3 (after 36 days);
at this stage the intensity data were collected again and the resulting structure was found to be identical to
that of the unaltered crystal. Therefore, in the HgI2.As4S4 adduct, the transition from realgar- to pararealgartype molecule appears to be reversible.
87
ms2-p5
Organoclay structure control
V. Cipolletti1, G. Guerra1, P. Longo1, M. Galimberti2, S. Giudice2, A. Lostritto2, L. Giannini2
1. Università di Salerno, Dipartimento di Chimica, 84084 - Fisciano (SA), Italy
2. Pirelli Tyre, 20126 – Milano, Italy
Clay minerals, as other layered solids, can incorporate organic guest molecules in their interlayer space.
The organoclay are compatible with organic materials and suitable to prepare hybrid organic-inorganic
composite materials with improvement of physical properties. Montmorillonite (MMT) is a cationic
layered clay, made of negatively charged layers with the interlayer galleries filled by alkali and alkaline
earth cations. These cations can be exchanged with alkylammonium cations to prepare organically modified
clays with the basal spacing d001 increased[1,2] (typically d001 ≈ 1.2 nm for MMT-Na).
Two different kinds of organoclays of montmorillonite with a double chain ammonium salt were obtained
in the presence of many different thermoplastic or elastomeric polymers. Independently of the chemical
nature of the polymer, all the obtained organoclays present a basal spacing of 4.0±0.1 nm or 6.00±0.05
nm (possibly corresponding to parrafin type perpendicular mono-layer and bi-layer intercalates) when the
mixing occurs in the absence and in the presence of a small amount of stearic acid respectively. This gives
an easy way to control the structure (and properties) of the organoclay in polymer composites.
Figure 1. Schematic representation of mono- and bi-layer MMT/amphiphile
intercalates.
Layered double hydroxide (LDH) are anionic synthetic clays made of positively charged brucite-like layers
with the interlayer space filled by anions (CO32-, Cl-, NO3-, etc) and water molecules. These anions can be
exchanged with organic anions to generate organoclay with the basal spacing d003 increased (typically d003
≈ 0.77 nm for carbonate LDH).
An organoclay of LDH with stearate anions were obtained in presence of glycerol, as reaction medium. It
presents a basal spacing of about 3.0 nm, possibly corresponding to paraffin-type mono-layer intercalate.
References
1. M. Galimberti, A. Lostritto, A. Spatola, G. Guerra, Chem.Mater., 19, 2495-2499 (2007).
2. M. Galimberti, S. Senatore, L. Conzatti, G. Costa, G. Giuliano, G. Guerra, Polym.Adv.Technol., 20, 135-142 (2009).
3. M. Galimberti, S. Senatore, A.lostritto, L. Giannini, L. Conzatti, G. Costa, G. Guerra, e-Polymers 057 (2009)
88
ms2-p6
Structural modifications of analbite at high pressure
N. Curetti1, L. Sochalski2, F. Nestola3, R.J. Angel2, P. Benna1 and E. Bruno1
1. Dipartimento di Scienze Mineralogiche e Petrologiche, Università di Torino, I-10125 Torino (Italy)
2. Department of Geosciences, Virginia Polytechnic Institute, Blacksburg, Virginia 24061 (U.S.A.)
3. Dipartimento di Geoscienze, Università di Padova, I-35137 Padova (Italy)
Crystals of low albite (NaAlSi3O8, Champorcher, Aosta Valley) were treated at T = 1000°C for 31 days and
at T = 1060°C for 28 days and then quenched in air. After the thermal treatments, the unit-cell parameters
at room pressure and temperature are a = 8.1554(7), b = 12.8736(7), c = 7.1086(4) Å, α = 93.469(4), β
= 116.436(8), γ = 90.289(5)°, V = 666.6 Å3, and indicate a complete Al,Si disorder. Investigations were
performed by single-cystal X-ray diffraction in situ at high pressure, using a diamond-anvil cell. The X-ray
intensity data were collected at a pressure of 0.0001, 1.2, 3.2, 5.5 and 7.3 GPa with a Gemini R Ultra
diffractometer (Oxford Diffraction). Analbite remains triclinic in space group C1 over the entire pressure
range. The compressional behavior shows that analbite is generally stiffer than ordered low albite (Benusa
et al. 2005). The O-O-O angles of the four-membered tetrahedral rings of the crankshaft chains show less
flexibility in analbite than in low albite.
Figure 1. Four–membered ring on (010) plane in low albite and in analbite.
The structure of low albite (Benusa et al. 2005) at pressures in excess of 4 GPa becomes elastically softer
than at lower pressures. In analbite no changes in compression pattern and in the rate of shear of the fourmembered rings with pressure up to P = 7.3 GPa are observed.
The unit-cell compression is anisotropic, as indicated by the unit strain tensors, with 48 % of the total
compression accommodated along a direction close to a* in the entire pressure range.
In the non-tetrahedral polyhedron the five shortest Na-O distances decrease linearly up to 7.3 GPa.
References
1. M.D. Benusa, R.J. Angel, N.L. Ross Am. Mineral. (2005), 90, 1115-1120
89
ms2-p7
HT behaviour of pargasite and kaersutite: expansivity
coefficients and dehydrogenation mechanisms
R.Oberti1, M.Zema1,2, S.Tarantino1,2 and M.Boiocchi3
1. CNR-Istituto di Geoscienze e Georisorse, UOS Pavia, 27100-Pavia
2. Università di Pavia, Dipartimento di Scienze della Terra, 27100-Pavia
3. Università di Pavia, Centro Grandi Strumenti, 27100-Pavia
Despite their importance in many petrogenetic contexts and their relevance for the release of water in
subduction zones, very few data are available on the HT behaviour of amphiboles, and almost all refer to
fluoro-amphiboles with very simple compositions, quite different from those of interest for Earth Sciences.
Therefore, we have undertaken a systematic investigation of the HT behaviour of different nature-occurring
C2/m and Pnma amphibole compositions. Experiments are done in situ on a single-crystal diffractometer
in the T range 25-1050°C, and no buffering is applied. The evolution of the unit-cell parameters is followed
at T steps of 25°C, and data collections are performed every 200-250°C in order to check changes in a) the
geometry of the crystal structure; b) the cation partitioning between the different sites; c) the beginning
and the mechanisms of dehydrogenation. The reversal path during cooling is also checked to discard the
presence of some crystal-chemical hysteresis. This work reports on the first results, which were obtained
on a completely dehydrogenated kaersutite with a composition preventing cation disorder (FR12) and on
a partially dehydrogenated pargasite with an Fe2+ content sufficient to allow complete dehydrogenation
at high temperature (DL5). Both the samples had been previously fully characterised by single-crystal
structure refinement, electron (EMP) and ion (SIMS) microprobe and Mössbauer spectroscopy[1]. The two
samples show linear variations of the unit-cell parameters, with the edges increasing (b > a > c) and the
β angle decreasing with T. Around 650°C, DL5 undergoes an abrupt decreases in the edges and increase
in the β angle, which are signals of dehydrogenation. After completion of the dehydrogenation process, a
further annealing experiment shows a behavior similar to that of FR12. The values of the linear thermal
expansion coefficients (α, ·10-6) for the unit-cell and the M sites are: FR12 (50-1050°C): αa 0.753(9), αb
1.27(1), αc 0.875(7), αβ -0.375(5), αV 3.12(1), αM(1) 2.5(2) αM(2) 4.2(3) αM(3) 3.7(3); DL5(OH)=0.9 (50-650°C):
αa 0.76(1), αb 1.22(4), αc 0.92(1), αβ -0.42(1), αV 3.12(3), αM(1) 2.13(7) αM(2) 3.1(2) αM(3)2.6(7); DL5 dehydr
(50-1050°C): αa 0.799(8), αb 1.26(5), αc 0.86(9), αβ -0.35(1), αV 3.10(1), αM(1) 2.2(2) αM(2) 2.9(3) αM(3) 3.3(1).
Thus the presence of (OH) groups mostly affects the expansivity of c and β. During the dehydrogenation
process, Fe2+ moves from the M(4) and M(2) sites to the M(1) site, where it oxidizes to allow local
electroneutrality after the loss of the proton at the coordinated O(3) oxygen atom. The complex pattern of
geometrical modifications occurring both during thermal annealing and during dehydrogenation will also
be discussed in detail.
References
1. A. Zanetti, G. Pedrazzi, R. Oberti (2000) Plinius 24, 220-221.
90
ms2-p8
High-pressure behaviour of AB2O6 (A=Fe,Mn; B=Nb,Ta)
oxides with columbite and tapiolite structures
M. Zema1,2, S.C. Tarantino1,2 and T. Boffa Ballaran3
1. Dipartimento di Scienze della Terra, Università di Pavia, 27100 - Pavia
2. CNR-IGG, UoS Pavia, 27100 - Pavia
3. Bayerisches Geoinstitut, University of Bayreuth, D-95447 - Bayreuth
Minerals of the columbite group have AB2O6 stoichiometry and composition within the quadrilateral formed
by four end-members: MnNb2O6, FeNb2O6, MnTa2O6 (orthorhombic, tri-α-PbO2 structure) and FeTa2O6
(tetragonal, tri-rutile structure). Orthorhombic members of this minerals family are called columbites or
tantalites, whereas those with tetragonal symmetry are known as tapiolites. They are characterised by an
intracrystalline cation exchange reaction between divalent and pentavalent cations which is responsible
for a polymeric isomorphic phase transition. These oxides have gained great attention because of their
excellent dielectric properties at microwave frequencies and attracted the interest of the telecommunication
industry for their application as dielectric resonators and filters.
In the present work, the structural evolution with pressure of two natural columbites, one ferrocolumbite
from Raode (Africa) and one manganocolumbite from Kragero (Norway), and one ferrotapiolite from
Kimito (Finland) have been determined by single-crystal XRD. All structural studies were carried out on
samples preliminarily annealed to attain the complete cation-ordered state.
In columbite, thermal expansion is linear and, in Fe-rich samples, slightly anisotropic with a and c showing
the largest variations with T;[1] the axial compressibility scheme is βb > βc ≥ βa and anisotropy is larger
in manganocolumbite.[2] Moreover, there is no inverse relationship between axial compressibility and
thermal expansion. HP-XRD data have been collected in order to characterise the different compression
mechanisms in ferro- and manganocolumbite. Five datasets have been collected for each crystal from room
P up to ca. 7 GPa. Octahedral volumes decrease linearly with P. The larger A site is more compressible
than B and in the Fe-rich sample. Compressibility along b is larger in the Mn-rich sample and results from
the sliding of the octahedral chains over each other.
For tapiolite, lattice parameters were measured at 18 P values up to 8.7 GPa and compared to data obtained
at HT. They show a continuous behaviour with P and the inverse relationship is not valid. No evidence
for phase transitions was found in the investigated P range. The P-V data have been fitted using a secondorder Birch-Murnaghan EoS. Four datasets have been collected up to 6.9 GPa and structure refinements
allowed to gain the compressibility mechanism in tapiolite which will be discussed in comparison to that
of columbite.
References
1. S.C. Tarantino, M. Zema, M. Pistorino, M.C. Domeneghetti Phys. Chem. Miner. (2003), 30, 590.
2. M. Pistorino, F. Nestola, T. Boffa Ballaran, M.C. Domeneghetti Phys. Chem. Miner. (2006), 33, 593.
91
ms3-p1
Surface polarity in intrinsically polar and in non-polar crystals.
Symmetry of crystal bulk and surface reconstruction
Dino Aquilano, Marco Bruno, Marco Rubbo
Università degli Studi di Torino, Dip. di Scienze Mineralogiche e Petrologiche, 10125 – Torino
The real surface profile of a (hkl) face rarely coincides with the ideal hkl lattice plane. In other words,
the hkl plane is a geometrical abstraction of the crystal structure, while to generate the corresponding
surface profile, one has to consider the face character along with its interactions with the mother phase.
Calculation shows that stability problems can arise, owing to the surface polarity, since the infinite 2D
array of iso-oriented surface dipole moments makes infinite the value of the electrical field in the surface
sites. Two classes of crystals are interested : intrinsically polar crystals, such as ZnS–wurtzite like (P63mc)
or ZnS–sphalerite like (F43m) lattices, and those, non-polar, where the polarity is the consequence of the
alternating layers of positive and negative charges (such as the {111} form of the NaCl – like lattice).
The real presence of such surfaces can be explained only by the foreign adsorption and/or by a surface
reconstruction that cancels out the surface dipoles. In any case, a criterion for surface reconstruction is
needed, also when dealing with the foreign adsorption. Reconstructions usually found in literature consist
in removing 50% of the atoms from the outmost hkl layer and in relocating them on its centre-symmetrical
crystal plane, regardless of the topology obtained from the atoms removal. This way is not self-consistent,
due to a serious drawback when dealing with the search for the minimum of the surface energy (γhkl) of the
reconstructed surfaces.
In this work we aim at finding a relationship between the reconstruction model, the 2D symmetry of a
given (hkl) surface and its specific surface energy γhkl value, and summarize our reconstruction of different
kind of polar surfaces: {111}-NaCl; {0001} and {01.2} of CaCO3 – calcite; {001} of UO2–uraninite
showing the CaF2 lattice. A peculiar criterion we adopted for {111}-NaCl and {0001}– calcite forms is the
“octopole” model proposed by Lacmann [1] and described in the following figure.
(a): Un-reconstructed and (b): Reconstructed (111) NaCl surfaces. The reconstructed face is made by 4(NaCl) molecules (octopoles):
its outermost layer contains only 1/4 of the available lattice sites, whereas the two layers below contain 3/4 and 4/4 of the sites,
respectively. Lines join the atoms belonging to the outermost layer.
From all these cases, it ensues that the absolute minimum of γhkl for reconstructed faces occurs when: i) one applies the “50%” model to the {01.2} form of calcite respecting the sole symmetry plane of the form;
ii)- the “octopole model”, respecting the A3 axis, is applied to both {111}-NaCl and {0001} – calcite iii)the reconstruction respecting the A4 axis is applied to the {001} form of UO2–uraninite.
Summing up and recollecting the Curie’s principle, the symmetry of the crystal bulk imposes its constraints
also to the reconstruction of the polar surfaces.
References
1. 1. R. Lacmann « Adsorption et Croissance Cristalline » Ed. CNRS vol.152, 195
92
ms3-p2
Mosaic GaAs crystals for hard-x-ray astronomy
C. Ferrari1, L. Zanotti1, A. Zappettini1, S. Arumainathan2 and C. Paorici3
1. CNR-IMEM Institute, 43010 Parma
2. Department of Nuclear Physics, University of Madras, 600 025, India
3. Phisics Department, Parma University, 43100 Parma
Recently the design of a Laue lens with field of view of 30 arcseconds for x-rays in the energy range
from 100 keV to 1 MeV has been proposed. Mosaic crystals are used as focussing elements in order to
increases the total diffracted intensity. The mosaic angular spread of the crystals is carefully determined as
a compromise between intensity and energy resolution of the Laue lens. According to the abovementioned
criteria copper and germanium crystals with typical mosaicity of 30 arcseconds have been studied for this
purpose.
In the present work we evaluate the use of GaAs crystals as optical elements for hard x-ray astronomy.
GaAs crystals have essentially the same electron density and lattice spacing as germanium, but because
of the spontaneous formation of “cellular structures” with dislocations at the boundaries between perfect
zones of the crystal, Czochralsky grown GaAs crystals exhibit some degree of mosaic structure.
By controlling the growth conditions the cellular structure responsible of the crystal mosaicity can be in
principle varied in a large range. Infact, for a given orientation, the grain-boundary (low) angle, which
defines the mosaicity, turns out to be related to the dislocation density if it can be assumed, in almost
dislocation-free single crystals, that all the dislocations contribute to the grain-boundary formation.
According to Jordan et al.[1] thermoelastic stress model, the dislocation density for a given orientation is
related to the difference between the total resolved shear stress and the critical resolved shear stress, both
quantities depending on the thermal field (and hence the growth conditions) during the growth process.
On the basis of this, the possibility of obtaining crystals with a given degree of mosaicity by tuning the
Czochralski growth conditions is presented. Several GaAs ingots grown with the encapsulating Czochralski
method have been characterized. Values of the full width at half maximum values ranging from 15 to 40
arcseconds of the measured diffraction peaks were found close to the proposed 30 arcsecond mosaicity.
Reference
1. A.S. Jordan, R. Caruso, A.R. von Neida The Bell System Technical Journal (1980), 59, N° 4.
93
ms3-p3
Sensitization of SnO2 and ZnO nanostructures
by CH3NH3SnCl3 hybrid particles
P. Ferro1, R. Mosca1, T. Besagni1, D. Calestani1, A. Zappettini1, M. Zha1, S. Iannotta1,2,
M. Nardi2, T. Toccoli2, J. J. Mares3, P. Hubík3, J. Kristofik3, F. Licci1
1. CNR-IMEM, Parma, Italy
2. CNR-IFN, Trento, Italy
3. Institute of Physics ASCR, v.v.i., Prague, Czech Republic
With the aim of developing metal oxide nanostructures optimally designed to match the physical
requirements of their applications, we tried to modify the surface of either ZnO tetrapods and SnO2
nanowires by evaporation of hybrid organic-inorganic self-assembled perovskites (surface sensitization)
and investigated the resulting photoluminescence (PL) properties.
Film of CH3NH3SnCl3 hybrid perovskite were thermally ablated on either ZnO tetrapods (TP) deposited
on quartz substrates [see L Zanotti et al., this conference] or SnO2 nanowires (NW) grown on alumina
substrates. By using a shadow mask hybrid was deposited only on one half of the ZnO TP and SnO2 NW
substrates, thus leaving bare nanostructures on the other half. PL measurements were performed on the two
portions of each substrate by using an excitation wavelength λ=325 nm.
We observed that hybrid has negligible effects on the PL spectra of ZnO TP, but significantly modify the
PL of SnO2 NWs. Bare SnO2 nanowires in fact show the usual broad featureless PL peak in the 400-600
nm range, while after hybrid deposition the peak shape is strongly modified with a slight red-shift. Since
the changes of NW PL do not scale with hybrid thickness, and, on the other hand, the PL efficiency of
the hybrid itself is quite modest to justify the phenomenon, we suggest that the observed effect has to be
imputed to the formation of interfaces due to the interaction between the nanostructure matrix and hybrid.
The mechanisms of such interaction and the consequent PL modification are presently investigated.
Figure 1. a)SEM image of SnO2 nanowires covered by hybrid film b) PL spectra of bare and hybrid-covererd SnO2 nanowires
94
ms3-p4
Pyrolytic MOVPE of CdTe:I on semi-insulating (111)B-CdTe
crystals for fabrication of nuclear radiation detectors
N. Lovergine1, P. Prete2, P. Paiano1, F. Marzo1, I. Farella1, A. Cola2 and A.M. Mancini1
1. Università del Salento, Dipartimento di Ingegneria dell’Innovazione, 73100 - Lecce
2. Consiglio Nazionale delle Ricerche, Istituto per la Microelettronica e i Microsistemi, Unità di Ricerca di
Lecce, 73100 - Lecce
Cadmium telluride (CdTe), in reason of its high mean atomic number, large X/γ-ray photon stopping power
and wide band-gap (1.45 eV at 300K) is one of the most promising semiconductors for the realization of
nuclear radiation detectors operating at non-cryogenic temperatures. CdTe-based detectors usually employ
In or Pt thin films to form a Schottky barrier (In) or an ohmic contact (Pt) onto semi-insulating CdTe
crystals. In recent years, homojunction-based CdTe detectors have been realized at low temperatures by
remote-plasma-assisted MOCVD, showing dark current values lower than for Schottky metal contact
detectors and good energy resolution[1]. P-i-n diode structures have the potential for very low dark currents
under high reverse bias conditions.
We report on conventional (pyrolitic) MOVPE for the growth of iodine-doped CdTe (CdTe:I) layers
on detector-grade (111)B-CdTe crystals and fabrication of test Al/n-CdTe:I/i-CdTe/Pt device structure,
a technological step towards a complete p-i-n homojunction diode structure. CdTe:I homoepitaxial
layers were grown on detector-grade (111)B-oriented crystals, using dimethylcadmium (Me2Cd), diisopropyltelluride (iPr2Te) and ethyliodide (EtI) as precursors. To ensure complete and reproducible
homoepitaxy on the (111)B surface, CdTe crystals went through a series of chemical and thermal surface
treatments, namely (i) etching in 2% Br2-methanol solution; (ii) in-situ H2 thermal cleaning at 350°C, the
latter followed by (iii) annealing in H2+Me2Cd vapours at 350°C[2]. Fully homoepitaxial CdTe:I layers
were then grown at temperatures between 330°C and 350°C under Cd-rich vapour conditions (Te:Cd
molar flow rate ratios among precursors between 0.50 and 0.33) and a EtI molar flow rate ~2 µmol/min.
Incorporation of I in CdTe epilayers was confirmed by SIMS and low temperature photoluminescence, and
showed to increase for low Te:Cd ratios in the vapour. Resistivity and Hall effect measurements showed
electron concentration in the 1016 cm-3 range. As-grown n-CdTe:I/i-CdTe structures were used to fabricate
M-i-n test devices. Their I-V characteristics showed a rectifying behaviour, with dark current values
(under reverse bias conditions) about two orders of magnitude lower than for Pt/i-CdTe/Pt detectors, and
comparable to In/i-CdTe/Pt structures.
References
1. M. Niraula, D. Mochizuki, T. Aoki, Y. Tomita, T. Nihashi, Y. Hatanaka, Nucl. Instrum. Meth. Phys. Res. A 458 (2001) 478.
2. M. Traversa, L. Tapfer, P. Paiano, P. Prete, F. Marzo, N. Lovergine, A.M. Mancini, Appl. Phys. A 91 (2008) 23.
95
ms3-p5
Theoretical growth morphology of organic semiconductors:
the case of oligocenes and oligotiophenes
M. Bruno1, F.R. Massaro2, and M. Moret2
1. Università di Torino, Dipartimento di Scienze Mineralogiche e Metrologiche, 10125 Torino
2. Università di Milano Bicocca, Dipartimento di Scienza dei Materiali, 20125 Milano
Acenes and tiophenes are the subject of intense studies due to their unique electronic properties associated
with intramolecular π-bonds and molecular packing. Pertinent literature shows that many efforts have
been aimed at developing new methods of synthesis, purification, and crystallization as well as fabricating
prototype electronic devices. Recent studies performed on high-purity organic semiconductor single
crystals have provided benchmarks for performance of thin films devices as well. However, a detailed
investigation of their structure/property relationships cannot forget the study of theoretical equilibrium and
growth crystal morphologies. Even in those cases in which a theoretical approach to crystal morphology
was pursued, authors consider only the crystallographic forms with simplest indices, so evaluating only
partially the correct crystal morphologies.
In the present work we have performed a complete PBC analysis (in the sense of Hartman-Perdok theory)
on different phases belonging to the oligocenes (naphtalene, antracene, tetracene, pentacene and rubrene)
and oligotiophenes (quatertiophene and sexitiophene). Having determined the character of the crystal faces
(which affects the growth mechanism), we have calculated the surface energies (in vacuum and at T =
0 K) of the most likely forms entering the final morphology by means of the Universal Force Field[1]
semiempirical potentials. We believe this is an appropriate and non-ambiguos approach for correctly
estimating the theorethical equilibrium morphology of these strategic organic crystals, without introducing
a bias when establishing which forms are present in the crystals.
Figure 1. Predicted equilibrium morphologies for rubrene (left) and quaterthiophene (right)
References
1. A.K. Rappe, C.J. Casewit, K.S. Colwell, W.A. Goddard, W.M. Skiff J. Amer. Chem Soc. (1992), 114, 10024.
96
ms3-p6
Transparent conductive oxide layers grown by Pulsed
Electron Deposition (PED) for thin film solar cells
S. Rampino, F. Bissoli, F. Pattini and E. Gilioli
IMEM – CNR, 43100 - Parma, Italy
During the last years, transparent conducting oxides (TCO) gained increasing importance in optical and
electronic devices. TCO generally belong to metal oxide compounds and they are applied for a broad variety
of applications, e.g. low-E glass, gas sensors, displays, and solar cells. In particular, Zinc Oxide (ZnO) and
Al-doped Zinc Oxide (AZO) find lots of application because of their properties such as excellent substrate
adherence, hardness, optical and piezoelectric behaviour, chemical stability in aggressive atmosphere and
their non-toxicity[1]. In photovoltaics, ZnO and AZO are used to realize transparent windows layers in
thin film solar cells, based on Cu(In,Ga)Se2 or amorphous silicon[2]. Several vacuum techniques enable
the deposition of these materials and Pulsed Electron Deposition (PED) seems to be a suitable system for
growing oxides with reduced costs. PED is a process in which a very short pulsed electron beam with high
power density (~500 MW/cm2) induces the ablation of the target material and its subsequent transport to
the substrate maintaining the target stoichiometry. This is particularly advantageous in the case of complex
and doped materials. PED offers unique advantages compared to other pulsed deposition techniques:
high efficiency of energy transfer from the e-beam to the target (about 30% vs. 0.1% for Pulsed Laser
Deposition) and very low installation and running costs (roughly 10% compared to PLD[3]). In this work
we report results of ZnO and AZO films grown by PED on quartz substrates: the corresponding structural,
morphological, electrical and optical properties were studied as a function of substrate temperature,
background pressure and deposition time. XRD characterizations show a preferential (002) orientation
beyond about 100 nm-thick films deposited onto amorphous quartz substrates, suggesting that the first
ZnO layers keep the same amorphous structure of the quartz underneath. These important results are
supported by an excellent optical transparency, exceeding 80% in the VIS and NIR region for all the
samples in a wide range of thickness from 80 to 2000 nm. Remarkable results for undoped ZnO and AZO
films are related to the electrical resistivity that exhibits a value in the range 1÷3x10-1 Ω∙cm and 5÷9x10-4
Ω∙cm respectively. These preliminary results confirm that PED seems to appear a reliable method for the
deposition of TCO films with excellent transparency in the UV-VIS range and good electrical conductivity,
and also a promising route to achieve a cost-effective solar cell fabrication.
References
1. V.R. Shinde, T.P. Gujar, C.D. Lokhande, Solar Energy Materials and Solar Cells (2007) 91, 1055.
2. T. Mahalingam, V.S. John, M. Raja, Y.K. Su, P.J. Sebastian, Solar Energy Materials and Solar Cells (2005), 88, 227.
3. T. Venkatesan, K.S. Harshvardhan, M. Strikovsky, J.Kim, “Recent Advance in the Deposition of Multi-Component Oxide
Films by Pulsed Energy Deposition”, Springer US, (2005), 385.
97
ms3-p7
Crystalline organic heterostructures: growth,
properties, and perspectives
A. Sassella
Università di Milano Bicocca, Dipartimento di Scienza dei Materiali, I-20125 - Milano
In the last decades, molecular organic semiconductors raised a great interest as possible alternative
materials to inorganic semiconductors in device technology. Independently of the specific molecules
chosen, thin crystalline films are the most suitable choice for device applications. Crystalline films and
heterostructures, possibly crystalline, with a precise orientation and sharp interfaces, can be obtained when
using properly selected and oriented organic single crystals as substrates, therefore exploiting the local
crystallo-chemical properties of the substrate surface. In this work, after a brief summary of the state of the
art on organic crystalline heterostructures, we choose rubrene (C42H28, 5,6,11,12-tetraphenyltetracene) as a
model compound for illustrating the possible role of a controlled growth; this material is, in the solid state,
the organic semiconductor displaying the highest charge mobility.
Figure 1. a) Structural formula of the rubrene molecule (H atoms are omitted); b) epitaxial crystalline island of rubrene grown on a
tetracene single crystal; as insets: high resolution AFM image of the island surface and sketch of the interface structure.
In particular, we present and discuss the study of thin films of rubrene grown on several substrates by
organic molecular beam epitaxy (OMBE), exploiting the potentiality of this technique to control the
purity, the thickness, the surface morphology and, which is the most important achievement, the structure
of the films. Crystalline organic substrates induce the solidification of rubrene in crystalline form, in
some cases with single crystalline order. We will discuss the mechanisms making possible the growth of
epitaxial rubrene thin films, i.e. crystalline and oriented films, thanks to a morphological and structural
characterization of the samples, performed by atomic force microscopy (AFM), and the comparison
with the results of optical spectroscopy measurements carried out before and after film deposition with
polarized light. As a perspective, we will show how these highly controlled structures obtained by OMBE
can be used as substrates for depositing an n-type organic semiconductor, for example fullerene (C60) or
perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA), thus obtaining p-n junctions, which can
be considered the basis for semiconductor devices.
98
ms3-p8
Method for large area deposition of ZnO tetrapod nanostructures
L. Zanotti1, D. Calestani1, M. Villani1, M. Zha1, A. Zappettini1 and C. Paorici1,2
1. IMEM - CNR, 43100 - Parma
2. Università degli Studi di Parma, Dipartimento di Fisica, 43100 - Parma
Among several morphologies ZnO presents one quite characteristic nano-crystalline structure, usually
reported as “tetrapod” (TP), which consists of four needle-shaped “legs” connected at one common end
and respectively arranged as axes of a tetrahedron (Fig. 1).
Using an appropriate vapor-solid process, ZnO TPs are produced in large quantity (tens of mg per run)
and, when removed from the growth reactor, they appear well assembled like a light white-grey “sponge”.
These aggregate structures mainly consist of TP nanocrystals, though usually they might also include
unreacted Zn metal particles, nanosized ZnO powders and/or partially oxidized ZnO1-x nanostructures/
powders. In order to “purify” as-grown TPs from the other undesired structures, the authors propose a
multi-step process summarized as following: (1) post growth thermal annealing in vacuum (evaporation
of metal Zn) and, subsequently, in oxygen atmosphere (oxidation of not completely reacted particles of
ZnO1-x); (2) suspension of all the reaction products in appropriate liquids, in which ZnO is insoluble, in
order to decant and to separate TPs from spurious structures; (3) room-temperature deposition of purified
ZnO TPs on proper substrates (glass, silicon, alumina, etc.), whose sizes can vary from a few square mm
up to many square cm depending on the specific application; (4) heating at moderate temperature under
low vacuum to remove traces of organic solvent and to favour the sticking of ZnO TPs on the substrates.
The described procedure is highly valuable as it allows the achievement of homogeneous distribution of
purified ZnO nanostructures on large substrates and a room-temperature deposition process which avoids
detrimental interaction of ZnO TPs with substrate material, or with metal contacts previously deposited
on the substrates. In practice, the proposed method is a new way to prepare large area films of metal
oxides nanostructures, ready for device production. Application of the process to gas sensor fabrication
and hybrid compounds (ZnO-MeS) preparation is also reported.
Figure 1. SEM image of obtained ZnO tetrapods
99
ms3-p9
A new approach for the synthesis of ZnO nanoparticles
sensitized with metal chalcogenides
L. Zanotti, A.Zappettini, M. Villani, D. Calestani and R. Mosca
IMEM - CNR, 43100 - Parma
The present communication is a response to renewed interest in nanostructure based “coupled compounds”,
like ZnO-MeX (where Me = Cd, Pb,... and X = S, Se) which can find extensive use in the fabrication
of a number of solid state devices, such as photoconductive, solar cells, electroluminescent cells,
photocatalysts.
Various oxide semiconductors, like TiO2 and ZnO, are known to have appropriate properties for these
applications, although there are some drawbacks associated with their use: (i) charge carrier recombination
occurs within a few nanoseconds, (ii) band edge absorption threshold does not allow the utilization of
visible light. One of the main approaches to overcome these particular limitations involves contacting of
the semiconductor particle with another semiconductor, called “sensitizer” (for example, nanostructured
ZnO particles combined with metal chalcogenides).
Infact it is known that in these coupled systems the absorption threshold is extended to the visible region
and the photogenerated electrons are quickly transferred from sulphide/selenide layer into to the lower
lying conduction band of ZnO, thus limiting recombination effects.
In order to produce this type of material we have combined ZnO nanoparticles, in the specific “tetrapod”
morphology, with nanoparticles of metal chalcogenides. The main innovative aspects of the preparation
procedure are the following:
■■ the use of appropriate organic solvents to keep both ZnO and the metal chalcogenides completely
suspended and dispersed in liquid phase;
■■ the in situ direct formation of metal chalcogenides keeping pH value in the range 6-8;
■■ the limited use of chemical reagents (no use of buffer solutions, ammonia salts or complexing
agents), i.e. only metal and sulphur/selenium precursors are involved;
■■ the possibility to deposit the “coupled compounds” in form of thin layers directly from the
liquid suspension onto the substrates (silicon, alumina, glass, TCO layers, etc.).
This paper reports details on the preparation procedure, results of morphological and structural investigations
(XRD, SEM), compositional analysis (EDS microanalysis) and optical-electrical measurements (UV-VIS
absorption, I-V, impedance spectroscopy,...), which point out the great potentiality of the proposed method
for the synthesis of different “sensitized nano-compounds”.
100
ms3-p10
CdZnTe crystal growth from the vapour phase under microgravity
conditions on board of the ESA Photon M3 mission
E. Bassano1, L. Carotenuto1, L. Zanotti2, A.Zappettini2, D. Calestani2, C. Paorici3and M. Fiederle4
1. Telespazio, Napoli
2. CNR-IMEM, Parma, Italy
3. Unversity of Parma, Physics Dept.
4. Freiburger Materialforschungszentrum FMF Albert-Ludwigs-Universität Freiburg D-79104 Freiburg,
Germany
CdZnTe crystals were grown by the vapour phase aboard of the ESA Photon-M3 mission. The growth
chamber was constituted by four crystallization zones maintained at different temperatures, so that it
was possible to study the transport rate of the compound as a function of temperature. The aim of the
experiment was the study of the effects of gravity on the transport of the vapor species during the growth
of CdZnTe crystals. For this reason, a model was developed for the unsteady flow of multi-component
gaseous mixtures, taking into account all cross-effects of the entropy production in the framework of
linear thermodynamics of irreversible processes and proper boundary conditions at crystal surfaces. A
3d unsteady numerical CFD code for the growth process simulation and a thermal code for the thermal
analysis of composite ampoule employed in space experiment were implemented, based on the thermofluid-dynamic model.
The four crystals grown under microgravity conditions and the four ones grown on earth were characterized
by profilometer, Scanning Electron Microscopy, and Microanalysis.
The effect of microgravity on transport rate was studied and compared with the model prediction. Results
show that also the Zn/Cd ratio in the source material and in the crystals was affected by microgravity. The
explanation of the former effect requires further investigations.
All the results are discussed in the frame of the new project that is being founded by ESA that concerns the
next flight scheduled in the 2010 aboard of the International Space Station.
101
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Stucture and property of isotactic butene-ethylene
copolymers prepared with metallocene catalysts
Rossella Aprea, Claudio De Rosa, Carmen Scarica, Finizia Auriemma, Odda
Ruiz de Ballesteros, Alberto Di Girolamo, Rocco Di Girolamo
Dipartimento di Chimica “Paolo Corradini”, Università di Napoli “Federico II”, 80126 Napoli (Italy).
It has recently been shown that the microstructure of isotactic polybutene (iPB) can be tuned by using
metallocene catalysts.[1] Samples of iPB characterized by different concentration of stereodefects show
different crystallization and physical properties. This principle can be exploited to modify the complex
polymorphic behaviour of iPB that has prevented the commercial development of iPB produced with
Ziegler-Natta catalysts, notwithstanding the interesting physical properties. In fact, manufactured articles
obtained with the classic technologies of processing of thermoplastic materials (moulding, extrusion etc.)
crystallize in the metastable form II that slowly transforms into the more stable form I. This spontaneous
transformation produces dimensional instability and deformation of the manufactured article preventing
commercial development of the product.
In this communication a detailed study of the polymorphic behavior and of the mechanical properties
of isotactic butene-ethylene copolymers (Bu-Et) prepared with metallocene catalysts is presented. The
incorporation of ethylene up to high concentrations and the random distribution of comonomeric units
allow studying the influence of the presence of ethylene as constitutional defect, on the structure, in
particular on the form II-form I transformation, and the physical properties of iPB.
The structural characterization of Bu-Et copolymers has shown that copolymers samples with low ethylene
concentration crystallize form the melt into form II, which transforms into form I by aging at room
temperature. Samples with ethylene contents higher than 4 wt% do not crystallize from the melt and the
obtained amorphous samples crystallize by aging at room temperature directly into form I. Therefore, the
presence of ethylene accelerates the transition of the form II into form I and samples with suitable ethylene
concentration (4-10 wt%) crystallize by aging at room temperature directly in form I.
The study of the mechanical properties has demonstrated that Bu-Et copolymers show interesting
mechanical properties of thermoplastic elastomers, which are not observed in the iPB homopolymer.
It has been observed a gradual variation of the mechanical parameters with increasing ethylene content,
with gradual decrease of the Young’s modulus and of the stress at yielding, in agreement with the decrease
of the crystallinity, and increase of the deformation at breaking and flexibility.
References
1. L. Resconi, I. Camurati, F. Malizia, Macromol. Chem. Phys. (2006), 207, 2257.
102
ms4-p2
Study of the crystallization kinetics of isotactic propenebutene copolymers from metallocene catalysts
Rossella Aprea, Claudio De Rosa, Manuela Muccio, Odda Ruiz de Ballesteros, Finizia Auriemma
Dipartimento di Chimica “Paolo Corradini”, Università di Napoli “Federico II”, 80126 Napoli (Italy)
Random copolymers of propylene with ethylene and butene are commercially produced world wide and
used mainly in the packaging market as materials for film applications, taking advantages of their good
transparency, higher impact strength and lower heat-seal temperature compared with isotactic polypropylene
(iPP) homopolymer. These advantages would be due to the incorporation of defects in the chain structure
that reduces crystallization tendency of iPP. The less perfect crystals have lower melting temperature
and density, resulting in higher clarity. The crystallization behavior and the mechanical properties of
random copolymers of propylene with ethylene, butene and hexene comonomers prepared with different
metallocene catalysts have been recently studied.[1-3] Incorporation of low amounts ethylene, butene and
hexene induces crystallization of γ form,[1,2] and produces great enhancement of ductility, flexibility and
toughness, compared to iPP.
In this communication the crystallization kinetics of samples of propene-butene (iPPBu) copolymers,
prepared with a metallocene catalyst, has been studied. This study allows determining the influence of
butene units on the crystallization kinetics of iPP, which in turn influences the crystallization of α and γ
forms and the material properties.
All as polymerized iPPBu copolymers crystallize as mixtures of α and γ forms of iPP and the amount of γ
form increases with increasing butene concentration. The iPPBu samples isothermally crystallize from the
melt in mixtures of α and γ forms, at any crystallization temperature Tc, and the amount of γ form increases
with increasing the crystallization temperature.
The study of crystallization kinetics has shown that the presence of butene units for concentration lower
than 10-13 mol% does not affect the rate of the crystallization form the melt of iPP. With increasing
butene content the crystallization rate strongly increases and the copolymers crystallize completely in
the α form. This can be explained by the fact that high concentrations of butene are well tolerated in the
crystal lattice of the kinetically favored α form, rather than in the γ form, with a corresponding increase of
the crystallization rate.
References
1. C. De Rosa, F. Auriemma, O. Ruiz de Ballesteros, L. Resconi, I. Camurati, Macromolecules (2007), 40, 6600.
2. C. De Rosa, F. Auriemma, O. Ruiz de Ballesteros, D. De Luca, L. Resconi, Macromolecules (2008), 41, 2172.
3. C. De Rosa, F. Auriemma, O. Ruiz de Ballesteros, L. Resconi, I. Camurati, Chem. Mater. (2007), 19, 5122.
103
ms4-p3
Effect of nucleating agent on the crystallization of
metallocene low stereoregular isotactic polypropylene
Finizia Auriemma, Maria Criscuolo, Claudio De Rosa, Fortunata Esposito
Dipartimento di Chimica “Paolo Corradini” - Università di Napoli “Federico II” - 80126 Napoli, Italy
The use of nucleating agents (NAs) is very common for obtainment of low cost manufactures of
semicrystalline thermoplastic polymers. The presence of a nucleating agent accelerates the crystallization
process through a heterogeneous nucleation mechanism, with the result that the production cycles
are shortened.[1] The use of sorbitol derivatives as NAs in the production of objects made by isotactic
polypropylene (iPP) with heterogeneous Ziegler-Natta catalysts is well known.
Nowadays, using metallorganic catalysts it is possible to obtain samples of iPP with different microstructures
and mechanical properties.[2] One of the most important problems of metallocene-made iPPs is that at a
given temperature the crystallization rate decreases with increasing the defect content. Moreover, since
NAs act through a heterogeneous nucleation mechanism, the resulting morphology and mechanical
properties may also be affected. Aim of this work is the study of the effect of the presence of NAs on the
crystallization rate and the mechanical properties of a metallocene made low stereoregular iPP sample,
characterized by elastomeric properties and high Young modulus due to the presence of a high level of
crystallinity.
Pseudo ternary mixtures consisting of a low stereo-regular iPP sample, bis-[(3,4-dimethylbenzylidene)sorbitol] (DMDBS) as AN and IRGANOX 1010 as antioxidant, have been prepared. The metallocene iPP
sample is characterized by a concentration of stereo-defects essentially represented by isolated rr triads of
11 mol %, and is free from regio-defects.
The composition of DMDBS in the mixtures has been varied in the range 0-1 wt% with respect to the
weight of the polymer, whereas the IRGANOX 1010 content has been fixed at 0.5 wt%.
The structural and thermal analyses have indicated that the presence of only 0,1 wt% of DMDBS has
already a strong effect on the crystallization. In fact, the crystallization temperature increases (Tc) of 17°C,
corresponding to an efficiency of the nucleating agent of about 59%. The addition of 1 wt% of DMDBS
produces an increase of Tc of about 25°C, which corresponds to an efficiency of the nucleating agent of
85%. The mechanical analysis indicates that the presence of NA does not influence significantly the good
elastomeric properties of the pure iPP. The increase of NA content however improves the transparency of
films with the same thickness.
References
1. M. Kristiansen, M. Werner, T. Tervoot, P. Smith Macromolecules (2003), 36, 5150.
2. C. De Rosa, F. Auriemma, A. Di Capua, L. Resconi, S. Guidotti, I. Camurati, I. E. Nifant’ev, I. P. Laishevtsev, J. Am. Chem.
Soc. (2004), 126, 17040.
104
ms4-p4
The crystallization of γ form in isotactic copolymers of propylene
Claudio De Rosa1, Finizia Auriemma1, Paolo Vollaro1, Maria D’Avino1, Luigi Resconi2
1. Dipartimento di Chimica “Paolo Corradini” - Università di Napoli “Federico II” 80126 Napoli, Italy
2. Basell Polyolefins, Centro Ricerche G. Natta Ferrara Italy
Recent extensive investigations of the crystallization properties of isotactic polypropylene (iPP) produced
with metallocene catalysts have demonstrated that the microstructure of the chains strongly influences
the polymorphic behavior of iPP.[1-3] Single-center metallocene catalysts allow a perfect control over
the chain microstructure, and iPP samples characterized by different kinds and amounts of regio- and
stereo-irregularities can be produced.[1] iPP samples characterized by chains including different types of
microstructural defects (stereodefects and regiodefects) or constitutional defects (i.e. comonomeric units)
generally crystallize as a mixture of the α and γ forms. A first important parameter that influences the
crystallization of the α and γ forms is the average length of the regular isotactic propylene sequences
<LiPP> (interruption effect).[2,3] Short regular isotactic sequences would induce crystallization of the γ
form. Since in metallocene-made iPPs and in propene-based isotactic copolymers the defects are randomly
distributed along the polymer chains, even a small amount of defects shortens the length of the regular
isotactic sequences, favoring the crystallization of the γ form. A second important parameter that influences
the crystallization of the α and γ is related to the different degrees of inclusion of stereodefects and
constitutional defects in the crystals of α and γ forms (inclusion effect).[3]
The crystalizzation behaviors of isotacic copolymers of propylene with 4-methy-1-pentene (iPP4MP) and
1-octene (iPPC8) have been studied. They have been synthesized with a metallocene catalyst. The amount
of the stereo- and regio-defects is negligible and nearly constant all over the series. Therefore, the effect
of the sole presence of comonomeric units on the polymorphism and the physical properties of iPP could
be analyzed. All iPP4MP and iPPC8 copolymers crystallize from the melt in mixtures of α and γ forms.
iPPC8 copolymers with a concentration of octene lower than 5.0 mol% crystallize essentially into the α
form, whereas samples with octene contents higher than 5.0 mol% crystallize in disordered modifications
intermediated between the α and γ forms.
The maximum amount of γ form obtained by isothermal crystallizations in iPP4MP and iPPC8 copolymers
is compared to those obtained for copolymers with ethylene, butene, pentene and hexene and is discussed
in terms of the effect of interruption of the regular isotactic sequences.
References
1. C. De Rosa, F. Auriemma, A. Di Capua, L. Resconi, S. Guidotti, I. Camurati, I. E. Nifant’ev, I. P. Laishevtsev J. Am. Chem.
Soc. (2004), 126, 17040.
2. C. De Rosa, F. Auriemma, O. Ruiz de Ballesteros, L. Resconi, I. Camurati Macromolecules (2007), 40, 6600.
3. C. De Rosa, F. Auriemma, O. Ruiz de Ballesteros, D. De Luca, L. Resconi, Macromolecules (2008), 41, 2172.
105
ms5-p1
Carbonic anhydrase inhibitors: comparison of aliphatic
sulfamate/bis-sulfamate adducts with isozymes II and IX
V. Alterio1, R.M. Vitale2, A. Innocenti3, J.Y. Winum4,
S.M. Monti1, C.T. Supuran3 and G. De Simone1
1.
2.
3.
4.
Istituto di Biostrutture e Bioimmagini-CNR, 80134 Napoli, Italy
Istituto di Chimica e Biomolecolare-CNR, 80078, Pozzuoli, Italy
Università degli Studi di Firenze, 50019 Sesto Fiorentino (Firenze), Italy
Université Montpellier II, Laboratoire de Chimie Biomoléculaire, 34296 Montpellier Cedex, France
Carbonic anhydrases (CAs, EC 4.2.1.1) constitute an ubiquitous family of metalloenzymes that catalyze the
reversible hydration of carbon dioxide to bicarbonate ion.[1] These enzymes represent an interesting target
for the design of pharmacological agents useful in the treatment or prevention of a variety of disorders such
as glaucoma, acid-base disequilibria, epilepsy, neuromuscular diseases and the management of hypoxic
tumors.[1,2] Two main approaches have been used to design CA inhibitors (CAIs), the tail and the ring
approaches. Aliphatic mono-[3] and bis-sulfamates[4] constitute a particular class of CAIs which cannot be
classified in neither one of these categories.
Mono-/bis-sulfamates incorporating 8-10 normal aliphatic chains (compounds 1-4), have been tested for
the inhibition of all the catalytically active human isozymes, showing a very interesting inhibition profile.
In particular, the bis-sulfamates showed higher affinity for the tumor-associated isozyme CA IX compared
to hCA II, whereas the opposite was true for the corresponding mono-sulfamates.
Here we report the crystal structures for aliphatic mono- and bis-sulfamates (1-4) in adduct with the
physiologically dominant isoform II, as well as modeling studies on two of these compounds (2,4) with the
isoform CA IX. This combined approaches give an interesting explanation for the experimentally observed
different affinities of this class of compounds toward the various isozymes, providing useful insights for
the design of more isozyme-selective inhibitors mainly targeting the tumor-associated CA IX.
References
1. C.T. Supuran Nat. Rev. Drug Discov. (2008), 7, 168.
2. E. Svastova, A. Hulikova, M. Rafajova, M. Zat’ovicova, A. Gibadulinova, A. Casini, A. Cecchi, A. Scozzafava, C.T.
Supuran, J. Pastorek, S. Pastorekova FEBS Lett. (2004), 577, 439.
3. J.Y. Winum, D. Vullo, A. Casini, J.L. Montero, A. Scozzafava, C.T. Supuran J. Med. Chem. (2003), 46, 5471.
4. J.Y. Winum, S. Pastorekova, L. Jakubickova, J.L. Montero, A. Scozzafava, J. Pastorek, D. Vullo, A. Innocenti, C.T. Supuran
Bioorg. Med. Chem. Lett. (2005), 15, 579.
106
ms5-p2
Crystal structure of the catalytic domain
of the tumor-associated Hca IX*
V. Alterio1, M. Hilvo2, A. Di Fiore1, C.T. Supuran3, P. Pan2, S. Parkkila2, A. Scaloni4,
J. Pastorek5, S. Pastorekova5, A. Scozzafava3, C. Pedone1, S.M. Monti1 and G. De Simone1
1.
2.
3.
4.
5.
Istituto di Biostrutture e Bioimmagini-CNR, 80134 Napoli, Italy
Institute of Medical Technology and School of Medicine, FI-33014 University of Tampere, Finland
Università degli Studi di Firenze, 50019 Sesto Fiorentino (Firenze), Italy
Proteomics and Mass Spectrometry Laboratory-CNR, 80147 Napoli, Italy
Institute of Virology-SAS, 84505 Bratislava, Slovak Republic
Carbonic anhydrases (CAs) are ubiquitous metallo-enzymes, acting as catalysts in the reversible hydration
of CO2 to HCO3- and H+.[1] All human CAs (hCAs) belong to the so-called α-class and differ widely in their
cellular localization: CA I-III, VII and XIII reside in the cytosol, CA IV, IX, XII and XIV are associated
with the cell membrane, CA VA-VB occur in mitochondria, whereas CA VI is secreted in saliva and milk.[1]
CA IX is a very peculiar member of the CA family since it is generally expressed in a very limited number
of normal tissues, whereas its overexpression is seen on the cell surface of a large number of solid tumors,
where it is invariably linked with the hypoxic phenotype.[2] It is a multi-domain protein consisting of an
N-terminal proteoglycan-like (PG) domain, a CA catalytic domain, a transmembrane segment (TM) and an
intracytoplasmic (IC) portion.[3] Here we report the X-ray crystallographic structure of the hCA IX catalytic
domain in complex with a classical, clinically used sulfonamide inhibitor.[4] The structure reveals a typical
α-CA fold, which significantly differs from the other CA isozymes when the protein quaternary structure
is considered. Thus, two catalytic domains of CA IX associate to form a dimer, which is stabilized by the
formation of an intermolecular disulfide bond. The active site clefts and the N-terminal regions of both
monomers are located on one face of the dimer (allowing for concomitant positioning of both PG domains
at the entrance to the active site clefts), while the C-termini are located on the opposite face to facilitate
protein anchoring to the cell membrane. This analysis provides the first structural background to justify
the various functions observed for the different CA IX domains. Moreover, on the basis of the structural
differences observed between CA IX and the other membrane-associated α-CA isoforms, further prospects
for the rational drug design of isozyme-specific CA inhibitors are also proposed.
References
1. C.T. Supuran Nat. Rev. Drug Discov. (2008), 7, 168.
2. C.C. Wykoff, N.J.P. Beasley, P.H. Watson, K.J. Turner, J. Pastorek, A. Sibtain, G.D. Wilson, H. Turley, K.L. Talks, P.H.
Maxwell, C.W. Pugh, P.J. Ratcliffe and A.L. Harris Cancer Res (2000), 60, 7075.
3. R. Opavsky, S. Pastorekova, V. Zelnik, A. Gibadulinova, E.J. Stanbridge, J. Zavada, R. Kettmann, and J. Pastorek Genomics
(1996), 33, 480.
4. V. Alterio, M. Hilvo, A. Di Fiore, C.T. Supuran, P. Pan, S. Parkkila, A. Scaloni, J. Pastorek, S. Pastorekova, A. Scozzafava,
C. Pedone, S.M. Monti and G. De Simone PNAS (2009), Submitted.
*This research was financed by a grant of the 6th Framework Programme (FP) of the European Union (DeZnIT project)
107
ms5-p3
The dynamic of the inner sphere water in lanthanide
DOTAM complexes: a neutron and X-ray study
R. Artali1, G. Bombieri1, F. Meneghetti1, S. Aime2, A. Mortillaro3, S.A. Mason4 and G.J. McIntyre 4
1.
2.
3.
4.
University of Milano, Dipartimento di Scienze Farmaceutiche “Pietro Pratesi”, 20133 - Milano (Italy)
University of Torino, Dipartimento di Chimica, 10125 - Torino (Italy)
BRACCO Imaging S.p.A. - Milano (Italy)
Institut Laue-Langevin, Grenoble (France)
It is well known the importance of the Ln-Hwater distances in the macrocyclic complexes of Ln used for
MRI imaging as they permit to calculate the overal rotational correlation time (τRO) related to the water
proton relaxivity. Merback et al.[1] calculated the τRO of the Ln(III)-Hwater vector assuming the water
molecule symmetry axis, aligning with the Ln(III)-Owater vector. More recently Caravan[2], using a new
model based on 1H ENDOR combined with 17O ENDOR [3], assessed that the water is oriented in its metal
coordination with an angle γ between Gd-O and the bisection of the two lone pairs, distributed within the
range 0°< γ <55°. The X-ray and neutron studies on [Ln(H2O)DOTAM](CF3SO3)•3H2O (Ln=Eu, Nd)
derivatives have permitted to define clearly the values of the distances Ln-Owater and Ln-Hwater particularly
in neutron experiments. The asymmetry of the Ln-Hwater or Ln-Dwater in the deuterated complexes, were
used to evidence a non symmetric orientation of the coordinated water with respect to the Ln-Owater axis,
with the two hydrogen or deuterium atoms bent towards the macrocyclic ligand, as shown by the ORTEP
view of the [Nd(H2O)DOTAM](CF3SO3)•3H2O structure determined by neutron diffraction at 65K.
References
1. F.A. Dunand,, A. Borel, A.E. Merbach JACS (2002) 124 (4), 710
2. P. Caravan ACS (2009) 195365
3. A.M. Raitsimring, A.V. Astashkin, D. Baute, D. Goldfarb, P. Caravan J. Phys. Chem. A (2004) 108 (35), 7318
108
ms5-p4
Structure and functional regulation of a mycobacterial
enzyme essential for daughter cell separation
F. Squeglia1, A. Ruggiero1, D. Marasco1,2, E. Pedone1, C. Pedone1,2 and R. Berisio1
1. Instituto di Biostrutture e Bioimmagini, CNR, I-80134 Napoli – Italy
2. Università degli Studi di Napoli “Federico II”, I-80134 – Napoli, Italy
Mechanisms which regulate bacterial exit from dormancy are the same which are responsible for cellular
division. Indeed, proteins which have been identified as responsible for resuscitation, like the Resuscitation
Promoting Factor Interacting Protein (RipA) play a key role in bacterial division, as they and are likely
responsible for septal peptidoglycan degradation[1,2,3]. RipA localizes at bacterial septa and has remarkable
effect on bacterial phenotype. Indeed, the deletion of the gene encoding for RipA induces decreasing
growth and an abnormal M. tuberculosis phenotype, consisting in branching and chaining bacteria[1]. This
makes RipA an excellent candidate as a drug target against Tuberculosis.
RipA was cloned, expressed and purified in native conditions. Crystals were obtained using vapour diffusion
techniques. The structure of RipA was solved by Multiwavelength Anomalous Dispersion using the
anomalous signal from the Se atoms of selenomethionine-labeled enzymes. For functional characterization
of the enzyme, lyophilized cells of M. lysodeikticus labeled with FITC were used as substrate.
The crystal structure of RipA allowed us to definitely characterize the enzyme function and its regulation
mechanism. Cell wall degradation experiments revealed that this enzyme is active as cell wall hydrolase,
by cleaving cell-wall peptide crosslinks. In parallel, mass spectrometry studies of the processed cell wall
material provided clues of the peptidase specificity. Altogether, these results provide the basis for the
rational design of low molecular weight enzyme inhibitors.
References
1. E.C. Hett, M.C. Chao, L.L. Deng, E.J. Rubin. PLOS Pathogens (2008), 4.
2. A. Ruggiero, B. Tizzano, A. Geerlof, E. Pedone, C. Pedone, M. Wilmanns, R. Berisio. Acta Crystallogr F (2007), 63, 870-873.
3. A. Ruggiero, B. Tizzano, E. Pedone, C. Pedone, M. Wilmanns, R. Berisio. J. Mol. Biol. (2009), 385, 153-62.
This work was supported by MIUR (FIRB Prot. RBRN07BMCT)
109
ms5-p5
Structural insights into revival of M. tuberculosis from latency
A. Ruggiero1, F. Squeglia1, E. Pedone1, C. Pedone1,2 and R. Berisio1
1. Instituto di Biostrutture e Bioimmagini, CNR, I-80134 Napoli – Italy
2. Università degli Studi di Napoli “Federico II”, I-80134 – Napoli, Italy
The interaction between M. tuberculosis and the human host after infection may manifest itself as a chronic
disease or as a latent (or dormant) infection, a state capable to evade host responses. The probability of
reactivation from dormancy is strongly affected by the type of host immune response and it is significantly
enhanced in immune-compromised patients, e.g. suffering from AIDS. Understanding and controlling the
entry and exit from dormancy is important in the development of new anti-tubercular therapies.
Resuscitation of dormant bacteria is promoted by resuscitation-promoting-factors, Rpfs, which are
secreted from slowly replicating bacteria close to dormant bacteria. These proteins are thought to cleave
peptidoglycans which constitute the cell wall[1]. Cell wall cleavage could alter cell wall mechanical
properties and favour cell division and/or release anti-dormancy factors[1]. Although these proteins are
targets for antibiotics and key proteins for the formulation of vaccines, available structural information
are scarce.
We have determined the first crystal structure of a Resuscitation Promoting Factor, RpfB .[2,3]. Beside aiming at a better understanding of the mechanism of exit from dormancy in M. tuberculosis, the
comprehension of the structural features associated to RpfB activity/inhibition will provide the basis for
the identification of molecules (pro-latency molecules) able to restrict bacterial life to the latent, nondangerous, state.
References
1. N.H. Keep.; J.M. Ward, M. Cohen-Gonsaud, B. Henderson, Trends Microbiol (2006), 14, 271-276.
2. A. Ruggiero, B. Tizzano, A. Geerlof, E. Pedone, C. Pedone, M. Wilmanns, R. Berisio. Acta Crystallogr Sect F Struct Biol
Cryst Commun. (2007), 63, 870-873.
3. A. Ruggiero, B. Tizzano, E. Pedone, C. Pedone, M. Wilmanns, R. Berisio. J. Mol. Biol. (2009), 385, 153-62.
This work was supported by MIUR (FIRB Prot. RBRN07BMCT)
110
ms5-p6
Structural studies on new furazan derivatives,
as potential Stat-3 inhibitors
G. Bombieri, C. Trucco, D. Masciocchi, A. Gelain, S. Villa and F. Meneghetti
Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche “P. Pratesi”, 20133 - Milano
Signal transduction and activator for transcription factor 3 (Stat-3) is a latent cytosolic protein member of
Stat family. It is a transcription factor that transmits cytoplasmic signals (e.g. from growth factors, polypeptide cytokines etc.) to the nucleus. Blocking constitutively activated Stat-3 signalling leads to apoptosis
of tumour cells but has no effects on normal cells suggesting that its inhibition could be a leading target
for cancer therapy[1]. In this research we focused on the discovery of new furazan derivatives, as potential
Stat-3 inhibitors, with the aim to identify the essential structure-activity requirements for the development
of novel active compounds. On this basis, we have analyzed the X-ray structures of four compounds having
the following general formula (Figure 1, left) and structure-activity relationship have been derived. The
drop in activity of the derivatives with respect to AVS-0288 (lead compound) could be due to the presence
of a more flexible lateral chain that could influence their orientation and interaction at the receptor site.
Figure 1. General formula of the X-Ray analyzed derivatives (left) and of the lead compound (right).
References
1. L. Costantino, D. Barlocco Curr. Med. Chem. (2008), 15, 834.
111
ms5-p7
Insights into the molecular basis of transcriptional activation in
Archaea: structural analysis of BldR from Sulfolobus solfataricus
A. Di Fiore1, G. Fiorentino2, R. M. Vitale3, R. Ronca2, P. Amodeo3,
C. Pedone1, S. Bartolucci2 and G. De Simone1
1. CNR, Istituto di Biostrutture e Bioimmagini, 80134, Naples, Italy.
2. Università degli Studi di Napoli Federico II, Dip. di Biologia Strutturale e Funzionale, 80126, Naples
3. CNR, Istituto di Chimica e Biomolecolare, 80078, Pozzuoli, Italy.
The multiple antibiotic resistance regulator (MarR) family is a significant class of transcriptional regulators,
since its members control a variety of biological functions, including resistance to multiple antibiotics,
organic solvents, household disinfectants and oxidative stress agents. Although the majority of the MarR
family members have been characterized as transcriptional repressors, examples of transcriptional activators
have also been reported.[1] BldR is a newly identified member of this family that has been demonstrated to
act as a transcriptional activator in stress response to aromatic compounds in the crenarchaeon Sulfolobus
solfataricus.[2] In particular, biochemical studies suggested that by binding to its own promoter, BldR
is able to induce autoactivation and increase the level of a coexpressed putative drug efflux transporter,
while by binding to the Sso2536 promoter, this protein stimulates accumulation of alcohol dehydrogenase
enzyme and, hence, the enzyme-catalyzed conversion of aldehydes into less toxic alcohols.
To provide the first detailed description of the molecular determinants present in an archaeal activator
of the MarR family responsible for its binding to DNA, we undertook a structural study on BldR. In
particular, here we report its X-ray crystal structure, together with a molecular modeling study on the
complex formed by BldR with its cognate DNA sequence.[3]
References
1. K. J. Newberry, M. Fuangthong, W. Panmanee, S. Mongkolsuk, R. G.Brennan. Mol. Cell. (2007), 28, 652.
2. G. Fiorentino, R. Ronca, R. Cannio, M. Rossi, S. Bartolucci. J. Bacteriol. (2007), 189, 7351.
3. A. Di Fiore, G. Fiorentino, R. M. Vitale, R. Ronca, P. Amodeo, C. Pedone, S. Bartolucci, G. De Simone. J. Mol. Biol. (2009),
388, 559.
112
ms5-p8
Novel gold(I)/gold(III) compounds bearing saccharinate
ligands: structural and solution chemistry, protein
binding behaviour and antiproliferative effects
A. Guerri1, L. Maiore,2, M.A. Cinellu2, L. Messori3
1. Università di Firenze, Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino (FI)
2. Università di Sassari, Dipartimento di Chimica, 07100 Sassari
3. Università di Firenze, Dipartimento di Chimica, 50019 Sesto Fiorentino (FI)
Gold compounds are of great interest for their attractive antiproliferative and cytotoxic properties and are
intensely investigated as a potential source of innovative drugs for cancer treatment [1]. Various gold(I)/
gold(III) saccharinate (Sac) complexes have been synthesized in order to obtain water-soluble and non
toxic compounds. Three different compounds were prepared for the present study: a disaccharinate Au(I)
complex; a mixed-ligand Au(I) complex with one saccharinate moiety and one PTA moiety as coordinating
groups; a square planar Au(III) monochloro trisaccharinate complex (Figure 1). The crystal structure of 3
has also been determined.
Figure 1. Schematic view of the three complexes
Figure 2. Crystal structure of [AuCl(Sac)3]-
Besides the solution behaviour, the interaction with protein has been tested by means of horse heart
cytochrome c as target. The antiproliferative and cytotoxic properties were evaluated in vitro toward
sensitive and resistant A2780 human ovarian carcinoma cell lines. These compounds turned out to
manifest a reasonable compromise between stability and reactivity. ESI MS analysis revealed that these
compounds react with the model protein cytochrome c, to highly different extents. Finally, the essay for the
antiproliferative properties of the three compounds shows that the mixed ligand gold(I) complex turned out
to be the most active whereas a very moderate activity was found for the disaccharinate gold(I) complex;
an intermediate activity was measured for the gold(II) complex.
References
1. 1.A. Casini, C. Hartinger, C. Gabbiani, E. Mini, P.J. Dyson, B.K. Keppler, L. Messori J. Inorg. Biochem. (2008), 102, 564.
113
ms5-p8
Crystal structure of Enterococcus faecalis Thymidylate
synthase in complex with a specific inhibitor
C. Pozzi1 ,M.P. Costi2, S. Ferrari2, R. Luciani2, M. Benvenuti1, S. Mangani1
1. Dipartimento di Chimica, Universita` di Siena, Siena 53100, Italy.
2. Dipartimento di Scienze Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, 41100 Modena.
Thymidylate synthase (TS) is an enzyme that catalyzes the reductive methylation of 2’-deoxyuridine
5’-monophosphate (dUMP) to thymidyne 5’-monophosphate (dTMP), using the cofactor 5,10-methylene5,6,7,8-tetrahydrofolate (mTHF) as a one–carbon donor and reductant [1]. This reaction is the only the novo
source of thymidylate for the cells [2]. The inhibition of TS leads to pronounced changes in cellular protein
and RNA, cessation of DNA replication and eventually cell death, a phenomenon termed thymineless
death [3].
Because of its critical function, considerable effort has been focused on the design of TS inhibitors for the
treatment of cancer [4]. Less attention has been directed towards the design of species-specific TS inhibitors
aimed at treating diseases caused by bacterial, fungal or opportunistic pathogens. However, taking into
account the rise in antibiotic resistant bacteria, the relative toxicity of treatments for fungal infections
and the poor therapies available for several opportunistic infections in immunocompromised patients, the
successful development of pathogen-specific TS inhibitors may offer an important alternative to current
antibiotic, antiparasitic and antifungal drugs [5,6]. TS enzymes show an highly conserved structure, but some
differences of the active site may be exploited for the design of inhibitors able to discriminate pathogen
TSs vs. human TS [7].
We have synthesized a library of compounds with original structure that have provided encouraging results
as specific inhibitors of bacterial enzymes. In order to explain the activity of these compounds and to reveal
the molecular basis for this specificity, we have obtained the crystal structure of Lactobacillus casei TS
(LcTS), Escherichia coli TS (EcTS) and of Enterococcus faecalis TS (EfTS) complexed with dUMP and
selective inhibitors. The 2.18 Å crystal structure of one EfTS complex presented here is the first EfTS
structure and shows that binding of the inhibitor is accompanied by large rearrangement of the protein,
determining the ordering of a mobile loop that appears disordered in the free enzyme.
In contrast to the previously determined crystal structures of the complexes of EcTS and LcTS with
inhibitors, that suggested multiple binding modes of these molecules into the active site, the complex
obtained for EfTS shows a well defined binding site for the compound.
The determination of the title crystal structure can provide the basis for the rational design of more powerful
and selective inhibitors towards bacterial targets.
References:
1.
2.
3.
4.
5.
6.
7.
114
K. Perry, E. Fraumann, et al. Proteins (1990), 8, 315.
C.W. Carreras, D.V. Santi Annu. Rev. Biochem. (1995), 64, 721.
J. Phan, S. Koli, W. Minor, R.B. Dunlap, S.H. Berger, L. Lebioda Biochemistry (2001), 40, 1897.
M.P. Costi Med. Res. Rev. (1998), 18, 21.
T.M. File Jr. Chest (1999), 115, 3S.
R.E. Chaisson, J.E. Gallant, J.C. Keruly, R.D. Moore Aids (1998), 12, 29.
T.A. Fritz, D. Tondi, J.S. Finer-Moore, M.P. Costi, R.M. Stroud Chemistry & Biology (2001), 8, 981
ms5-p9
Cross-talking of the chain termini in the swapping process
Filomena Sica1,2, Antonello Merlino1,2, Anna Balsamo1, Carmine
Ercole1, Delia Picone1, Lelio Mazzarella1,2
1. Department of Chemistry, University of Naples “Federico II”, Naples
2. Istituto di Biostrutture e Bioimmagini, CNR, 80134 Naples, Italy.
3D domain swapping is the process by which two or more protein molecules exchange part of their
structure to form intertwined dimers or higher oligomers. Bovine pancreatic ribonuclease, RNase A, is
able to swap both the C-terminal β-strand (residues 116-124) [1] and the N-terminal α-helix (residues 1-13)
[2]
, thus forming two different dimers. Cis-trans isomerization of the Asn113-Pro114 peptide group was
observed when the protein forms the C-terminal swapped dimer. To study the effect of the substitution of
Pro114 on the swapping process of RNase A, we have prepared and characterized the P114A monomeric
and dimeric variants of the enzyme. The mutation affects the capability of the N-terminal α-helix to swap
and the stability of the two swapped dimeric forms. These results, which are discussed on the bases of
crystallographic data collected on the monomeric and C-terminal swapped form of the P114A variant,
reveal a cross-talk between the chain termini in the swapping process of RNase A.
References
1. Y. Liu, P.J.Hart, M.P. Schlunegger, and D. Eisenberg. Proc. Natl. Acad. Sci. USA (1998), 95, 3437.
2. Y. Liu, G.Gotte, ,M. Libonati, and D. Eisenberg, Nature Struct. Biol. (2001), 8, 211.
115
ms5-10
Structural characterization of the redundant
thioredoxin system of Sulfolobus solfataricus
A. Ruggiero1, M. Masullo2, M.R. Ruocco3, P. Arcari3, A.Zagari1,4, L. Vitagliano1
1. Istituto di Biostrutture e Bioimmagini, CNR, I-80134 Napoli
2. Dipartimento di Scienze Farmacobiologiche, Università degli Studi ”Magna Graecia” di Catanzaro, 88021
Catanzaro.
3. Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, 80131 Napoli, Italy
4. Dipartimento delle Scienze Biologiche, Sez.di Biostrutture, Università di Napoli Federico II, 80134 Napoli
Living organisms have developed efficient biological mechanisms for scavenging reactive oxygen species
produced by metabolism. The thioredoxin system, composed by thioredoxin (Trx), thioredoxin reductase
(TrxR), and NADPH plays a crucial role in regulating the redox state of the cells and in protecting them
against oxidative stress. Although this system is ubiquitous among organisms of all three domains of
life, most of the functional and structural investigations have been hitherto focused on eukaryal and
eubacteryal Trx systems. The analysis of the Sulfolobus solfataricus genome reveals that the thioredoxin
system is particularly intricate in this organism. Indeed, the presence of multiple putative TrxRs and the
coexistence of two distinct thioredoxin (SsTrxA2 and SsTrxA1) genes have been detected. The functional
characterization of the system has shown that two distinct Trxs are substrates for the thioredoxin reductase
SsTrxRB3. [1] In order to elucidate structure-function and structure-stability relationships of S. solfataricus
Trx system, we have undertaken combined crystallographic and spectroscopic analyses of the proteins
involved. The characterization of SsTrxRB3 has provided clues on the determinants of its dual function
(thioredoxin reductase and NADH oxidase) and of its thermostability.[2] The elucidation of SsTrxA2
structure [3,4] have revealed a peculiar dimeric organization as the redox active center of the protein is buried
by the monomer-monomer interface. Furthermore, on the basis of the 3D structure, we also suggested that
the shortening of the loop connecting secondary structure elements may play an important role in the
remarkable SsTrxA2 stability. These observations are confirmed by the analysis of the 3D structure of
SsTrxA1, which is currently in progress.
References
1. Grimaldi, P. Ruocco, MR. Lanzotti, MA. Ruggiero, A. Ruggiero, I., Arcari, P. Vitagliano, L. Maullo, M. Extremophiles
(2008),12,553.
2. Ruggiero, A. Masullo, M. Ruocco, MR. Grimaldi, P. Lanzotti, MA. Arcari, P. Zagari A, Vitagliano, L. Biophysical and
Biochimica Acta (2009),1794,554.
3. Ruggiero, A. Lanzotti, MA. Ruocco, MR. Grimaldi, P. Marasco, D., Arcari, P. Masullo, M. Zagari A, Vitagliano, L. Acta
Crystallogr F (2009), F65, 604.
4. Ruggiero, A. Ruocco, MR. Grimaldi, P. Marasco, D., Arcari, P. Masullo, M. Zagari A, Vitagliano, L. Proteins (2009),
revision submitted.
116
ms5-p11
A statistical survey in the protein data bank
searching for a 4-cysteines ring
A. Zagari
Dipartimento delle Scienze Biologiche, Università di Napoli “Federico II”, 80134, Napoli
Disulfide bridges play a fundamental role in the folding and the stabilization of a large number of proteins
and polypeptides. With the increase of the structural content of the Protein Data Bank (PDB)[1] almost
every aspect related to disulfide bond formation has been analysed. As a result, disulfide bonds were found
to be involved in a large variety of structural motifs that have been widely described and reviewed in the
literature.[2]
This work is aimed at searching highly rare motifs containing disulfide bonds. A search for four Cysteines,
forming a Ring (4CR) embodying 2 disulfide bonds, was carried out against all entries in the PDB.
Searching the crystallographic subset, only few protein molecules, all dimeric, were found to embody this
peculiar structural feature, which establishes a covalent link between two different polypeptide chains. In
contrast, in a peptide studied in solution by NMR, the 4 cysteines moiety includes only residues from one
chain.
A comparative analysis provided evidence for similarity and difference. Despite the very small number of
4CR found in the PDB, it emerged that 4CR motif may serve to gain a specialized function.[3]
4CR motif in the crystal structure of a PDZ domain
References
1. H.M Berman, et al.. Acta Crystallogr. (2002), D58, 899–907.
2. D.Majhen, J. Gabrilovac, M. Eloit, J.S. Richardson, A. Ambriović-Ristov Biochem. Biophys. Res. Commun.
(2006), 348, 278-87.
3. A. Zagari (2009), Biopolymers (submitted)
117
ms5-12
Structural studies of Nhm1, a key enzyme in the
nuclear and cytoplasmic metabolism of RNA
Luigi De Colibus 1, Lijie Sun2, John McCarthy 2 and Robert J.C.Gilbert 1
1. Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford
2. Interdisciplinary Biocentre, University of Manchester
mRNA turnover plays a key role in control of gene expression both by setting the basal level of gene
expression and as a site of regulatory responses. mRNA turnover is also used to remove aberrant mRNAs,
contributing to quality control in mRNA biogenesis.
Two general paths of mRNA decay have been identified downstream of the deadenylation event in
eukaryotic cells.
-a decapping enzyme consisting of two subunits, Dcp1p and Dcp2p, removes the 5′ cap structure, exposing
the transcript to digestion by a 5′→ 3′ exonuclease, and generating m7GDP.
-mRNAs can be degraded in a 3′→5′ direction by the cytoplasmic exosome. This generates a range of
m7Gppp-oligonucleotides.
While heterodimeric Dcp1-Dcp2 decaps full-length mRNAs, the DcpS type of “scavenging” enzyme
typically hydrolyses the m7GDP and m7Gppp- oligonucleotides generated by the two pathways above.
Recently, we have identified and biochemically characterized a Schizosaccharomyces pombe DcpS ortholog,
called Nhm1. Unlike mammalian DcpS and yeast Dcs1, this enzyme is able to catalyse the decapping
of capped mRNAs considerably longer than 10 nucleotides. Fluorescence and immunofluorescence
microscopy show that Nhm1 is located both in the nucleus and in the cytoplasm. We have solved crystal
structures for Nhm1 in the Apo form, in complex with a non-hydrolysable GTP analogue, and in complex
with m7GpppG as an H244N mutant. This mutation prevents enzyme turnover and has allowed us to
view atomic details of Nhm1’s characteristic catalytic histidine triad motif, and shed light on the catalytic
mechanism of the enzyme. Catalysis involves the generation of an asymmetric dimer in which one
monomer is in an open conformation and inactive and the other in a closed conformation and active. Each
monomer alternatively swaps between conformers via a 30 Å swing. Altogether these data provide new
insight into the mechanism of action of an enzyme that is involved in both cytoplasmic and nuclear RNA
metabolism.
118
ms5-p13
Copper(I)-mediated protein-protein interactions
result from suboptimal interaction surfaces
Banci L, Bertini I, Calderone V, Della-Malva N, Felli IC, Neri S, Pavelkova A, Rosato A.
The homeostasis of metal ions in cells is the result of the contribution of several cellular pathways that
involve transient, often weak, protein-protein interactions. Metal transfer typically implies the formation
of adducts where the metal itself acts as a bridge between proteins, by coordinating residues of both
interacting partners. Here we addressed the interaction between the human copper(I)-chaperone HAH1
and one metal-binding domain of one of its partners, namely the P-type copper-transporting ATPase
ATP7A. The adduct was structurally characterized in solution, in the presence of copper(I), and through
X-ray crystallography, upon replacing copper(I) with cadmium(II). Further insight was obtained through
molecular modelling techniques and site-directed mutagenesis. It is found that the interaction involves a
relatively small interface (less than 1000 A2) with a low fraction of non-polar atoms. These observations
provide a possible explanation for the low affinity of the two apo-proteins. It appears that electrostatics
is important in selecting which domain of the ATPase is able to form detectable amounts of the metalmediated adduct with HAH1.
119
ms6-p1
XRPD characterization of new luminescent
Ce(IV) amino phosphonates
F. Costantino1, P. L. Gentili1 and N. Audebrand2
1. Dipartimento di Chimica e CEMIN , Università di Perugia, 06123 Perugia
2. Sciences Chimiques de Rennes (UMR-CNRS 6226, 1-ENSCR) Universite´ de Rennes 1, 35042 Rennes
France, Cedex
The synthesis and characterization of new metal phosphonates is one of the older but still persistent research
field in the fundamental and applicative material chemistry because of their application in many field of
solid-state chemistry like catalysis, molecular recognition, gas-storage and for photochemical purposes.1
In particular the synthesis of new lanthanide phosphonates is a promising research field in the material
chemistry for the possibility to tune the photochemical properties by choosing the opportune metalbuilding block combination.
In this contribution we show the synthesis and the structural characterization of a new family of Ce aminobis phosphonates and diamino tetra- phosphonates.
All the structures of these derivatives have been solved “ab-initio” from laboratory X-Ray powder
diffraction data, using the real space global optimization procedures, implemented in the program FOX.2
All these compounds have three-dimensional pillared structure in which the layers, composed of CeO7
(or CeO8) polyhedra and PO3C tetrahedra, are connected by the organic moieties belonging to the aminophosphonic group.3
Figure 1. structures of two Ce(IV) bis- (left) and tetra- (right) phosphonates
References
1. J. G. Mao, Coordination Chemistry Reviews (2007) 251 1493
2. V. Favre-Nicolin, R. Cerny, J. Appl. Crystallogr. (2002) 35 734
3. F. Costantino, P.L. Gentili and N. Audebrand Inorg. Chem. Comm. 12 (2009) 406
120
ms7-p1
Small angle X-ray scattering (SAXS) as a tool to study
polymer blends with low contrast in electron density.
Finizia Auriemma1, Claudio De Rosa1, GiovanGiuseppe Giusto1, Geoffrey R. Mitchell2
1. Dipartimento di Chimica “Paolo Corradini”, Università di Napoli “Federico II”, 80126 Napoli, (Italy)
2. Polymer Science Centre, J. J. Thomson Physical Laboratory, University of Reading, Reading RG6 6AF, UK
Use of scattering methods for probing inhomogeneities such as thermal composition fluctuations in
polymer blends is well known. This kind of approach is generally performed resorting to small angle
neutron scattering experiments (SANS). Neutrons have the particularly important advantages of strong
scattering contrast and deep penetration into materials, which are achieved preparing blends in which a
component is totally or partially deuterated. With use of SANS the phase diagrams for a variety of polymer
blends have been detailed determined and a conclusive level of basic understanding has been achieved in
this field.[1] In particular, the role of concentration fluctuations on phase separation at the critical points
have been deeply understood in terms of general theory of critical phenomena.[1] In the case of commercial
samples, the use of SANS technique is limited due to the necessity of using deuterated samples especially
in the case of polyolefins based samples, due to low contrast of scattering density length between the two
components.
Here we demonstrate that small angle X-ray scattering (SAXS) may be used as a valuable tool to study
polymer blends, even in the cases where the contrast in electron density between the two components is low.
To this aim model blends of two metallocene-made isotactic polypropylene (iPP) samples characterized
by a different degree of stereoregularity have been analyzed using synchrotron light in time-resolving
SAXS experiments during consecutive heating-cooling runs. It is shown that non trivial structural and
mechanistic information may be obtained without resorting to more sophisticated experiments based on
SANS technique and deuterium labelling of polymers.
References
1. D. Schwahn Adv. Poly, Sci. (2005), 183, 1.
121
ms7-p2
Crystal structure solution of small or medium
sized molecules at non-atomic resolution
Benedetta Carrozzini1, Rocco Caliandro1, Giovanni Luca Cascarano1,
Carmelo Giacovazzo1,2, Annamaria Mazzone1 and Dritan Siliqi1
1. Istituto di Cristallografia, CNR, 70126 - Bari.
2. Dipartimento Geomineralogico, Università di Bari, 70125 - Bari
Data resolution is the most critical limit for the success of the ab initio crystal structure solution. Electron
density maps, calculated by Fourier syntheses with coefficients based on structure factors, are usually
affected by truncation effects due to the limited data resolution. To overcome this limit, two methods
have recently been proposed, namely the correction of resolution bias in electron-density maps [1,2] and the
extrapolation of the structure factors beyond the data resolution limit[3,4]. The first method has successfully
been applied to powder data and the second to protein data. Neither of them has been applied to singlecrystal data from small or medium-sized molecules. A third technique, the active use of the PSI-0 triplets
in a tangent procedure, was applied to small molecules in the early days of crystallography[5], but it
soon became obsolete because of the great success of methods combining reciprocal and direct space
techniques.
A new procedure, actively involving the above auxiliary algorithms in the phasing process, has been
implemented in SIR2008, the ab initio program of the package ILMILIONE[4]. It aims at reducing the
resolution bias by exploiting the extrapolation of unobserved high-resolution reflections and by relocating
the peaks in more correct positions, modifying also the peak profile to better fit the effective atomic electron
densities. Applications to a large set of test structures show that this new procedure can be successfully
accomplished, making more robust and effective the determination of the crystal structure[6].
References
1.
2.
3.
4.
5.
6.
122
Altomare, A., Cuocci, C., Giacovazzo, C., Kamel, G. S., Moliterni, A. & Rizzi, R. (2008). Acta Cryst. A64, 326–336.
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A. & Rizzi, R. (2008). J. Appl. Cryst. 41, 592-599.
Caliandro, R., Carrozzini, B., Cascarano, G.L., De Caro, L., Giacovazzo, C. & Siliqi, D. (2007). J.Appl. Cryst. 40, 883-890.
Caliandro, R., Carrozzini, B., Cascarano, G.L., De Caro, L., Giacovazzo, C. & Siliqi, D. (2007). J.Appl. Cryst. 40, 931-937.
Cascarano, G.L. & Giacovazzo, C. (1995). Acta Cryst. A51, 820-825.
Caliandro, R., Carrozzini, B., Cascarano, G.L., Giacovazzo, C., Mazzone A. & Siliqi, D. (2009). J.Appl. Cryst. 42, 302-307.
ms7-p3
Il Milione: a package for automatic protein structure determination
M.C. Burla4, R. Caliandro1, M. Camalli3, B. Carrozzini1, G.L. Cascarano1,
C. Giacovazzo1,2, A. Mazzone1 G. Polidori4, D. Siliqi1 and R. Spagna3
1.
2.
3.
4.
CNR - Istituto di Cristallografia, 70126 - Bari
Università di Bari – Dipartimento Geomineralogico,70125 – Bari
CNR - Istituto di Cristallografia, 00016 – Area della Ricerca di Roma 1
Università di Perugia – Dipartimento di Scienze della Terra, 06100 – Perugia
Il Milione[1] is a suite of computer programs devoted to the structure solution of macromolecules. It is able
to solve and refine crystal structures using the following techniques:
1. Ab initio. Early figures of merit rank the trial phase sets provided by Patterson or Direct Methods.
Phase extension and refinement have been powered to solve proteins up to 2.0 Å resolution; new
algorithms[2,3], using unobserved reflections properly extrapolated from the observations, have
been developed.
2. SIR-MIR, SIRAS-MIRAS, SAD-MAD. The program automatically performs the following
steps: evaluation of structure factor moduli of the heavy/anomalous scatterers substructure,
location of the substructure and phasing of the protein using this information.
3. Molecular Replacement (REMO). An atomic model is positioned in the protein cell by
exploiting experimental reflection moduli at limited resolution and by using novel rotation and
translation functions derived from probabilistic distributions.
4. Phase extension and improvement using Electron Density Modification (EDM) procedures and
extrapolation of reflections beyond the observed resolution (Free Lunch algorithm) [3].
5. An iterative model completion procedure (DEA) [4] based on a combination of an external
Automatic Model Building software and Modification of the Difference Fourier Map (DEDM[5])
and EDM.
New features and results on known and unknown protein structures will be illustrated.
Il Milione (version 2.2) is available, free for academic users, for Linux, Mac and Windows platforms.
References
1. M.C.Burla, R. Caliandro, M. Camalli, B. Carrozzini, G.L. Cascarano, L. De Caro, C. Giacovazzo, G. Polidori D. Siliqi, R.
Spagna - J. Appl. Cryst. (2007), 40, 609-613.
2. R. Caliandro, B. Carrozzini, G.L. Cascarano, L. De Caro, C. Giacovazzo, D. Siliqi – Acta Cryst. (2005), D61, 1080-1087.
3. R. Caliandro, B. Carrozzini, G.L.Cascarano, L. De Caro, C. Giacovazzo and D. Siliqi. – J. Appl. Cryst. (2007) 40,931-937.
4. R. Caliandro, B. Carrozzini, G.L. Cascarano, C. Giacovazzo, A. Mazzone, D. Siliqi – Acta Cryst. (2009), D65, 477-484.
5. R. Caliandro, B. Carrozzini, G.L. Cascarano, C. Giacovazzo, A. Mazzone, D. Siliqi – Acta Cryst. (2009), D65, 249-256.
123
ms7-p4
The MCX beamline at ELETTRA
A. Lausi1, P. Scardi2,3, M Leoni2,, J. Plaisier1, G Zerauschek1, A. Benedetti3, and P. Riello3
1. Sincrotrone Trieste, 34012 Basovizza (TS)
2. Dip. Ing. Materiali, Univ. di Trento, Mesiano, 38050 Trento
3. Dipartimento di Chimica Fisica, Univ. di Venezia, 30170 Venezia-Mestre
With the completion of the commissioning phase in fall 2008, the new powder diffraction beamline at
ELETTRA is open to users since February 2009. The new beamline allows to perform a wide range of nonsingle crystal diffraction experiments: grazing angle diffraction and reflectivity, residual stress and texture
analysis, phase identification and structural studies, kinetic studies, anomalous scattering and DAFS. In
order to fulfill the required flexibility in terms of beam characteristics at the experiment, ranging from spot
focus to line focus and to parallel beam, the optics of the line consist of two mirrors and a wider range (2.1
to 23 keV) monochromator: a first Pt-coated cylindrical mirror collimates the beam on the horizontally
focusing Si (111) double crystal monochomator in 1:1 configuration. The second - vertical focusing platinum coated mirror is flat and bendable, with a radius adjustable from 6 km to flat. The photon intensity
has been measured in excess of 1011 ph/s, with a energy resolution of about 2 10-4 at the Cu K-edge.
The standard instrument available in the experimental station is a four-circle diffractometer with motorized
sample holder; the standard optics in the diffracted beam consist of a single-crystal analyzer and scintillation
counter. A hot blower heater is available to control the temperature of the sample. As an alternative setup to the 4-circle diffractometer the beamline can be equipped with an oven coupled to a translating IP
detector for fast collection of XRD patterns and kinetics studies.
124
ms8-p1
Novel zirconium(IV) complexes bearing (amidomethyl)pyridine
(NN-) and amidomethylpyrrolidepyridine (-NNN-) ligands:
catalyst structure and stereoselectivity of olefin polymerization.
Liana Annunziata1, Daniela Pappalardo2, Consiglia Tedesco1 and Claudio Pellecchia3
1. Università degli Studi di Salerno, Dipartimento di Chimica, 84084 Fisciano (SA), Italy.
2. Università del Sannio, Dipartimento di Studi Geologici ed Ambientali, 82100 Benevento, Italy.
The understanding of the correlations between catalyst structure and stereoselectivity of polymerization
is one of the most fascinating issue in the olefin polymerization catalysis. In this contribution we describe
recent results concerning solid state characterization of novel zirconium complexes bearing (amidomethyl)
pyridine (NN-) or amidomethylpyrrolidepyridine (-NNN-) and their activity in olefin polymerization.
Zirconium(IV) complex bearing amidomethylpyrrolidepyridine ligand showed a “time averaged” Cssymmetric structure in solution and slightly distorted square pyramidal geometry in the solid state (scheme
1). Interestingly, an agnostic interaction between metal and hydrogen atom on C(23) was detected. Despite
the pre-catalyst structure, isotactic polyolefins with narrow molecular weight distributions were produced[1]
Bis(pentafluoro-N-((pyridin-2-yl)methyl)anilinato)zirconium(IV) complexes were synthesized and
characterized by RX single crystal. Interestingly, while the dichloride derivative, prepared via traditional
routes, showed a distorted octahedral geometry with C1-symmetry, the reaction between Zr(NMe2)4 and
Lig1H led to the 7-coordinate compound in which one dimethylamino group had been exchanged with one
ortho fluoride on the perfluorophenyl ring of the ligand via an aromatic nucleophilic substitution reaction
(Lig1)(Lig1*)ZrF(NMe2) (Scheme 2). Treatment of complexes with AliBu2H and methylalumoxane (MAO)
yields active, multisite ethylene and propylene polymerization catalysts.[2]
Scheme 1
Scheme2
References
1. L. Annunziata, D. Pappalardo, C. Tedesco, C. Pellecchia Macromolecules (2009) ASAP
2. L. Annunziata, D. Pappalardo, C. Tedesco, C. Pellecchia Organometallics (2009), 28, 688.
125
ms8-p2
Polymorphism and thermal stability of nicergoline
D. Capsoni1, M. Bini1, S. Ferrari1, V. Massarotti1, P. Di Martino2,
R. Gobetto3, R. Censi2, L. Malaj2, L. Pellegrino3
1. Università di Pavia, Dip. di Chimica Fisica “M. Rolla”, 27100 - Pavia
2. Università di Camerino, Dip. di Scienze Chimiche, 62032 - Camerino
3. Università di Torino, Dip. di Chimica I.F.M., 10127 - Torino
Nicergoline
(10α-methoxy-1,6-dimethylergoline-8β-methanol-5’-bromonicotinate,
C24H26BrN3O3)
is a semisynthetic ergot derivative, used for its α-adrenolytic and vasodilating effects on the vascular
system and for its stimulating action on cerebral and peripheral metabolism. Two polymorphic forms
have been obtained by crystallization at different temperatures. Form I crystallizes in the triclinic P1
s.g., with a=7.729Å, b=8.695Å, c=17.030Å, α=100.90°, β=98.67°, γ=93.04°, Z=2[1]; form II belongs to
the orthorhombic P21P21P21 s.g., with a=11.507Å, b=13.219Å, c=14.753Å, Z=4[2]. In this work both
nicergoline polymorphs have been crystallized at room temperature by different solvents. Form I is
obtained by crystallization from ethilacetate, form II is cristallized from tetrahydrofurane (THF), methanol,
ethanol, acetone, dichloroethane, acetonitrile. The combined use of different techniques – Differential
Scanning Calorimetry (DSC), thermogravimetric Analysis (TGA), 13C CPMAS-NMR spectroscopy, high
temperature X-Ray powder diffraction (HT-XRPD), Scanning Electron Microscopy (SEM) - allowed to
evaluate the thermal stability of the two crystallographic forms. While form I is stable up to the melting
point (135°C), form II shows a different stability with temperature depending on the crystallization solvent.
The Form II obtained from acetonitrile, when heated at 124°C, undergoes the structural transition to the
orthorhombic phase, that is retained down the room temperature after cooling. Differently, the other form
II samples melt and decompose in the temperature range 113-123°C, depending on the crystallization
solvent used in the synthesis. The structural changes with temperature have been investigated by structural
refinement with the Rietveld method.
Figure 1. Molecular structure of nicergoline
References
1. M. Husàk, B. Kratochvil, J. Ondraček, J. Maixner, A. Jerolov, J. Stuchlik Z. Kristallogr. (1994) 209, 260.
2. M. Husàk, J. Had, B. Kratochvil, L. Cvak, J. Stuchlik, A. Jegorov Collect. Czech. Chem. Commun. (1994) 59, 1624.
126
ms8-p3
A combined XRPD and vibrational study of the thermal
treatment of palygorskite-indigo to produce Maya blue
G. Croce1, M. Milanesio1, W. van Beek1,2 and M. Sanchez del Rio2
1. Università del Piemonte Orientale, DISTA, I-15121 – Alessandria
2. European Synchrotron Radiation Facility, F-38043 – Grenoble Cedex
The heating process (30-200ºC) of a palygorskite-indigo mixture has been monitored in situ by synchrotron
powder diffraction and Raman spectroscopy at the same time. During this process, the colorant and the
clay interact to form Maya blue, a pigment highly resistant to degradation. It is shown that the formation
of a very stable pigment occurs in the 70-130 ºC interval when palygorskite starts to loose zeolitic water,
accompanied by a reduction of the crystallographic a parameter, and interacting with the clay in such a way
that the indigo chromophore, which includes C=C and C=O bonds, is altered.
Mid- and Near-Infrared spectroscopic work and microporosity measurements are employed to study the
rehydration process after the complex formation, evidencing a inhibition of the rehydration of Maya blue
as compared with palygorskite. These results are consistent with the blocking of the palygorskite tunnel
entrance by a single or several indigo molecules.
Figure 1. Evolution of the [110] peak intensity and peak position versus temperature for a)
palygorskite, and b) palygorskite and indigo (1% wt).
127
ms8-p4
Molecular dynamics simulations of aggregated states:
insights into amyloid fibers and their toxic precursors
Esposito1, A. De Simone2, F. Stanzione1, C. Pedone1, L. Vitagliano1
1. Istituto di Biostrutture e Bioimmagini, CNR, I-80134 Napoli
2. Department of Chemistry, University of Cambridge, Cambridge UK
The insurgence of severe neurodegenerative diseases is frequently associated with insoluble amyloid-like
fibrils formed by proteins and peptides that often possess a globular fold in their physiological state. The
structural characterization of these fibrils has long been hampered by the low solubility and the noncrystalline nature of these aggregates. The high resolution structure of several amyloid-like peptides[1]
offered an atomic detailed model, denoted as cross-β spine steric zipper, for amyloid-like fibrils. In order
to obtain further insights into the structure determinants of amyloid fiber structure/formation and to
analyse the effects of crystal packing on aggregated structures, we have undertaken molecular dynamics
simulations on a variety of different models arranged in a cross-β spine structure[2-5]. Indeed, we have
studied steric zipper interfaces containing large polar and/or aromatic residues as well as small and/or
hydrophobic residues. The analysis of large aggregates formed by the peptide GNNQQNY have shown
that these assemblies can adopt either twisted or flat β-sheeted structures[2].
In recent years, new data have suggested that small soluble precursors of amyloid fibers are the actual
toxic species. Using GNNQQNY as model system we have carried extensive replica exchange molecular
dynamics simulations on small aggregates of this peptide. The analysis of these small-sized models has
provided information on the structural properties of possible intermediate states along the fiber formation
pathway[6,7]. Furthermore, these data have offered new hints on the structural aspects of amyloid oligomer
formation and toxicity[6], also consistent with data available on polyglutamine systems[4].
References
1. R. Nelson, M.R. Sawaya, M. Balbirnie, A.O. Madsen, C. Riekel, R. Grothe, D. Eisenberg Nature (2005), 435, 773 and
ibidem (2007), 447, 453.
2. L. Esposito, C. Pedone, L. Vitagliano PNAS (2006), 103, 11533.
3. A. De Simone, C. Pedone, L.Vitagliano Biochem. Biophys. Res. Commun. (2008), 366, 806.
4. L. Esposito, A. Paladino, C. Pedone, L. Vitagliano Biophys. J. (2008), 94, 4031.
5. L. Vitagliano, A. De Simone, F. Stanzione, L. Esposito Biopolymers (2009) Epub Mar 11.
6. A. De Simone, L. Esposito, C. Pedone, L. Vitagliano Biophys. J. (2008), 95, 1965.
7. L. Vitagliano, L. Esposito, C. Pedone, A. De Simone Biochem. Biophys. Res. Commun. (2008), 377, 1036.
128
ms8-p5
Exploring PHM active site: characterization of novel inhibitors
using a combined experimental and computational approach
E. Langella1, S. Pierre2, W. Ghattas2, M. Giorgi3, M. Réglier2,
M. Saviano1, R. Hardré2 and L. Esposito1
1. Istituto di Biostrutture e Bioimmagini, CNR, 80134 Napoli, Italy.
2. Aix-Marseille Université, Institut des Sciences Moléculaires de Marseille, équipe BiosCiences, UMR-CNRS
Normandie-Niemen, 13397 Marseille Cedex 20, France.
3. Aix-Marseille Université, Spectropole, FR1739-CNRS, Normandie-Niemen, 13397 Marseille Cedex 20,
France.
Peptidylglycine α-Hydroxylating Monooxygenase (PHM) is involved in the biosynthesis of α-amidated
neuropeptides and peptide hormones. Due to the role played by specific α-amidated peptides in different
human diseases, PHM represents a potential target for drug design [1,2].
In this framework, we carried out a structure-activity study of new compounds derived from a well-known
PHM substrate analog, the olefinic compound 4-phenyl-3-butenoic acid (PBA) [3]. In order to investigate
the substrate-like behavior of PBA and similar compounds, as well as to map putative binding pockets for
new inhibitors, we designed, synthesized, and tested different PBA derivatives both in vitro and in silico.
Docking calculations were performed by using AUTODOCK 4.0 package[4].
Figure 1. Binding pockets of crystallographic IYG molecole and compound 2d
We demonstrated that it is possible to increase the affinity of PBA for PHM by appropriate functionalization
of its aromatic nucleus. Results from docking calculations revealed novel features of the enzyme active site
that can be used to design new molecules able to modulate PHM activity.
References
1.
2.
3.
4.
F. N. Bolkenius, A. J. Ganzhorn, Gen. Pharmacol. (1998), 31, 655.
D. J. Merkler, A. S. Asser, L. E. Baumgart, N. Carballo et al., Bioorg. Med. Chem. (2008), 16, 10061.
W. J. Driscoll, S. Konig, H. M. Fales, L. K. Pannell, B. A. Eipper et al., Biochemistry (2000), 39, 8007.
G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Huey, W. E. Hart et al., J. Comput.Chem. (1998), 19, 1639.
129
ms8-p6
Understanding the Mechanism of H2 activation from the experimental
and computed structures of a model of [Fe-Ni]-hydrogenase
Carlo Mealli, Giovanni La Penna, Andrea Ienco, Abdelatif Messaoudi
ICCOM-CNR, 50019 Sesto Fiorentino (FIRENZE)
[Fe-Ni]-hydrogenases are enzymes that catalyze the splitting of H2 into 2H+ and 2e-.1 Ogo et al.2 reported a
simple Ru-Ni model which allow focusing on some specific aspects of the protein. The crystal structures
of a precursor diamagnetic complex and a high spin product of its reaction with H2 have been reported
The figure shows that this product contains a bridging hydride between the metals. This seems particularly
relevant because the third bridge at the [Fe-Ni]-hydrogenases has never been fully clarified to be an actual
hydrogen atom.3 Also, the presence of a high spin Ni(II) ion in the product is consistent with the two
different ground states that are involved in the mechanism of the protein. The reaction occurs at RT and
increases the acidity of the water solution, consistently with the abstraction of H+ from H2. Our DFT
calculations indicate that an aggregate between three H2O molecules and the counterion (triflate or nitrate)
have sufficient basicity for the heterolysis of H2. The study, besides reproducing the known experimental
structures, depicts a series of intermediates and transition states. The proton is abstracted from the H2
molecule initially η2 coordinated to Ru(II), but then the remaining hydride shifts to a bridging position
and force the change of spin state at Ni(II). By following subsequent experimental indications,4 we then
analyzed the behavior of a second H2 molecule in the system. This not only scrambles its atoms with the
bridging hydride, but it can also loses a proton, similarly abstracted from the anion-water aggregate. The
overall balance is that the two bonding electrons of one H2 molecule end up reducing the Ru-Ni dication to
an uncharged species, while two protons are released. The theoretical modeling highlights basic geometry/
electronic structure relations, which provide useful hints also for the behavior of the much more complex
protein.
References
1. F. Armstrong Curr. Opin. Chem. Biol. (2004), 8, 133.
2. S. Ogo, R. Kabe, K. Uehara, B. Kure, T. Nishimura, S.C. Menon, R. Harada, S. Fukuzumi, Y. Higuchi, T. Ohhara, T. Tamada,
R. Kuroki Science (2007), 316, 585.
3. C. Mealli, T.B. Rauchfuss Angew. Chem. Engl. Int. Ed. (2007), 46, 8942.
4. B. Kure, T. Matsumoto, K. Ichikawa, S. Fukuzumi, Y. Higuchi, T. Yagid, S. Ogo Dalton Trans. (2008), 4747.
130
ms8-p7
Multi-technique structural characterization of
drug/hydrotalcite nanocomposites
M. Milanesio1, D. Viterbo1, G. Croce1, F. Carniato1, E.
Conterosito1, L. Palin1, V. Ambrogi2, L. Perioli2
1. DISTA, Università del Piemonte Orientale, 15121 Alessandria, Italy
2. Dipartimento di Chimica e Tecnologia del Farmaco, Università di Perugia, 06123, Perugia, Italy.
Hydrotalcites (Htlc) are inorganic layered hydroxides containing exchangeable anions, in which the
lamellar plane is constituted by bivalent and trivalent metals octahedrally coordinated to six hydroxyl
groups. The increasing interest for these materials is due to their numerous applications in particular in
catalysis and in pharmaceutical formulations. In the last case an improvement of the dissolution rate of
poorly water soluble drugs and prolonged drug release may be achieved. The use of hydrotalcites for
intercalating anionic sunscreens was also proposed, with the purpose of improving the sunscreen photostability. The comprehension of the structural features of these hybrid organic-inorganic materials and the
transformations induced by external stimuli is fundamental to understand the stability of the materials and
to identify the optimal modifications to produce improved materials and/or formulations. X-ray powder
diffraction (XRPD) patterns were collected both on a XRPD X’TRA by Thermo Electron laboratory
diffractometer and with synchrotron radiation (SNBL. Grenoble). The analysis of the patterns was
performed using the Topas program. The structural information is poor because of the layered morphology
of the samples and their medium to low crystallinity. FT-Raman spectra, TGA measurements and solid
state NMR data together with molecular orbital calculation complemented the XRPD data. The case of
EUS-HTLC sunscreen system (see pictures) has been analyzed in more detail. Indexing allowed to define
a triclinic unit cell: a=7.955(1)Ǻ , b=5.734(1) Ǻ, c=22.448(2) Ǻ, α=96.62(1)°, β=79.55(1)°, χ=78.42(1)°, a
multiple of the non-intercalated HTLS form. The interlayer spacing of 21.779(1) Ǻ can accommodate two
facing molecules intercalated by about half a molecule. Raman and NMR spectra of the composite show
the interactions between the EUS molecule and the layered inorganic material. The theoretical calculations
were performed to optimize the molecular geometry and to calculate the Raman frequencies: the calculated
frequencies confirmed that the intercalated EUS molecule is in the anionic form.
XRPD pattern and tentative crystal structure by NMR-and Raman-aided
structure solution
131

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