DCTC13 II Congresso Nazionale della Divisione di Chimica Teorica

Transcript

II Congresso della Divisione di Chimica Teorica e Computazionale della SCI – Padova 20-22.02.2013
DCTC13
II Congresso Nazionale della Divisione di
Chimica Teorica e Computazionale della
Società Chimica Italiana
20-22 febbraio 2013
Padova, Centro Culturale ‘San Gaetano’
Comitato Scientifico
GIANFRANCO PACCHIONI (Univ. Milano Bicocca, Presidente DCTC-SCI)
ORLANDO CRESCENZI (Univ. Napoli “Federico II”)
DARIO DUCA (Univ. Palermo)
LUCIANA MARINELLI (Univ. Napoli “Federico II”)
ANTONINO POLIMENO (Univ. Padova)
FABRIZIO SANTORO (ICCOM-CNR, Pisa)
MAURO STENER (Univ. Trieste)
MAURIZIO CASARIN (Univ.Padova)
Comitato Organizzatore
ALESSANDRO BAGNO (Univ. Padova)
MAURIZIO CASARIN (Univ. Padova)
ALBERTA FERRARINI (Univ. Padova)
DANIEL FORRER (Univ. Padova)
DIEGO FREZZATO (Univ. Padova)
GIORGIO J. MORO (Univ. Padova)
LAURA ORIAN (Univ. Padova)
GIULIA PARISIO (Univ. Padova)
ANTONINO POLIMENO (Univ. Padova)
GIACOMO SAIELLI (Univ. Padova)
MAURO STENER (Univ. Trieste)
Segreteria
E-mail: [email protected]
Sito web
http://www.chimica.unipd.it/dctc13
I
Università degli Studi CNR Padova
di Padova
Dipartimento di
Scienze Chimiche
Con la sponsorizzazione di
Hewlett Packard
E4 Computer Engineering
II
PROGRAMMA
Mercoledì 20 Febbraio
14:15-14:30
Apertura del Congresso (G. Pacchioni, U. Milano Bicocca, Presidente DCTC
della SCI)
Sessione 1
Chairman: A. Polimeno (Dip. di Scienze Chimiche, Padova)
Invited: Gianfranco Tantardini
14:30-15:00 Dip. di Chimica Fisica ed Elettrochimica, U. Milano
Theoretical studies of C-based nanostructures
Enrico Bodo (U. “La Sapienza”)
15:00-15:15 The structure of ionic liquids from a molecular perspective: recent theoretical
and experimental results
Claudio Greco (U. Milano Bicocca)
15:15-15:30 DFT-based design of molecular functionality: the case of hydrogenases
biomimetic models
Daniele Toffoli (Middle East Technical University)
15:30-15:45 Density functional theory for molecular multiphoton ionization in the
perturbative regime
Giuseppe Suffritti (U. Sassari)
15:45-16:00 Structure and dynamics of hydrated Na vermiculite clay studied by CarParrinello molecular dynamics simulations
16:00-16:30 Coffee Break
Sessione 2
Chairman: F. Santoro (ICCOM-CNR, Pisa)
Invited – Benedetta Mennucci (ERC Starting Grant)
Dip. di Chimica e Chimica Industriale, U. Pisa
16:30-17:00
The interplay between environment and excited state processes in
(supra)molecular systems: a quantum chemical picture
Livia Giordano (U. Milano Bicocca)
17:00-17:15 Charging of gold atoms on doped MgO and CaO: identifying the key parameters
by DFT calculations
17:15-17:30
Tiziana Marino (U. Calabria)
Catalytic mechanism of the arylsulfatase promiscuous enzyme
17:30-17:45
Vincenzo Villani (U. Basilicata)
H-transfer termination mechanisms in polyolefin homogeneous catalysis
17:45-18:00
Anna Ferrari ( U. Torino )
Modified ion pair interaction for water dimers on supported MgO ultrathin films
18:00-19:00 Poster session
III
Giovedì 21 Febbraio
Sessione 3
Chairman: M. Stener (Dip. Scienze Chimiche e Farmaceutiche, Trieste)
Invited – Emilia Sicilia
Dip. di Chimica, U. della Calabria (Cosenza)
09:00- 09:30
Catalytic generation of hydrogen assisted by metal-based homogeneous
catalysts: computational insights
Antonio Laganà ( U. Perugia )
09:30- 09:45 Towards a Virtual Research Community for chemistry, molecular and materials
science and technology
Filippo Lipparini ( U. Pierre et Marie Curie )
09:45- 10:00 A very fast divide and conquer discretization algorithm for the Polarizable
Continuum Model
Anna Painelli ( U. Parma )
10:00-10:15 Tuning the nature of the fluorescent state: a substituted polycondensed dye as a
case study
Giosuè Costa ( U. Catanzaro )
10:15-10:30 Identification and characterization of new DNA G-Quadruplex binders selected
by a combination of ligand and structure-based virtual screening approaches
Sessione 4
Chairman: A. Laganà (Dip. Chimica, Perugia)
Invited – Sonia Coriani
Dip. Scienze Chimiche, U. Trieste
11:00-11:30
Correlated response methods to model absorption, ionization and scattering
phenomena
11:30-11:45
Michele Pavone ( U. “Federico II” )
Ab-initio DFT+U Study of Sr-doped LaMO3 (M=Cr, Mn)
11:45-12:00
Nazzareno Re ( U. “D’Annunzio” )
Computational investigation of IR spectra of electrospray ionized biomolecules
Alessandro Biancardi ( U. Pisa )
An investigation of the photophysical properties of minor groove bound and
12:00-12:15
intercalated molecular probes for nucleic acids, through QM and spectroscopic
tools
Davide Presti ( U. Modena-Reggio Emilia )
12:15-12:30 Benchmarking periodic dispersion-corrected DFT calculations for the prediction
of molecular crystal polymorphism
12:30-14:30 Pausa
IV
Sessione 5
Chairman: O. Crescenzi (Dip. di Chimica, Napoli)
14:3015:00
Invited – Anna Bernardi
Dip. di Chimica Organica ed Industriale, U. Milano
Design of mono- and polyvalent mimics of oligosaccharides
15:0015:15
Emanuele Coccia ( U. L’Aquila )
Protein field effect on the dark state of 11-cis Retinal in Rhodopsin by Quantum
Monte Carlo/Molecular Mechanics
15:1515:30
Roberto Orlando ( U. Torino )
Massively parallel CRYSTAL program for large unit cell ab initio calculations
15:3015:45
Cecilia Coletti ( U “D’Annunzio” )
Coulomb Sturmian Orbitals and Hyperspherical Harmonics as building blocks for
quantum chemical applications
15:4516:00
Ivan Carnimeo ( Scuola Normale Superiore di Pisa )
DFTB/PCM and TD-DFTB/PCM approaches for calculation of spectroscopical
properties of large systems in solution
16:0016:30
Coffee Break
Sessione 6
Chairman: D. Duca (Dip. di Fisica e Chimica, Palermo)
16:3017:00
Invited – Andrea Vittadini
ISTM-CNR Padova
Structure and reactivity of metal-supported self-assembled molecular layers from
first principles
17:0017:15
Elisa Gambuzzi ( U. Modena Reggio Emilia )
Silicate and aluminosilicate glasses: probing network arrangement by solid state
NMR spectroscopy and accurate first principle calculations
17:1517:30
Lucas Viani ( U. Pisa )
Spatial and Electronic Correlations in the PE545 Light-Harvesting Complex
17:3017:45
Fabio Grassi ( U. Piemonte Orientale )
A First Principles Study of Capping Energies and Electronic States in PbSe
Nanocrystals
17:4518:00
Remedios Cortese ( U. Palermo )
Selective hydrogenation of 2-methyl-3-butyn-2-ol on Pd catalysts
18:0019:00
Poster session
19:0020:00
Assemblea della Divisione
V
Venerdì 22 Febbraio
Sessione 7
Chairman: M. Casarin (Dip. di Scienze Chimiche, Padova)
Invited - Francesco Tarantelli
Dip. di Chimica, U. Perugia
09:00-09:30
Charge displacement analysis: a different view of bonding, from non-covalent
interactions to coordination chemistry
Oliviero Andreussi ( U. Pisa )
09:30-09:45 Self-consistent continuum solvation (SCCS) in periodic electronic-structure
calculations
Ana Belen Munoz Garcia ( U. “Federico II” )
09:45-10:00 Unveiling structure-property relationships in Perovskite-oxide based electrodes
for solid oxide fuel cell applications
Marco De La Pierre ( U. Torino )
10:00-10:15 Ab initio simulation as the key tool to interpret the IR reflectance spectra of
crystalline solids
Simone Casolo ( U. Milano )
10:15-10:30 Eley-Rideal hydrogen recombination on graphite: ab-inito molecular dynamics
of an astrophysical gas-surface reaction
Sessione 8
Chairman: L. Marinelli (Dip. di Chimica Farmaceutica, Napoli)
Invited - Alessandro Fortunelli
11:00-11:30 IPCF-CNR Pisa
Global optimization methods in chemistry
David Picconi ( Technische Universitaet Muenchen )
11:30-11:45 A strategy for nonadiabatic quantum-classical dynamics of semirigid molecules.
Investigating the photostability of nucleobases
11:45-12:00
Alessandro Erba ( U. Torino )
Ab initio temperature effect on one-electron properties of solids
12:00-12:15
Elisa Frezza ( U. Padova )
The phase diagram of hard helices: classical DFT and Monte Carlo simulations
Leonardo Belpassi ( ISTM-CNR Perugia )
12:15-12:30 Recent advances and perspectives in 4-component Dirac-Kohn-Sham
calculations
12:30-14:15 Pausa
Sessione 9
Chairman: G. Pacchioni (Dip. di Scienza dei Materiali, Milano Bicocca)
Invited - Maurizio Recanatini
14:15-14:45 Dip. di Farmacia e Biotecnologie, U. Bologna
Computational studies on the hERG potassium channel
VI
Invited - Chiara Cappelli (Medaglia Roetti)
Scuola Normale Superiore, Pisa
14:45-15:15
Bridging the gap between theory and experiment: modeling solvent effects on
molecular properties and spectroscopies
Invited - Alfonso Pedone (Targa Scrocco)
Dip. di Scienze Chimiche e Geologiche, U. Modena e Reggio Emilia
15:15-15:45
Computational simulations of solid state NMR spectra: a new era in structure
determination of oxide glasses
Invited - Vincenzo Barone (ERC Advanced Grant)
15:45-16:15 Scuola Normale Superiore, Pisa
Toward a multifrequency virtual spectrometer
VII
VIII
SOMMARIO
INVITED LECTURES
TOWARD A MULTIFREQUENCY VIRTUAL SPECTROMETER ............................... 3
Vincenzo Barone
DESIGN OF MONO- AND POLYVALENT MIMICS OF OLIGOSACCHARIDES........ 4
Anna Bernardi
BRIDGING THE GAP BETWEEN THEORY AND EXPERIMENT: MODELING
SOLVENT EFFECTS ON MOLECULAR PROPERTIES AND SPECTROSCOPIES . 5
Chiara Cappelli
CORRELATED RESPONSE METHODS TO MODEL ABSORPTION, IONIZATION
AND SCATTERING PHENOMENA............................................................................ 6
Sonia Coriani
GLOBAL OPTIMIZATION METHODS IN CHEMISTRY ............................................. 7
Alessandro Fortunelli
THE INTERPLAY BETWEEN ENVIRONMENT AND
EXCITED STATE
PROCESSES IN (SUPRA)MOLECULAR SYSTEMS: A QUANTUM CHEMICAL
PICTURE.................................................................................................................... 9
Benedetta Mennucci
THEORETICAL STUDIES OF C-BASED NANOSTRUCTURES ............................. 10
Rocco Martinazzo, Matteo Bonfanti, Simone Casolo, Gian Franco Tantardini
COMPUTATIONAL SIMULATIONS OF SOLID STATE NMR SPECTRA: A NEW
ERA IN STRUCTURE DETERMINATION OF OXIDE GLASSES ............................ 11
Thibault Charpentier, Maria Cristina Menziani, Alfonso Pedone
COMPUTATIONAL STUDIES ON THE hERG POTASSIUM CHANNEL ................. 12
Maurizio Recanatini, Matteo Masetti
CHARGE DISPLACEMENT ANALYSIS: A DIFFERENT VIEW OF BONDING, FROM
NON-COVALENT INTERACTIONS TO COORDINATION CHEMISTRY................. 13
Francesco Tarantelli
IX
CATALYTIC GENERATION OF HYDROGEN ASSISTED BY METAL-BASED
HOMOGENEOUS CATALYSTS: COMPUTATIONAL INSIGHTS ............................ 14
Emilia Sicilia, Valeria Butera, Nino Russo
STRUCTURE AND REACTIVITY OF METAL-SUPPORTED SELF-ASSEMBLED
MOLECULAR LAYERS FROM FIRST PRINCIPLES ............................................... 15
Andrea Vittadini
COMUNICAZIONI ORALI
SELF-CONSISTENT CONTINUUM SOLVATION (SCCS) IN PERIODIC
ELECTRONIC-STRUCTURE CALCULATIONS....................................................... 19
Oliviero Andreussi, Nicola Marzari
AN INVESTIGATION OF THE PHOTOPHYSICAL PROPERTIES OF MINOR
GROOVE BOUND AND INTERCALATED MOLECULAR PROBES FOR NUCLEIC
ACIDS, THROUGH QM AND SPECTROSCOPIC TOOLS ...................................... 20
Alessandro Biancardi, Tarita Biver, Benedetta Mennucci
THE STRUCTURE OF IONIC LIQUIDS FROM A MOLECULAR PERSPECTIVE:
RECENT THEORETICAL AND EXPERIMENTAL RESULTS .................................. 21
E. Bodo, R. Caminiti
DFTB/PCM AND TD-DFTB/PCM APPROACHES FOR CALCULATION OF
SPECTROSCOPICAL PROPERTIES OF LARGE SYSTEMS IN SOLUTION ......... 22
Carnimeo I., Scalmani G., Barone V.
PROTEIN FIELD EFFECT ON THE DARK STATE OF 11-CIS RETINAL IN
RHODOPSIN BY QUANTUM MONTE CARLO/MOLECULAR MECHANICS .......... 23
Emanuele Coccia, Daniele Varsano , Leonardo Guidoni
COULOMB STURMIAN ORBITALS AND HYPERSPHERICAL HARMONICS AS
BUILDING-BLOCKS FOR QUANTUM CHEMICAL APPLICATIONS....................... 24
Cecilia Coletti, Danilo Calderini, Vincenzo Aquilanti
SELECTIVE HYDROGENATION OF 2-METHYL-3-BUTYN-2-OL ON Pd
CATALYSTS............................................................................................................. 25
Remedios Cortese, Francesco Ferrante, Antonio Prestianni, Dario Duca
IDENTIFICATION AND CHARACTERIZATION OF NEW DNA G-QUADRUPLEX
BINDERS SELECTED BY A COMBINATION OF LIGAND AND STRUCTUREBASED VIRTUAL SCREENING APPROACHES ..................................................... 26
Costa G., Alcaro S., Musetti C., Distinto S., Casatti M., Zagotto G., Artese A., Parrotta L., Moraca F., Ortuso F.,
Maccioni E., Sissi C.
X
AB INITIO SIMULATION AS THE KEY TOOL TO INTERPRET THE IR
REFLECTANCE SPECTRA OF CRYSTALLINE SOLIDS ........................................ 28
M. De La Pierre, C. Carteret, R. Dovesi
AB INITIO TEMPERATURE EFFECT ON ONE-ELECTRON PROPERTIES OF
SOLIDS .................................................................................................................... 29
Alessandro Erba, Cesare Pisani, Matteo Ferrabone, Roberto Dovesi
MODIFIED ION PAIR INTERACTION FOR WATER DIMERS ON SUPPORTED MgO
ULTRATHIN FILMS.................................................................................................. 30
Anna Maria Ferrari, Livia Giordano
THE PHASE DIAGRAM OF HARD HELICES: CLASSICAL DFT AND MONTE
CARLO SIMULATIONS ............................................................................................ 31
Elisa Frezza, Alberta Ferrarini, Hima Bindu Kolli, Achille Giacometti, Giorgio Cinacchi
SILICATE
AND ALUMINOSILICATE
GLASSES:
PROBING
NETWORK
ARRANGEMENT BY SOLID STATE NMR SPECTROSCOPY AND ACCURATE
FIRST PRINCIPLE CALCULATIONS....................................................................... 32
Elisa Gambuzzi, Alfonso Pedone, Maria Cristina Menziani, Thibault Charpentier
CHARGING OF GOLD ATOMS ON DOPED MgO AND CaO: IDENTIFYING THE
KEY PARAMETERS BY DFT CALCULATIONS....................................................... 34
Livia Giordano, Stefano Prada, Gianfranco Pacchioni
A FIRST PRINCIPLES STUDY OF CAPPING ENERGIES AND ELECTRONIC
STATES IN PbSe NANOCRYSTALS ....................................................................... 35
Fabio Grassi, Mario Argeri, Lorenzo Canti, Maurizio Cossi, Alberto Fraccarollo, Leonardo Marchese
DFT-BASED DESIGN OF MOLECULAR FUNCTIONALITY: THE CASE OF
HYDROGENASES BIOMIMETIC MODELS ............................................................. 36
Claudio Greco, Maurizio Bruschi, Piercarlo Fantucci, Luca De Gioia
TOWARDS A VIRTUAL RESEARCH COMMUNITY FOR CHEMISTRY,
MOLECULAR AND MATERIALS SCIENCE AND TECHNOLOGIES....................... 37
Antonio Laganà, Alessandro Costantini
A VERY FAST DIVIDE AND CONQUER DISCRETIZATION ALGORITHM FOR THE
POLARIZABLE CONTINUUM MODEL .................................................................... 39
Filippo Lipparini, Benjamin Stamm, Eric Cancès,Yvon Maday, Benedetta Mennucci
CATALYTIC MECHANISM OF THE ARYLSULFATASE PROMISCUOUS ENZYME
................................................................................................................................. 40
Tiziana Marino, Nino Russo
XI
UNVEILING STRUCTURE-PROPERTY RELATIONSHIPS IN PEROVSKITE-OXIDE
BASED ELECTRODES FOR SOLID OXIDE FUEL CELL APPLICATIONS............. 41
Ana B. Muñoz-García, Michele Pavone, Emily A. Carter
MASSIVELY PARALLEL CRYSTAL PROGRAM FOR LARGE UNIT CELL AB INITIO
CALCULATIONS ...................................................................................................... 42
Roberto Orlando
TUNING THE NATURE OF THE FLUORESCENT STATE: A SUBSTITUTED
POLYCONDENSED DYE AS A CASE STUDY........................................................ 43
Cristina Sissa, Valentina Calabrese, Marco Cavazzini, Luca Grisanti, Francesca Terenziani, Silvio Quici, Anna
Painelli
AB-INITIO DFT+U STUDY OF Sr-DOPED LaMO3 (M=Cr, Mn)................................ 44
Michele Pavone, Ana B. Muñoz-Garcia, Emily A. Carter
A STRATEGY FOR NONADIABATIC QUANTUM-CLASSICAL DYNAMICS OF
SEMIRIGID MOLECULES. INVESTIGATING THE PHOTOSTABILITY OF
NUCLEOBASES....................................................................................................... 45
David Picconi, Francisco José Avila Ferrer,Roberto Improta, Alessandro Lami, Fabrizio Santoro
BENCHMARKING PERIODIC DISPERSION-CORRECTED DFT CALCULATIONS
FOR THE PREDICTION OF MOLECULAR CRYSTAL POLYMORPHISM .............. 47
Davide Presti, Alfonso Pedone, Maria Cristina Menziani
COMPUTATIONAL INVESTIGATION OF IR SPECTRA OF ELECTROSPRAY
IONIZED BIOMOLECULES...................................................................................... 49
Roberto Paciotti, Cecilia Coletti, Nazzareno Re, Maria Elisa Crestoni, Simonetta Fornarini
STRUCTURE AND DYNAMICS OF HYDRATED Na VERMICULITE CLAY STUDIED
BY CAR-PARRINELLO MOLECULAR DYNAMICS SIMULATIONS ........................ 50
Giuseppe B. Suffritti, Pierfranco Demontis, Marco Masia
DENSITY FUNCTIONAL THEORY FOR MOLECULAR MULTIPHOTON
IONIZATION IN THE PERTURBATIVE REGIME ..................................................... 51
Daniele Toffoli, Piero Decleva
SPATIAL AND ELECTRONIC CORRELATIONS IN THE PE545 LIGHTHARVESTING COMPLEX........................................................................................ 52
Lucas Viani, Carles Curutchet, Benedetta Mennucci
H-TRANSFER TERMINATION MECHANISMS IN POLYOLEFIN HOMOGENEOUS
CATALYSIS.............................................................................................................. 53
Vincenzo Villani, Gaetano Giammarino
XII
POSTER
P01 FULLY AUTOMATED PROCEDURE TO EVALUATE ELASTIC AND
PIEZOELECTRIC CONSTANTS .............................................................................. 57
Elisa Albanese, Alessandro Erba, Bartolomeo Civalleri
P02 DFT AND TDDFT STUDY OF UNSYMMETRICAL SQUARAINES ADSORBED
ON PbSe SURFACES.............................................................................................. 58
Mario Argeri, Claudia Barolo, Maurizio Cossi, Fabio Grassi, Leonardo Marchese
P03 MODELING OF SPIRAL HALLOYSITE NANOTUBES ................................... 60
Francesco Ferrante, Nerina Armata, Giuseppe Lazzara, Stefana Milioto
P04 IMPROVING THE COMPARISON OF COMPUTATIONAL DATA WITH
EXPERIMENTAL ABSORPTION AND EMISSION SPECTRA. BEYOND THE
VERTICAL TRANSITION APPROXIMATION........................................................... 61
Francisco Avila, Javier Cerezo, Emiliano Stendardo, Roberto Improta, Fabrizio Santoro
P05 BERYLLIUM OXIDE NANOTUBES AND THEIR CONNECTION TO THE FLAT
MONOLAYER........................................................................................................... 62
J. Baima, A. Erba, M. Rérat, R. Orlando, R. Dovesi
P06 THE NEAR-EDGE X-RAY-ABSORPTION FINE-STRUCTURE OF O2
CHEMISORBED ON Ag(110) SURFACE STUDIED BY DENSITY FUNCTIONAL
THEORY................................................................................................................... 63
Oscar Baseggio, Mauro Stene, Michele Romeo, Giovanna Fronzon
P07 FUNCTIONAL EFFECTS ON THE TDDFT INVESTIGATIONS IN
ORGANOMETALLIC PHOTOCHEMISTRY ............................................................. 64
Luca Bertini, Maurizio Bruschi, Claudio Greco, Luca De Gioia, Piercarlo Fantucci, Giuseppe Zampella
P08 STUDY OF THE SPECIATION OF THE [Cu(HGGG)(Py)] COMPLEX IN
WATER SOLUTION USING DFTB AND DFT APPROACHES ................................ 65
Maurizio Bruschi, Luca Bertini, Vlasta Bonačić-Koutecký, Luca De Gioia, Roland Mitrić, Giuseppe Zampella,
Claudio Greco, Piercarlo Fantucci
P09 ARE THE NONADIABATIC TRANSITION RATES TRANSFERABLE AMONG
DIFFERENT ENVIRONMENTS?.............................................................................. 66
Valentina Cantatore, Giovanni Granucci, Maurizio Persico
P10 THEORETICAL ADSORPTION OF METHANE, HYDROGEN AND CARBON
DIOXIDE IN POROUS AROMATIC FRAMEWORKS (PAFs)................................... 68
L. Canti, A. Fraccarollo, M. Cossi, L. Marchese
XIII
P11 THEORETICAL INVESTIGATIONS OF SRTI1-XMXO3-δ (M = Co, Ni, Cu)
DOPED-PEROVSKITE SYSTEMS: EFFECTS OF THE DOPING ON THE
FORMATION OXYGEN VACANCIES ...................................................................... 70
Silvia Carlotto, Andrea Vittadini, Antonella Glisenti, Marta Maria Natile
P12 ASSESSMENT OF THE GEOMETRICAL CORRECTION FOR THE BSSE IN
DFT CALCULATIONS FOR MOLECULAR CRYSTALS .......................................... 71
B. Civalleri, M. Alessio
P13 AB INITIO MODELING OF METAL-ORGANIC FRAMEWORKS: INSIGHTS ON
STRUCTURE-PROPERTY RELATIONSHIPS ......................................................... 72
B. Civalleri, E. Albanese, L. Valenzano, R. Orlando
P14 AB INITIO SIMULATION OF SPECTROSCOPIC AND OPTICAL PROPERTIES
OF NOVEL POROUS GRAPHENE PHASES .......................................................... 73
M. De La Pierre, P. Karamanis, J. Baima, R. Dovesi
P15 AB INITIO MÖSSBAUER ISOMER SHIFT AND QUADRUPOLE SPLITTINGS
OF 57Fe WITH CRYSTAL ......................................................................................... 74
S. Casassa, A. M. Ferrari
P16 DESIGN OF NOVEL WO3-BASED MATERIALS WITH TAILORED OPTICAL
AND PHOTO-REDOX OR CATALYTIC PROPERTIES ........................................... 75
Cristiana Di Valentin, Fenggong Wang, Massimo Rosa, Gianfranco Pacchioni
P17 COMPETITIVE SOLVATION OF K+ BY C6H6 AND H2O IN THE K+-(C6H6)n(H2O)m (n=1-4; m= 1-6) AGGREGATES................................................................... 76
Noelia Faginas Lago, M. Albertí
P18
COMPUTATIONAL APPROACHES EMPLOYED IN THE SusFuelCat
PROJECT................................................................................................................. 77
Francesco Ferrante, Nerina Armata, Remedios Cortese, Fabrizio Lo Celso, Antonio Prestianni, Dario Duca
P19 CHEMICAL REACTION BETWEEN AMINO-FUNCTIONALIZED PORPHYRIN
AND CYANURIC CHLORIDE ON SILVER: A STM/DFT STUDY............................. 78
Daniel Forrer, Marco Di Marino, Francesco Sedona, Mauro Sambi, Andrea Vittadini, Maurizio Casarin
P20 MOLECULAR SIMULATION OF H2 AND CH4 ADSORPTION IN POROUS
DIPEPTIDE CRYSTALS........................................................................................... 79
Alberto Fraccarollo, Maurizio Cossi, Angiolina Comotti, Leonardo Marchese
P21 TOWARDS BULK THERMODYNAMICS VIA NONEQUILIBRIUM METHODS:
THE COMPRESSIBILITY FACTOR OF GASEOUS METHANE AS CASE STUDY. 80
Mirco Zerbetto, Diego Frezzato
XIV
P22 EFFECT OF TERMINAL OLIGO(ETHYLENE GLYCOL) ON THE STRUCTURE
OF ALKYLTHIOL SAMs: A MOLECULAR DYNAMICS INVESTIGATION ............... 81
Piero Gasparotto, Giulia Parisio, Alberta Ferrarini
P23
QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS MODELLING
AND PREDICTION OF ORGANIC POLLUTANTS BEHAVIOUR IN THE
ENVIRONMENT ....................................................................................................... 82
Paola Gramatica, Stefano Cassani, Nicola Chirico, Simona Kovarich, Ester Papa
P24 MODELLING OF THE ELECTROOPTICAL PROPERTIES OF LIQUID
CRYSTALS: THE MOLECULAR ORIGIN OF THE ELECTROCLINIC EFFECT ...... 83
Cristina Greco, Alberta Ferrarini
P25 REFINEMENT AND VALIDATION OF THE AMBER FORCE FIELD FOR α, α
DIALKYLATED PEPTIDES....................................................................................... 84
Sonja Grubisic, Giuseppe Brancato, Vincenzo Barone
P26 DIELECTRIC NLO PROPERTIES OF POLYACETYLENE.............................. 85
R. Dovesi, M. Ferrabone, M. Ferrero, B. Kirtman, V. Lacivita, R. Orlando, M. Rérat
P27 AB INITIO INVESTIGATION OF ELECTRONIC AND VIBRATIONAL
CONTRIBUTIONS TO NONLINEAR DIELECTRIC PROPERTIES OF ICE ............. 86
A. Mahmoud, J. Baima, S. Casassa
P28 ELECTRONIC PROPERTIES OF H2Pc AND CuPc FILMS: AN EXPERIMENTAL
AND THEORETICAL STUDY................................................................................... 87
Giulia Mangione, Maurizio Casarin, Roberto Verucchi, Marco Nardi
P29 COHESIVE ENERGY OF MOLECULAR CRYSTALS THROUGH AB INITIO
POST-SCF HYBRID METHODS .............................................................................. 88
Lorenzo Maschio, Bartolomeo Civalleri, Kamal Sharkas, Julien Toulouse, Andreas Savin
P30 AB INITIO ANALYTICAL INFRARED AND RAMAN INTENSITIES FOR
PERIODIC SYSTEMS THROUGH A CPHF/KS METHOD....................................... 89
Lorenzo Maschio, Bernard Kirtman, Michel Rérat, Roberto Orlando, Roberto Dovesi
P31 COLLECTING AND VALIDATING LDHA CONFORMATIONS FOR AN
ENSEMBLE-BASED VIRTUAL SCREENING .......................................................... 90
Rosa Buonfiglio, Maria Ferraro, Federico Falchi, Andrea Cavalli, Matteo Masetti, Maurizio Recanatini
P32 MOLECULAR DYNAMICS OF MACROMOLECULAR SYSTEMS IN LIPID
BILAYERS ................................................................................................................ 91
Roberta Galeazzi, Luca Massaccesi, Giovanna Mobbili, Michela Pisani
XV
P33 THE LIPID BILAYER PERMEABILITY OF MOLECULAR SOLUTES: BEYOND
THE STANDARD SOLUBILITY-DIFFUSION MODEL.............................................. 92
Giulia Parisio, Alberta Ferrarini
P34 SMOOTH FILLING OF THE SOLVENT-EXCLUDING VOLUME WITH
SPHERES ................................................................................................................ 93
Christian Silvio Pomelli
P35 THEORETICAL STUDY OF THE PHOTOIONIZATION CROSS SECTIONS OF
METALLOCENES .................................................................................................... 94
P. Decleva, A. Ponzi
P36 THE SOFT X-RAY ABSORPTION SPECTRUM OF THE ALLYL FREE
RADICAL .................................................................................................................. 95
M. Alagia, E. Bodo, P. Decleva, S. Falcinelli, A. Ponzi, R. Richter, S. Stranges
P37
BENCHMARKING
PERIODIC
DISPERSION-CORRECTED
DFT
CALCULATIONS FOR THE PREDICTION OF MOLECULAR CRYSTAL
POLYMORPHISM .................................................................................................... 96
P38 FROM PHENYL CHLORIDES TO α,n-DIDEHYDROTOLUENES (α,n-DHTs)
VIA PHENYL CATIONS. A CASSCF INVESTIGATION ........................................... 98
Davide Ravelli, Stefano Protti, Maurizio Fagnoni, Angelo Albini
P39 ELECTRONIC AND EPR SPECTRA OF THE SPECIES INVOLVED IN
[W 10O32]4- PHOTOCATALYSIS. A RELATIVISTIC DFT INVESTIGATION............... 99
Davide Ravelli, Daniele Dondi, Maurizio Fagnoni, Angelo Albini, Alessandro Bagno
P40
NITROGEN AND CARBON K-EDGE NEXAFS SPECTRA OF MODEL
SYSTEMS FOR C5H5N ON Si(100) : A DFT SIMULATION ................................... 100
M. Romeo, G. Balducci, M. Stener, G. Fronzoni
P41 COARSE-GRAINED MD SIMULATIONS OF THE MESOMORPHIC
BEHAVIOUR OF 1-HEXADECYL-3-METHYLIMIDAZOLIUM NITRATE ................ 102
G. Saielli, Y. Ji, R. Shi, G. A. Voth, Y. Wang
P42 RELATIVISTIC DFT CALCULATIONS OF XENON NMR PARAMETERS IN
VAN DER WAALS SYSTEMS ................................................................................ 103
G. Saielli, A. Bagno
P43 ORBITAL RELAXED DENSITY MATRIX AT LOCAL MP2 LEVEL FOR
PERIODIC SYSTEMS: FORMAL ASPECTS AND IMPLEMENTATION ................ 104
Simone Salustro, Lorenzo Maschio
XVI
P44 DEVELOPMENT OF A RELIABLE FORCE FIELD FOR CLASSICAL MD
SIMULATIONS IN ALUMINOSILICATES, ENABLING FAST PARALLEL
COMPUTATIONS................................................................................................... 105
Andrea Gabrieli, Marco Sant, Pierfranco Demontis, Giuseppe B. Suffritti
P45 A GENERAL ALL-COORDINATES QUANTUM-DYNAMICAL APPROACH FOR
DESCRIBING THE VIBRONIC LINESHAPE OF ELECTRONIC CIRCULAR
DICHROISM SPECTRA IN EXCITON-COUPLED DIMERS .................................. 106
Fabrizio Santoro
P46 PHOTOPHYSICS & PHOTOCHEMISTRY OF CARBONYL CAROTENOIDS: A
COMBINED CASSCF AND TD-DFT STUDY ......................................................... 107
Mireia Segado, Francisco Jose Avila Ferrer, Fabrizio Santoro, Chiara Cappelli, Mariangela Di Donato, Andrea
Lapini, Manuela Lima, Roberto Righini
P47 IRON GALL INKS AS 3D COORDINATION POLYMERS A DFT STUDY USING
PERIODIC BOUNDARY CONDITIONS.................................................................. 108
Sara Zaccaron, Marco Bortoluzzi, Renzo Ganzerla
P48 INTEGRATED APPROACHES TO NMR SPIN RELAXATION IN FLEXIBLE
BIOMOLECULES: APPLICATION TO OLIGOSACCHARIDES.............................. 109
Mirco Zerbetto, Dmytro Kotsyubynskyy, Maria Soltesova, Jozef Kowalewski, Goran Widmalm, Antonino
Polimeno
P49 SPECTROSCOPIC PROPERTIES OF THIOPHENE BASED EUROPIUM βDIKETONATE COMPLEXES: A THEORETICAL STUDY ...................................... 110
Ugo Cosentino, Claudio Greco, Giorgio Moro, Luca Bertini, Malgorzata Biczysko, Vincenzo Barone
P50 COMPUTATIONAL SPECTROSCOPY FOR SYSTEMS IN THE CONDENSED
PHASE: NICOTINE AS A TEST CASE .................................................................. 112
Franco Egidi, Julien Bloino, Chiara Cappelli, Vincenzo Barone
P51
QUANTUM
CHEMISTRY
WITHOUT
WAVEFUNCTIONS:
NEW
PROSPECTIVES.................................................................................................... 113
Stefano Conte
P52 PREDICTING THE SPIN-STATE ENERGETICS AND NMR OF IRON
COMPLEXES BY DFT .......................................................................................... 114
Andrea Borgogno, Federico Rastrelli, Alessandro Bagno
INDICE DEGLI AUTORI ....................................................................................... 117
LISTA DEI PARTECIPANTI ................................................................................. 121
XVII
XVIII
INVITED LECTURES
2
TOWARD A MULTIFREQUENCY VIRTUAL SPECTROMETER
Vincenzo Barone
Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy
Within the plethora of modern experimental techniques, vibrational, electronic,
and resonance spectroscopies are uniquely suitable to probe static and dynamic
properties of molecular systems under realistic environmental conditions and in
a non-invasive fashion. However, the outcome of spectroscopic studies is rarely
interpretable without the support of theoretical treatments providing a link
between chemical/electronic structure and spectroscopic properties.
Furthermore, the development of more and more sophisticated experimental
techniques poses correspondingly stringent requirements on the quality of the
models employed to interpret spectroscopic results, and on the accuracy of the
underlying chemical-physical descriptions. The predictive and interpretative
ability of computational spectroscopy can be clearly demonstrated by state-ofthe-art methods available for small molecular systems, which at present yield
results comparable to the most accurate experimental measurements. However,
the definition of efficient computational approaches aimed at spectroscopic
studies of large, complex molecular systems is in general a non-trivial task, and
the basic requirement is that such effective models need to reflect a correct
physical picture. On these grounds, the present contribution aims to present and
analyze several examples illustrating the current status of computational
spectroscopy approaches applicable to medium-to-large molecular system in the
gas phase and in more complex environments. Particular attention is devoted to
theoretical models able to provide data as close as possible to the results directly
available from experiment, in order to avoid ambiguities in the interpretation of
the latter. The examples range from anharmonic frequencies and IR-Raman
intensities of medium size systems, to vibrationally resolved UV-Vis spectra of
molecules in solution, to the direct simulation of the ESR spectral line-shapes.
The point is also made that computational spectroscopy studies of more complex
macro-systems are becoming feasible.
Suitable multi-scale approaches aiming at spectroscopic properties of complex
molecular systems, of drug design, materials science, nanotechnology, etc.
interest, which exploits the new capacities offered by the constant increase in
computer performances, will be employed in the development of a research
environment for advanced modelling of “soft matter” within the ERC-DREAMS
project.
[1] Barone, V.; Baiardi, A.; Biczysko, M.; Bloino, J.; Cappelli, C.; Lipparini, F.; Phys. Chem.
Chem. Phys. 2012, 14, 12404-12422.
3
DESIGN OF MONO- AND POLYVALENT MIMICS OF
OLIGOSACCHARIDES
Anna Bernardi
Università degli Studi di Milano, Dipartimento di Chimica,
via Golgi 19, 20133Milano, Italy
Interference with oligosaccharide-mediated recognition events can be achieved
using functional mimics of carbohydrates, that could thus be used to
modulate/alter signal transmission, or to prevent the onset of diseases. In recent
years our laboratory has designed and prepared glycomimetic ligands of wellknown target lectins1 (cholera toxin, DC-SIGN, MBL, PA-IIL). This
presentation will focus on our attempts to use standard computational tools for
the design of a group of mono- and polyvalent mimics of oligomannosides,
directed towards the dendritic cell receptor DC-SIGN.2 Problems deriving from
the specific features of carbohydrate-protein interactions will be highlighted and
the computational predictions will be compared with experimental data obtained
from a variety of biochemical techniques (X-ray, NMR, ITC, SPR,
ultracentrifugation).
[1]. Bernardi, A.; Cheshev, P. Chemistry Eur. J. 2008, 14, 7434-7441
[2] a) Varga, N.; Sutkeviciute, I.; Guzzi, C.; McGeagh, J.; Petit-Haertlein, I.; Gugliotta, S.;
Weiser, J.; Angulo, J.; Fieschi, F.; Bernardi, A. Chemistry – Eur. J., 2013. accepted; b)
Thépaut, M.; Guzzi, C.; Sutkeviciute, I.; Sattin, S.; Ribeiro-Viana, R.; Varga, N.;
Chabrol, E.; Rojo, J.; Angulo, J.; Bernardi, A.; Nieto, P.M.; Fieschi, F. J. Am. Chem.
Soc. 2013, http://dx.doi.org/10.1021/ja3053305
4
BRIDGING THE GAP BETWEEN THEORY AND EXPERIMENT:
MODELING SOLVENT EFFECTS ON MOLECULAR PROPERTIES
AND SPECTROSCOPIES
Chiara Cappelli
Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)
& Dipartimento di Chimica e Chimica Industriale, Università di Pisa,
via Risorgimento 35, I-56126 Pisa (Italy)
Effective in silico simulation of response and spectroscopic properties of
molecular systems in their natural environment is among the most significant
tasks of contemporary theoretical and computational chemistry in view of the
increasing reliability of the results coupled to the quite straightforward
disentanglement of the role of different effects. However, the production of
calculated spectroscopic data directly comparable to their experimental
counterparts is particularly challenging in the case of solvated systems, that
being mainly due to two reasons.
First, the extraction of absolute data, especially intensity values, from spectra of
solvated systems is far from being trivial, so that raw experimental values are
often treated by means of some kind of theoretical assumptions (usually relying
on classical theories) in order to extract from them the molecular property.
Second, from the purely theoretical and computational point of view, in order to
obtain calculated values directly comparable to experiments, the models to be
used should reliably represent the experimental sample, i.e., the physical model
should be as realistic as possible, which in practice means that all the physical
interactions in the sample and between the sample and the probing field have to
be taken into account in the model.
Among the possible strategies which can be exploited to account for solvent
effects on molecular properties and spectroscopies, a relevant role is played by
continuum solvation models [1], due to their well-documented accuracy in
describing the structure and properties of solvated systems at a low
computational cost.
An overview of the continuum solvation approach to molecular properties and
spectroscopies is given [2], with special emphasis on vibrational spectroscopy.
[1] Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999.
[2] Cappelli, C. “Continuum solvation approaches to vibrational properties” in Mennucci,
B.; Cammi, R. Eds. “Continuum Solvation Models in Chemical Physics: from Theory to
Application”, Wiley, Chichester, 2007, pp. 167-179.
5
CORRELATED RESPONSE METHODS TO MODEL ABSORPTION,
IONIZATION AND SCATTERING PHENOMENA
Sonia Coriani
Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste,
via Licio Giorgieri 1, 34127 Trieste, Italty
An overview of our recent work on the extension of Linear Coupled Cluster
Response Theory to compute Near-Edge Absorption Fine Structures [1,2,3],
photoionization cross-sections [5] as well as other linear response properties of
atoms and molecules in resonant frequency regions [3,4] will be presented.
[1] S. Coriani, O. Christiansen, T. Fransson, P. Norman, Phys. Rev. A 2012, 85, 022507.
[2] S. Coriani, T. Fransson, O. Christiansen, P. Norman J. Chem. Theory Comp. 2012, 8,
1616.
[3] T. Fransson, S. Coriani, O. Christiansen, P. Norman, Submitted to J. Chem. Phys.
[4] S. Coriani, J. Kauczor, P. Norman, O. Christiansen, to be submitted.
[5] J. Cukras, S. Coriani, P. Decleva, O. Christiansen, P. Norman, to be submitted.
6
GLOBAL OPTIMIZATION METHODS IN CHEMISTRY
Alessandro Fortunelli
CNR-IPCF, via Giuseppe Moruzzi 1, 56124, Pisa, Italy
A wide variety of systems of chemical interest present a potential energy surface
exhibiting a wealth of low-energy local minima, whose number grow
exponentially with the system size, separated by appreciable barriers (“rugged
potential energy surface”). The predictive description of such systems is a major
challenge for theoretical and computational chemistry because of the need of
achieving information on global observables (those ultimately determining the
system structural response) on the basis of local (limited) information. Searching
for the lowest-energy configuration (the global minimum) is the first challenge,
and techniques for addressing it are named global optimization (GO) methods.
In this talk, recent advances in GO methods will be illustrated, which are based
on the combination of random sampling and structural recognition (order
parameter) algortithms, their improved efficiency and capabilities, and their
application to selected topics. We will focus in particular on the structure and
properties of supported metal nanoparticles and nanoalloys1,2,3, ranging from
very small clusters via a density-functional basin-hopping (DF-BH) algorithm,
their mobility and growth phenomena and the topic of “surface magic clusters”,
to large particles via combined density-functional empirical-potential (DF-EP)
or empirical-potential global-optimization (EP-GO) searches with the possibility
of creating exotic metal-on-oxide phases. Current developments to feasibly
reconstruct the topology of local minima and saddle points in the energy hypersurface so as to extend GO techniques into the dynamic régime will also be
discussed in two different directions: (i) a
predictive computational methodology in the
form of a reactive global minimization
(RGO) approach4 to study the catalytic
activity of very small (sub-nanometer or
ultranano) supported metal clusters, and (ii)
to study boundary motion and creep in
nanophase materials, showing that reactive
configurational search techniques produce
correct predictions when compared with
accelerated MD methods, thus opening up
new
avenues
of
materials
science
5, 6
computational design .
7
[1] R. Ferrando et al. “Interface-stabilized exotic phases of metal-on-oxide nanodots”, ACS
Nano 2008, 2, 1849.
[2] G. Barcaro et al. “Patchy Multishell Segregation in Pd-Pt Alloy Nanoparticles”, NanoLett.
2011, 11, 1766.
[3] G. Barcaro et al. “Interface effects on the magnetism of CoPt supported nanostructures”,
NanoLett. 2011, 11, 5542.
[4] F. R. Negreiros et al. “A first-principles theoretical approach to heterogenous
nanocatalysis”, Nanoscale 2012, 4, 2018.
[5] L. Gragnaniello et al. “Ordered Arrays of Size-Selected Oxide Nanoparticles”, Phys. Rev.
Lett. 2012, 108, 195507.
[6] H. Van Swygenhoven, A.Fortunelli, A. Caro, unpublished.
8
THE INTERPLAY BETWEEN ENVIRONMENT AND EXCITED
STATE PROCESSES IN (SUPRA)MOLECULAR SYSTEMS: A
QUANTUM CHEMICAL PICTURE
Benedetta Mennucci
Dipartimento di Chimica e Chimica Industriale, Università di Pisa,
via Risorgimento 35, 56126 Pisa, Italy
Molecular systems in their electronically excited states play a fundamental role
in many fields of science. In most cases, their photochemistry and photophysics
are strongly affected, if not entirely determined, by the surrounding
environment. In addition, when the excited state processes involve a
supramolecular structure, a further specificity of the environment is that of
influencing the interactions among the molecular subunits. For this reason, a
proper integration of models that take into account the effects of the
environment into a quantum-mechanical (QM) description is necessary. In this
talk, it will be shown that models based on hybrid QM/classical descriptions
(either continuum or discrete, or their combination) represent a valid
computational strategy but only if mutual polarization effects between the QM
and the classical part are possible and all the main physical specificities of the
environment are properly taken into account [1]. Examples of applications of
these methods to different molecular and supramolecular phenomena
(absorption, emission and energy transfer) in the presence of environments of
increasing complexity will be presented and discussed.
[1] B. Mennucci, Phys. Chem. Chem. Phys., 2013, DOI: 10.1039/C3CP44417A
9
THEORETICAL STUDIES OF C-BASED NANOSTRUCTURES
Rocco Martinazzo, Matteo Bonfanti, Simone Casolo, Gian Franco Tantardini
Università degli Studi di Milano, Dipartimento di Chimica
Graphene isolation in 2004 by the Machenster group initiated an explosion of
scientific activity which promises to change our everyday life. Thanks to its
extraordinary electronic, optical and mechanical properties it is an ideal
candidate for ultrafast electronic and optical devices, flexible electronic,
functional lightweight components and advanced batteries. Being one-atom
thick – it is indeed the first truly two-dimensional material ever produced – it is
extremely sensitive to the presence of adsorbed atoms and molecules and, more
generally, to defects such as vacancies, holes and/or substitutional dopants. This
property, apart from being useful for molecular sensor devices, can also be
employed to tune graphene electronic properties.
Here, we briefly review the basic features of atomic-scale defects that can be
useful for material design, and the chemistry behind them [1-4]. The focus will
be on the so-called pz vacancies, i.e. those defects which cause the
disappearance of a carbon pz orbital from the π-π* band systems, either because
of a strong (chemical) bond with a lattice atom or because of the removal of a
carbon atom. The contribution will thus cover the issues of clustering of
adatoms, their magnetic behavior, analogies and differences with carbon atom
vacancies and their debated magnetic properties, the possibility of nanostructuring the substrate to tailor specific properties, and the role of edges in the
adsorption process. We will also touch a few dynamical issues, e.g. the role of
the above defects in limiting graphene electronic transport properties, and the
reactivity of H atoms to form H2 molecules.
[1] M. Bonfanti, S. Casolo, G. F. Tantardini, A. Ponti and R. Martinazzo, “A few simple
rules governing hydrogenation of graphene dots”, J. Chem. Phys. 2011, 135, 164701.
[2] R. Martinazzo, S. Casolo and G.F. Tantardini, “The effect of atomic-scale defects and
dopants on graphene electronic structure”, in: Physics and applications of Graphene –
Theory, Editor: S. Mikhailov, Intech (2011).
[3] S. Casolo, R. Martinazzo and G.F. Tantardini, “Band Engineering in Graphene with
Superlattices of Substitutional Defects”, J. Phys. Chem. C 2011, 115, 3250.
[4] R. Martinazzo, S. Casolo and G. F. Tantardini, “Symmetry-induced band-gap opening in
graphene superlattices”, Phys. Rev. B 2010, 81, 245420.
10
COMPUTATIONAL SIMULATIONS OF SOLID STATE NMR
SPECTRA: A NEW ERA IN STRUCTURE DETERMINATION OF
OXIDE GLASSES
Thibault Charpentier,1 Maria Cristina Menziani2, Alfonso Pedone2
(1)
(2)
CEA, IRAMIS, SIS2M, CEA-CNRS UMR 3299, 91191 Gif-sur-Yvette cedex (France)
Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Modena e
Reggio Emilia, Via G. Campi 183, 41125 Modena (Italy)
In this communication a computational approach which couples molecular
dynamics and DFT simulations for the calculation of NMR parameters, line
widths and shapes of the spectra of oxide glasses will be presented.1,2 Emphasis
is given to the decisive role of this approach both as interpretative tool for a
deeper understanding of the spectral behavior of complex systems and as
predictive instrument to map NMR data into a distribution of structural
parameters and backwards.
This approach will be applied to ‘simple’ network former glasses and more
complex silicates, aluminosilicate, phosphosilicate and borosilicate glasses of
scientific relevance.3-6
[1] Pedone, A.; Charpentier, T.; Menziani, M. C. Phys. Chem. Chem. Phys. 2010, 12, 6054.
[2] Charpentier, T.; Kroll, P.; Mauri, F. J. Phys. Chem. C 2009, 113, 7917.
[3] Pedone, A.; Charpentier, T.; Malavasi, G.; Menziani, M. C. Chem. Mater. 2010, 22, 5644.
[4] Pedone, A.; Charpentier, T.; Menziani, M. C. J. Mater. Chem. 2012, 22, 12599.
[5] Pedone, A.; Gambuzzi, E.; Malavasi, G.; Menziani, M. C. Theor. Chem. Acc. 2012 131,
1147.
[6] Pedone, A.; Gambuzzi, E.; Menziani, M. C. J. Phys. Chem. C 2012, 115, 14599.
11
COMPUTATIONAL STUDIES ON THE hERG POTASSIUM CHANNEL
Maurizio Recanatini, Matteo Masetti
Department of Pharmacy and Biotechnology, University of Bologna,
Via Belmeloro 6, I-40126, Bologna.
The voltage-gated hERG potassium channel (Kv 11.1) is expressed in several
organs and tissues, and in the heart, it is responsible for the rapid component of
the delayed K+ current (Ikr), which plays a fundamental role in the
repolarization phase of the cardiac action potential [1]. Alterations in the hERG
functionality have been associated to a potentially lethal proarrhythmic
condition known as long QT syndrome-type 2 (LQTS2) [2]. The hERG
dysfunction caused by an accidental block by drugs is of pivotal importance in
the pharmaceutical research area since, although rare in occurrence, its
seriousness has raised severe concerns about drug safety [3]. In this scenario,
assessing the blockade activity at the early stages of a drug discovery process, as
well as the possibility to develop drugs specifically designed to contrast the
block, is highly desirable [4]. On the other hand, the occurrence of inherited
LQTS2 forms has been related to the expression of functionally assembling
albeit non-conductive mutants. From this perspective, investigating the ion
conduction at an atomistic detail opens promising possibilities to understand the
mechanisms leading to altered channel functionality.
From a computational point of view, dealing with the hERG channel poses
several issues that must be addressed with diverse and specific techniques,
ranging from well established quantitative structure-activity relationship
methods to the most advanced biophysical simulations. In this presentation,
several aspects of the hERG modeling will be covered, with a special emphasis
on the identification of new molecules able to modulate the channel
functionality.
[1] Tseng, G.-N. J. Mol. Cell. Cardiol. 2001, 33, 835−849.
[2] Sanguinetti, M. C.; Tristani-Firouzi, M. Nature 2006, 440, 463−469.
[3] Recanatini, M.; Poluzzi, E.; Masetti, M.; Cavalli, A.; De Ponti, F. Med. Res. Rev. 2005,
25, 133−166.
[4] Xu, X.; Recanatini, M.; Roberti, M.; Tseng, G.-N. Mol. Pharmacol. 2008, 73,
1709−1721.
12
CHARGE DISPLACEMENT ANALYSIS: A DIFFERENT VIEW OF
BONDING, FROM NON-COVALENT INTERACTIONS TO
COORDINATION CHEMISTRY
Francesco Tarantelli
Dipartimento di Chimica, Università di Perugia, e ISTM-CNR
Assessing reliably the presence, extent, and effects of charge transfer (CT) is
notoriously a controversial, elusive goal in several areas of chemistry. And yet
CT is a long-standing, ubiquitous staple of chemical reasoning, useful to
interpret and model many experimental observations and features of chemical
interactions. We review here a simple theoretical approach, based on the socalled charge-displacement curves [1], which has proved to be helpful to
ascertain and measure the extent of CT taking place when two species interact.
This is especially useful for non-covalent interactions such as hydrogen
bonding where, for example, we have conclusively established that an
experimentally detectable, strongly anisotropic, CT characterizes even weakly
bound water binary complexes [2] (where water may act as donor or acceptor
depending on orientation) but not other similar hydride adducts. By careful
comparison with the experiments, we have been able to estimate the
stabilization energy associated with CT at 2-3 meV per millielectron
transferred, a rate which we find remarkably constant across a range of systems.
A simple physical model for the kinetic energy loss accompanying electron
delocalization helps to rationalize these findings [3]. Similarly useful results
have been obtained clarifying the role of CT in halogen bonding. Among other
successful fields of application of the CD analysis is coordination chemistry,
where the popular Dewar-Chatt-Duncanson model of the bonding, in terms of
donation and back-donation components, can be put for the first time on a firm
quantitative basis [4]. This has been instrumental, for example, for elucidating
some aspects of gold(I) coordination chemistry,
a gold mine ;-) of modern catalysis but still little
understood, and in particular the key role played
by back-donation, previously widely believed to
be marginal. The forward and backward CT
components have also been put in quantitative
relation with experimental observables such as
ligand IR frequency and geometric distortion,
opening the way for useful interpretative models.
[1] L. Belpassi, I. Infante, F. Tarantelli, L. Visscher, J. Am. Chem. Soc. 2008, 130,
1048-1060.
[2] L. Belpassi, M.L. Reca, F. Tarantelli, L.F. Roncaratti, F. Pirani, D. Cappelletti, A. Faure,
Y. Scribano, J. Am. Chem. Soc. 2010, 132, 13046-13058.
[3] D. Cappelletti, E. Ronca, L. Belpassi, F. Tarantelli, F. Pirani, Acc. Chem. Res. 2012, 45,
1571-1580.
[4] N. Salvi, L. Belpassi, F. Tarantelli, Chem. Eur. J. 2010, 16, 7231-7240.
13
CATALYTIC GENERATION OF HYDROGEN ASSISTED BY
METAL-BASED HOMOGENEOUS CATALYSTS:
COMPUTATIONAL INSIGHTS
Emilia Sicilia, Valeria Butera, Nino Russo
Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Ponte P. Bucci
Cubo 14c, 87030 Arcavacata di Rende (Italy), [email protected]
Interest in sustainable non-hydrocarbon-based fuels for transportation has grown
as the recognition that the supply of fossil fuels is limited and the deleterious
environmental effects of burning them has come into public focus. The use of
hydrogen (H2) has been proposed as an alternative, but its use in pure form is
undesirable due to the high pressures or low temperatures required to store
useful quantities. Currently, there are three leading alternative methodologies to
store H2: sorbents (nanoporous materials), metal hydrides, and so-called
chemical hydrides. We have concentrated our efforts [1,2] on the investigation
of the mechanistic aspects of the processes for the release of H2 from chemical
hydrides assisted by homogeneous metal-based catalysts. Here, the outcomes of
our computational analysis of some reactions for the catalytic generation of
hydrogen from potential hydrogen storage materials, such as amine-boranes,
will be presented. All the presented results show how the intervention of
theoretical investigation is essential to disentangle the mechanistic details
experimentally envisaged and to provide precious hints for the improvement of
existing catalysts
[1] Chowdhury, S.; Himo, F.; Russo, N.; Sicilia, E. J. Am. Chem. Soc. 2010 132, 4178-4190.
[2] Butera, V.; Russo, N.; Sicilia, E. Chem. Eur. J. 2011 17, 14586-14592.
14
STRUCTURE AND REACTIVITY OF METAL-SUPPORTED
SELF-ASSEMBLED MOLECULAR LAYERS
FROM FIRST PRINCIPLES
Andrea Vittadini†
CNR-ISTM, DiSC, and CR-INSTM “Village”, via Marzolo 1, 35131, Padova.
The autonomous ordering and assembly of molecules on well-defined solid
surfaces represent a promising route to the fabrication of functional molecular
devices of nanometer size [1]. To this end, achieving a good and reproducible
control over the composition and the structure of molecular layers is obviously
mandatory. Precious indications in this respect can be provided by accurate
investigations where surface science experiments (such as scanning tunnelling
microscopy) and theoretical calculations are carried out synergistically. In this
talk, I will discuss the results obtained by applying this approach to the case of
iron phthalocyanine layers supported on Ag(110). In particular, I will show that
the adsorbate-support coupling can be suitably steered acting on the coverage.
This in turn allows to take control of the oxygen reduction reaction—a key
process in energy conversion and storage.
[1] Barth, J. V.; Costantini, G.; Kern, K. Nature 2005, 437, 671-679.
†
In collaboration with, V. Barone, M. Casarin, A. Cossaro, M. Di Marino, D. Forrer, L.
Floreano, M. Pavone, M. Sambi, F. Sedona, E. Tondello.
15
16
COMUNICAZIONI ORALI
17
18
SELF-CONSISTENT CONTINUUM SOLVATION (SCCS) IN PERIODIC
ELECTRONIC-STRUCTURE CALCULATIONS
Oliviero Andreussi,a,b Nicola Marzarib
a
b
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Italy
Theory and Simulations of Materials (THEOS), École Polytechnique Fédérale de Lausanne,
Switzerland
The solvation model proposed by Fattebert and Gygi [1] and Scherlis et al. [2] is
reformulated [3], overcoming some of the numerical limitations encountered and
extending its range of applicability. The resulting self-consistent continuum
solvation (SCCS) model has been implemented in the public-domain PWSCF
package of the Quantum-ESPRESSO distribution [4] (an open-source massively
parallel environment for electronic-structure simulations, based on densityfunctional theory and beyond, periodic-boundary conditions, plane-wave basis
sets, and pseudo-potentials to represent ion-electron interactions). The SCCS
model provides a very effective and compact fit of computational and
experimental data, whereby the static dielectric constant of the solvent and one
parameter allow to fit the electrostatic energy provided by the PCM model with
a mean absolute error of 0.3 kcal/mol on a set of 240 neutral solutes. Two
parameters allow to fit experimental solvation energies on the same set with a
mean absolute error of 1.3 kcal/mol. A detailed analysis of these results, broken
down along different classes of chemical compounds, shows that several classes
of organic compounds display very high accuracy, with solvation energies in
error of 0.3-0.4 kcal/mol, whereby larger discrepancies are mostly limited to
self-dissociating species and strong hydrogen-bond forming compounds. When
applied to the study of charged solutes, the SCCS model shows remarkable
results for positive ions, with solvation energies of organic cations in error of 2.2
kcal/mol, whereby larger discrepancies are found for negative ions, with errors
in the same range of other computational tools (~4-5 kcal/mol).
[1] Fattebert, J. L.; Gygi, F. J. Comput. Chem. 2002, 23, 662.
[2] Scherlis, D.; Fattebert, J. L.; Gygi, F.; Cococcioni, M.; Marzari, N. J. Chem. Phys. 2006,
124, 074103.
[3] Andreussi, O.; Dabo, I.; Marzari, N.; J. Chem. Phys. 2012, 136, 064102.
[4] Giannozzi, P. ; et al. J. Phys.: Condens. Matter 2009, 21, 395502.
19
AN INVESTIGATION OF THE PHOTOPHYSICAL PROPERTIES OF
MINOR GROOVE BOUND AND INTERCALATED MOLECULAR
PROBES FOR NUCLEIC ACIDS, THROUGH QM AND
SPECTROSCOPIC TOOLS
Alessandro Biancardi, Tarita Biver, Benedetta Mennucci
Dipartimento di Chimica e Chimica Industriale, via Risorgimento 35, 56126 – Pisa
The fluorescence of molecular probes for nucleic acids is well known to show
complex changes due to both intercalation and minor groove binding [1, 2]. To
investigate this behavior, quantum-mechanical calculations using timedependent density functional theory (TDDFT), coupled with polarizable
continuum and/or atomistic models, were performed [3, 4, 5] in combination
with spectroscopic measurements of the probe in the different environments,
ranging from a homogeneous solution to the minor groove or intercalation
pockets of double stranded nucleic acids. The overall data collected provided
information on the features of the “light-switch” by fluorescent probes and the
comparison between experimental and calculated photophysical properties
allowed to explain and rationalize both shifts and quenching/enhancing effects
on fluorescence due to solvation, dimerization, intercalation and minor groove
binding.
[1] Neidle, S; Nature Chemistry 2012, 4, 594.
[2] Pichon, A; Nature Chemistry 2012, 4, 593.
[3] Biancardi, A.; Biver, T.; Marini, A.; Mennucci, B.; Secco, F. Phys. Chem. Chem. Phys.
2011, 13, 12595.
[4] Biancardi, A.; Biver, T.; Mennucci, B.; Secco, F. Phys. Chem. Chem. Phys. 2013
(accepted, DOI: 10.1039/C3CP44058C).
[5] Biancardi, A.; Biver, T.; Barone, G.; Mennucci, B.; Secco, F. (in preparation).
20
THE STRUCTURE OF IONIC LIQUIDS FROM A MOLECULAR
PERSPECTIVE: RECENT THEORETICAL
AND EXPERIMENTAL RESULTS
E. Bodo, R. Caminiti
Dept. of Chemistry, University of Rome “La Sapienza”, Italy
Among the most exciting and successful materials developed and studied in the
last twenty years, ionic liquids [1] are among those that can certainly claim one
of the most rich field of applications in industry and in applied technological
research. We have recently analyzed the behavior of such compounds by using a
variety of theoretical approaches including: abinitio gas phase cluster optimizations, molecular
dynamics simulations of the bulk phases and abinitio first principle molecular dynamics. The
collaboration with experimental groups allows the
validation of our results with precise
measurements such as X-ray and Neutron
structures, Raman and NEXAFS spectra.
We shall report some of the most recent results
obtained in our group [2,3] focusing in particular
on the studies of protic ionic liquids and their
complex liquid structure due to hydrogen bonding
features.
[1] Rogers, R. D., Plechkova, N. V., Seddon, K. R., Eds. “Ionic Liquids: From Knowledge to
Application”; ACS Symp. Ser.; 2009; Vol. 1030; Plechkova, N. V.; Seddon, K. R.,
Chem. Soc. Rev. 2008, 37, 123–150.
[2] E. Bodo, R. Caminiti, J. Chem. Phys. A 2010, 114, 12506; E. Bodo, M. Chiricotto and R.
Caminiti, J. Phys. Chem. B 2011, 115, 14341-14347.
[3] E. Bodo, P. Postorino, S. Mangialardo, G. Piacente, F. Ramondo, F. Bosi, P. Ballirano,
and R. Caminiti, J. Phys. Chem. B 2011, 115 13149-13161. L. Gontrani ,E. Bodo, A.
Triolo, F. Leonelli, P. D’Angelo, V. Migliorati, R. Caminiti., J. Phys. Chem. B 2012,
116, 13024-13032.
21
DFTB/PCM AND TD-DFTB/PCM APPROACHES FOR CALCULATION
OF SPECTROSCOPICAL PROPERTIES OF LARGE SYSTEMS
IN SOLUTION
Carnimeo I.,a,b Scalmani G.,c Barone V.d,b
a
Universita’ degli Studi di Pisa, Dipartimento di Chimica e Chimica Industriale,
Via Risorgimento, 35 – 56126 – Pisa, Italia
b
INFN, Sezione di Pisa
c
Gaussian, Inc., 340 Quinnipiac Street Building 40,
Wallingford, Connecticut 06492, United States
d
Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa
A new computational approach, has been recently proposed for the
modellization of large systems in solution [1]. DFTB method has been
integrated with the Polarizable Continuum Solvent Model, in order to take into
account the polarization effects induced by the bulk of the solvent on the
spectroscopical properties of the solute. The implementation of the ground state
first and second derivatives allows geometry optimizations and harmonic
frequency calculations in different solvents. The PCM contribution to the gas
phase TD-DFTB [2] response matrices has been also implemented, in order to
compute the solvatochromic
shifts of the excited state
properties. The new approach
has been first tested on several
organic molecules, in order to
provide a general overview of
the performances, also in
comparison
with
other
solvation models proposed for
the DFTB method [3-5]. Then,
vibrational frequencies and
excitation energies have been computed for Uracil and Red Nile in solution, and
a good agreement with results obtained using more accurate metods has been
found.
[1] Barone V., Carnimeo I., Scalmani G., JCTC, 2012 (just accepted).
[2] Trani F., Scalmani G., Zheng G., Carnimeo I., Frisch M. J., Barone V., JCTC 2011, 7,
3304.
[3] Lu, Z.; Liu, H.; Elstner, M.; Yang, W., Reviews of modern quantum chemistry: a
celebration of the contribution of Robert G. Parr, 2002, 1606.
[4] Hou, G.; Zhu, X.; Cui, Q., JCTC 2010, 6, 2303.
[5] Xie, L.; Liu, H., J. Comp. Chem. 2002, 23, 1404.
22
PROTEIN FIELD EFFECT ON THE DARK STATE OF
11-CIS RETINAL IN RHODOPSIN BY QUANTUM MONTE
CARLO/MOLECULAR MECHANICS
Emanuele Coccia,a Daniele Varsanob , Leonardo Guidonia
a
Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’Aquila,
via Vetoio, 67100, L’Aquila, Italy
b
Dipartimento di Fisica, “Sapienza” – Università di Roma,
piazzale Aldo Moro 5, 00185, Rome, Italy
The accurate determination of the geometrical details of the dark state of 11-cis
Retinal in Rhodopsin represents a fundamental step for the rationalization of the
protein role in the optical spectral tuning in the vision mechanism [1].
We have calculated high-level geometries in gas phase and in protein
environment using the correlated Variational Monte Carlo method [2-5]. The
Bond Length Alternation of the conjugated carbon chain of the chromophore in
gas phase shows a significant reduction when moving from the ß-ionone ring to
the nitrogen whereas, as expected, the protein environment reduces the
electronic conjugation.
The proposed dark state structure is fully compatible with solid-state NMR data
reported by Carravetta et. al. [J. Am. Chem. Soc. 2004, 126, 3948-3953].
TDDFT/B3LYP calculations on such geometries show a blue opsin shift of 0.28
and 0.24 eV induced by the protein for S1 and S2 states, consistently with
literature spectroscopic data. The effect of the geometrical distortion alone is a
red shift of 0.21 and 0.16 eV with respect to the optimized gas phase
chromophore [5].
[1] Palczewski, K. Annuv. Rev. Biochem. 2006, 75, 743-767.
[2] Foulkes, W. M. C.; Mitas, L.; Needs, R. J.; Rajagopal, G. Rev. Mod. Phys. 2001, 73, 3383.
[3] Casula, M.; Attaccalite, C.; Sorella, S. J. Chem. Phys. 2004, 121, 7110-7126.
[4] Coccia, E.; Guidoni, L. J. Comput. Chem. 2012, 33, 2332-2339.
[5] Coccia, E.; Varsano, D.; Guidoni, L. J. Chem. Theor. Comput., doi:10.1021/ct3007502.
23
COULOMB STURMIAN ORBITALS AND HYPERSPHERICAL
HARMONICS AS BUILDING-BLOCKS FOR QUANTUM CHEMICAL
APPLICATIONS
Cecilia Coletti,a Danilo Calderini,b Vincenzo Aquilantic
a
Dipartimento di Farmacia, Università G. d’Annunzio Chieti-Pescara,
Via dei Vestini, 66100 Chieti
b
Scuola Normale Superiore di Pisa, Via Consoli del Mare, 2, 56126 Pisa
c
Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, 06100 Perugia
In the last years, Sturmian orbitals are emerging as an interesting alternative to
Slater-type and Gaussian-type orbitals to solve quantum chemistry problems
[1,2]. One of their main strengths lies in the complete reciprocity between these
basis sets in configuration space and their counterparts in momentum space,
hyperspherical harmonics. Because the superposition integrals between these
functions can be written as elements of angular momentum algebra and its
generalizations [3], they can also be used to connect alternative Sturmian bases,
arising from the separation of the hydrogenic Schrödinger equation in different
sets of coordinates [4]. This provides a most powerful tool to be exploited for
building up the most appropriate basis sets to solve multielectron and/or
multicenter problems. Moreover, this approach is completely general and can be
extended to any dimension, allowing, for instance, the use of alternative basis
sets to deal with the d-dimensional hydrogen atom, though the usual
tridimensional Sturmians (and the corresponding O(4) hyperspherical
harmonics) are most commonly employed in applications.
The quantum mechanics of atoms and molecules can be discussed in terms of
the breaking of the hyperspherical symmetry of a d-dimensional hydrogenoid
atom, d=3(N-1) for N body Coulomb problems, due to the introduction of
further charged particles (electrons and/or nuclei). Thus, in configuration space,
Sturmian basis functions can be used as expansion basis sets to build up atomic
and molecular orbitals. Additionally, one can choose among alternative
hyperspherical harmonics pertaining to different subgroup chain reductions of
the original (d+1)-dimensional rotation group and thus possessing different
symmetry properties [5].
[1] Avery, J.; Avery, J. Generalized Sturmians and Atomic Spectra. 2006, World Scientific,
Singapore.
[2] Calderini, D.; Cavalli, S.; Coletti, C.; Grossi, G.; Aquilanti, V. J. Chem. Sci, 2012, 124,
187.
[3] Aquilanti, V.; Caligiana, A.; Cavalli, S.; Coletti, C. Int. J. Quantum Chem, 2003, 92, 212.
[4] Aquilanti, V., Cavalli, S., Coletti, C. Chem. Phys. Lett., 2001, 344, 587.
[5] Aquilanti, V.; Cavalli, S.; Coletti, C.; Di Domenico, D.; Grossi, G. Int Rev Phys Chem,
2001, 40, 673.
24
SELECTIVE HYDROGENATION OF 2-METHYL-3-BUTYN-2-OL
ON Pd CATALYSTS
Remedios Cortese, Francesco Ferrante, Antonio Prestianni, Dario Duca
Dipartimento di Fisica e Chimica dell’Università,
viale delle Scienze Ed. 17, I-90128 Palermo
In the frame of the heterogeneous catalysis, it is well known that size and shape
effects play a primal role in driving activity and selectivity [1] and sometimes in
giving structure-sensitive reactions [2]. Recently, Crespo-Quesada et al. [3]
reported that the 2-methyl-3-butyn-2-ol (MBY) selective reduction on palladium
is strongly influenced both by the metal planes – namely, {100} and {111} –
and by the reaction site topologies involved in the hydrogenation while the
adsorption energies drove the catalytic kinetics. In fact, triple to double-bond
reduction seemed to occur four times faster on surface sites with respect to edge
or corner sites. Conversely, double to single-bond reduction seemed to occur
almost exclusively on edge sites. Moreover, {100}
and {111} planes would seem to be more active in
the triple-bond and double-bond hydrogenation,
respectively. In order to understand and,
hopefully, drive these structure-sensitive effects
Density Functional Theory (DFT) calculations
were performed. A Pd30 cluster was employed as
the model for the catalyst. This was cut from a fcc
palladium fragment, to obtain both (100) and
(111) faces (see Figure 1). Different sites and Figure 1. Pd30 cluster, showing both
binding modes were considered to describe either the (100) and (111) faces
the MBY or 2-methyl-3-buten-2-ol (MBE)
interaction and hydrogenation, occurring on the palladium surface. Kinetic
studies on MBY and MBE hydrogenation over the Pd30 cluster showed very
close activation energy values, irrespective of the surface species considered. On
the contrary, the MBY and MBE adsorption energies on the different sites of the
palladium faces and the corresponding structural changes were peculiar to the
different adsorbed species and plane sites and could be easily connected to the
activation of the unsaturated bonds hence to the reactivity of the differently
adsorbed species. These results, finally, confirmed the already claimed structure
sensitivity of the title reaction and, moreover, the higher reactivity of MBY with
respect of MBE, which was also observed [3].
[1] Duca, D.; Barone, G.; Varga, Zs. Catal. Letters, 2001, 72 (1-2), 17–23.
[2] Bond, G. C. Metal-Catalysed Reaction of Hydrocarbons, Springer NY, 2005.
[3] Crespo-Quesada, M.; Yarulin, A.; Jin, M.; Younan, X.; Kiwi-Minsker, L. J. Am. Chem.
Soc., 2011, 133 (32),12787–12794.
25
IDENTIFICATION AND CHARACTERIZATION OF NEW DNA
G--QUADRUPLEX BINDERS SELECTED BY A COMBINATION OF
LIGAND AND STRUCTURE-BASED VIRTUAL SCREENING
APPROACHES
Costa G.,a Alcaro S.,a Musetti C.,b Distinto S.,c Casatti M.,b Zagotto G.,b
Artese A.,a Parrotta L.,a Moraca F.,a Ortuso F.,a Maccioni E.,c Sissi C.b
a
Dipartimento di Scienze della Salute, Università di Catanzaro, Campus “Salvatore Venuta”,
Viale Europa, 88100 Catanzaro, Italy
b
Department of Pharmaceutical and Pharmacological Sciences, University of Padova,
Via Marzolo 5, 35131, Padova, Italy
c
Department of Life and Environmental Sciences, University of Cagliari,
Via Ospedale 72, 09124 Cagliari, Italy
G-quadruplex structures are nucleic acid arrangements assumed by guanine-rich
sequences and stabilized by the planar pairing of four guanines through eight
Hoogsteen hydrogen bonds. These sequences are found in crucial positions of
the genome, such as at telomeric ends, ribosomal DNA (rDNA), RNA, or gene
promoter regions (for example, c-myc, bcl-2, or c-kit) [1].
Nowadays, it has been demonstrated that DNA G-quadruplex arrangements are
involved in cellular aging and cancer, thus boosting the discovery of selective
binders for these DNA secondary structures. By taking advantage of available
structural and biological information on these structures, we performed a high
throughput in silico screening of commercially available molecules databases by
merging ligand- and structure-based approaches by means of docking
experiments.
Figure 1: Virtual screening workflow.
Compounds selected by the virtual screening procedure were then tested for
their ability to interact with the human telomeric G-quadruplex folding by
circular dichroism, fluorescence spectroscopy, and photodynamic techniques.
Interestingly, our screening succeeded in retrieving a new promising scaffold for
G-quadruplex binders characterized by a psoralen moiety.
26
[1] Huppert, J. L. Biochimie 2008, 90, 1140-1148.
27
AB INITIO SIMULATION AS THE KEY TOOL TO INTERPRET THE
IR REFLECTANCE SPECTRA OF CRYSTALLINE SOLIDS
M. De La Pierre,a C. Carteret,b R. Dovesia
a
b
Dipartimento di Chimica, Università degli Studi di Torino, Italy
Laboratoire de Chimie Physique et Microbiologie pour l’Environnement,
Université de Lorraine, France
Quantum-mechanical simulation by means of hybrid HF-DFT functionals has
demonstrated very high accuracy in the prediction of IR frequencies and
intensities of crystalline solids [1,2]. Such an achievement nowadays represents
the starting point for the advanced application of simulation in the
characterization of the IR reflectance spectra.
These spectra contain a high amount of information, which is accessible through
the relations among reflectance spectrum, dielectric function and
frequencies/intensities of the vibrational modes. The extraction of these data
from the spectra requires a delicate best-fit process involving a large number of
parameters. Simulation here plays a crucial role, providing the full set of
fundamental modes with accurate frequencies and intensities, which is the ideal
starting guess for the best-fit. Low intensity fundamentals are identified,
whereas peaks not corresponding to fundamental computed modes are
recognized as combinations or overtones. Overall, a straightforward scheme can
be built, that permits the interpretation of almost all the spectral features of the
spectra. Examples are discussed [3,4] to illustrate the effectiveness of the
synergy between simulation and experiments.
[1] R. Dovesi, M. De La Pierre, A.M. Ferrari, F. Pascale, L. Maschio, C. M. ZicovichWilson, Am. Miner. 2011, 96, 1787.
[2] R. Demichelis, H. Suto, Y. Noël, H. Sogawa, T. Naoi, C. Koike, H. Chihara, N.
Shimobayashi, M. Ferrabone, R. Dovesi, Mon. Not. R. Astron. Soc. 2012, 420, 147.
[3] C. Carteret, M. De La Pierre, M. Dossot, F. Pascale, A. Erba, R. Dovesi, J. Chem. Phys.
2013, 138, 014201.
[4] M. De La Pierre, C. Carteret, R. Orlando, R. Dovesi, submitted to J. Comput. Chem.
28
AB INITIO TEMPERATURE EFFECT ON ONE-ELECTRON
PROPERTIES OF SOLIDS
Alessandro Erba,* Cesare Pisani, Matteo Ferrabone, Roberto Dovesi
Dipartimento di Chimica, Università di Torino, via Giuria 5 10125, Torino, Italy
* E-mail: [email protected]
Quite recently, the entrance into a new age of molecular quantum chemistry has
been declared: “In the fourth age we are able to incorporate into our quantum
chemical treatment the motion of nuclei [...] and compute accurate, temperaturedependent, effective properties, thus closing the gap between measurements and
electronic structure computations” [1]. Nowadays, a variety of solid state ab
initio quantum chemical methods is available for the study of many properties of
the ground state of crystals at zero temperature.
In this contribution, we present and discuss two schemes: (i) a fully ab initio
technique for the determination of atomic anisotropic displacement parameters
(ADP) of crystalline materials within the harmonic approximation to the lattice
potential [2]; (ii) a harmonic Monte Carlo ab initio approach for the description
of nuclear motion effects on the electronic density matrix of crystalline materials
[3]: in the frame of the Born-Oppenheimer approximation, nuclear motions in
crystals can be simulated rather accurately using a harmonic model. In turn, the
electronic first-order density matrix can be expressed as the statistically
weighted average over all its determinations each resulting from an
instantaneous nuclear configuration.
Such schemes have been developed within the formalism of all-electron atomcentered basis sets, one-electron Hamiltonians (Hartree-Fock, Densityfunctional-theory, hybrids) and periodic boundary conditions, and implemented
in the CRYSTAL program for solid state quantum chemistry.
[1] A. G. Császár, C. Fábri, T. Szidarovszky, E. Mátyus, T. Furtenbacher, and G. Czakó,
Phys. Chem. Chem. Phys. 2012, 14, 1085.
[2] A. Erba, M. Ferrabone, R. Orlando and R. Dovesi, J. Comput. Chem. 2013, 34, 346.
[3] C. Pisani, A. Erba, M. Ferrabone and R. Dovesi, J. Chem. Phys. 2012, 137, 044114.
29
MODIFIED ION PAIR INTERACTION FOR WATER DIMERS ON
SUPPORTED MgO ULTRATHIN FILMS
Anna Maria Ferrari,a Livia Giordanob
a
Dipartimento di Chimica IFM, Università di Torino and NIS –Nanostructured Interfaces and
Surfaces – Centre of Excellence. V. P. Giuria 7, 10125 Torino, Italy
b
Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca,
via Cozzi 53, 20125 Milano, Italy
The dissociation of water dimers at MgO(100) surface and MgO ultra-thin films
on Ag(100) has been studied by means of pure DFT and hybrid functionals
calculations. We demonstrate that at the intermediate regime between the
isolated molecule and the water monolayer, barrierless dissociation of water
occurs when assisted by another water molecule. The metal support had been
showed to crucially influence the overall process. Indeed, on the metal
supported ultrathin film, the dissociated form is noticeably stabilized, at variance
with the MgO(100) surface, where the dissociated fragments can easily
recombine. The stabilization of the dissociated charged fragments arises from
the polarization of the electron density at the oxide-metal interface and by the
polaronic distortion of the oxide film. The presence of the metallic substrate
strongly weakens the interaction after the dissociation, by changing the nature of
the newly formed ion pair, with possible consequence of the dynamics and the
reactivity of water fragments on the oxide ultra-thin film.
30
THE PHASE DIAGRAM OF HARD HELICES:
CLASSICAL DFT AND MONTE CARLO SIMULATIONS
Elisa Frezza,a Alberta Ferrarini,a Hima Bindu Kolli,b
Achille Giacometti,b Giorgio Cinacchic
a
Dipartimento di Scienze Chimiche, Università di Padova,
via Marzolo 1, 35131 Padova, Italy
b
Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari di Venezia,
Dorsoduro 2137, 30123 Venezia, Italy
c
Departamento de Física Téorica de la Materia Condensada, Universidad Autónoma de
Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
Since the early Onsager work [1], there have been several demonstrations that
purely hard-core repulsions are sufficient for the formation of ordered phases.
Recent investigations have revealed the unexpected complexity of the ordered
structures obtained by changing the shape of hard particles [2]. The helix is a
typical structural motif in nature: for example, polynucleotides, proteins and
collagen fibres are all right-handed helices [3]. Rigid and semiflexible helical
polymers can exhibit ordered phases, whose features are only partially
understood. We have investigated the phase diagram in systems of hard helical
particles, using classical DFT and Monte Carlo computer simulations.
Motivation of this work resides in the ubiquity of the helical shape motif in
many natural and synthetic polymers, as well as in the well known importance
that the details of size and shape have in determining the phase behaviour and
properties of soft condensed matter systems. We discuss the differences with the
corresponding spherocylinder phase diagram [4] and find that the helix
parameters affect the phase behaviour and the existence of the nematic phase.
We find that at high helicities Onsager theory significantly departs from
numerical simulations even when improvements are included to account for the
non-convexity of particles. The discrepancies increase with increasing density
and upon going from the isotropic to the ordered phases. The unexplored
compact structure realm occurring for such non-convex objects at high densities
and pressures will also be briefly discussed.
[1] Onsager, L. Ann. N.Y. Acad. Sci.1949, 51, 627–659.
[2] Damasceno, P.; Engel, M.; Glotzer, S.C. Science 2012, 337, 453–457.
[3] Hamley, I. Soft Matter 2010, 6, 1863-1871.
[4] Bolhuis, P.; Frenkel, D. J. Chem. Phys. 1996, 106, 666-687.
31
SILICATE AND ALUMINOSILICATE GLASSES: PROBING
NETWORK ARRANGEMENT BY SOLID STATE NMR
SPECTROSCOPY AND ACCURATE FIRST PRINCIPLE
CALCULATIONS
Elisa Gambuzzi,a Alfonso Pedonea, Maria Cristina Menziani,a
Thibault Charpentierb
a
Università degli Studi di Modena e Reggio Emilia, Dip. di Scienze Chimiche e Geologiche,
via G. Campi 183, 41125 Modena, Italia
b
Commissariat à l’Energie Atomique, IRAMIS / SIS2M / LSDRM, CEA Saclay SIS2M,
Bât 125, F-91191 Gif-sur-Yvette cedex, FRANCE
Silicate and aluminosilicate glasses play an important role in nuclear waste
confinement and are the ideal reference systems to study geological processes.
The full understanding of glass properties and potentiality strongly depend on
their structure. Solid State Nuclear Magnetic Resonance is very sensitive to a
topological and chemical disorder around active nuclei and has arisen as the
most promising experimental technique for amorphous structural elucidation[1].
Nevertheless, accurate correlations between experimental data and structural
features must be found. This can be reached by a synergic experimentalcomputational approach that couple MD-DFT/GIPAW calculations to
experimental spectra.
In this contribution we will report the
investigation of the glass structure by
17
O, 27Al and 29Si NMR spectroscopy
[2], [3], [4]. The results evidence how
network chemical disorder contributes
to Qn species detection and, therefore, to
network polymerization quantification.
Moreover,
they
confirm
some
hypothesis made by experimentalists
about the deshielding effect of Al
vicinity on 29Si and 27Al nuclei.
Network modifier Ca and Na cation postions have been thoroughly investigated
analyzing MD-derived models. The effect of their
vicinity on NMR parameters of network nuclei can
be accurately predicted and this helps in describing
the limits of well known correlations that relate
isotropic chemical shift to intertetrahedral angles,
paving the way to the elaboration of more effective
relationships[4].
32
[1] Edèn, M.; Annu. Rep. Prog. Chem., Sect. C 2012, 108, 177-221.
[2] Pedone, A.; Gambuzzi, E; Malavasi, G.; Menziani, M. C.; Theo. Chem. Acc 2013, 131,
1147.
[3] Pedone, A.; Gambuzzi, E; Menziani, M. C.; J. Phys. Chem. C 2012, 116, 14599−14609.
[4] Gambuzzi, E.; Pedone, A.; Menziani, M. C.; Angeli, F.; Caurant, D.; Charpentier T.;
submitted to Geo. Cosmo. Acta, 2013.
33
CHARGING OF GOLD ATOMS ON DOPED MgO AND CaO:
IDENTIFYING THE KEY PARAMETERS BY DFT CALCULATIONS
Livia Giordano, Stefano Prada, Gianfranco Pacchioni
via Cozzi 53, 20125 Milano
The use of transition metals I as dopants is a versatile way to change the
properties of oxide materials. One example is the possibility to induce charge
transfer from the TM to species adsorbed on the oxide surface. In the case of
wide-gap alkaline-earth oxides, such as MgO and CaO, the charge transfer is
determined by the respective position of the energy levels of the impurity and
the adsorbate and resides in the capability of the TM to be stabilized in various
oxidation states [1]. The structural and electronic properties of Cr- and Modoped MgO and CaO are investigated by Density Functional Theory (DFT)
calculations. The problem of band gap description and energy levels alignment
in DFT is addressed by comparing the results obtained with standard GGA,
GGA+U and hybrid exchange-correlation functionals. The ability of the
impurity ion to transfer one electron to the adsorbed species is considered for the
case of electronegative Au adatoms. The study of the thermodynamic stability of
the TM ions shows that Mo impurities are stable in the oxide lattice as Mo3+ or
Mo+4 but can assume also higher oxidation states and are therefore able to
transfer electrons to adsorbed gold. Conversely, Cr impurities are stabilized as
Cr3+ and the high cost of further oxidation results in absence of charge transfer
to gold on both Cr-doped MgO and Cr-doped CaO [2].
[1] Shao, X.; Prada, S.; Giordano, L.; Pacchioni, G.; Nilius, N.; Freund, H.-J. Angew. Chem.
Int. Ed. 2011, 50, 11525-11527.
[2] Stavale, F.; Shao, X.; Nilius,N.; Freund, H.-J.; Prada, S.; Giordano, L.; Pacchioni, G. J.
Am. Chem. Soc. 2012, 134, 11380-11383.
34
A FIRST PRINCIPLES STUDY OF CAPPING ENERGIES AND
ELECTRONIC STATES IN PbSe NANOCRYSTALS
Fabio Grassi, Mario Argeri, Lorenzo Canti, Maurizio Cossi,
Alberto Fraccarollo, Leonardo Marchese
Dipartimento di Scienze e Innovazione Tecnologica, Centro Interdisciplinare Nanosistemi,
Università del Piemonte Orientale “Amedeo Avogadro”, Viale T. Michel 11, 15121,
Alessandria, Italy. [email protected]
Semiconductor quantum dots (QDs) are a relatively recent family of materials
characterized by a marked dependence of physico-chemical properties on size
and morphology. This intrinsic tunability makes them excellent candidates for
applications in different fields such as molecular imaging, quantum computing
and photovoltaics.
In the present work, PbSe QDs were modelled by extracting clusters of cubic,
cuboid, cuboctahedral and octahedral morphology from the cubic PbSe lattice.
The effects of ligand adsorption, cluster stoichiometry and morphology on
electronic structure have been investigated. Addition energies of different
ligands were also calculated. Calculations were performed at DFT level with
B3-LYP functional for geometry optimizations and B-LYP for electronic
structures, with a modified LANL2DZ basis set with polarization functions for
Pb, Se and S and 6-31G** for all other elements.
Results indicate a strong dependence of electronic structure on cluster
stoichiometry, with a 1:1 relationship between intra-band states and the number
of excess Pb or Se atoms, whereas ligand adsorption appears to be of little
influence (Figure 1). Average addition energy of capping molecules to cluster
surface has been shown to decrease, albeit irregularly, as the number of
adsorbed ligands increases.
Figure 1: Density of states of trimethylphosphineoxide (TMPO, top), Pb59Se56
(middle) and Pb59Se56 with adsorbed TMPO (bottom).
35
DFT-BASED DESIGN OF MOLECULAR FUNCTIONALITY:
THE CASE OF HYDROGENASES BIOMIMETIC MODELS
Claudio Greco,a Maurizio Bruschi,a Piercarlo Fantucci,b Luca De Gioiab
a
Dipartimento di Scienze dell’Ambiente e del Territorio, e di Scienze della Terra, e
b
Dipartimento di Biotecnologie e Bioscienze; Università di Milano-Bicocca,
Piazza della Scienza 1-2, 20126, Milano (Italia)
[FeFe]-hydrogenases are H2-evolving enzymes featuring a Fe6S6 active site, i.e.
the “H-cluster”. The latter is composed by a Fe2S2 subsite bearing CO and CN–
ligands (the [2Fe]H subcluster) and a ferredoxin-like Fe4S4 subsite called “[4Fe4S]H”. The [2Fe]H subsite directly interacts with substrates. Hundreds of
synthetic complexes structurally related to the [2Fe]H site have been described
so far. Many of those closely resemble the [2Fe]H geometry, but are much less
efficient than the enzyme in catalysing H+ reduction. This suggests that the
interplay between the [2Fe]H subcluster and the protein matrix has a central role
for the enzyme function, an issue that we investigated by quantum chemical and
mixed quantum/classical approaches. Theory showed that H+ binding to the
[2Fe]H assembly is concomitant with e– transfer between the [2Fe]H and the
[4Fe-4S]H subsites [1]. Synthetic efforts aiming at the reproduction of this key
feature were later published, but proved unsuccessful. Our computational results
indicated that previously used redox-active organic ligands are actually unable
to establish proper electronic communication with synthetic Fe2S2 cores [2],
while metallocene-based non-innocent ligands were predicted to have superior
properties [2,3]. Experimental results confirmed the latter point [4]. We also
used QM/MM modeling to study the process of H2 binding to the enzyme [5];
results suggest that H2 and [FeFe]-hydrogenases cellular redox partners
(ferredoxins) can establish an electronic interplay of functional relevance.
[1] Bruschi, M.; Greco, C.; Kaukonen, M.; Fantucci, P.; Ryde, U.; De Gioia, L. Angew.
Chem. Int. Ed. 2009, 48, 3503-3506.
[2] Greco, C.; De Gioia, L. Inorg. Chem. 2011, 50, 6987-6995.
[3] Greco, C. Inorg. Chem., in press.
[4] Camara, ; Rauchfuss, T. B. Nat. Chem. 2012, 4, 26-30.
[5] Greco, C.; Bruschi, M.; Fantucci P.; Ryde, U.; De Gioia, L. J. Am. Chem. Soc. 2011, 46,
18742-18749.
36
TOWARDS A VIRTUAL RESEARCH COMMUNITY FOR
CHEMISTRY, MOLECULAR AND MATERIALS SCIENCE
AND TECHNOLOGIES
Antonio Laganàa, Alessandro Costantinib
a
Department of Chemistry, University of Perugia, Perugia, Italy
b
INFN, Perugia, Italy
Thanks to the progress made during the EGEE and the EGI-inspire European
projects, the Chemistry, Molecular and Materials Science and Technologies
(CMMST) community has set up a proposal aimed at establishing a CMMST
Virtual Team (VT) of the European Grid Infrastructure (EGI) devoted to
grounding the assemblage of a homonimous Virtual Research Community (see
https://wiki.egi.eu/wiki/Virtual_team).
Virtual Research Communities (VRCs) are groups of like-minded individuals
organised by discipline or computational model. A VRC can establish a support
relationship, formalised through a Memorandums of Understanding (MoU), with
EGI. EGI VRCs have typically an established presence in their field and
represent well-defined scientific research communities. Multi-national scientific
communities can draw many benefits from having a VRC partnership with EGI.
For example, they can benefit from the resources and support that are available
within the National Grid Initiatives (the main stakeholders of EGI.eu), they can
benefit from the workshops and forums organised by EGI, they can receive
support on resolving specific technical issues with EGI services, and they
become involved in the user-focussed evolution of EGI’s production
infrastructure.
The VT project will take the first step towards the setup of a CMMST VRC, by
documenting the structure that such a VRC should have to represent the
CMMST community in EGI, the technologies, resources and services that
already exist within EGI and could be used to satisfy the requirements of the
CMMST VRC; the technologies that need to be developed or brought into EGI,
then integrated with the production infrastructure so the VRC members can
efficiently manage and use TASKS.
The VT will investigate how to exploit the capabilities of the existing EGI tools
in building distributed workflows and “workflows of workflows” from various
software packages, including
- Molecular Simulators (like GEMS the Grid Empowered Molecular Simulator);
- Electronic structure computation (like GAUSSIAN, GAMES, CRYSTAL,
etc.);
- Quantum and classical molecular dynamics computation (like ABC,
GROMACS, MCTDH, VENUS96, DL_POLY, RWAVEPR, etc.);
37
- Statistical averaging to produce physical observables;
- Distributed database and knowledge repositories (G-LOREP).
Support to the Belong Research Laboratories endorsing the VT are: CNAF (I),
UNIPG (I), UPV (ES), UB (ES), TUW (PL), Univ. Toulouse (FR), FORTH
(GR), Univ. Groningen (NL), Univ. Thessaloniki (GR)
38
A VERY FAST DIVIDE AND CONQUER DISCRETIZATION
ALGORITHM FOR THE POLARIZABLE CONTINUUM MODEL
Filippo Lipparini,aBenjamin Stammb,c, Eric Cancès,dYvon Madayb,e,
Benedetta Mennuccif
a
UPMCUnivParis 06,Institut du Calcul et de la Simulation, 75005 Paris, France
UPMCUnivParis 06, UMR 7598, Laboratoire J.-L. Lions, 75005 Paris, France
c
CNRS, UMR 7598, Laboratoire J.-L. Lions, 75005 Paris, France
d
CERMICS, INRIA-Ecole des Ponts, Université Paris-Est, 6 and 8 Avenue Blaise Pascal,
77455 Marne-la-ValléeCedex 2, France
e
Division of Applied Mathematics, Brown University,
182 George Street, Providence, RI 02912, USA
f
Via Risorgimento 35, 56126 Pisa, Italy
b
In this contribution we present a divide and conquer method to efficiently solve
the integral equations involved in the Polarizable Continuum Model1(PCM), and
in particular in its Conductor-like approximation2,3, for a Van der Waals
molecular cavity.The spirit of our new algorithm is the one of Schwarz Domain
Decomposition method4for overlapping domains, as the spheres that form the
Van der Waals cavity. On the single sphere, the Conductor-like PCM problem is
diagonal in the Spherical Harmonics basis: the diagonal block (i.e., the one
associated to a specific sphere) of the matrix obtained with our algorithm will be
diagonal. Furthermore, as only the spheres overlapping with the reference one
will give contributions, the matrix is also block sparse for large molecules:
linear scaling with respect to the dimension of the system can be easily obtained
using a simple Jacobi iterative scheme. The Jacobi scheme allows for an
embarrassingly parallel implementation, which, together with the linear scaling
properties of the algorithm, result in a very fast computation of the solvation
energy.
[1] Tomasi, J.; Mennucci, B.; Cammi, R.Chem. Rev. 2005, 105, 2999-2093.
[2] Klamt, A.; Schuurmann, G. J. Chem. Soc., Perk. Trans. 1993, 2, 799-805.
[3] Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995-2001.
[4] Schwarz, H.A. Vierteljahrsschrift der NaturforschendenGesellschaft in Zürich 1870, 15,
272-286.
39
CATALYTIC MECHANISM OF THE ARYLSULFATASE
PROMISCUOUS ENZYME
Tiziana Marino, Nino Russo
Department of Chemistry, Università della Calabria 87036, Arcavacata di Rende (Italy)
The Pseudomonas aeruginosa aryl sulfatase (PAS) enzyme catalyzes the
hydrolysis of the original p-nitrophenyl-sulfate (PNPS) substrate such as that of
the promiscuous p-nitrophenyl-phosphate (PNPP) one with comparable kinetics.
Figure: Active site of the PAS and its two substrates.
With the aim of elucidating the working mechanism of this enzyme having
“broad substrate specificity”, a full quantum chemical study has been performed
at the density functional level [1]. Although the potential energy surfaces of the
two examined reactions are almost similar, the rate determining step is different
(nucleophile attack for PNPS versus nucleophile activation for PNPP).
The calculated ∆∆G between two reactions (0.7 kcal/mol) is in agreement with
that obtained converting to barriers the available experimental kinetic data (1.6
kcal/mol, applying classical transition-state theory) at the same temperature
(T=298.15 K).
Furthermore, the influence of the dispersion contributions on both investigated
reactions has been also taken into account.
[1] Marino T.; Russo N.; Toscano M. Chem.-Eur. J, DOI:10.1002/chem.201201943.
40
UNVEILING STRUCTURE-PROPERTY RELATIONSHIPS IN
PEROVSKITE-OXIDE BASED ELECTRODES FOR SOLID OXIDE
FUEL CELL APPLICATIONS
Ana B. Muñoz-García,a Michele Pavone,a Emily A. Carter b
a
Dipartimento di Scienze Chimiche, Universitá di Napoli Federico II, Comp. Univ. M. S.
Angelo, Via Cintia 21, 80126 Napoli. [email protected]
b
Department of Mechanical and Aerospace Engineering, Program in Applied and
Computational Mathematics, and the Andlinger Center for Energy and the Environment,
Princeton University, Princeton, NJ, 08544-5263 USA.
Solid oxide fuel cell (SOFC) devices generate electricity and high-quality heat
with high efficiency and low pollution from flexible fuel sources. However,
current SOFCs operate at temperatures too high (900-1000°C) to be effective in
terms of materials durability, thus limiting widespread use of this technology.
Therefore, considerable effort is being devoted to developing new SOFCs that
can operate at lower, intermediate temperatures (600-800°C). In many cases, the
cathode material poses the greatest challenge. It is difficult to simultaneously
retain adequate oxygen reduction reaction (ORR) rates and high oxide ion
mobility at intermediate temperatures. Complex perovskite-type transition metal
oxides have been the materials of choice. The key factors determining the
relative usefulness of these materials are: high-temperature stability, ability to
catalyze the ORR at reasonable rates and sufficiently high electronic
conductivity. In this talk, simple quantum mechanical analyses of LaMO3 (M =
Cr, Mn, Fe, Co) materials will be discussed, providing new insights into what
drives the relative ease of formation of oxygen vacancies, which is a prerequisite
for and predictor of oxide ion bulk diffusion [1]. Moreover, a promising new
SOFC electrode material based on Sr2Fe(1+x)Mo(1-x)O6-δ (SFMO) will be
presented [2, 3]. In particular, the theoretical analysis of the electronic structure
allows us to elucidate the origin of SFMO non-stoichiometry and the attendant
mixed ion-electron conductor character so important for intermediate
temperature fuel cell operations.
[1] Pavone, M.; et al., Energy Environ. Sci. 2011, 4, 4933-4937.
[2] Muñoz-García, A. B.; et al., Chem. Mater. 2011, 23, 4525-4536.
[3] Muñoz-García, A. B.; et al., J. Am. Chem. Soc. 2012, 134, 6826-6833.
41
MASSIVELY PARALLEL CRYSTAL PROGRAM FOR LARGE UNIT
CELL AB INITIO CALCULATIONS
Roberto Orlando
Dipartimento di Chimica, Università di Torino, Via Pietro Giuria 5, 10125 Torino.
The electronic structure and properties of crystals can be calculated ab initio
with CRYSTAL [1] at different levels of approximation ranging from HartreeFock (HF) to Kohn-Sham (KS) Density Functional Theory (DFT), including use
of hybrid functionals. The CRYSTAL program is based on the use of Gaussiantype orbitals, which allows easy interpretation of the electronic structure and
direct comparison with molecular fragments.
The present release of the code, CRYSTAL09 (http://www.crystal.unito.it),
enables fully automated and efficient search for minimum energy structures and
the computation of a variety of properties including structural, elastic,
piezoelectric, dielectric, magnetic and electronic properties, simulation of
vibration spectra. Extensive use of symmetry and low computational
requirements make the program efficient and suitable for the study of complex
structures with ordinary computer facilities. Use of standard parallel linear
algebra libraries now permit large-scale calculations for systems containing
thousands of atoms in the unit cell with good scalability over thousands of
processors on High Performance Computers (HPC). In the impending new
release of the program memory storage has been fully reorganized and
optimized with removal of all static limits; data distribution is also enhanced [2].
Thus, crystals containing more than 100000 basis functions in the unit cell can
now be handled efficiently and quasi-linear scaling with the unit cell size has
been achieved on HPCs. Full parallelization has also been extended to the
calculation of the full set of “properties” available in CRYSTAL. The new
capabilities of the program, which enable investigation of complex problems
such as materials in the nanoscale [3] or biological systems [4], will be
illustrated.
[1] Dovesi, R.; Orlando, R.; Civalleri, B.; Roetti, C.; Saunders, V. R.; Zicovich-Wilson, C.
M. Z. Kristallogr. 2005, 39, 571-573.
[2] Orlando, R.; Delle Piane, M.; Bush, I. J.; Ugliengo, P.; Ferrabone, M.; Dovesi, R. J.
Comput. Chem. 2012, 33, 2276–2284.
[3] Garcia-Castello, N.; Prades, J. D.; Orlando, R.; Cirera, A. J. Phys. Chem. C 2012, 116,
22078–22085.
[4] Rimola, A.; Aschi, M.; Orlando, R.; Ugliengo, P. J. Am. Chem. Soc. 2012, 134,
10899−10910.
42
TUNING THE NATURE OF THE FLUORESCENT STATE:
A SUBSTITUTED POLYCONDENSED DYE AS A CASE STUDY
Cristina Sissa,a Valentina Calabrese,b Marco Cavazzini,b Luca Grisanti,a
Francesca Terenziani,a Silvio Quici,b Anna Painellia
Dipartimento di Chimica Università di Parma and INSTM UdR-Parma
b
Istituto di Scienze e Tecnologie Molecolari (ISTM) CNR
We present an extensive spectroscopic analysis of
an elongated polycondensed dye with donor–
acceptor substitution. The charge-transfer (CT)
state, polarized along the long molecular axis, is
close in energy to a local excitation (LE) of the
polycondensed system, roughly polarized along
the short molecular axis, making this system
particularly suitable to investigate the LE/CT
interplay. An essential-state model is presented
that quantitatively reproduces absorption and
fluorescence spectra, as well as fluorescence
emission and excitation anisotropy spectra
collected in solvents of different polarity and
viscosity. A sound basis is set for the
understanding of how relaxation of polar
solvents affects the nature of low-lying
excitations.
The
markedly
different
fluorescence
emission
and
excitation
anisotropy spectra measured in glassy and
liquid
polar
solvents
unambiguously
demonstrate the major role played by solvent
relaxation in the definition of fluorescence
properties of the dye.1
[1] C. Sissa et al., Chem. Eur. J. 2013, 19, 924 – 935.
43
Charge-Transfer
(CT) Excitation
C 4H 9
N
N
Local
Excitation (LE)
C 4H 9
Non-polar solvent Polar solvent
Potential Energy Surfaces (eV)
a
LE
emission
CT
emission
Solvation Coordinate
AB-INITIO DFT+U STUDY OF Sr-DOPED LaMO3 (M=Cr, Mn)
Michele Pavone,a Ana B. Muñoz-Garcia,a Emily A. Carterb
a
Dipartimento di Scienze Chimiche, Universitá di Napoli Federico II, Comp. Univ. M. S.
Angelo, Via Cintia 21, 80126 Napoli. [email protected]
b
Department of Mechanical and Aerospace Engineering, Program in Applied and
Computational Mathematics, and the Andlinger Center for Energy and the Environment,
Princeton University, Princeton, NJ, 08544-5263 USA.
Perovskite-type transition metal oxides have many technological applications,
from solid oxide fuel cells (SOFC) to oxygen and proton membranes, from
colossal magneto-resistance to ferroelectric devices. The key to such a success is
the ease of tuning the ABO3 chemical formula with aliovalent substitutions at
the A and/or B sites. The resulting p-/n-doped electronic structure alters and
determines the properties of the perovskite. Therefore, proper modelling of these
features is crucial to support and guide a rational design of new and more
effective materials. In this contribution we will discuss the cases of La(1x)Sr(x)CrO3 (LSC) and La(1-x)Sr(x)MnO3 (LSM) with x equal to 0 and 0.25. Both
LSC and LSM have been successfully applied as SOFC interconnects and
cathodes, respectively [1]. The presence of holes formed upon Sr substitution for
La affects the transition-metal d-states and induces formation of M4+ species.
The very localized nature of transition metal d-orbitals and the well-known selfinteraction error (SIE) of standard density functional theory (DFT) makes it
challenging to capture the correct physics of these materials. Within this context,
we will discuss the ab initio DFT+U approach [2] and will compare its
performance against the very popular PBE semi-local density functional [3] and
the HSE06 hybrid functional [4]. Our results show how important it is to correct
the SIE in order to produce accurate electronic features and also for gaining
important insights into the charge and oxide transport mechanisms in these
materials [5].
[1] Ishihara, T. (Ed.) Perovskite Oxide for Solid Oxide Fuel Cells, Springer, 2009.
[2] Mosey, N.J.; et al. J. Chem. Phys. 2008, 129, 014103.
[3] Perdew, J.P.; et al., Phys. Rev. Lett. 1996, 77, 3865-3868.
[4] Heyd, J.; et al., J. Chem. Phys. 2006, 124, 219906.
[5] Pavone, M.; et al., Energy Environ. Sci. 2011, 4, 4933-4937.
44
A STRATEGY FOR NONADIABATIC QUANTUM-CLASSICAL
DYNAMICS OF SEMIRIGID MOLECULES. INVESTIGATING THE
PHOTOSTABILITY OF NUCLEOBASES
David Picconi,a Francisco José Avila Ferrer,b,c Roberto Improta,d
Alessandro Lami,b Fabrizio Santorob
a
Technische Universitt München, Lehrstuhl für Theoretische Chemie,
Lichtenbergstraße 4, D-85747 Garching, Germany
b
Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici
(ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
c
University of Málaga, Physical Chemistry, Faculty of Science, Málaga 29071, Spain
d
Consiglio Nazionale dell Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR),
via Mezzocannone 16, I-80134, Napoli, Italy
Semirigid molecules, whose excited state behaviour has an essentially
vibrational nature, are of great importance in many fields of photochemistry.
Particular interest is devoted to the description of the dynamical processes
occurring after a photoexcitation to a set of nonadiabatically coupled electronic
states.
The theoretical simulation by means of
quantum wave packet propagations
represents one of the best ways to describe
the quantum effects of the molecular
motion, thus the internal conversion
processes. Besides, this opens the route to
the description of nonadiabatic effects in different spectroscopic signals, by
means of eigenstate-free time-dependent calculations.[1]
The purpose of this contribution is to illustrate a general time-dependent
procedure to study the photophysics of internal conversion processes in large
semirigid molecules. With this intent, we model the potential energy surfaces
within the most general quadratic approximation, thus including the Duschinsky
mixing between normal modes, and describing the inter-state coupling through
a term linear in the coordinates.[2] This model is reminescent to those routinely
used for the eigenstate-based computations of single-state vibronic spectra.[3]
The dimensionality of the system is reduced with a rigorous standard approach,
which has been developed recently,[4] and allows to define a new set of
coordinates partitioned into groups, defining a hierarchy of effective
Hamiltonians, depending on few ad hoc degrees of freedom, for which the timedependent Schrödinger equation can be solved exactly. The different quantum
dynamical results (state populations, spectra) converge rapidly going on with the
hierarchy, and it is shown that the convergence improves when the remaining
coordinates are included as a ‘classical bath’.[5]
45
As an example, it will be illustrated how this scheme was applied to the
simulation of ππ*/nπ* internal conversions in nucleobases, a process whose
importance for the DNA photostability is intensely debated in literature.
[1] Lami, A.; Santoro F. in Computational Strategies for Spectroscopy: from Small
Molecules to Nanosystems, edited by V. Barone, chap. 10, p. 475 (wiley, Chichester,
UK, 2010).
[2] Köppel, H.; Domcke, W.; Cederbaum, L. S. Adv. Chem. Phys. 1984, 57, 59.
[3] Biczysko, M.; Bloino, J.; Santoro, F.; Barone, V. in Computational Strategies for
Spectroscopy: from Small Molecules to Nanosystems, edited by V. Barone, chap. 8, p.
361 (wiley, Chichester, UK, 2010).
[4] Picconi, D.; Lami, A.; Santoro, F. J. Chem. Phys. 2012, 136, 244104.
[5] Picconi, D.; Avila Ferrer, F. J.; Improta, R.; Lami, A.; Santoro, F. Faraday Discuss.
2012, 163.
46
BENCHMARKING PERIODIC DISPERSION-CORRECTED DFT
CALCULATIONS FOR THE PREDICTION OF MOLECULAR
CRYSTAL POLYMORPHISM
Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia,
Via G. Campi 183, 41125 Modena, Italy
Periodic Density Functional Theory (DFT) calculations employing the PBE,
PBE0 and B3LYP functionals coupled with different dispersion-correction
schemes (-D and –TS) have been applied to the para-diiodobenzene (p-DIB)
molecular crystal in order to determine how
they perform in reproducing the energetic and
crystal geometry of its two well known
polymorphs. Our results [1] showed that, when
properly
corrected,
DFT
calculations
successfully predict the relative stability of the
α (Fig.1) and β phases at zero temperature, in
good agreement with Diffusion Monte-Carlo (DMC) calculations [2]. Among
the two dispersion corrections employed, the recently proposed Tkatchenko and
Scheffler (TS) scheme [3] performs much better than the original Grimme
scheme (D) [4]. This is imputable to the accurate nonempirical method used to
obtain the dispersion coefficients in the former
approach.
We are currently benchmarking the TS scheme
also against a polar system, such as the oxalyl
dihydrazide (Fig.2). This simple molecule
gives rise to five different phases, in which the
competition of intermolecular H-bond and
dispersive interactions makes the prediction of
the relative stability very challenging. The TS scheme leads to a nice agreement
with experiment both for structures and thermodynamics.
The TS and other analogous models for dispersion-correction are still not
commonly used in computational chemistry but the results reported in literature
denote the accuracy of such methods to describe long-range interactions.
In our opinion, they can play a fundamental role to better understand the
chemical and physical nature of weak interactions – not only in the field of
molecular crystals – opening a new era for the design and the prediction of
increasingly complex systems, as requested from the market.
47
[1] Pedone A.; Presti D.; Menziani M.C.; Chem. Phys. Lett. 2012, 541, 12-15.
[2] Hongo K.; Watson M. A.; Sànchez-Carrera R. S.; Iitaka T.; Aspuru-Guzik A.; J. Phys.
Chem. Lett. 2010, 1, 1789.
[3] Tkatchenko A.; Scheffler M.; Phys. Rev. Lett. 2009, 102, 073005.
[4] Grimme S.; J. Comput. Chem. 2006, 27, 1787.
48
COMPUTATIONAL INVESTIGATION OF IR SPECTRA OF
ELECTROSPRAY IONIZED BIOMOLECULES
Roberto Paciotti,a Cecilia Coletti,a Nazzareno Re,a Maria Elisa Crestoni, b
Simonetta Fornarinib
a
Dipartimento di Farmacia, Università G. d’Annunzio Chieti-Pescara,
Via dei Vestini, 66100 Chieti
b
Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza,
P.le A. Moro 5, 00185, Roma, Italy.
IR vibrational spectroscopy is a widespread technique for the characterization of
molecules in gas phase, allowing the detection of motifs and signatures
occurring in relevant processes. In particular, IR spectroscopy of organic
molecules is known to be highly sensitive to hydrogen bonding, a feature that
makes this technique very appealing for a detailed structural characterization.
The extremely low density of gas phase ions requires the use of a sensitive
‘action’ spectroscopy approach such as IRMPD (IR Multiple Photon
Dissociation). The interpretation of the experimental spectra needs a strong
computational support to correctly assign the main features corresponding to the
vibrational signatures and to identify populated isomers and/or conformers,
particularly when processes involving aminoacids or peptides are investigated.
However, the computed spectrum is extremely sensible to the employed level of
theory [1], to the basis set size and to the inclusion of anharmonicity effects in
the calculation [2]. Furthermore, because IRMPD experiments are carried out at
room temperature, the contribution of all the accessible conformers has to be
considered [3].
In this work, the effect of all these aspects was individually taken into account to
accurately reproduce the IRMPD spectrum of the O-sulfoserine anion and
cation, paying special attention to the characterization of the sulfonation
vibrational signatures. Indeed, sulfonation occurs as a common enzymatic
modification of endogenous substances and drugs and has recently been
discovered and characterized in serine and threonine residues.
[1] Zevereva, E.E.; Shagidullin, A.R.; Katsyuba, S.A. J. Phys. Chem. A 2011, 115, 63-69.
[2] Barone, V. J. Chem. Phys. 2004, 120, 3059.
[3] C. Coletti , N. Re, D. Scuderi, Ph. Maitre, B. Chiavarino, S. Fornarini, F. Lanucara, R.K.
Sinhayc, M.E. Crestoni, Phys.Chem.Chem.Phys., 2010, 12. 13455-13467.
49
STRUCTURE AND DYNAMICS OF HYDRATED Na VERMICULITE
CLAY STUDIED BY CAR-PARRINELLO MOLECULAR DYNAMICS
SIMULATIONS
Giuseppe B. Suffritti,a Pierfranco Demontis,a Marco Masia,a,b
a
Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, and
Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM),
Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari
b
Istituto Officina dei Materiali, CNR, UOS SLACS, Via Vienna 2, 07100 Sassari
Car-Parrinello molecular dynamics simulations are applied to unravel the
structure of vermiculite clay at the hydration level found in the natural mineral.
The structure and the vibrational spectra of the aluminosilicate sheet is well
known and is well reproduced by the simulations. However, the structures of the
interlayer content at the ambient conditions, Na cations and hydration water
molecule (4 H2O per Na+), as proposed in X-ray diffraction experimental papers
seemingly are not in full agreement with the results of neutron diffraction
experiments found in literature, yielding only the density profile perpendicular
to the aluminosilicate sheets, but including hydrogens. Our calulations
reproduce this density profile, and show that the interlayer content is remakably
disordered, with some Na cations located midway between the sheets and some
others lying closer to the to the clay surface. The amount of the adsorbed water
is not sufficient to form a complete hydration shell for the cations, nor a
continuous hydrogen bond network, as most water molecules are also hydrogen
bonded to the basal oxygens of the sheets. Anomalous Na+ – Na+ and water –
water radial distribution functions suggest the presence two different Na+ – Na+
distances, depending on the interposition of water between cations, which
indeed were found by X-ray diffractions, and loose water – water hydrogen
bonds. On the other hand, X-ray diffraction studies proposed a more symmetric
distribution of water and cations, but were able to locate only about one half of
the interlayer content, as the occupancies of all atoms were partial. The
symmetric distributions probably were originated by the constraints of the
crystal symmetry group chosen for the structure refinement. Yet, at least for the
cations, the average computed positions, although affected by large errors, are
compatible with those reported in the experimental works. By adding two more
water molecules per Na+, a completely different structure of the interlayer
content results from the calculations. Water molecules form two parallel plane
sheets showing an unusual hexagonal structure and the cations remain midway
between the sheets at crystallographic positions and at regular distances.
50
DENSITY FUNCTIONAL THEORY FOR MOLECULAR
MULTIPHOTON IONIZATION
IN THE PERTURBATIVE REGIME
Daniele Toffoli,a Piero Declevab
a
Department of Chemistry, Middle East Technical University, 06531 Ankara, Turkey.
Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste,
Via L. Giorgieri 1, I-34127, Trieste, Italy and CNR-IOM DEMOCRITOS, Trieste, Italy
b
A general implementation of the lowest nonvanishing order perturbation theory
for the calculation of molecular multiphoton ionization cross sections is
proposed in the framework of density functional theory. Bound and scattering
wave functions are expanded in a multicentric basis set and advantage is taken
of the full molecular point group symmetry, thus enabling the application of the
formalism to medium-size molecules. Multiphoton ionization cross sections and
angular asymmetry parameters have been calculated for the two- and fourphoton ionization of the H2+ molecule, for linear and circular light polarizations.
Both fixed and random orientations of the target molecule have been considered.
To demonstrate the efficiency of the proposed methodology, the two-photon
cross section and angular asymmetry parameters for the HOMO and HOMO-1
orbital ionization of benzene are also presented.
51
SPATIAL AND ELECTRONIC CORRELATIONS IN THE PE545
LIGHT-HARVESTING COMPLEX
Lucas Viani a, Carles Curutchet b, Benedetta Mennucci a
a
via Risorgimento 35, 56126 Pisa, Italy
b
Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona,
Av. Joan XXIII s/n, 08028 Barcelona, Spain
The recent discovery of long-lasting quantum coherence effects in
photosynthetic pigment–protein complexes has challenged our view of the role
that protein motions play in light-harvesting processes. Several groups have
suggested that correlated fluctuations involving the pigments site energies and
couplings could be at the origin of such unexpected behavior. Here we combine
molecular dynamics simulations with quantum mechanics/molecular mechanics
calculations to analyze the degree of correlated fluctuations in the PE545
complex of Rhodomonas sp. strain CS24. We find that correlations between the
motions of the chromophores, which are significantly assisted by the water
solvent, do not translate into appreciable site energy correlations but do lead to
significant cross-correlations of energies and couplings. Such behavior, not
observed in a recent study on the Fenna–Mathews–Olson complex, seems to
provide phycobiliproteins with an additional fundamental mechanism to control
quantum coherence and light-harvesting efficiency compared with chlorophyllcontaining complexes.
52
H-TRANSFER TERMINATION MECHANISMS IN POLYOLEFIN
HOMOGENEOUS CATALYSIS
Vincenzo Villani, Gaetano Giammarino
Dipartimento di Scienze, Università degli Studi della Basilicata,
Campus di Macchia Romana, Potenza (Italy)
The understanding of the reaction mechanisms in homogeneous polymerization
of olefins is today a challenging topic1-3.
Fujita et al.1 have been the first to highlight the living behaviour, in which the
ability of the polymer chain to terminate is removed, in post-metallocene Tibased catalysts.
showed
that
the
Mecking
et
al.2
bis(enolatoimine)Ti catalyst, with orthofluorinated aryl groups, is also able to achieve
the same living behaviour. Via NMR, the key
role of F-bond interactions was proposed.
We study Mecking’s catalysts, using DFT
calculations on a parallel platform running
GAUSSIAN09, at the triple ζ plus polarization
with Becke-Perdew exchange-correlation level.
The stationary structures have been localized
and energy barriers of activation determined.
Normal mode analysis and intrinsic reaction
coordinates have been performed. The key role
of fluorine interactions both in propagation and termination steps has been made
clear.
An alternative H-transfer to the ligand in the termination mechanism is
proposed.
[1] Terao, H.; Iwashita, A.; Matsukawa, N.; Ishii, S.; Mitani, M.; Tanaka, H.; Nakano, T.;
Fujita, T. ACS Catal. 2011, 1, 254-265.
[2] Bryliakov, K. P.; Talsi, E. P.; Möller, H. M.; Baier, M. C.; Mecking, S. Organometallics
2010, 29, 4428-4430.
[3] Villani, V.; Giammarino, G. Macromolecules 2010, 43, 5917-5918.
53
54
COMUNICAZIONI POSTER
55
56
FULLY AUTOMATED PROCEDURE TO EVALUATE ELASTIC AND
PIEZOELECTRIC CONSTANTS
Elisa Albanese, Alessandro Erba, Bartolomeo Civalleri
Dipartimento di Chimica e Centro di Eccellenza NIS, Università di Torino,
via Pietro Giuria 7, Torino, 10125, ITALIA
A fully automated procedure to evaluate the independent second- and third-order
elastic constants (SOEC and TOEC) and piezoelectric coefficients has been
implemented in the periodic ab-initio CRYSTAL[1] code. This procedure can
handle any space group of 1D, 2D and 3D periodic systems. The automated
scheme provides, by exploiting the symmetry, to find the minimal set of strains
required to get all the independent coefficients and then apply them to the
unstressed structure. This procedure was partially already implemented for the
SOEC[2], but only now it has been made fully automatic and extended to TOEC
and piezoelectricity calculation.
The SOEC are related to the strain second derivatives of the total energy, and
the TOEC, that provide information on the nonlinear elasticity of the materials,
to the strain third derivatives:
in which Voigt’s notation is used (I, j, k = 1, 2, ..., 6) and V is the equilibrium
volume. The evaluation of elastic constants is accomplished by using a stressstrain relationship based on a total energy calculation, then second and third
derivatives of the energy as a function of crystal deformation are numerically
evaluated by means of the analytical gradients.
The approach used for computing the piezoelectric coefficients involves the
computation of the intensity of polarization induced by strain through the Berry
phase’s (BP) theory[3]. In short, the piezoelectric constants are related to the
derivatives of BP φ with respect to the strain components εk according to:
where e is the electron charge and aji is the i-th cartesian component of the j-th
direct lattice basis vector aj. Different systems are used to test the numerical
stability and the accuracy of the new procedure, especially for the piezoelectric
constants and TOEC that appear more delicate than for the SOEC[2]. α-quartz
and ZnO have been selected as test cases for piezoelectric constants and silicon
for TOEC. Furthermore, the effect of the DFT functionals on the piezoelectric
coefficients has been analysed.
[1] Dovesi, R. et. al. CRYSTAL09 User’s Manual. University of Torino: Torino, 2009.
[2] Pergen, W. F.; Criswell, J.; Civalleri B.; Dovesi R. Comp. Phys. Comm., 2009, 180,
1753-1759.
[3] Catti M.; Noel Y.; Dovesi.R. J. Phys. Chem. Solids, 2003, 11, 2183.
57
DFT AND TDDFT STUDY OF UNSYMMETRICAL SQUARAINES
ADSORBED ON PbSe SURFACES
Mario Argeri,a Claudia Barolo,b Maurizio Cossi,a Fabio Grassi,a
Leonardo Marchesea
a
DISIT, Università del Piemonte Orientale A. Avogadro,
Viale Teresa Michel 11, 15121 Alessandria, Italy
b
Department of Chemistry, NIS Centre of excellence, Università di Torino,
Via Pietro Giuria 7,10125 Torino, Italy
Recently considerable efforts have been spent to study Dye Sensitized Solar
Cells (DSSC), which represent an attractive alternative to traditional solid state
technology for converting sunlight to electricity at low cost. Several kinds of
dyes are employed as sensitizers and among them the most successful in
obtaining high power conversion efficiency (PCE) are the ruthenium
polypyridyl complexes, yelding above 11% PCEs. In spite of this good level of
efficiency, the main disadvantage of the Ru-complexes is the lack of absorption
in the far-red/near IR region. To improve the absorption capacity of the dye
layer, new sensitizers, characterized by a wider spectral match with the solar
emission, have been recently explored. Among the different classes of near-IR
dyes, squaraines received a special attention due to their good photo- and
thermal stability and the research is mainly focused on unsymmetrical
squaraines, rather than on symmetric ones, since it is thought that this
asymmetry favors the directionality of the charge transfer. One recent
advancement in photovoltaics technology is the use of semiconductor quantum
dots (QDs) as sensitizers: such devices are known as Quantum Dot Sensitized
Solar Cells (QDSSCs). This line of research has attracted considerable interest
due to the tunability of the QD band gap and to multiple exciton generation
(MEG), that is the production of several electron-hole bound states by means the
absorption of a single photon, which in principle enables to overcome the
Shockley-Queisser efficiency limit. One of the most promising semiconductor
materials for the purpose above is the Lead Selenide, PbSe, within which the
MEG takes place, although the quantum yield of such process is still debated. It
is believed that the use of a squaraine dye as a linker molecule between the PbSe
QD and the TiO2 layer could be a possible further research development. In this
work we study the adsorption properties of some unsymmetrical squaraines,
coded as VG0 and VG0-NH2 , on PbSe surfaces in order to investigate the
stability of PbSe-squaraine adduct. Furthermore we calculate at TDDFT level
the absorption spectra of squaraines above both in the free and adsorbed case to
gain insight about changes in dye’s optical properties due to the adsorption on
PbSe.
58
[1] C. Barolo, M.Graetzel, M. Nazeeruddin et. al. Chem. Commun. 2012, 48, 2782-2784.
59
MODELING OF SPIRAL HALLOYSITE NANOTUBES
Francesco Ferrante, Nerina Armata, Giuseppe Lazzara, Stefana Milioto
Dipartimento di Fisica e Chimica – Università degli Studi di Palermo,
viale delle Scienze Ed. 17 I-90128 Palermo
Halloysite is an economically viable clay mineral, belonging to the kaolinite
group and occurring in nature with a hollow tubular shape. The size of halloysite
nanotubes are between 500 and 1000 nm in I and 15-100 nm in inner diameter,
depending on the deposit. The general stoichiometry is Al2Si2O5(OH)4·n H2O
with n=0 for the anhydrous (Halloysite 7Å) and n=2 for the fully hydrated
halloysite (Halloysite 10Å). The crystal structure is described as a layer formed
by two building blocks: [SiO4] tetrahedra and [AlO6] octahedra. Water
molecules in Halloysite 10Å are sitting between two consecutive layers. This
material finds application in ceramics, cements and fertilisers industry and,
recently, as template in nanotechonology. In fact, thanks to its peculiar shape,
halloysite is considered a promising entrapment system for loading, storage and
controlled release system for various species [1].
The modeling approach is an helpful tool in the prediction and interpretation of
the interactions occuring between adsorbed species and inner and/or outer
nanotube surfaces. Even though a preliminary study on the adsorption process
could be obtained from a flat monolayer of kaolinite model or single-walled
halloysite nanotube [2], it is necessary to build up a more realistic model of the
hollow spiral nanotube. To this aim the starting geometries of Halloysite 7Å and
Halloysite 10Å have been generated by means of a program based on the
analitycal properties of Archimedean spiral. Geometry optimization of the
supercells so obtained (some of which exceed 2500 atoms) has been perfomed
by means of Self Consistent Charges Density Functional Tight Binding
employing the DFTB+ program [3]. These investigations, which represent the
first attempts to model the hydrated halloysite spiral nanotube, allowed to obtain
information on the [SiO4] tetrahedra and [AlO6] octahedra distortions necessary
to the spiral formation and on the water molecules organization on the
Halloysite 10Å outer surfaces and between the arms of its spiralling geometry.
[1] Lvov, Y. M., et al. ACS Nano 2008, 2, 814-820.
[2] Guimarães, L., et al. J. Phys. Chem. C 2010, 114, 11358-11363.
[3] Aradi B., et al. J. Phys. Chem. A 2007, 111, 5678-5684.
60
IMPROVING THE COMPARISON OF COMPUTATIONAL DATA
WITH EXPERIMENTAL ABSORPTION AND EMISSION SPECTRA.
BEYOND THE VERTICAL TRANSITION APPROXIMATION
Francisco Avila,a,b Javier Cerezo,c Emiliano Stendardo,d
Roberto Improta,d Fabrizio Santoroa
a
CNR–Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo
Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca,
via G. Moruzzi 1, I-56124 Pisa, Italy
b
University of Málaga, Physical Chemistry, Málaga, 29071, Spain
c
Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
d
CNR–Consiglio Nazionale delle Ricerche, Istituto di Biostrutture Biommagini (IBB-CNR)
Via Mezzocannone 16, I-80136, Napoli, Italy.
We carefully investigate the relationship between computed data[1.2] and
experimental electronic spectra. We compare vertical transition energies EV and
characteristic features of the spectrum like the maximum max and the first
moment M1, taking advantage on an analytical expression of M1 of an electronic
spectrum in terms of the initial and final-state potential energy surfaces, allows
to investigate the molecular factors that cause their differences. Simulations of
the absorption and emission spectra of several prototypical chromophores gives
lineshapes in very good agreement with experiments. Analysis of the simulated
spectra reveals that differences among EV, max and M1 are of the order of tenths
of eV, i.e. comparable to the expected accuracy of the most accurate
computational methods. Our results indicate that the customary comparison of
experimental max and computational EV, without taking into account vibrational
effects, is no more an adequate measure of the
performance of an electronic method, whereas
comparison of M1 and/or 0-0 transition
frequencies provides more robust results. Some
rules of thumbs are proposed to help
rationalize which kind of correction one should
expect when comparing EV, M1 and max.[3]
Figure 1 Schematical relationship
between spectral and computed
[1] Santoro, F.; Fcclasses a Fortran 77 code, 2008 http://village.pi.iccom.cnr.it
[2] Avila Ferrer F. J.; Santoro F. Phys. Chem. Chem. Phys. 2012, 14, 13549-13563.
[3] Avila Ferrer, F. J.; Cerezo, J.; Stendardo, E.; Improta, R.; Santoro, F. Submitted.
61
BERYLLIUM OXIDE NANOTUBES AND THEIR CONNECTION TO
THE FLAT MONOLAYER
J. Baima,a A. Erba,a M. Rérat,b R. Orlando,a R. Dovesia
a
Dipartimento di Chimica and Centre of Excellence NIS (Nanostructured Interfaces and
Surfaces), Università di Torino, via Giuria 5, IT-10125 Torino (Italy)
b
Equipe de Chimie Physique, IPREM UMR5254, Universit de Pau et des Pays de l’Adour,
FR-64000 Pau (France)
Single-walled zigzag Beryllium Oxide (BeO) nanotubes are simulated with an
ab initio quantum chemical method. The (n,0) family is investigated in the range
from n = 8 (32 atoms in the unit cell and tube radius R = 3.4 Å) to n = 64 (256
atoms in the cell and R = 27.1 Å). The trend towards the hexagonal monolayer
(h-BeO) in the limit of large tube radius R is explored for a variety of properties:
rolling energy, elastic modulus, piezoelectric constant, vibration frequencies,
infrared (IR) intensities, oscillator strengths, electronic and nuclear contributions
to the polarizability tensor. Three sets of IR-active phonon bands are found in
the spectrum. The first one lies in the 0 – 300 cm-1 frequency range and exhibits
a very peculiar behavior: the vibration frequencies do tend regularly towards
zero when R increases while their IR intensities do not; the nature of these
normal modes is unveiled by establishing a connection between them and the
elastic and piezoelectric constants of h-BeO. The second (680 – 730 cm−1 ) and
third (1000 – 1200 cm−1 ) sets tend regularly, but with quite different speeds, to
the optical modes of the h-BeO layer. The vibrational contribution of these
modes to the two components (parallel and perpendicular) of the polarizability
tensor is also discussed. Simulations are performed using the Crystal program
which fully exploits the rich symmetry of this class of one-dimensional periodic
systems: 4n symmetry operators for the general(n,0) tube.
62
THE NEAR-EDGE X-RAY-ABSORPTION FINE-STRUCTURE OF O2
CHEMISORBED ON Ag(110) SURFACE STUDIED BY DENSITY
FUNCTIONAL THEORY
Oscar Baseggioa, Mauro Stenera,b, Michele Romeoa, Giovanna Fronzonia,b
a
Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste,
Via L. Giorgieri 1, I-34127 TRIESTE – ITALY
b
Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali,
INSTM, Unità di Trieste
The adsorption of O2 on the silver surface has been studied since many decades,
since it has important implications in the oxygen dissociation, in the oxidation of
surface and in catalytic processes. In the present work the NEXAFS at the O K
edge of O2 adsorbed on the Ag(110) surface has been calculated employing a
DFT methodology, while the surface has been simulated employing finite size
clusters of large size (Ag156). Although the infinite nature of the surface would
lead to employ computational schemes with periodic boundary conditions, the
NEXAFS process, where the core hole transition is very localized on a specific
atomic site, can be properly described with cluster models of finite size. This has
two important practical advantages: first molecular quantum chemistry codes
can be directly applied to describe this phenomenon, second most
implementations with periodic boundary conditions cannot describe properly
core orbitals due to the cutoff of plane wave momentum, problem which is
circumvented introducing pseudopotentials. Present NEXAFS spectra have been
calculated from dipole transition moments between initial core orbital and final
virtual one, taking the dipole component along the electric vector polarization
and employing a code developed in the authors research group [1]. Comparison
between experimental [2] and present calculated NEXAFS allows a clear
assignment of the spectral features as well as some suggestions about a deviation
from the ideal adsorption geometry.
[1] Fronzoni, G.; Balducci, G.; De Francesco, R.; Romeo, M.; Stener, M. J. Phys. Chem. C,
2012, 116, 18910-18919.
[2] Pawela-Crew, J.; Madix, R. J.; Stöhr, J. Surf. Sci. 1995, 339, 23-28.
63
FUNCTIONAL EFFECTS ON THE TDDFT INVESTIGATIONS IN
ORGANOMETALLIC PHOTOCHEMISTRY
Luca Bertini,a Maurizio Bruschi,b Claudio Greco,b Luca De Gioia,a
Piercarlo Fantucci,a Giuseppe Zampellaa
a
Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca
Piazza della Scienza, 2; 20126 Milan – Italy
b
Department of Environmental Sciences, Università degli Studi di Milano-Bicocca,
Piazza della Scienza, 1, 20126 Milan, Italy
The photochemistry of an organometallic complex can be investigated by means
of excited state PESs explorations along relevant coordinates computed on the
ground state PES1 or by means of Time-Dependent Density Functional Theory
(TDDFT) geometry optimizations.2 The case of the CO photolysis of
Fe2(S2C3H6)(CO)6, a model of the [FeFe] hydrogenases catalytic site in
considered.3 Upon irradiation with near UV light, Fe2(S2C3H6)(CO)6 undergoes
CO photolysis with the formation of the 32e- Fe2(S2C3H6)(CO)5 species and
successively a solvent adduct.
One of the open question regarding this process is to understand if the photodissociated CO ligand is the apical or equatorial one. The picture that emerges
the from excited state PESs explorations carried out along the Fe-C bond
stretching coordinates change as a function of the functional adopted (BP86 and
PBE0), while TDDFT geometry optimization picture is less influenced by the
type of functional.
[1] Dunietz, B. D.; Dreuw, A.; Head-Gordon, M.; J. Phys. Chem. B, 2003, 107, 5623-5629.
[2] Bertini, L.; Greco, C.; De Gioia, L.; Fantucci, P.; J. Phys. Chem. A, 2009, 113, 56575670.
[3] Marhenke, J.; Pierri, A. E.; Lomotan, M.; Damon, P. L.; Ford, P. C.; Works, C. Inorg.
Chem. 2011, 50, 11850-11852.
64
STUDY OF THE SPECIATION OF THE [Cu(HGGG)(Py)] COMPLEX IN
WATER SOLUTION USING DFTB AND DFT APPROACHES
Maurizio Bruschia, Luca Bertini,b Vlasta Bonačić-Koutecký,c Luca De Gioia,b
Roland Mitrić,d Giuseppe Zampella,b Claudio Greco,a Piercarlo Fantuccib
a
Department of Environmental Science, University of Milano-Bicocca,
Piazza della Scienza 1, I-20126 Milano, Italy.
b
Department of Biotechnologies and Biosciences, University of Milano-Bicocca,
Piazza della Scienza 2, I-20126 Milano, Italy.
c
Institut für Chemie, Humboldt-Universität zu Berlin,
Brook-Taylor-Strasse 2, D-12489 Berlin, Germany.
d
Fachbereich Physik, Freie Universität zu Berlin, Arnimallee 14, D-14195 Berlin, Germany.
DFTB and DFT methods have been employed as a part of a new computational
protocol for the study of speciation of metal-peptide complexes hydrated in a
sphere of water molecules, considering as an example, the Cu(II) complex
[Cu(HG1G2G3)(Py)(W)] (H=histidine, G=glycine, Py=pyridine and W=H2O),
which contains the species [Cu(HG1G2G3)] related to compounds formed by the
interaction of the Cu2+ ion with the prion protein.1 The DFTB calculations were
possible thanks to a careful parameterization of the atom-atom repulsive energy
terms for Cu-H, Cu-C, Cu-N, and Cu-O. The speciation process is carried out by
computing different DFTB steered molecular dynamics (SMD) trajectories, in
which one or two selected ligands are dissociated, to form well defined pentaand tetra-coordinated different forms. The last frame of each trajectory is
subjected to geometry optimization both at DFTB and DFT level, leading to
different isomers. From the corresponding energy values a rank of relative
stability of the isomers can be established. The computational protocol here
developed is of general applicability to other metal-peptide systems and
represents a new powerful tool for the study of speciation of metal-containing
systems in water solution. For the Cu(II) complex investigated the results allow
to conclude that in the presence of pyridine the lowest energy isomer is the fivecoordinated form CuNHNG1NG2OG2NPy. To this conclusion converge, with
substantial agreement, DFTB and DFT-TZVP results, the last including both 84
and 40 water molecules. This agreement represents a very encouraging result for
a large scale application of our computational protocol in the study of speciation
of other copper-peptide systems.
[1] Bruschi, M.; Bertini, L.; Bonačić-Koutecký, V.; De Gioia, L.; Mitrić, R.; Zampella, G.;
Greco, C.; Fantucci P. J. Phys Chem. B 2012, 116, 6250-6260.
65
ARE THE NONADIABATIC TRANSITION RATES TRANSFERABLE
AMONG DIFFERENT ENVIRONMENTS?
Valentina Cantatore, Giovanni Granucci, Maurizio Persico
via Risorgimento 35, 56126 Pisa
10
m.d. values
1
Figure 1
-1
0.1
transition rate, fs
We want to investigate the
transferability of the nonadiabatic
transition rates in different
environments when expressed as
functions of few dynamical
variables. As a test case, we
choose the photoisomerization of
both isomers (trans and cis) of
0.01
0.001
0.0001
1e-05
1e-06
*
azobenzene excited in the n→ π
1e-07
0
0.5
1
1.5
2
2.5
3
S0-S1 energy difference, eV
band, because of our previously
acquired experience with this problem [1]. As first hypothesis we have taken as
independent dynamical parameters the energy difference between the two
electronic states ∆E and the kinetic energy of the four atom of the CNNC azogroup Ek,4 (PNAD: Parametrized NonAdiabatic Dynamics). Figure 1 shows the
Langevin fs-1
transition rates T(S1→ S0) obtained for single integration time steps in a swarm
of about 200 trajectories starting
10
hopping rates
f(x)
from trans-azobenzene. To store
1
and retrieve the T(k→ l) data we
0.1
distribute them in a grid according
to the ∆E and Ek,4 variables. We
0.01
tested the transferability of the
0.001
transition rates to the case of a
solvent of medium viscosity,
Figure 2
0.0001
modeled by integrating the
trajectories
by
Langevin’s
1e-05
1e-05
0.0001
0.001
0.01
0.1
1
10
equation.
The
Langevin’s
vacuo fs-1
dynamics shows a considerably
slower decay with respect to vacuum in the case of the trans→ cis photoisomerization (see Figure 3), while the rate is almost unaffected in the
cis→ trans case. In spite of this, by comparing the average transition rates
obtained for each cell in the ∆E/Ek,4 grid we find essentially the same values
(see figure 2). In the attempt to simplify and accelerate the nonadiabatic
66
trajectory calculations, we used the transition rate data computed in vacuo to
simulate the decay in the Langevin case. We applied a stochastic algorithm in
order to represent the extreme variability of the transition rate data. At each step
of the trajectory we pick at random a transition rate from the appropriate ∆E/Ek,4
cell in the grid. These tests show that our method is able to reproduce in a very
good manner the differences in the decay times for simulations run in different
environments (see Figure 3). The photo-isomerization quantum yields for
cis→ trans isomerization are almost unaffected by the solvent and are well
reproduced by the PNAD dynamics. For
1
S model dynamics
S PNAD vacuo
the trans→ cis case the solvent causes a
S mod. dyn. Langevin
S PNAD Langevin
0.8
rise in the quantum yields (from 0.33 to
0.37), a counterintuitive effect that was
0.6
Figure 3
already observed and explained in
0.4
simulations with an explicit solvent. Up
to now we were not able to obtain the
0.2
same effect by PNAD simulations. The
reproduction of the quantum yield is a
0
0
500
1000
1500
2000
particularly hard test because the fate of
time (fs)
a trajectory depends on fine details
concerning the geometry and nuclear momenta at the time of the hopping from
the excited to the ground state.
1
1
1
fraction of trajectories
1
[1] Cusati T., Granucci G., Persico M. J. Am. Chem. Soc. 2011, 128, 194312.
67
THEORETICAL ADSORPTION OF METHANE, HYDROGEN AND
CARBON DIOXIDE IN POROUS AROMATIC FRAMEWORKS (PAFs)
L. Canti, A. Fraccarollo, M. Cossi, L. Marchese
Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale
“Amedeo Avogadro”, Viale T. Michel 11, 15121, Alessandria, Italy.
Porous aromatic frameworks (PAF) are synthetic materials with 3D structure of
diamond where the sp3 carbon atoms are joined by short-to-long (poly)aromatic
chains [1]. These materials haves some of the highest specific surface areas
observed for organic microporous frameworks and are likely to be excellent
adsorbents for methane, hydrogen and carbon dioxide.
In the present work, the Grand Canonical Montecarlo (GCMC) technique was
used to model this newly developed class of materials which are obtained from a
diamond structure replacing each C-C covalent bond with phenyl rings or
polyaromatic chains. Materials PAF-30n (n = 1,2,3,4), where n is the number of
phenyl rings inserted in the C−C bonds, have been studied (Fig. 1) [2]. The
ability of these materials to adsorb gases at different pressures and at different
temperatures has also been investigated, along with their BET surface area.
Ab initio calculations were performed at DFT level, with the 6-31G(d,p) and 6311+G(d,p) basis sets, using Gaussian03(G03) package. The structural
properties of PAF-30n models were estimated using the GEPOL procedure,
implemented in G03 as part of the Polarizable Continuum Model of solvation.
Methane, hydrogen and carbon dioxide adsorption isotherms were simulated
using the Sorption module included in Materials Studio package, in a series of
Grand Canonical Monte Carlo (GCMC) simulations.
Simulations (Fig. 2) show that some members of the PAF family have great
potential as methane and carbon dioxide adsorbents. These results are based on
ideally crystalline materials and lower performances are expected in actual
working conditions, but these materials are very promising candidates for many
applications involving gas adsorption.
Fig.1. Top to bottom: aromatic building
block, tridimensional structure of the unit
cell, and skeletal volume defined as a
collection of atomic spheres by the GEPOL
procedure for the PAF-30n, n=1−4.
68
Fig.2 . Example of GCMC adsorption isotherms: methane in PAF-30n at 298K. The density
of free gaseous methane (from EOS) is shown for comparison. The black square indicates the
storage target proposed by DOE at 35 bar, 298 K.
[1] T. Ben, H, Ren, S. Ma, D. Cao, J. Lan, X. Jing, W. Wang, et al. Angewandte Chemie.
2009, 48(50), 9457-60.
[2] M. Cossi, G. Gatti, L. Canti, L. Tei, M. Errahali and L. Marchese., Langmuir 2012,
28(40), 14405-14.
69
THEORETICAL INVESTIGATIONS OF SrTi1-XMXO3-δδ (M = Co, Ni, Cu)
DOPED-PEROVSKITE SYSTEMS: EFFECTS OF THE DOPING ON
THE FORMATION OXYGEN VACANCIES
Silvia Carlotto,a Andrea Vittadini,b Antonella Glisenti,a Marta Maria Natileb
a
Dipartimento di Scienze Chimiche, Università degli Studi di Padova,
Via F. Marzolo 1, 35131, Padova, Italy
b
CNR-ISTM, Via F. Marzolo 1, 35131 Padova, Italy
SrTiO3 is a prototype of ABO3 perovskite-type oxides, a class of materials with
a wide range of technological applications, such as gas sensors, solid oxide fuel
cells, electrochemical and memory devices and catalyst [1]. An important role in
determining the properties of these materials is played by oxygen vacancies,
whose formation is favoured by dopants. Thus, the material properties can in
principle be tuned by a careful doping of the host. In this habit, accurate
theoretical calculations can be useful in suggesting suitable strategies to
manipulate and enhance the number of oxygen vacancies in this material to tune,
for example, its catalytic properties [2].
We present a study where density functional theory (DFT) calculations are
employed to study how the electronic structure of SrTiO3 is modified by the
introduction of diluted (~6%) substitutional M dopants (M = Co, Ni and Cu).
The effects of the doping on the stability of vacancies is also investigated, both
in the bulk material and at the (001) surface. The influence of the theoretical
approach (DFT vs. DFT+U) on the results is finally examined. Overall, our
results show that doping has strong effects on the host material, and that these
effects are sensitive to the dopant chemical identity.
[1] The Chemical Physics of Solid Surfaces – Oxide Surfaces, edited by P. Woodruff
(Elsevier, Amsterdam, 2001).
[2] Rodiguez, J. A.; Azad, S.; Wang, L. –Q.; Garcia, J.; Etxeberria, A.; Gonzalez, L. J. Chem.
Phys. 2003, 118, 6562-6571.
70
ASSESSMENT OF THE GEOMETRICAL CORRECTION FOR THE
BSSE IN DFT CALCULATIONS FOR MOLECULAR CRYSTALS
B. Civalleri, M. Alessio
Dipartimento di Chimica, Università di Torino, Via P. Giuria 7, 10125 Torino, Italy
When using incomplete atom centered basis sets, the computed interaction
energies in a supermolecular approach are subject to the basis set superposition
error (BSSE). It arises from an unbalance basis set expansion of monomers with
respect to the molecular adduct. The BSSE can give binding where there is none
and prevent the use of small-to-medium size basis set (e.g. 6-31G(d)) which are
still widely employed for large systems, as well as for solids. The removal of the
spurious BSSE binding is also crucial to avoid artefact in the molecular
geometry when dispersion corrections are included (e.g. DFT-D2).
The BSSE is usually taken into account by using the well-known Boys-Bernardi
counterpoise (BB-CP) correction [1]. However, it is limited to intermolecular
BSSE and the correction of the potential energy surface is complicate. Recently,
Kruse and Grimme [2] proposed a semi-empirical counterpoise-type correction
in molecular systems which depends only on the molecular geometry and is
denoted as geometrical counterpoise (gCP). It consists of an atom pair-wise
potential that corrects for the inter- and intra-molecular BSSE in supermolecular
HF or DFT calculations.
In the present work, the gCP method has been extended to periodic systems and
implemented in a development version of the CRYSTAL code [3]. Here we
show preliminary results on the application of the gCP method to molecular
crystals. Simple molecular solids (e.g. N2, CO2, CO, C6H6, ...) are used as test
cases and comparison is done with the BB-CP results and large basis sets (e.g.
QZVP). Results are encouraging but not as good as for the original set of
molecular adducts used for setting up the empirical correction. This is likely due
to the inadequacy of the fitted parameters to fully correct BSSE in molecular
crystals. Furthermore, the inclusion of a dispersion correction to DFT shows that
a recalibration of the method is needed to improve results.
[1] Boys, S.; Bernardi, F. Mol. Phys. 1970, 19, 553.
[2] Kruse, H.; Grimme, S. J. Chem. Phys. 2012, 136, 154101.
[3] Dovesi, R.; et al. CRYSTAL09 User’s Manual, 2010, Torino.
71
AB INITIO MODELING OF METAL-ORGANIC FRAMEWORKS:
INSIGHTS ON STRUCTURE-PROPERTY RELATIONSHIPS
B. Civalleri,a E. Albanese,a L. Valenzano,b R. Orlandoa
a
Dipartimento di Chimica, Università di Torino, Via Giuria 7, 10125 Torino, Italy
b
Department of Chemistry, MichiganTech University, Houghton, MI, USA
Metal-organic frameworks (MOFs) are a relatively new class of materials that
combine inorganic moieties (a metal ion or a cluster), acting as connectors, with
organic linkers to form a porous three-dimensional framework. The combination
of different connectors and linkers makes MOFs very versatile materials with
interesting and promising applications in many fields, namely: gas adsorption,
storage and separation, catalysis and photocatalysis, gas sensors, nonlinear
optics [1]. A better understanding of their properties is then important to guide
tailoring and engineering of new MOFs with improved capabilities. In this
respect, ab-initio modeling offers a useful tool to get new insight into the
structure-property relationships of MOFs from an atomistic point of view.
Here, we give an brief overview of our recent results on a throughout theoretical
characterization and prediction of structural, electronic, vibrational, elastic and
adsorption properties of various MOFs [2,3,4,5]. Among them: (i) adsorption of
small molecules (e.g. CO, CO2) in open metal MOFs such as MOF74(Mg,Ni,Zn) [2], Ni-BPB [3] and Ni-BTP. (ii) Electronic properties (i.e. band
gap, refractive index, ...) of a set of selected MOFs [4,5]. For example, the
semiconductor-like character of IRMOF-1 can be tuned by changing the organic
linker or by its functionalization. Also, the role of metal ions will be highlighted
for MOF-74(Mg,Ni,Zn).
All results were obtained through a fully periodic ab-initio approach with the
CRYSTAL program.[6]
[1] Special issue: “Metal-Organic Frameworks”, Chem. Soc. Rev. 2009, 38, 1201.
[2] Valenzano, L.; Civalleri, B.; Chavan, S. et al. J. Phys. Chem. C 2010, 114, 11185;
Valenzano, L.; Civalleri, B.; Sillar, K.; Sauer, J. J. Phys. Chem. C 2011, 115, 21777.
[3] Albanese, E..; Civalleri, B.; et al. J. Mater. Chem. 2012, 22, 22592.
[4] Civalleri, B.; Napoli, F.; Noel, Y.; Roetti, C. et al. CrystEngComm 2006, 8, 364
[5] Valenzano, L.; Civalleri, B.; Chavan, S.; Bordiga, S. et al. Chem. Mater. 2011, 23, 1700.
[6] Dovesi, R.; et al. CRYSTAL09 User’s Manual, 2010, Torino.
72
AB INITIO SIMULATION OF SPECTROSCOPIC AND OPTICAL
PROPERTIES OF NOVEL POROUS GRAPHENE PHASES
M. De La Pierre,a P. Karamanis,b J. Baima,a R. Dovesia
a
b
Dipartimento di Chimica, Università degli Studi di Torino, Italy
Institut Pluridisciplinaire de Recherche sur l’Environnement et les Matériaux,
Université de Pau et des Pays de l’Adour, France
We present a detailed periodic ab initio quantum-mechanical simulation of two
recently proposed systems, namely hydrogenated porous graphene (HPG) and
biphenyl carbon (BPC), using hybrid HF-DFT functionals and all-electron
Gaussian-type basis sets [1]. The equilibrium geometry, the vibrational spectrum
(including IR intensities), the full set of components of the polarizability and
hyperpolarizability tensors are provided, the latter evaluated through a CoupledPerturbed KS/HF scheme. IR and Raman spectra for the two systems are quite
different, and differ also from graphene, thus permitting their experimental
identification. It is then shown that small defects inserted into the graphene sheet
lead to finite values for the in-plane components of the static
(hyper)polarizability tensors, spanning a relatively large range of values. By
dehydrogenation of porous graphene into biphenyl carbon, a noteworthy
enhancement of the non-linear optical properties through the static second dipole
hyperpolarizability can be achieved. Vibrational contributions to the
polarizability are negligible for both systems.
[1] M. De La Pierre, P. Karamanis, J. Baima, R. Orlando, C. Pouchan, and R. Dovesi,
accepted for publication in J. Phys. Chem. C.
73
AB INITIO MÖSSBAUER ISOMER SHIFT AND QUADRUPOLE
SPLITTINGS OF 57Fe WITH CRYSTAL
S. Casassa, A. M. Ferrari
Dipartimento di Chimica, Università di Torino and NIS-Nanostructured Interfaces
and Surfaces-Center of Excellence, Via P. Giuria 7, 10125, Torino, Italy
When a γ photon interacts with a nucleus a spin transition, from a lower to an
higher spin status, can be promoted. The transition can be accompanied by three
different effects, originated by interaction of the nucleus with both the electric
and the magnetic field. The isotropic effect and the quadrupolar interaction, due
to the isotropic and anisotropic contribution of the electric field respectively, has
been calculated with the ab initio quantum-mechanic periodic CRYSTAL code
[1] for 57Fe.
Both the influence of the basis set and the Hamiltonian have been investigated.
Comparison with experimental data and previous literature results [2] are
presented and commented. The calibration of the isomer shift of 57Fe represents
the starting point for detailed investigation of this nucleus in metallorganic
compound.
[1] R. Dovesi, V.R. Saunders, C. Roetti, R. Orlando, C.M. Zicovich-Wilson, F. Pascale, K.
Doll, N.M. Harrison, B. Civalleri, I.J. Bush I.J. et al., CRYSTAL09 User’s Manual
(Universita` di Torino, Torino, 2010) [http://www.crystal.unito.it].
[2] U.D. Wdowik and K. Ruebenbauer, Phys. Rev. B 2007, 76, 155118.
74
DESIGN OF NOVEL WO3-BASED MATERIALS WITH TAILORED
OPTICAL AND PHOTO-REDOX OR CATALYTIC PROPERTIES
Cristiana Di Valentin, Fenggong Wang, Massimo Rosa, Gianfranco Pacchioni
via Cozzi 53, 20125 Milano
In this presentation we review some recent examples, based on density
functional theory calculations, of different approaches to design novel WO3based materials with peculiar photo-redox, optical or catalytic properties:
doping, controlled defectivity or oxide clusters deposition on activated surfaces.
Periodic calculation have been performed with hybrid functional methods and an
atomic basis set approach, as implemented in the CRYSTAL code. Hybrid
functionals provide a more accurate description of the semiconductors electronic
structure (e.g. band gap values, spin localization) with respect to standard LDA
or GGA functionals.
The first example is doped-WO3 [1] for photocatalytic water splitting. Doping
inorganic solids with impurity atoms is a consolidated method to modify their
chemical and electronic properties. Since the position of the conduction and
valence band edges of WO3 fits the oxidation potential for O2 evolution but not
the reduction potential for H2 evolution, a positive shift of both edges would be
highly beneficial for one-photon water splitting. Calculations indicate that such
an effect can be obtained by W substitution with larger metal cations such as Hf
[2].
The second examples is defective WO3-x which is well-known for its
electrochromic properties above a certain degree of oxygen deficiency. The
origin of the electrochromic effect in WO3 is, however, still an open issue. We
propose [3] a rationalization based on a charge state variation of the oxygen
vacancy defects and we also show that these present rather anisotropic
properties.
The third example is a catalytic system based on (WO3)3 clusters deposited on
the rutile (110) TiO2 surface which is found to catalyze the formaldehyde
polymerization reaction at very low temperatures. We propose [4] a novel
radical reaction path with very low activation barriers which is triggered by the
presence of extra electrons on the (WO3)3 clusters as induced by a defective
TiO2 support.
[1] F. Wang, C. Di Valentin, G. Pacchioni, J. Phys. Chem. C 2012, 116, 8901.
[2] F. Wang, C. Di Valentin, G. Pacchioni, ChemCatChem 2012, 4, 476.
[3] F. Wang, C. Di Valentin, G. Pacchioni, Phys. Rev. B 2011, 84, 073103.
[4] C. Di Valentin, M. Rosa, G. Pacchioni, J. Am. Chem. Soc. 2012, ASAP.
75
COMPETITIVE SOLVATION OF K+ BY C6H6 AND H2O IN THE
K+-(C6H6)n-(H2O)m (n=1-4; m= 1-6) AGGREGATES.
Noelia Faginas Lago,a M. Albertíb
a
b
Dipartimento di Chimica, Università di Perugia, Perugia (Italy)
IQTCUB, DepartamentdeQuíımica Física,Universitat de Barcelona, Barcelona (Spain)
The competitive solvation of the potassium ion by benzene and water is
investigated at molecular level by means of Molecular Dynamics simulations on
the K+-(C6H6)n-(H2O)m (n=1-4; m=1-6) ionic aggregates. The preference of K+
to bind (C6H6) or (H2O) is investigated in the range of temperatures in which
isomerization process are likely by adding water and benzene to the K+-(C6H6)n
and K+-(H2O)m aggregates, respectively. Hydrogen bonds and the π-hydrogen
bond, in spite of their weakness with respect to the K+-π and K+-(H2O)
interactions, play an important role in stabilizing different isomers, thus favoring
isomerization processes. Accordingly with experimental information it has been
found that K+ bind preferably (C6H6) better than (H2O) and that the
fragmentation of (C6H6) is only observed for aggregates containing four
molecules of benzene
Fig.1 Two dimensional map of the probability density of the water molecules
drown as a plane parallel to that of the aromatic ring for the K+-(C6H6)n-(H2O)m
76
COMPUTATIONAL APPROACHES EMPLOYED IN THE
SusFuelCat PROJECT
Francesco Ferrante, Nerina Armata, Remedios Cortese, Fabrizio Lo Celso,
Antonio Prestianni, Dario Duca
Dipartimento di Fisica e Chimica dell’Università,
viale delle Scienze Ed. 17, I-90128 Palermo
Aim of the FP7 EU SusFuelCat project [1] is the
biomass conversion for sustainable green–fuel
production, to reduce the reliance of Europe on fossil
fuel and to provide environmentally friendly energy.
Aqueous phase reforming (APR) is one of the most
competitive ways for the production of liquid and
gaseous fuels from biomass. APR enables processing of
wet biomass resources without energy intensive drying
and additional hydrogen production from water by the
water-gas-shift reaction. Catalysis technology is a key in
APR. Hence, the project aims at a concentration of the
European expertise in industry and academia in this
area, and more specifically the synthesis, production, optimization and further
know-how of hydrothermally stable carbon supported catalysts.
Role of the group – from the Dipartimento di Fisica e Chimica dell’Università di
Palermo – in the project concerns theoretical studies, in the field of the involved
experimental project-systems. Model calculations will focus on local
carbonaceous support properties, formation of the metal (Ni, Pt, Ru, Pd)
supported nanostructures and specific metal-metal interactions within metallic or
bimetallic (Pt-Ru) nano-clusters. Ab initio and/or DFT paradigms in the frame of
cluster approaches will be used. A selection of catalyst prepared by experimental
partners will be considered hence a selection of model catalysts will be
performed. Effects of the reaction solvent (water) on the supported metal cluster
will be studied also with the introduction of discrete water molecules. An
integrated in silico approach will be performed on the kinetics vs. structuralresults, regarding APR elementary events and reactions. In fact, the fully
atomistic QM calculations and MD simulations utilized for the description of the
structural characteristics of the carbonaceous supports and metal-containing
catalysts will be employed as starting material for the whole characterization of
the kinetic properties of the reactions in which the catalysts are involved.
[1] SusFuelCat: Sustainable fuel production by aqueous phase reforming – understanding
catalysis and hydrothermal stability of carbon supported noble metals. GA: CP-IP
310490 http://cordis.europa.eu/projects/rcn/106702_en.html.
77
CHEMICAL REACTION BETWEEN AMINO-FUNCTIONALIZED
PORPHYRIN AND CYANURIC CHLORIDE ON SILVER:
A STM/DFT STUDY
Daniel Forrer,a Marco Di Marino,b Francesco Sedona,b Mauro Sambi,b
Andrea Vittadini,a Maurizio Casarinb
a
b
Istituto di Scienze e Tecnologie Molecolari, CNR e
Dipartimento di Scienze Chimiche, Università di Padova
5,15-bis(4-aminophenyl)-10,20-diphenylporphyrin (TPP(NH2)2) reacts with
cyanuric chloride (CC) on Ag(100) at room temperature, leading to the
formation
of
5,15-bis(4-cyanamidophenyl)-10,20-diphenylporphyrin
(TPP(NHCN)2). The reaction product self-organize on the Ag(100) surface and
forms two phases, which show largely different surface density. Density
functional theory (DFT) calculations show that different intermolecular bond
types stabilize the two phases. Indeed, in the sparser network molecules interact
mainly through strong, directional hydrogen bonds, while in the denser phase
weak, non-directional van der Waals interactions dominate. The cyanamide
moiety exists in two forms related by a tauromerism. Interestingly, the each
phase is composed by one single tautomer, while the other isomer forms the
other phase. In fact, the sparser, h-bonded network promotes the formation of
the cyanamide isomer, while in the denser packing the diimide moiety is the
most stable.
78
MOLECULAR SIMULATION OF H2 AND CH4 ADSORPTION
IN POROUS DIPEPTIDE CRYSTALS
Alberto Fraccarollo,a Maurizio Cossi,a Angiolina Comotti,b Leonardo Marchesea
a
Dipartimento Scienze e Innovazione Tecnologica, Università Piemonte Orientale,
Viale T. Michel 11, 15121 Alessandria, Italy
b
Department of Materials Science, University of Milano Bicocca,
Via R. Cozzi 53, 20125 Milano, Italy
The storage and separation of important gases, such as H2, N2, CH4, and CO2, is
a challenging research field, due to the impending energy crisis and related
global pollution that are dramatic issues today [1]. The work presented here is the
result of an investigation of the adsorption properties of eight different porous
dipeptide crystals, which exhibit different pore networks. The adsorption
isotherms of H2 and CH4 were simulated using Grand Canonical Monte Carlo
method, following a previous simulation of CO2 and N2 with the same method
[2]
. The simulation were compared to experimental data where available [3]. In
order to study the influence of the pore structure on the adsorption performance,
pore size distributions, contour maps and snapshots were analysed and
visualised. Finally, the accessible volume and surface area were calculated and
compared to experimentally determined values, where available [4] to obtain an
estimation of the quality of the experimental sample prior to adsorption
measurements.
[1] Wenliang Li, Jingping Zhang, Haichao Guo, Godefroid Gahungu, J. Phys. Chem. C
2011,115, 4935–4942.
[2] Angiolina Comotti, Alberto Fraccarollo, et al., CrystEngComm, 2013, Advance Article,
DOI: 10.1039/c2ce26502h.
[3] Angiolina Comotti, Silvia Bracco, Gaetano Distefano, Piero Sozzani, Chem. Commun.
2009, 284–286.
[4] Dmitriy V. Soldatov, Igor L. Moudrakovski, Eugeny V. Grachev, John A. Ripmeester, J.
Am. Chem. Soc., 2006, 128, 6737-6744.
79
TOWARDS BULK THERMODYNAMICS VIA NONEQUILIBRIUM
METHODS: THE COMPRESSIBILITY FACTOR OF GASEOUS
METHANE AS CASE STUDY
Mirco Zerbetto, Diego Frezzato
via Marzolo 1, I-35131 Padova
In the last decade, the so-called “Work Fluctuations Theorems” have been
largely applied to build (both experimentally and numerically) free-energy
profiles of molecular systems subjected to steered transformations along some
coordinate(s) of interest [1]. In particular, the Jarzynski equality (JE) can be seen
as the archetype of these tools. In the essence, the distribution of the amount of
work, required to drive the (nonequilibrium) transformation according to a
freely chosen protocol, is employed to compute the free-energy difference
between initial and final (equilibrium) states; at the computational level, the
efficiency of the JE lays in replacing a cumbersome calculus of configurational
partition functions with simulation of few system’s trajectories in the steered
transformations.
To the best of our knowledge, up to now this nonequilibrium approach has been
focused only on single-molecule studies (complex molecular systems or supramolecular aggregates). Typical applications are encountered in biological
contexts, e.g. probing the internal energetics in proteins and in protein-ligand
complexes. Here we explore the applicability of the nonequilibrium tool to bulk
homogeneous systems where the target is the determination of an equation of
state given an estimation of the free-energy density. We adopt the gaseous
methane as case study, aiming at the construction of the profile of the
compressibility factor versus the gas pressure at fixed temperature. This goes
through the evaluation of the pressure itself from the thermodynamic derivative
of the Helmholtz free-energy. The latter is achieved by applying the JE with a
“total morphing” schedule where the bulk state is let to “chemically grow up”
from the ideal-gas state according to a prescribed protocol, which gradually
turns on the intermolecular pair-interaction potential while the molecules
explore the 3D-space via Markovian moves (a basic Monte Carlo “preferential
sampling” with periodic boundary conditions propagator was employed).
Preliminary calculations performed with a suitably parametrized Lennard-Jones
pair-potential show a good agreement with experimental data.
[1] Jarzynski, C. Annu. Rev. Condens. Matter Phys. 2011, 2, 329-351.
80
EFFECT OF TERMINAL OLIGO(ETHYLENE GLYCOL) ON THE
STRUCTURE OF ALKYLTHIOL SAMs: A MOLECULAR DYNAMICS
INVESTIGATION
Piero Gasparotto, Giulia Parisio, Alberta Ferrarini
via Marzolo 1 – 35131 Padova (Italy)
Self-assembly of organosulfur compounds to form monolayers on metal surfaces
is a spontaneous process, which has been widely exploited to modulate the
interactions of surfaces and nanoparticles. The relationship between the
chemical structure of self-assembled monolayers (SAMs), their organization and
their properties has been extensively investigated by experimental and
computational methods. However most studies have focussed on alkylthiol
monolayers and much less is known on the organization of monolayers of
different chemical nature. An important class of SAMs is represented by
oligo(ethylene glycol) (OEG) terminated alkylthiols. First proposed by Prime
and Whitesides in 1991 [1], these have become very popular because of some
peculiarities, the most important of which is protein resistance. This behaviour
has been the object of several experimental studies: some of them have pointed
out the importance of single molecule properties, like the amphiphilic character
of OEG and its conformational preferences, while others have stressed the role
of the packing density, the presence of defects and the surface coverage.
Here we present a Molecular Dynamics (MD) study of hydrated OEGterminated alkylthiol monolayers adsorbed on Au(111). We have examined
systems differing in the relative length of the alkyl and ether part of the chains
and in the density of coverage of the gold surface and we have investigated the
effects of these factors on the structural properties of the SAM. In particular we
have focussed on interplay between conformation of the chains, organization of
the monolayer and interaction with water.
[1] Prime, K. L.; Whitesides, G. M. Science 1991, 252, 1164-1167.
81
QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS
MODELLING AND PREDICTION OF ORGANIC POLLUTANTS
BEHAVIOUR IN THE ENVIRONMENT
Paola Gramatica, Stefano Cassani, Nicola Chirico,
Simona Kovarich, Ester Papa
QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of
Theoretical and Applied Sciences, University of Insubria, via J.H.Dunant 3, 2100 Varese.
The predictive modelling approach, based on the development and validation of
Quantitative Structure-Activity Relationships (QSARs), is highly useful in the
screening of chemicals that are of recognized high concern in the environment,
and also for the prioritization of compounds that haven’t experimental data or
that have not yet been synthesized. Computational chemistry is the basis of
QSAR models as the chemical structure must be carefully designed, minimized
and translated in useful numerical information through various theoretical
molecular descriptors. Some problems related to this preliminary and
fundamental input for QSAR models will be addressed in this presentation [1].
The chemometric QSAR approach is mainly focused on the rigorous validation
of the models by different validation tools to verify their predictivity, in
particular for chemicals not used during the model development (external
validation) [2]. Some examples of useful QSAR models, developed at
University of Insubria, for the prediction of the atmospheric chemical reactivity
of Volatile Organic Compounds [3], of the PBT behaviour [4] and of the soil
sorption of pesticides [5], using the proprietary software QSARINS [6] will be
presented.
[1] Gramatica, P.; Cassani, S.; Roy, P.P.; Kovarich, S.; Yap, C.W.; Papa E. Mol. Inform.
2012, 31, 817-835.
[2] Chirico, N.; Gramatica, P. J. Chem. Inf. Model. 2011, 51, 2320–2335 and 2012, 52,
2044-2058.
[3] Roy, P.P.; Kovarich, S.; Gramatica. P. J. Comput. Chem. 2011, 32, 2386-2396.
[4] Papa, E.; Gramatica, P. Green Chem. 2010, 12, 836-843.
[5] Gramatica, P.; Giani, E.; Papa, E. J. Mol. Graph. Model, 2007, 25, 755-766.
[6] Chirico, N.; Papa, E.; Kovarich, S.; Cassani, S.; Gramatica, P. QSARINS, software for
QSAR MLR model development and validation. 2012. University of Insubria, Varese,
Italy. http://www.qsar.it
82
MODELLING OF THE ELECTROOPTICAL PROPERTIES OF
LIQUID CRYSTALS: THE MOLECULAR ORIGIN OF THE
ELECTROCLINIC EFFECT
Cristina Greco, Alberta Ferrarini
Department of Chemical Sciences, University of Padova, Italy
Liquid crystals (LC) exhibit a variety of electrooptical phenomena, which are at
the basis of different applications. An intriguing example is represented by the
electroclinic (EC) effect, which is a tilt of the optical axis about an electric field,
perpendicular to the optical axis itself. It was originally observed in
macroscopically achiral smectic and nematic samples made of chiral molecules
[1], but its molecular origin remained controversial. More recently, observation
of the EC effect in a helically distorted sample of achiral molecules was
interpreted as a sign of “top-down” induced deracemization [2].
Here we present a molecular model for the EC effect. By combining a proper
account of the molecular and sample symmetry with a molecular level modeling
we can provide a consistent description of the EC effect and quantitatively
predict the material coefficients that govern this phenomenon. A detailed
molecular level description is needed, in terms of molecular geometry, electric
dipole and polarizability. In particular, a representation of the molecular
polarizability with local resolution [3] is essential in the case of the helically
distorted environment. We will present some examples and discuss the role of
the molecular and phase chirality. Interestingly, we show that molecular
chirality is not needed for the EC effect in the helical sample configuration, so
contrasting the recent claims of a deracemization mechanism.
[1] Li, Z.; Petschek, R. G.; Rosenblatt, C. Phys. Rev. Lett. 1989, 62, 796-799.
[2] Basu, R.; Pendery, J. S.; Petschek, R.G.; Lemieux, R. P.; Rosenblatt, C. Phys. Rev. Lett.
2011, 107, 237804: 1-4.
[3] Thole B.T. Chem. Phys. 1981, 59, 341-350.
83
REFINEMENT AND VALIDATION OF THE AMBER FORCE FIELD
FOR α, α DIALKYLATED PEPTIDES
Sonja Grubisic, a, b Giuseppe Brancato a , Vincenzo Barone a
a
Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
b
Center for Chemistry, IHTM, University of Belgrade,
Njegoseva 12, 11001 Belgrade, Serbia.
The popular biomolecular AMBER (ff99SB) force
field has been extended and supplemented with new
parameters for the simulations of peptides containing
cyclic α,α dialkylated residues.1 Together with the
recent set of nitroxide parameters2 this extension
allows to treat the TOAC residue (TOAC, 2,2,6,6tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic
acid) widely used as spin label in protein studies. All
the conformational minima of the Ac-Ac6C-Nme
(Ac=Acetyl, Ac6C=1-aminocyclohexaneacetic acid,
Nme=Methylamino) and Ac-TOAC-Nme dipeptides
have been examined in terms of geometry and relative
energy stability by Quantum Mechanical (QM)
computations employing an hybrid density functional
(PBE0) and for an extended training set of conformers with various folds. We
further advance simulation accuracy of Aib based peptides (Aib, alphaaminoisobutyric acid) by improving relevant parameters of original
AMBER99SB force field. Here, we used as reference data new high-level
quantum-mechanical calculations with an added empirical dispersion correction,
namely B3LYP-D. A very good agreement between QM and MM (molecular
mechanics) data has been obtained in most of the investigated properties,
including solvent effects. Molecular dynamics (MD) simulations of TOAC and
Aib based polypeptides have been carried out to validate the resulting force
field against available experimental data. The proposed force field accurately
describes the conformation and dynamical behavior of the TOAC/Aib
polypeptides in solvents with high and low polarity, in a good agreement with
experimental and QM data.
[1] Grubisic, S. ; Brancato, G; Pedone, A.; Barone, V. Phys. Chem. Chem. Phys. 2012, 14,
15308-15320.
[2] Stendardo, E. ; Pedone, A. ; Cimino, P. ; Menziani, M. C. ; Crescenzi, O. ; Barone, V.
Phys. Chem. Chem. Phys. 2010, 12, 11697-11709.
84
DIELECTRIC NLO PROPERTIES OF POLYACETYLENE
R. Dovesi,a M. Ferrabone,a M. Ferrero,a,c B. Kirtman,b
V. Lacivita,a R. Orlando,a M. Rératc
a
Università di Torino, Italy
University of Santa Barbara, USA
c
Université de Pau et des Pays de l’Adour, France
b
In the past decades, nonlinear optics (NLO) has given great impetus to the
development of laser, optical-communication and data-storage technologies.
Meanwhile, engineering at nano-length scale has caught on with the detection of
remarkable NLO properties by a number of nanomaterials, such as organic πconjugated systems (polyenes, graphene and carbon nanotubes). Electronic and
ionic contributions to the (hyper)polarizabilities of polyacetylene have been
simulated[1,2] through the Coupled-Perturbed Hartree-Fock/Kohn-Sham
computational scheme implemented in the CRYSTAL code[3].
Huge
differences are observed on the longitudinal hyperpolarizability tensor
component γL when different functionals are used: for the infinite model the
ratio between LDA and HF becomes 1010[1]. On the basis of previous
systematic comparisons including DFT, HF, Moller-Plesset (MP2) and coupled
cluster results on finite chains, we can argue that the HF results are the most
reliable for the infinite polymer. In most cases, the HF vibrational contribution is
comparable to, or larger than the corresponding static electronic contribution[2].
The effect of the basis set is also explored, being particularly important for the
non-periodic direction perpendicular to the polymer plane.
[1] V. Lacivita, M. Rérat, R. Orlando, M. Ferrero and R. Dovesi J. Chem. Phys. 2012, 136,
114101.
[2] V. Lacivita, M. Rérat, B. Kirtman, R. Orlando, M. Ferrabone and R. Dovesi J. Chem.
Phys. 2012, 137, 014103.
[3] R. Dovesi, V. R. Saunders, C. Roetti, R. Orlando, C. M. Zicovich-Wilson, F. Pascale, B.
Civalleri, K. Doll, N. M. Harrison, I. J. Bush, P. D’Arco, and M. Llunell,
CRYSTAL09 User’s Manual (University of Torino, Torino, 2009).
85
AB INITIO INVESTIGATION OF ELECTRONIC AND VIBRATIONAL
CONTRIBUTIONS TO NONLINEAR DIELECTRIC PROPERTIES
OF ICE
Mahmoud, J. Baima, S. Casassa
Dipartimento di Chimica, Università di Torino and NIS-Nanostructured Interfaces
and Surfaces-Center of Excellence, Via P. Giuria 7, 10125, Torino, Italy
The electronic and vibrational contribution to (hyper)polarizabilities for
hexagonal ordinary ice has been investigated. Calculations have been carried out
by the Finite Field Nuclear Relaxation (FF-NR) method [1], recently
implemented in the CRYSTAL code, combined with the Coupled Perturbed
Kohn-Sham (CPKS) method [2] at the B3LYP/[6-311Gdp2(f)] level for the
electronic (hyper)polarizabilities (α , β, γ ) . Through a Berry phase approach
static and electronic dielectric constants have been evaluate on different models
of ice.
The vibrational (ionic) contribution to the nonlinear optical properties have been
calculated by the FF-NR method on the non periodic direction for slabs of ice
with a space group Pna21 with increasing thickness, and by extrapolating these
values, the vibrational contribution to (hyper)polarizabilities can be obtained for
the periodic system. The correlation between the dielectric properties and the
different structures of ice have been observed.
[1] D. M. Bishop , M. Hasan, and B. Kirtman, J. Chem. Phys. 1995, 103, 4157.
[2] M. Ferrero, M. Rérat, R. Orlando, and R. Dovesi, J. Comput. Chem. 2008, 29, 1450.
86
ELECTRONIC PROPERTIES OF H2Pc AND CuPc FILMS:
AN EXPERIMENTAL AND THEORETICAL STUDY
Giulia Mangione,a Maurizio Casarin,a Roberto Verucchi,b Marco Nardib,c
a
Dipartimento di Scienze Chimiche, Università di Padova,
Via F. Marzolo 1, 35131 Padova, Italy
b
Istituto dei Materiali per l’Elettronica ed il Magnetismo, sezione FBK di Trento,
IMEM–CNR, Via alla Cascata 56/C – Povo, 38123, Italy
c
Institut fur Physik, Humboldt-Universität zu Berlin,
Newtonstrasse 15, 12489 Berlin, Germany
Films of phthalocyanine (H2Pc) and of its open-shell copper complex (CuPc)
deposited on amorphous gold have been studied by combining the outcomes of
several synchrotron based spectroscopic tools (X-ray photoelectron
spectroscopy (XPS), UV photoelectron spectroscopy (UPS) and near-edge X-ray
absorption fine structure spectroscopy (NEXAFS)) with the results of density
functional theory (DFT) calculations. The assignment of experimental evidences
has been guided by the results of DFT and time dependent DFT (TDDFT)
numerical experiments carried out on the isolated molecules. With specific
reference to CuPc NEXAFS data collected at the N K-edge, they have been
assigned by using the open-shell TDDFT1 in the framework of the zeroth order
regular approximation (ZORA) scalar relativistic approach. Besides the good
agreement between theory and experiment, the combined use of NEXAFS data
and DFT/TDDFT outcomes ultimately testified the significant ionic contribution
characterizing the Cu–Pc interaction.
[1] Wang, F.; Ziegler, T. Mol. Phys. 2004, 102, 2585-2595.
87
COHESIVE ENERGY OF MOLECULAR CRYSTALS THROUGH AB
INITIO POST-SCF HYBRID METHODS
Lorenzo Maschio,a Bartolomeo Civalleri,a Kamal Sharkas, b
Julien Toulouse, b Andreas Savin b
a
Dipartimento di Chimica, and Centre of Excellence NIS (Nanostructured Interfaces and
Surfaces), Università di Torino, via Giuria 5, I-10125 Torino (Italy)
b
Laboratoire de Chimie Théorique, Université Pierre et Marie Curie and
CNRS, 75005 Paris, France
A proper quantitative evaluation of intermolecular interaction energies is a
prerequisite for an understanding of molecular aggregation modes in condensed
phases, and hence for prediction and control of structural, thermodynamic, and
physical properties of materials. Recently, quantum chemical methods have
advanced to the point that cohesion energies of elementary molecular aggregates
are more easily calculated than measured,[1] and, in general, molecular
modeling is nowadays accepted and even widely encouraged as a complement,
and in some cases even a substitute, of expensive experimental investigation.
In this contribution we present the adaptation to periodic crystals of hybrid
functionals combining Hartree-Fock exchange and second-order Møller-Plesset
correlation with a semilocal exchange-correlation density functional.[2]
Cohesive energies have been computed of a set of benchmark molecular
crystals. DFT calculations with the CRYSTAL program (www.crystal.unito.it)
are combined with the Local-MP2 method[3] implemented in CRYSCOR
(www.cryscor.unito.it). Thanks to the use of density-fitting techniques for the
fast evaluation of electron repulsion integrals and efficient parallelization,[4] the
overall cost is manageable even for routine calculations, and significantly
reduces the steep basis set dependence of the MP2 method alone.
[1] (a) L. Maschio, B. Civalleri, P. Ugliengo, A. Gavezzotti, J Phys Chem A. 2011, 115(41);
(b) L. Maschio, D. Usvyat, B. Civalleri, CrystEngComm 2010, 12, 2429.
[2] K. Sharkas, J. Toulouse, and A. Savin, J. Chem. Phys. 2011, 134, 064113.
[3] C. Pisani, M. Schütz, S. Casassa, D. Usvyat, L. Maschio, M. Lorenz, and A. Erba, Phys.
Chem. Chem. Phys., 2012, 14, 7615.
[4] (a) L. Maschio, D. Usvyat, F. R. Manby, S. Casassa, C. Pisani, and M. Schütz, Phys. Rev.
B 2007, 76, 075101; (b) L. Maschio and D. Usvyat, Phys. Rev. B 2008, 78, 073102; (c)
L. Maschio, J. Chem. Theory Comput. 2011, 7, 2818.
88
AB INITIO ANALYTICAL INFRARED AND RAMAN INTENSITIES
FOR PERIODIC SYSTEMS THROUGH A CPHF/KS METHOD
Lorenzo Maschio,a Bernard Kirtman,b Michel Rérat,c
Roberto Orlando,a Roberto Dovesi a
a
Dipartimento di Chimica, and Centre of Excellence NIS (Nanostructured Interfaces and
Surfaces), Università di Torino, via Giuria 5, I-10125 Torino (Italy)
b
Department of Chemistry and Biochemistry, University of California,
Santa Barbara, California 93106, USA
c
Equipe de Chimie Physique, Universitè de Pau, 64000 Pau, France
The theoretical simulation of the infrared (IR) and Raman vibrational spectra of
crystalline materials can be an extremely powerful tool to support and
complement the analysis of experimental data. In this connection it is of great
importance not only to determine the position of the absorption peaks, i.e. the
frequency of vibrational modes, but also the corresponding peak intensities.
Periodic codes that allow one to compute IR or Raman intensities mainly adopt
a density functional theory (DFT) CPKS approach together with a plane wave
basis set calculation.[1] Although there are previous calculations in the literature
that use atom-centered gaussian type orbitals (GTOs) as a basis set,
implementations of IR intensities in general purpose electronic structure
programs have been often limited to systems with one-dimensional
periodicity,[2] and we are not aware of any implementation of Raman intensities
for crystals adopting GTOs.
In this contribution a fully analytical formulation will be presented that allows to
compute the IR[3] and Raman intensities of crystalline periodic systems, as
recently implemented in the CRYSTAL program, which uses a local Gaussian
type basis set. The formalism is based on the combination of energy gradients of
the integrals with a Coupled Perturbed Hartree-Fock/Kohn Sham (CPHF/KS)
scheme [4] for the response of the density with respect to the electric field. It
avoids numerical differentiation with respect to wave vectors and with respect to
atomic coordinates. No perturbation equations for the atomic displacements
need to be solved. Several tests have been carried out to verify numerical
stability, consistency in one, two and three dimensions, and applicability to large
unit cells.
[1] S. Baroni, S. de Gironcoli, A. Dal Corso, P. Giannozzi, Rev. Mod. Phys. 2001, 73, 515.
[2] A. Izmaylov and G. Scuseria, Phys. Rev. B 2008, 77, 165131.
[3] L. Maschio, B. Kirtman, R. Orlando and M. Rérat, J. Chem. Phys. 2012, 137, 204113
[4] M. Ferrero; M. Rérat; B. Kirtman; R. Dovesi, J. Chem. Phys. 2008, 129, 244110.
89
COLLECTING AND VALIDATING LDHA CONFORMATIONS FOR
AN ENSEMBLE-BASED VIRTUAL SCREENING
Rosa Buonfiglio,a Maria Ferraro,a Federico Falchi,a Andrea Cavalli,a,b
Matteo Masetti,a Maurizio Recanatinia
a
Department of Pharmacy and Biotechnology, University of Bologna,
Via Belmeloro 6, I-40126, Bologna.
b
Department of Drug Discovery and Development, Istituto Italiano di Tecnologia,
Via Morego 30, I-16163 Genova.
Human lactate dehydrogenase (LDH; EC 1.1.27) is a tetrameric enzyme
responsible for the NADH dependent conversion of pyruvate to lactate. Five
isoforms of the enzyme are possible basing on the assembly of two subunits, M
and H (also known as A and B, respectively). The M4 homotetramer (or LDHA)
is mainly found in tissues such as skeletal muscle and plays a key role in
anaerobic metabolism [1]. The shift in energy production from oxidative
phosphorylation to glycolysis (Warburg effect) is considered as an adaptive
response of cancer cells to adverse hypoxic conditions typical of solid tumors.
By catalyzing glycolytic metabolism, LDHA functions as tumor promoter, and
for this reason in recent years this enzyme has emerged as an anticancer target
[2].
The aim of this study is the development and validation of a computational
protocol to be used in prospect for an ensemble-based Virtual Screening in
search for novel LDHA inhibitors. In particular, 1) the large scale rearrangement
of a 12 aa-long loop (which is known to be involved in substrate recognition)
was sampled by means of the hybrid-REMD method [3], and 2) the ensemble of
resulting conformations was analyzed by combining network and cluster
analysis. Finally, 3) the best ranked conformations were validated by their
ability to discriminate active compounds versus decoys generated by the DUD-E
database [4], and active versus inactive compounds taken from the BindingDB
[5].
[1]. Granchi, C.; Bertini, M.; Macchia, M.; Minutolo, F. Curr. Med. Chem. 2010, 17, 672697.
[2] Le, A.; Cooper, C.M; Gouw, A.M.; Dinavahi, R.; Maitra, A.; Deck, L.M.; Royer, R.E.;
Vander Jagt, D.L.; Semenza, G.L.; Dang, C.V. Proc. Natl. Acad. Sci. USA 2010, 107,
2037-2042.
[3] Okur, A.; Wickstrom, L.; Layten, M.; Geney, R.; Song, K.; Hornak, V.; Simmerling C. J.
Chem. Theory Comput. 2006, 2, 420–433.
[4] Huang, N.; Shoichet, B.K.; Irwin, J.J. J. Med. Chem. 2006, 49, 6789–6801.
[5] Böde, C.; Kovács, I.A.; Szalayb, M.S.; Palotaib, R.; Korcsmárosb, T.; Csermely, P. FEBS
Lett. 2007, 581, 2776-2782.
90
MOLECULAR DYNAMICS OF MACROMOLECULAR SYSTEMS
IN LIPID BILAYERS
Roberta Galeazzi,a Luca Massaccesi, a Giovanna Mobbili, a Michela Pisanib
a
Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche,
via Brecce Bianche, Ancona, Italy
b
S.I.M.A.U., Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy
The accurate atomistic knowledge of the structure and dynamics of membranes
has become in the last decade a new challenge due to its peculiar fluid character
under physiological conditions, and to the lack of experimental data that are
directly interpretable in terms of positions and motions of atoms.[1]
Furthermore, the availability of high performance parallel computing has
opened new ways to study lipid bilayers in atomic detail and thus full atom
molecular dynamics simulations are able to compute a detailed picture of
structure and dynamics of membranes [2].
In this study we presents our results in this field of research, focusing both to the
characterization of membrane receptors in POPC bilayers and to the structural
and dynamics picture of DOPC based mixed composition lipid bilayers.
[1] D.P. Tieleman, S.J. Marrink, H.J.C. Berendsen, Biochimica et Biophysica Acta 1997,
1331, 235–270.
[2] S.E.Feller, “Computational Modeling of Membrane Bilayers”, Current Topics in
Membrane, Volume 60, 2008, Elsevier edition.
.
91
THE LIPID BILAYER PERMEABILITY OF MOLECULAR SOLUTES:
BEYOND THE STANDARD SOLUBILITY-DIFFUSION MODEL
Giulia Parisio, Alberta Ferrarini
via Marzolo 1 – 35131 Padova (Italy)
Besides active and mediated transport processes, small solutes and drug-like
molecules can permeate the lipid matrix of biological membranes by a diffusion
process driven by a concentration gradient between the water regions at the two
membrane sides. The solubility-diffusion (SD) model originally proposed in
1974 relates the membrane permeability coefficient of a solute to its local
partition and diffusion coefficient in the heterogeneous environment of the lipid
bilayer.[1] In 1994 a computational method based on this model was proposed,
which has become the standard approach for the calculation of permeability
coefficients from Molecular Dynamics simulations.[2] Intrinsic to this approach
is the reduction of permeation to an effective translational process, where any
other degree of freedom of the permeant molecule is assumed to be irrelevant.
Here we present a revision of the SD model of membrane permeability and
propose a more general approach, which goes beyond the usual approximations.
The theory is recast in the general framework of a roto-translational FokkerPlanck equation, and the classical SD expression for permeability is recovered
when the permeation rate is determined by solute translation. A solution of the
problem is achieved by describing the global kinetics of translocation in terms of
transitions between adjacent free energy minima.[3] The expression for the
permeability coefficient, in terms of the rates of the transitions along all the
possible translocation paths, is rationalized within discrete path sampling
theory.[4] Selected examples illustrate the multi-dimensional approach
compared to the standard mono-dimensional approximation.
[1] Diamond, J. M.; Szabo, G.; Katz, Y. J. Membr. Biol. 1974, 17, 148-152.
[2] Marrink, S.-J.; Berendsen, H.J.C. J. Phys. Chem. 1994, 98, 4155-4168.
[3] Parisio, G.; Sperotto, M. M.; Ferrarini, A. J. Am. Chem. Soc. 2012, 134, 12198-12208.
[4] Wales, D. J. Mol. Phys. 2002, 100, 3285-3305.
92
SMOOTH FILLING OF THE SOLVENT-EXCLUDING VOLUME
WITH SPHERES
Christian Silvio Pomelli
Dipartimento di Farmacia – Università di Pisa, Via Bonanno 33, 56126 Pisa, Italy.
Email:[email protected]
The solvent-excluding volume is the portion of space outside the van der Walls
volume that is inaccessible by a spherical solvent probe. Thus volume is usually
described using MSDOT [1] or GEPOL [2] algorithms. However both are
unable to produce a continuous and differentiable description of the solventexcluding volume and surface in terms of a collection of simple geometrical
objects. This fact leads to numerical artefacts and catastrophes when we deal
with non-rigid molecules (like in automated geometry optimization procedures).
The method proposed in this contribution uses a different strategy based on:
The decomposition of the solvent-excluding volume
in contributions related to pairs and triples of atoms
[3].
The filling of these contributions with fixed radii
auxiliary (non-atomic) spheres.
A smoothly disposal of the auxiliary spheres that are
not longer useful.
The resulting set of auxiliary spheres is continuous
and differentiable with respect the molecular
geometry.
[1] M. L. Connolly, Science 1983, 221, 709–713.
[2] J. L. Pascual-Ahuir and E. Silla J. Comp. Chem. 1990, 11, 1047-1060.
[3] C.S. Pomelli and J. Tomasi J. Comp. Chem. 1998, 19, 1758-1776.
93
THEORETICAL STUDY OF THE PHOTOIONIZATION
CROSS SECTIONS OF METALLOCENES
P. Decleva, A. Ponzi
Dipartimento di Scienze Chimiche, Università di Trieste,
via L. Giorgieri 1, 34127 Trieste, Italy
Strong oscillations in molecular photoemission cross sections, which persist up
to hundreds of eV above threshold, have been first detected in C60, both in the
solid state and gas phase. In the course of a theoretical investigation into
photoemission from transition metal sandwiches, the same phenomenon has
been uncovered in Magnesium Cyclopentadienyl (MgCp2) [1].
While it was assumed that photoionization profiles were essentially unstructured
beyond some 100 eV above threshold, there is mounting evidence of notable
structures which persist at high energies.
The present work concerns the study of high energy structures in the
photoionization of a series of metallocenes.
The simulation approach, based on an accurate solution of the scattering
problem in a Density Functional framework, provides excellent reproduction of
the MgCp2 features. The computational approach utilizes a discretization of both
bound and continuum functions in a multicenter basis of B-spline functions
times spherical harmonics [2, 3].
The two outermost valence ionizations of MgCp2, HOMO and HOMO-1,
corresponding to the in-phase and out-of-phase combinations of the highest p
orbitals of the cyclopentadienyl rings, have been studied. The results obtained
are compared to the analogous results for MgCp*2 and BeCp*2.
The theoretical data show that the features of photoionization cross sections are
dependent on the electronic effects (the presence of methyl groups determines
different cross section profiles for MgCp and MgCp*2) and on the structural
effects, related in our study to the different values of the metal –
cyclopentadienyl ring distance.
It appears that long range oscillations in molecular photoemission cross sections
are a general phenomenon, which can convey important information on the
geometric and electronic structure of the target.
[1] Decleva, P.; Fronzoni, G.; Stener, M.; De Simone, M.; Coreno, M.; Green, J.C.; Hazari,
N.; Plekan, O. J. Chem. Phys. 2005, 122, 234301
[2] Stener, M.; Fronzoni, G.; Decleva, P. J. Chem. Phys. 2005, 122, 234301.
[3] Bachau, H.; Cormier, E.; Decleva, P.; Hansen, J. E.; Martin, F. Rep. Prog. Phys. 2001, 64,
1815.
94
THE SOFT X-RAY ABSORPTION SPECTRUM
OF THE ALLYL FREE RADICAL
M. Alagia,a E. Bodo,b P. Decleva,c S. Falcinelli,d A. Ponzi,c
R. Richter,e S. Stranges a,b
a
IOM-CNR, Laboratorio TASC, 34149 Basovizza, Trieste, Italy
Dipartimento di Chimica, Università degli studi di Roma “La Sapienza”,
piazzale Aldo Moro 5, 00185 Roma, Italy
c
Dipartimento di Scienze Chimiche, Università di Trieste,
via L. Giorgieri 1, 34127 Trieste, Italy
d
Dipartimento di Ingegneria Civile ed Ambientale, Università degli Studi di Perugia,
via G. Duranti 93, 06125 Perugia, Italy
e
Elettra-Sincrotrone Trieste, Area Science Park, 34149 Basovizza, Trieste, Italy
b
The allyl radical is the simplest p-conjugated electron system in organic
chemistry. This molecule is presently one of the better understood polyatomic
hydrocarbon radicals owing to its role as a model system to study chemical
dynamics of radicals. [1]
The present work is therefore aiming at reporting the first XAS of this radical
and providing a detailed spectral assignment by means of a joint experimental
and theoretical investigation.
A supersonic He seeded beam of hyperthermal allyl radicals was crossed by a
high resolution synchrotron radiation (SR) in the focus of a 3D ion momentum
imaging time-of-flight (TOF) spectrometer to investigate the soft X-ray
absorption and fragmentation processes. The XAS, recorded as Total-Ion-Yield
(TIY), is dominated by C1s electron excitations from either the central carbon
atom, CC, or the two terminal carbon atoms, CT, to the frontier orbitals, the
semi-occupied-molecular-orbital (SOMO) and the lowest-unoccupiedmolecular-orbital (LUMO).
The number of transitions and their excitation energies and oscillator strengths
are properly described by ab initio calculations performed at the CASSCF level.
The failure of the one electron description of the XAS of the open shell radical
and the required MCSCF approach emphasized the importance of the multireference nature of the corehole states of the allyl molecule.
The lowest lying core excitation of the allyl radical displays a rich vibrational
structure with sharp features in the experimental XAS. In order to analyze these
spectral features, we have used the method FC-Classes, developed by Santoro at
al. [2], to compute the vibronic structure of the optical transition. The main
features of this vibrational structure have been explained in terms of excitation
of the CH2 twist mode and the stretching of the two C–H bonds of this group.
[1] Fischer, I.; Chen, P.; J. Phys. Chem. A, 2002, 106, 4291.
[2] Santoro, F.; Improta, R.; Lami, A.; Bloino, J.; Barone, V. J. Chem. Phys., 2007, 126,
084509.
95
BENCHMARKING PERIODIC DISPERSION-CORRECTED
DFT CALCULATIONS FOR THE PREDICTION OF
MOLECULAR CRYSTAL POLYMORPHISM
Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia,
Via G. Campi 183, 41125 Modena, Italy
Periodic Density Functional Theory (DFT) calculations employing the PBE,
PBE0 and B3LYP functionals coupled with different dispersion-correction
schemes (-D and –TS) have been applied to the para-diiodobenzene (p-DIB)
molecular crystal in order to determine how
they perform in reproducing the energetic and
crystal geometry of its two well known
polymorphs. Our results [1] showed that, when
properly
corrected,
DFT
calculations
successfully predict the relative stability of the
α (Fig.1) and β phases at zero temperature, in
good agreement with Diffusion Monte-Carlo (DMC) calculations [2]. Among
the two dispersion corrections employed, the recently proposed Tkatchenko and
Scheffler (TS) scheme [3] performs much better than the original Grimme
scheme (D) [4]. This is imputable to the accurate nonempirical method used to
obtain the dispersion coefficients in the former
approach.
We are currently benchmarking the TS scheme
also against a polar system, such as the oxalyl
dihydrazide (Fig.2). This simple molecule
gives rise to five different phases, in which the
competition of intermolecular H-bond and
dispersive interactions makes the prediction of
the relative stability very challenging. The TS scheme leads to a nice agreement
with experiment both for structures and thermodynamics.
The TS and other analogous models for dispersion-correction are still not
commonly used in computational chemistry but the results reported in literature
denote the accuracy of such methods to describe long-range interactions.
In our opinion, they can play a fundamental role to better understand the
chemical and physical nature of weak interactions – not only in the field of
molecular crystals – opening a new era for the design and the prediction of
increasingly complex systems, as requested from the market.
96
[1] Pedone A.; Presti D.; Menziani M.C.; Chem. Phys. Lett. 2012, 541, 12-15.
[2] Hongo K.; Watson M. A.; Sànchez-Carrera R. S.; Iitaka T.; Aspuru-Guzik A.; J. Phys.
Chem. Lett. 2010, 1, 1789.
[3] Tkatchenko A.; Scheffler M.; Phys. Rev. Lett. 2009, 102, 073005.
[4] Grimme S.; J. Comput. Chem. 2006, 27, 1787.
97
FROM PHENYL CHLORIDES TO α,n-DIDEHYDROTOLUENES
(α
α,n-DHTs) VIA PHENYL CATIONS. A CASSCF INVESTIGATION
Davide Ravelli, Stefano Protti, Maurizio Fagnoni, Angelo Albini§
PhotoGreen Lab, Department of Chemistry, University of Pavia,
Viale Taramelli 12, 27100 Pavia, Italy. Fax: +39 0382 987323; Tel: +39 0382 987316
E-mail:[email protected], website: www.unipv.it/photochem
We recently reported that irradiation of the three isomeric (nchlorobenzyl)trimethylsilanes in methanol-water opened a novel access (by a
double elimination process) to the corresponding didehydrotoluenes (α,n-DHTs;
see Scheme, left part).[1]
.
CH 2SiMe3
CH 2SiMe3
CH2
Only the α,3-DHTs were
∆
CH2
hν -Cl.+
previously generated in
(hν)
+
-SiMe
3
Protic
.
.
solution through the Myers- Cl
Solvent
Saito
protocol
(the
α,n-DHT
cycloaromatization
of
New approach
Classical approach
enyne-allenes; see Scheme,
right part).
This finding prompted the present computational study aimed at rationalizing
the pathways involved in our approach.[2] The work revealed that efficient Inter
System Crossing (Conical Intersection located) leads to the lowest-lying triplet
state of the silanes that fragments to give the corresponding triplet aryl cations.
Delocalization of the positive charge on the benzene ring plays a key role in the
desilylation of these cations. In the case of para- and ortho- isomers, these have
a radical/radical cation character and desilylate directly to yield the
corresponding DHTs likewise in the triplet state (whereas desilylation has found
to be not favored in the corresponding singlets). On the other hand, the metaphenyl cation has a radical/radical cation structure in both spin states and thus
has available two potential accesses to the different spin states of the
corresponding DHT.
[1] Protti, S.; Ravelli, D.; Mannucci, B.; Albini, A.; Fagnoni, M. Angew. Chem. Int. Ed. 2012,
51, 8577-8580.
[2] Ravelli, D.; Protti, S.; Fagnoni, M.; Albini, A. submitted.
§
S.P. acknowledges MIUR, Rome (FIRB-2008 RBFR08J78Q) for financial support. This
work has been supported by the Fondazione Cariplo (grant no. 2011-1839). This work was
funded by the CINECA Supercomputer Center, with computer time granted by ISCRA
COMPDHT (HP10CZEHG6) project.
98
ELECTRONIC AND EPR SPECTRA OF THE SPECIES INVOLVED IN
[W10O32]4- PHOTOCATALYSIS. A RELATIVISTIC
DFT INVESTIGATION
Davide Ravelli,a Daniele Dondi,a Maurizio Fagnoni, a
Angelo Albini,a Alessandro Bagnob §
a
PhotoGreen Lab, Department of Chemistry, University of Pavia,
Viale Taramelli 12, 27100 Pavia, Italy. Fax: +39 0382 987323; Tel: +39 0382 987316.
E-mail: [email protected], website: www.unipv.it/photochem
b
Department of Chemistry, University of Padova,
via Marzolo 1, 35131 Padova, Italy.
The usefulness and versatility of polyoxometalates (POMs) in many areas of
chemistry is widely recognized in the literature. POMs are routinely
characterized by spectroscopic techniques such as NMR and IR; robust
computational methods have been developed for the prediction of these spectra,
and the electronic structure of these species has also been extensively
investigated. Conversely, their electronic and EPR spectra are comparatively
less understood and studied. This is relevant not only for their characterization
by UV-Vis spectroscopy, but – most importantly – also for understanding their
photoreactivity.
In a recent work, [1] we showed that the prediction of the UV spectrum of
POMs requires the inclusion of a solvation model and relativistic effects. GGA
functionals are not suitable for such calculations, but hybrid functionals allow
for a reliable calculation of transition energies and oscillator strengths, albeit at a
much higher computational cost. In practice, it is found that a small number of
hybrids, such as PBE0, provide optimal results. Overall such calculations turned
out to be quite demanding; nevertheless, the problem is partly alleviated by the
use of a frozen-core basis set.
On this basis, we have undertaken an investigation of the electronic spectra of
[W10O32]4- (see Figure), its mono[W10O32]5- and bi-reduced forms [W10O32]6,
by relativistic DFT calculations; we have
also modeled the EPR properties of
[W10O32]5- and its protonated forms. The
study has led to a sound understanding of
the involved transitions and the EPR spectra
thereof, as well as predictions concerning
NMR spectra. [2]
[1] Ravelli, D.; Dondi, D.; Fagnoni, M.; Albini, A.; Bagno, A. J. Comput. Chem. 2011, 32,
2983-2987.
[2] Ravelli, D.; Dondi, D.; Fagnoni, M.; Albini, A.; Bagno, A. Phys Chem. Chem. Phys.,
DOI: 10.1039/C2CP43950F.
99
NITROGEN AND CARBON K-EDGE NEXAFS SPECTRA OF MODEL
SYSTEMS FOR C5H5N ON Si(100) : A DFT SIMULATION
M. Romeo, G. Balducci, M. Stener, G. Fronzoni
Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste,
Via L. Giorgieri 1, I-34127 – TRIESTE
Adsorption of organic molecules on semiconductor surfaces has been attracting
a growing attention for its importance in emerging technologies. Fundamental
research on the covalent bonding of molecules with the surface can provide
useful information on the organic/semiconductor interface. The NEXAFS
spectroscopy [1] represents a powerful technique to investigate the orientation
and geometry of molecules adsorbed on surfaces and is widely used to
characterize adsorbate structures, often in concert with theoretical calculations
[2]. The computational simulation of NEXAFS spectra of such systems
represents a significant challenge both for a proper modelling of the adsorbate as
well as for the size of the system itself, which needs theoretical methods capable
to fulfill requirements of accuracy and computational economy. Here we present
a DFT-TS [3,4] simulation of the NEXAFS spectra of pyridine adsorbed on a
regular Si (100) – 2x2 surface by considering several adsorption models [5,6].
The models have been previously optimized through periodic calculations
performed with the Quantum Espresso code, then suitable finite clusters have
been cutted out from the optimized periodic structures and used for the
simulation of the angle resolved NEXAFS spectra [7] of the adsorbed molecule
by employing traditional molecular DFT techniques through the use of the ADF
code. The results show a good match with the experimental spectra and this
highlight the fact that the calculated polarized spectra can provide important
informations on specific details of the adsorbtion geometries and that the
methodology employed is reliable to describe the K-shell spectra of finite
models of such solid state problems.
100
[1] J.Stöhr – NEXAFS Spectroscopy, Springer – Verlag, 1992
[2] G. Fronzoni, G. Balducci, R. De Francesco, M. Romeo and M. Stener, J. Phys. Chem. C
2012, 116 (35), 18910–18919.
[3] John C. Slater – Advances in Quantum Chemistry, vol.6, pp. 1-92, Academic Press New
York · London, 1972.
[4] David A. Liberman – Physical Review B, Third Series, vol. 62, n. 11, pp. 6851-6853, 15
September, 2000-I.
[5] R. Coustel, N. and Witkowski, J. Phys. Chem. C 2008, 112, 14102–14107.
[6] R. Coustel, N. Witkowski et al., Phys. Rev. B 2012, 85, 035323.
[7] ADF External Utility®, a Fortran implementation to compute angle-resolved spectra from
ADF®, 2011 – source: www.archivemr.cz.cc
101
COARSE-GRAINED MD SIMULATIONS OF THE MESOMORPHIC
BEHAVIOUR OF 1-HEXADECYL-3-METHYLIMIDAZOLIUM
NITRATE
G. Saielli,a Y. Ji,b R. Shi,b G. A. Voth,c Y. Wangb
a
ITM-CNR, Unità di Padova, Via Marzolo, 1 – 35131 Padova.
b
ITP-CAS, 55 E. Zhongguancun Rd., Beijing, China
c
Department of Chemistry, 5735 S. Ellis Av., Chicago – IL (USA)
Ionic Liquid crystals (ILCs) are a new class of materials composed of typical
cation-anion combinations as usually found in ionic liquids (Ils), but exhibiting
mesomorphism similarly to liquid crystals (LCs). The prototypes of such
systems are 1-alkyl-3-methylimidazolium salts with various anions, such as Cl-,
Br-, BF4-, NO3- and alkyl chains of at least 14 carbon atoms [1].
In the present work we have used MD simulations to characterize the phase
behavior of a coarse-grained force-field (CG-FF) model initially developed for
1-alkyl-3-methylimidazolium nitrates [2], that is systems with an alkyl chain of
few carbon atoms. Moreover, only the isotropic liquid phase (the only one
exhibited by the short chain imidazolium Ils, besides the crystal phase) was
considered in the parameterization of the CG-FF model.
For [C16mim][NO3] the ionic smectic phase has been indentified between 500
and 560 K [3]. We have characterized the structure and order parameters of the
three phases observed, the crystal phase, the smectic A phase and the isotropic
phase and compared with experimental data. Moreover, we have analyzed in
detail the dynamics of cations and anions in the SmA phase and compared the
results with the known behavior of pure LCs, LCs mixtures, which may share
with ILCs an alternation of layers, and lyotropic liquid crystals which also share
with ILCs a layered lamellar phase with alternating hydrophobic and charged
regions [4].
Finally we have investigated the effect of the chain length on the relative weight
of electrostatic vs van der Waals interactions through a properly defined
heterogeneity order parameter (HOP) finding a discontinuity for C14 carbon
chains, in remarkable agreement with the experimental observations of the
appearance of a LC phase in imidazolium salts [5].
[1]
Bradley,A.E.; Hardacre, C.; Holbrey, J.D.; Johnston, S.; McMath,
Nieuwenhuyzen, M. Chem. Mater. 2000, 14, 629.
[2] Wang, Y.; Feng, S.; Voth, G.A. J. Chem. Theory Comput. 2009, 5, 1091.
[3] Saielli, G. Soft Matter 2012, 8, 10279.
[4] Saielli, G.; Voth, G.A.; Wang, Y. submitted
[5] Ji, Y.; Shi, R.; Wang, Y.; Saielli, G. J. Phys. Chem. B 2013, 117, on-line.
102
S.E.J.;
RELATIVISTIC DFT CALCULATIONS OF XENON NMR
PARAMETERS IN VAN DER WAALS SYSTEMS
G. Saielli,a A. Bagnob
a
b
ITM-CNR, Unità di Padova, Via Marzolo, 1 – 35131 Padova.
Dipartimento di Scienze Chimiche, Via Marzolo, 1 – 35131 Padova.
Relativistic DFT methods have proven to be a valuable aid in the prediction and
interpretation of NMR data of heavy nuclei. In this contribution we will discuss
two recent results concerning the well-known NMR probe 129Xe where weak
non-covalent interactions played a fundamental role. The first example is that of
xenon encapsulated in a cryptophane, 1, which undergoes a dramatic deshielding
upon permetallation of the cryptophane, 2, see Figure 1a). The relative ∆δexp for
129
Xe inside the cryptophane, is 277 ppm. Relativistic ZORA-DFT calculations
have allowed to disentangle the various contributions to the chemical shift
variation due to solvent, charge redistribution and spin-orbit coupling and the
calculated ∆δcalc of 281 ppm, is in remarkable agreement with the experiments.
The second example concerns the spin-spin coupling between unbound spins,
that is van der Waals complexes. ZORA-DFT calculations of the coupling
constant between 129Xe and 1H of pentane, in structures obtained from snapshots
of a classical MD simulation (see Figure 1b) of a xenon-pentane mixture,
predicted the existence of an average through-space spin-spin coupling
Jcalc(129Xe,1H) of −3.2 Hz. This has been confirmed by SQUID NMR
experiments, Jexp(129Xe,1H) = −2.7 ± 0.6.
a)
b)
[2] Bagno, A.; Saielli, G. Chem. Eur. J. 2012, 18, 7341-7345.
[1] Ledbetter, M.; Saielli, G.; Bagno, A.; Tran, N.; Romalis, M. Proc. Natl. Acad. Sci. USA
2012, 109, 12393-12397.
103
ORBITAL RELAXED DENSITY MATRIX AT LOCAL MP2 LEVEL
FOR PERIODIC SYSTEMS: FORMAL ASPECTS AND
IMPLEMENTATION
Simone Salustro, Lorenzo Maschio
Dipartimento di Chimica, Università degli Studi di Torino,
via P. Giuria 5, I-10125 Torino (Italy)
In this poster an orbital relaxed density matrix formalism for periodic systems
will be presented. The generic quantum mechanical wavefunction is a very huge
object that gives us, with respect of its dimension, just few fragments of
information about the system of interest. Nevertheless, using the wavefunction
itself as starting point, it is possible to define a simpler object that leads to the
same information: the density matrix. Treating the electron correlation as a
perturbation of the Hartree-Fock description, its effects can be taken into
account. CRYSCOR[1] is an ab initio software capable to describe crystalline
solids at a correlated level, exploiting the HF wavefunction provided by
CRYSTAL[2]. In particular, CRYSCOR implements the MP2 post-HF method
within the Saebø-Pulay local[3] approach. Since the MP2 method is not a
variational theory, Lagrangian techniques[4], that have been quite recently
developed for molecules[5], must be used in order to obtain the expression of
the correction to the HF density matrix.
[1] Pisani, C.; Schütz, M.; Casassa, S.; Usvyat, D.; Maschio, L.; Lorenz, M.; Erba, A., Phys.
Chem. Chem. Phys., 2012, 14, 7615.
[2] Dovesi, R.; Orlando, R.; Civalleri, B.; Roetti, C.; Saunders, V.R.; Zicovich-Wilson, C.M.,
Z. Kristallogr. 2005, 220, 571–573.
[3] Pulay, P.; Saebø S.; Theor. Chim. Acta 1986, 69, 357.
[4] Usvyat, D.; Schütz, M. J. Phys.: Conf. Ser. 2008, 117, 012027.
[5] Helgaker, T.; Jørgensen, P.; Olsen, J. Molecular Electronic-Structure Theory, Wiley,
2000.
104
DEVELOPMENT OF A RELIABLE FORCE FIELD FOR CLASSICAL
MD SIMULATIONS IN ALUMINOSILICATES, ENABLING
FAST PARALLEL COMPUTATIONS
Andrea Gabrieli, Marco Sant, Pierfranco Demontis, Giuseppe B. Suffritti
Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari,
via Vienna 2, 07100 Sassari, Italy, email: [email protected]
The development of a new force field for fast molecular dynamics simulations in
flexible aluminosilicates is presented [1]. This force field is in CHARMM
functional form. As initial guess, the parameters are taken from previous works
of both our group [2] and other authors [3], which are subsequently optimized
by comparison with ab-initio data and experimental vibrational spectra, see Fig.
1. We validated the obtained force field checking its ability to reproduce the
crystallographic structures of silicalite and zeolites Na A, Ca A, Na Y, and Na
X.
Figure 1. IR spectra for silicalite: experimental [2] (dots), classical MD
(dashes), ab-initio (line).
This new force field can be exploited within the most widespread computational
packages, allowing the execution of large-scale simulations in a parallel
environment.
[1] Gabrieli, A. ; Sant, M. ; Demontis, P. ; Suffritti, G. B. J. Phys. Chem. C 2013, 117, 503509.
[2] Demontis, P.; Suffritti, G. B.; Bordiga, S.; Buzzoni, R. J. Chem. Soc., Faraday Trans.
1995, 91, 525-533.
[3] Nicholas, J. B.; Hopfinger, A. J.; Trouw, F. R.; Iton, L. E. J. Am. Chem. Soc. 1991, 113,
4792-4800.
105
A GENERAL ALL-COORDINATES QUANTUM-DYNAMICAL
APPROACH FOR DESCRIBING THE VIBRONIC LINESHAPE OF
ELECTRONIC CIRCULAR DICHROISM SPECTRA
IN EXCITON-COUPLED DIMERS
Fabrizio Santoro
Consiglio Nazionale delle Ricerche – CNR, Istituto di Chimica dei Composti Organo
Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca,
Via G. Moruzzi 1, I-56124 Pisa, Italy
In this contribution we present a computational approach [1] to simulate the
vibronic lineshapes of absorption and ECD spectra in exciton-coupled dimers
[2]. Our method is based on a time-dependent expression of the spectra [3] that
are computed though the quantum dynamics of suitable wave packets moving on
coupled diabatic states localized on the monomers; it is general and
straightforwardly applicable when the electronic potential energy surfaces of the
monomer excitation can be described within harmonic approximation [1]. At
variance with previous theoretical treatments [4, 5], our method allows to
include the effect of all the vibrational modes of the system, accounting for
geometry displacements, frequency changes and normal-modes (Duschinsky)
mixing. This is possible exploiting a hierarchical representation of the
Hamiltonian in blocks [6], defined so that few blocks (few coordinates) describe
accurately the short-time dynamics (and hence the low- intermediate-resolution
spectra) of the full system. The application to a “dimer” of anthracene (156
normal modes) delivers absorption and ECD spectra in the region of the 1La
monomer transition in very nice agreement with the experiment [7].
Furthermore, the hierarchical representation allows the qualitative assignment of
the main vibronic features of the spectra in terms of transitions to states of welldefined “effective” vibrational modes.
[1] Padula D, Picconi D, Di Bari L, Lami A, Pescitelli G, Santoro F, J Phys Chem B
submitted.
[2] Harada, N.; Nakanishi, K.; Berova, N. In Comprehensive Chiroptical Spectroscopy;
Berova, N.; Woody, R. W.; Polavarapu, P.; Nakanishi, K., Eds.; Wiley: New York,
2012, 1, 115.
[3] Seibt, J.; Engel, V. The Journal of chemical physics 2007, 126, 074110.
[4] Pawlikowski, M.; Zgierski, M. Z. The Journal of Chemical Physics 1982, 76, 4789–4797
[5] Guthmuller, J.; Zutterman, F.; Champagne, B. The Journal of chemical physics 2009,
131, 154302.
[6] Picconi, D.; Lami, A.; Santoro, F. The Journal of Chemical Physics 2012, 136, 244104.
[7] Harada, N.; Takuma, Y.; Uda, H. Journal of the American Chemical Society 1978, 100,
4029.
106
PHOTOPHYSICS & PHOTOCHEMISTRY OF CARBONYL
CAROTENOIDS: A COMBINED CASSCF AND TD-DFT STUDY
Mireia Segado1, Francisco Jose Avila Ferrer2 , Fabrizio Santoro2 ,
Chiara Cappelli3,, Mariangela Di Donato4,5, Andrea Lapini4,
Manuela Lima4, Roberto Righini4
1
Dipartimento di Chimica e Chimica Industriale, Università di Pisa via Risorgimento, 35
I-56126 Pisa (Italy) & INSTM, UdR Pisa, Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, via Risorgimento, 35 I-56126 Pisa (Italy);
2
ICCOM-CNR, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy;
3
Dipartimento di Chimica e Chimica Industriale, Università di Pisa via Risorgimento, 35
I-56126 Pisa (Italy) & Scuola Normale Superiore Piazza dei Cavalieri, 7 I-56126 Pisa (Italy),
4
LENS (European laboratory for non linear spectroscopy)
via N. Carrara 1, 50019 Sesto Fiorentino (FI) Italy;
5
Dipartimento di Chimica ‘Ugo Schiff’, Universita’ di Firenze,
via della Lastruccia 13, 50019 Sesto Fiorentino (FI), Italy.
The aim of this work is to clarify the nature of the evolution of the first bright
electronic, the nature of low lying electronic states and elucidate the role ICT
states in apocarotenals. The study is focused on two carotenoids; trans-8’-apoβ-carotenal and trans-12’-apo-β-carotenal. The ordering of the low-lying
excited electronic states is very important to define the photochemical properties
of these carotenoids. As polyenes, if C2h symmetry is assumed in polyene
backbone, 1 Ag − symmetry is predicted for the ground state (S0) of the
carotenoid and the presence of several low lying singlet excited states including
21 Ag −,11 Bu -,11 Bu+. In last years the photophysics of carotenoids was be
described as a three-state model involving S0 , S1 (1 A− ) and S2 (1 Bu+ ). But It
is still a controversy on carotenoids containing electron withdrawing
substituents, where mesurements in different solvents show lifetime shortening
induced by solvent polarity within the possible presence of an ICT state.
Transient infrared spectroscopy (T1D-IR) and transient 2D infrared
spectroscopy (T2D-IR) are used to investigate the ultrafast excited state
relaxation dynamics. The best features for CASSCF/MS-CASPT2 and TDDFT
quantum methods are combined in order to computed and elucidate: a)
vibrational resolved absorption electronic spectra, b) nature of low lying excited
states c) equilibrium geometries and Hessians of ground and low lying excited
state states in order to analyze the geometrical and frequencies changes,
focusing on the normal modes active in the IR for the ground and excited states.
Based on this global analysis we propose a photochemical mechanism for these
systems where only 21 Ag − ,11 Bu + excited state are involved and we suggest
11 Bu + excited state as the ICT state.
107
IRON GALL INKS AS 3D COORDINATION POLYMERS.
A DFT STUDY USING PERIODIC BOUNDARY CONDITIONS
Sara Zaccaron, Marco Bortoluzzi, Renzo Ganzerla
Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia,
Dorsoduro 2137, 30123 Venezia, Italy
Iron gall inks can be prepared mixing an iron salt (usually ferrous sulfate
heptahydrate) and gallic acid (3,4,5-trihydroxybenzoic acid). Thanks to their
indelibility, these blue-black inks have been the most important writing material
in the past, widely used until the 20th century. Although, documents containing
iron gall dyes show noticeable degradation phenomena, such as browning and
embrittlement, caused by the interaction between metallo-gallate inks and
cellulose. Unfortunately, molecular structures and electronic features of iron gall
complexes are still not completely ascertained.
In the present communication we report the electronic structure of a 3D ironbased coordination polymer having formula [(Fe3L3)3-]∞ (H4L = gallic acid). It
has been studied applying DFT-based computational methods in combination
with periodic boundary conditions and plane-waves or numerical basis sets. The
model compound has been built on the basis of reported experimental structural
parameters. [1] Data regarding the ground-state spin multiplicity, the magnetic
interactions among the primitive cells, the charge and spin distributions, the
oxidation states, the frontier bands and the band gap have been computed.
Moreover, the simulation of the optical properties shows consistency between
the calculated absorption spectrum and the commonly reported spectra for iron
gall dyes, validating the model here proposed for the electronic structure of
[(Fe3L3)3-]∞,
We acknowledge the CINECA Award N. HP10CRPVUO, 2011 for the
availability of high performance computing resources and support.
[1] a) Wunderlich, C.H. Z Anorg Allg Chem. 1991, 598-599, 371. b) Wunderlich, C.H.
Restauro 1994, 100, 414. c) Zaccaron, S., Bortoluzzi, M., Ganzerla, R. Computational
studies on iron-based coordination polymers of interest in cultural heritage, Atti del
Primo Congresso Nazionale della Divisione di Chimica Teorica e Computazionale della
società Chimica Italiana, pp. 112, Pisa, 22-23 febbraio 2012. d) Zaccaron, S.,
Bortoluzzi, M., Ganzerla, R, J. Coord. Chem., Submitted. e) Zaccaron, S., Bortoluzzi,
M., Ganzerla, R, Sciences at Ca’ Foscari, Submitted.
108
INTEGRATED APPROACHES TO NMR SPIN RELAXATION IN
FLEXIBLE BIOMOLECULES: APPLICATION TO
OLIGOSACCHARIDES
Mirco Zerbetto,a Dmytro Kotsyubynskyy,a Maria Soltesova,b
Jozef Kowalewski,b Goran Widmalm,b Antonino Polimenoa
a
Dipartimento di Scienze Chimiche, Università degli Sutdi di Padova, Padova 35131, Italy
b
Department of Physical, Inorganic and Structural Chemistry, Stockholm University,
10691 Stockholm, Sweden
We address the interpretation of molecular dynamics
from nuclear magnetic resonance measurements
(NMR) of flexible molecules via stochastic modeling.
We focus our attention to the family of flexible
molecules which internal relevant dynamics, with
respect to NMR observables, is expressed in terms of
torsion angles. Thus, we deal with molecules that
from the point of view of the NMR spectroscopy can
be associated to chains of rigid fragments connected
by joints around which torsion is possible. The complete dynamics comprises
the, coupled, global tumbling and internal flexibility. Here we apply two
different approaches to the interpretation of slow dynamics of close- and openchain oligosaccharide molecules, which have a primary interest in the fields of
biology (e.g. cellular recognition) and of theoretical/computational chemistry, as
tunable case-study systems. In particular, we apply a mesoscopic two-body
approach [1, 2] to close-chain cyclodextrins and a many-body diffusive model
approach [3] to selected open-chain oligosaccharides, in which torsion angles
are explicitly taken into account. We also show that by merging the stochastic
treatment to quantum mechanical, molecular dynamics, and hydrodynamics
methods, many of the molecular properties entering the stochastic model can be
evaluated a priori leaving a very reduced set of (or even none) free parameters
to be determined by fitting.
[1] Polimeno, A.; Freed, J. H. J. Phys. Chem. 1995, 99, 10995-11006.
[2] Zerbetto, M.; Kotsyubynskyy, D.; Kowalewski, J.; Widmalm, G.; Polimeno, A. J. Phys.
Chem. B 2012, 116, 13159-13171.
[3] Kotsyubynskyy, D.; Zerbetto, M.; Soltesova, M.; Engström, O.; Pendrill, R.; Kowalewski,
J.; Widmalm, G.; Polimeno, A. J. Phys. Chem. B 2012, 116, 14541-14555.
109
SPECTROSCOPIC PROPERTIES OF THIOPHENE BASED
EUROPIUM β-DIKETONATE COMPLEXES:
A THEORETICAL STUDY
Ugo Cosentinoa, Claudio Grecoa, Giorgio Morob, Luca Bertinib,
Malgorzata Biczysko,c Vincenzo Baronec
a
Dipartimento di Scienze dell’Ambiente e del Territorio e di Scienze della Terra, Università di
Milano-Bicocca; Piazza della Scienza 1, 20126 Milano, Italy
b
Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca;
Piazza della Scienza 2, 20126 Milano, Italy
c
Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
e-mail: [email protected]
Due to their photophysical properties, Lanthanide complexes with π-conjugated
ligands can act as light antennae, and thus find applications in several
technological fields. [1]One of the most studied class of ligands is constituted by
β-diketonateligands (β-DK) in view of their noticeable emission properties due
to the effectiveness of the energy transfer (ET) from this ligand to the Ln(III)
ion. In particular, europium β-DK complexes have attracted more interest in
optoelectronic applications because of their strong and narrow red emission.
(2) Br-TTA
(1) TTA
CF3
Phen
N
S
N
O
(3) DTDK
S
O
S
O
H3C
S
CF3
Br
O
S
CF3
S
O
O
(4) MeT-TTA
O
O
Here we present the results of our theoretical investigation on the spectroscopic
properties of the Eu(TTA)3Phen (1), Eu(Br-TTA)3Phen (2), Eu(DTDK)3Phen
(3), and Eu(MeT-TTA)3Phen (4) complexes (Scheme 1 for ligand structures),
the photophysical characterization of which has been recently reported in
literature. [2]
The adiabatic transition energies from the lowest triplet states of compounds (1)(4) have been determined in CH2Cl2solution by the ∆SCF method at the DFT
theory level, using the PBE1PBE and the CAM-B3LYP hybrid functionals.
Calculations, performed with the Gaussian 09 program, were done by using for
the Europium ion a large-core quasi-relativistic effective core potential (ECP)
110
and the related [5s4p3d]-GTO valence basis set and for the ligand atoms, the 631G* basis.
As a result, the adiabatic transitions of compounds (1)-(4) calculated in solution
including ZPE corrections by the two functional well reproduce the
experimental 0-0 transitions determined from phosphorescence spectra of the
corresponding Gd3+ complexes. These results confirm the reliability of the
adopted computational procedure in calculating the lowest triplet state energy of
these complexes, a critical parameter in determining the photoluminescence
quantum yields of these systems.
[1] Bünzli, J-C. G.; Piguet, C. Chem. Soc. Rev. 2005, 34, 1048.
[2] Freund, C.; Porzio, W.; Giovanella, U.; Vignali, F.; Pasini, M.; Destri, S.; Mech, A.; Di
Pietro S.; Di Bari, L.; Mineo, P., Inorg. Chem. 2011, 50, 5417.
111
COMPUTATIONAL SPECTROSCOPY FOR SYSTEMS IN THE
CONDENSED PHASE: NICOTINE AS A TEST CASE
Franco Egidi,a Julien Bloino,a,b Chiara Cappellia,c , Vincenzo Baronea
a
b
Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
CNR, Istituto di Chimica dei Composti Organometallici, UOS di Pisa,
Via G. Moruzzi 1, 56124 Pisa, Italy
c
Via Risorgimento 35, 56126 Pisa, Italy
Reliable computations of spectroscopic parameters for flexible molecules in
condensed phases require a proper account of stereo-electronic, dynamic, and
environmental effects [1,2] if they are to be compared directly to experiment. In
the framework of last-generation density functionals, these effects can be
introduced by second order vibrational perturbation theory [4,5] coupled to
polarizable continuum models [6,7]. In this communication we present a
thorough computational spectroscopic analysis of nicotine as a test case which
includes the calculation of the NMR shieldings and spin-spin couplings, optical
rotation, infra-red and vibrational circular dichroism spectra, and raman optical
activity spectra to show the reliability and applicability of our methodology.
[1] Barone, V.; Improta, R.; Rega, N. Acc. Chem. Res. 2008, 41, 605-616.
[2] Barone, V.; Baiardi, A.; Biczysko, M.; Bloino, J.; Cappelli, C.; Lipparini, F.; Phys. Chem.
Chem. Phys. 2012, 14, 12404-12422.
[3] Barone, V. J. Phys. Chem. A 2004, 108, 4146-4150.
[4] Barone, V. J. Chem. Phys. 2005, 122, 014108.
[5] Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999-3093.
[6] Mennucci, B. WIREs Comput. Mol. Sci. 2012, 2, 386-404.
112
QUANTUM CHEMISTRY WITHOUT WAVEFUNCTIONS:
NEW PROSPECTIVES
Stefano Conte
Department of Chemistry, University of Pisa, Italy
Electron Correlation has a crucial role in modern Quantum Chemistry: the direct
calculation of the two-electron reduced density matrix (2-RDM) requires the
trasformation of the N-electron wave function to density matrix. A variational 2RDM procedure, using first-order semidefinite programming, has been shown to
capture multireference correlation effects important at non-equilibrium
geometries. The nonvariational calculation of the 2-RDM requires the contracted
Schroedinger equation. In fact the many-electron problem might be reducible to
only two electrons: the energy of any atom or molecule can be expressed as a
linear functional of the 2-RDM with only density matrix, without wave
functions, because electrons are indisinguishable with only pairwise interactions.
The 2-RDM had to be costrained to represent a many-electron density matrix:
these constraints have called N-reperesentability conditions and become known
as the N-representability problem. These 2-RDM methods have been applied in
a variety of problems including (i) the conical intersections in methylene and
bicyclobutane, (ii) the biolumniscence of fireflies, (iii) quantum phase
transitions, (iv) the study of the ground-state motion of nuclei within the BornOppenheimer approximation. These 2-RDM methods have the ability to treat
moderate-to-strong Electron Correlation in Chemistry and Physics that is
especially difficult for traditional wave functions methods.
[1] R. McWeeny, “Quantum Chemistry: the first seventy years”, Spiers Memorial Lectures,
Faraday Discussions, 135, 2007.
[2] J. Schiff, B. Poirier, “Quantum Mechanics without Wave Functions”, J. Chem. Phys.
2012, 136.
[3] D. A. Mazziotti, “Quantum Chemistry without Wave Functions”, Accounts of Chemical
Research of the ACS 2006, 39, 3.
[4] J. A. Coleman, V. I. Yukonov, “Reduced Density Matrices”, Springer-Verlag, New York,
2000.
[5] D. A. Mazziotti, “Reduced-Density-Matrix Mechanics”, Wiley, New York, 134, 2007.
[6] D. A. Mazziotti, “Two-Electron Reduced Density Matrix as the Basic Variable in ManyElectron Quantum Chemistry and Physics”, Chemical Reviews of the ACS 2011.
113
PREDICTING THE SPIN-STATE ENERGETICS AND NMR
OF IRON COMPLEXES BY DFT
Andrea Borgogno, Federico Rastrelli, Alessandro Bagno*
Department of Chemistry, University of Padova.
*[email protected]
Many transition-metal complexes can exist in different electron configurations,
leading in turn to different spin states. The most studied example is probably
that of iron(II) (d6). According to the kind of coordinated ligands, Fe(II)
complexes may exist as a singlet (S=0), triplet (S = 1) or quintet (S = 2) state.
Likewise, Fe(III) complexes (d5) can exist in the S = 1/2, S = 3/2 and S = 5/2
states. Similar situations occur also in the case of other transition metals, of
course.
The spin state of a given complex is not always straightforward to predict. Also,
when the separation between the energy of such states is small, even subtle
changes in the ligands cause a switch in the relative stability. This phenomenon
acquires a major significance whenever the spin transition can be triggered by
external factors such as temperature or light, giving rise to spin-crossover
(SCO), which is being investigated for information storage. [1]
It is therefore desirable to be able to predict and probe the spin state of such
complexes, since this capability would allow to design complexes and monitor
their properties. Here, we have applied DFT methods to the prediction of the
relative energies of the spin states of a variety of Fe(II,III,IV) complexes (Figure
1). These results are then employed for the prediction of paramagnetic NMR
spectra, which allows one to simplify the interpretation of experimental results
compromised by line broadening and paramagnetic shifts. [2] In order to achieve
this goal, a computational method that is sufficiently accurate and inexpensive
for NMR calculations [3] is required. Thus, the performance of several (GGA,
meta-GGA and hybrid) density functionals has been tested, and B3LYP* was
found to provide the best results. These results were used to compute the NMR
spectra of several Fe complexes in various spin states.
Figure 1: Examples of Fe(II) A, Fe(III) B and Fe(IV) investigated complexes.
114
[1] Halcrow M. A., Chem. Soc. Rev. 2011, 40, 4119-4142.
[2] Bertini I., Luchinat C., Parigi G., “Solution NMR of Paramagnetic Molecules
Applications to Metallobiomolecules and Models”, Elsevier, Amsterdam, 2001.
[3] Bagno A., Rastrelli F., Chem. Eur. J. 2009, 15, 7990-8004.
115
116
INDICE DEGLI AUTORI
Cavalli, A. ..................................................................... 90
Cavazzini, M................................................................. 43
Cerezo, J. ...................................................................... 61
Charpentier, T. ........................................................ 11; 32
Chirico, N. .................................................................... 82
Cinacchi, G. .................................................................. 31
Civalleri, B.................................................. 57; 71; 72; 88
Coccia, E....................................................................... 23
Coletti, C................................................................. 24; 49
Comotti, A. ................................................................... 79
Conte, S....................................................................... 113
Coriani, S. ....................................................................... 6
Cortese, R. .............................................................. 25; 77
Cosentino, U. .............................................................. 110
Cossi, M...................................................... 35; 58; 68; 79
Costa, G. ....................................................................... 26
Costantini, A. ................................................................ 37
Crestoni, M. E............................................................... 49
Curutchet, C.................................................................. 52
A
Alagia, M. ..................................................................... 95
Albanese, E. ............................................................57; 72
Albertí, M...................................................................... 76
Albini, A..................................................................98; 99
Alcaro, S........................................................................ 26
Alessio, M. .................................................................... 71
Andreussi, O.................................................................. 19
Aquilanti, V................................................................... 24
Argeri, M.................................................................35; 58
Armata, N................................................................60; 77
Artese, A. ...................................................................... 26
Avila Ferrer, F. J. ............................................45; 61; 107
B
Bagno, A. ...................................................... 99; 103; 114
Baima, J.............................................................62; 73; 86
Balducci, G.................................................................. 100
Barolo, C. ...................................................................... 58
Barone, V. ...........................................3; 22; 84; 110; 112
Baseggio, O................................................................... 63
Bernardi, A...................................................................... 4
Bertini, L. ........................................................64; 65; 110
Biancardi, A. ................................................................. 20
Biczysko, M. ............................................................... 110
Bindu Kolli, H............................................................... 31
Biver, T. ........................................................................ 20
Bloino, J. ..................................................................... 112
Bodo, E. ..................................................................21; 95
Bonačić-Koutecký, V. ................................................... 65
Bonfanti, M. .................................................................. 10
Borgogno, A................................................................ 114
Bortoluzzi, M. ............................................................. 108
Brancato, G. .................................................................. 84
Bruschi, M.........................................................36; 64; 65
Buonfiglio, R................................................................. 90
Butera, V. ...................................................................... 14
D
De Gioia, L. ...................................................... 36; 64; 65
De La Pierre, M. ..................................................... 28; 73
Decleva, P. ........................................................ 51; 94; 95
Demontis, P........................................................... 50; 105
Di Donato, M. ............................................................. 107
Di Marino, M. ............................................................... 78
Di Valentin, Cristiana ................................................... 75
Distinto, S. .................................................................... 26
Dondi, D. ...................................................................... 99
Dovesi, R. ....................................... 28; 29; 62; 73; 85; 89
Duca, D. .................................................................. 25; 77
E
Egidi, F. ...................................................................... 112
Erba, A.............................................................. 29; 57; 62
F
Faginas Lago, N............................................................ 76
Fagnoni, M.............................................................. 98; 99
Falchi, F. ....................................................................... 90
Falcinelli, S. .................................................................. 95
Fantucci, P. ....................................................... 36; 64; 65
Ferrabone, M........................................................... 29; 85
Ferrante, F......................................................... 25; 60; 77
Ferrari, A. M. .......................................................... 30; 74
Ferrarini, A. ................................................ 31; 81; 83; 92
Ferraro, M. .................................................................... 90
Ferrero, M. .................................................................... 85
Fornarini. S. .................................................................. 49
Forrer, D. ...................................................................... 78
Fortunelli, A.................................................................... 7
Fraccarollo, A. .................................................. 35; 68; 79
Frezza, E. ...................................................................... 31
Frezzato, D.................................................................... 80
Fronzoni, G. .......................................................... 63; 100
C
Calabrese, V. ................................................................. 43
Calderini, D................................................................... 24
Caminiti, R. ................................................................... 21
Cancès, E....................................................................... 39
Cantatore, V. ................................................................. 66
Canti, L. ..................................................................35; 68
Cappelli, C. .....................................................5; 107; 112
Carlotto, S. .................................................................... 70
Carnimeo, I.................................................................... 22
Carter, E. A. ............................................................41; 44
Carteret, C. .................................................................... 28
Casarin, M...............................................................78; 87
Casassa, S...................................................................... 86
Casatti, M. ..................................................................... 26
Casazza, S. .................................................................... 74
Casolo, S. ...................................................................... 10
Cassani, S. ..................................................................... 82
117
Moro, Giorgio ............................................................. 110
Muñoz-Garcia, A. B...................................................... 44
Muñoz-García, A. B...................................................... 41
Musetti, C. .................................................................... 26
G
Gabrieli, A................................................................... 105
Galeazzi, R. ................................................................... 91
Gambuzzi, E.................................................................. 32
Ganzerla, R.................................................................. 108
Gasparotto, P................................................................. 81
Giacometti, A. ............................................................... 31
Giammarino, G.............................................................. 53
Giordano, L. ................................................................. 34
Giordano, L. .................................................................. 30
Glisenti, A. .................................................................... 70
Gramatica, P.................................................................. 82
Granucci, G. .................................................................. 66
Grassi, F. .................................................................35; 58
Greco, Claudio ..........................................36; 64; 65; 110
Greco, Cristina .............................................................. 83
Grisanti, L. ................................................................... 43
Grubisic, S..................................................................... 84
Guidoni, L. .................................................................... 23
N
Nardi, M........................................................................ 87
Natile, M. M.................................................................. 70
O
Orlando, R............................................. 42; 62; 72; 85; 89
Ortuso, F. ...................................................................... 26
P
Karamanis, P. ................................................................ 73
Kirtman, B...............................................................85; 89
Kotsyubynskyy, D....................................................... 109
Kovarich, S.................................................................... 82
Kowalewski, J. ............................................................ 109
Pacchioni, G............................................................ 34; 75
Paciotti, R. .................................................................... 49
Painelli, A. .................................................................... 43
Papa, E. ......................................................................... 82
Parisio, G. ............................................................... 81; 92
Parrotta, L. .................................................................... 26
Pavone, M. .............................................................. 41; 44
Pedone, A.................................................... 11; 32; 47; 96
Persico, M. .................................................................... 66
Picconi, D. .................................................................... 45
Pisani, C........................................................................ 29
Pisani, M. ...................................................................... 91
Polimeno, A. ............................................................... 109
Pomelli, C. S. ................................................................ 93
Ponzi, A. ................................................................. 94; 95
Prada, S......................................................................... 34
Presti, D. ................................................................. 47; 96
Prestianni, A............................................................ 25; 77
Protti, S. ........................................................................ 98
L
Q
Lacivita, V..................................................................... 85
Laganà, A. ..................................................................... 37
Lami, A. ........................................................................ 45
Lapini, A. .................................................................... 107
Lazzara, G. .................................................................... 60
Lima, M....................................................................... 107
Lipparini, F.................................................................... 39
Lo Celso, F.................................................................... 77
Quici, S. ........................................................................ 43
I
Improta, R. ..............................................................45; 61
J
Ji, Y. ............................................................................ 102
K
R
Rastrelli, F................................................................... 114
Ravelli, D................................................................ 98; 99
Re, N............................................................................. 49
Recanatini, M.......................................................... 12; 90
Rérat, M. ........................................................... 62; 85; 89
Richter, R...................................................................... 95
Righini, R.................................................................... 107
Romeo, M. ............................................................ 63; 100
Rosa, M......................................................................... 75
Russo, N.................................................................. 14; 40
M
Maccioni, E. .................................................................. 26
Maday, Y....................................................................... 39
Mahmoud, A. ................................................................ 86
Mangione, G.................................................................. 87
Marchese, L.................................................35; 58; 68; 79
Marino, T. ..................................................................... 40
Martinazzo, R................................................................ 10
Marzari, N. .................................................................... 19
Maschio, L. .....................................................88; 89; 104
Masetti, M. ..............................................................12; 90
Masia, M. ...................................................................... 50
Massaccesi, L. ............................................................... 91
Mennucci, B. .................................................9; 20; 39; 52
Menziani, M. C. ..........................................11; 32; 47; 96
Milioto, S. ..................................................................... 60
Mitrić, R........................................................................ 65
Mobbili, G..................................................................... 91
Moraca, F. ..................................................................... 26
S
Saielli, G. ............................................................ 102; 103
Salustro, S. .................................................................. 104
Sambi, M....................................................................... 78
Sant, M........................................................................ 105
Santoro, F................................................ 45; 61; 106; 107
Savin, A. ....................................................................... 88
Scalmani, G................................................................... 22
Sedona, F. ..................................................................... 78
Segado, M. .................................................................. 107
Sharkas, K..................................................................... 88
Shi, R. ......................................................................... 102
118
Varsano, D. ................................................................... 23
Verucchi, R. .................................................................. 87
Viani, L. ........................................................................ 52
Villani, V. ..................................................................... 53
Vittadini, A. ...................................................... 15; 70; 78
Voth, A. ...................................................................... 102
Sicilia, E........................................................................ 14
Sissa, C.......................................................................... 43
Sissi, C. ......................................................................... 26
Soltesova, M................................................................ 109
Stamm, B....................................................................... 39
Stendardo, E. ................................................................. 61
Stener, M............................................................... 63; 100
Stranger, S..................................................................... 95
Suffritti, G. B......................................................... 50; 105
W
Wang, F......................................................................... 75
Wang, Y...................................................................... 102
Widmalm, G................................................................ 109
T
Tantardini, G. F. ............................................................ 10
Tarantelli, F................................................................... 13
Terenziani, F. ................................................................ 43
Toffoli, D. ..................................................................... 51
Toulouse, J. ................................................................... 88
Z
Zaccaron, S. ................................................................ 108
Zagotto, G. .................................................................... 26
Zampella, G. ........................................................... 64; 65
Zerbetto, M. .......................................................... 80; 109
V
Valenzano, L. ................................................................ 72
119
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degli Studi di
Scienze Chimiche
Padova
Gruppo di
Scuola
Chimica Teorica e Normale
Computazionale
Superiore
Dipartimento di
Università di
Chimica e
Chimica
Pisa
Industriale
Dipartimento di
Chimica e
Università di
Pisa
Chimica
Industriale
Università
Dipartimento di
degli Studi di
Chimica
Torino
Dipartimento di
Chimica
Dipartimento di
Chimica
Università di
Perugia
Laganà
noelia
[email protected]
Dipartimento di
chimica
Università di
Perugia
Lipparini
Filippo
[email protected]
Institut du calcul
et de la simulation
Université
Pierre et
Marie Curie
Mahmoud
Agnes Nora
[email protected]
Dipartimento di
Chimica IFM
Università di
Torino
Mangione
Giulia
[email protected]
Dipartimento di
Scienze Chimiche
Università di
Padova
[email protected]
Chimica
Farmaceutica e
Tossicologica
Università
degli studi di
Napoli
"Federico II"
Università
della Calabria
Marinelli
Luciana
Marino
Tiziana
[email protected]
Dipartimento di
Chimica e
Tecnologie
Chimiche
Martinazzo
Rocco
[email protected]
Dipartimento di
Chimica
Maschio
Lorenzo
[email protected]
Dipartimento di
Chimica
Masetti
Matteo
[email protected]
Massaccesi
Luca
[email protected]
Mennucci
Benedetta
Moro
Università
degli Studi di
Milano
Università
degli Studi di
Torino
Dipartimento di
Farmacia e
Biotecnologia
Dipartimento di
Scienze della Vita
e dell'Ambiente
Università
Politecnica
delle Marche
[email protected]
Dipartimento di
Chimica
Università di
Pisa
Giorgio
[email protected]
Dipartimento di
Biotecnologie e
Bioscienze
Università di
MilanoBicocca
Moro
Giorgio
[email protected]
Dipartimento di
Scienze Chimiche
Università di
Padova
Moro
Stefano
[email protected]
Dipartimento di
Scienze del
Farmaco
Università di
Padova
Università di
Bologna
Università di
Napoli
“Federico II”
Università
degli studi di
Padova
Munoz
Garcia
Ana Belen
[email protected]
Dipasrtimento di
Scienze Chimiche
Orian
Laura
[email protected]
Dipartimento di
Scienze Chimiche
Orlando
Roberto
[email protected]
Dipartimento di
Chimica
Università di
Torino
Pacchioni
Gianfranco
[email protected]
Dipartimento di
Scienza dei
Materiali
Università
Milano
Bicocca
125
Painelli
Anna
[email protected]
Dipartimento di
Chimica
Università di
Parma
Parisio
Giulia
[email protected]
Dipartimento di
Scienze Chimiche
Università di
Padova
Pavone
Michele
[email protected]
Dipartimento di
Scienze Chimiche
Pedone
Alfonso
[email protected]
Dipartimento di
Scienze Chimiche
e Geologiche
Picconi
David
[email protected]
Lehrstuhl fur
Theoretische
Chemie
Polimeno
Antonino
[email protected]
Dipartimento di
Scienze Chimiche
Pomelli
Christian
Silvio
[email protected]
Dipartimento di
Farmacia
Università di
Pisa
[email protected]
Dipartimento di
Scienze chimiche
e farmaceutiche
Università di
Trieste
Università di
Modena e
ReggioEmilia
Ponzi
Aurora
Università di
Napoli
“Federico II”
Università di
Modena e
Reggio
Emilia
Technische
Universitaet
Muenchen
Università
degli Studi di
Padova
Presti
Davide
[email protected]
Dipartimento di
Scienze Chimiche
e Geologiche
Ravelli
Davide
[email protected]
Dipartimento di
Chimica
Università di
Pavia
[email protected]
Dipartimento di
Farmacia
Università G.
D'Annunzio
ChietiPescara
Re
Nazzareno
Dipartimento di
Farmacia e
Biotecnologia
Dipartimento di
Scienze Chimiche
e Farmaceutiche
Istituto per la
Tecnologia delle
Membrane, Unità
di Padova
Università di
Bologna
Recanatini
Maurizio
[email protected]
Romeo
Michele
[email protected]
Saielli
Giacomo
[email protected]
Salustro
Simone
[email protected]
Dipartimento di
Chimica
Sant
Marco
[email protected]
Dipartimento di
Chimica e
Farmacia
Università
degli Studi di
Torino
Universita'
degli Studi di
Sassari
Santoro
Fabrizio
[email protected]
ICCOM
CNR
126
Università
degli Studi di
Trieste
CNR
[email protected]
Dipartimento di
Chimica e
Chimica
Industriale
Università di
Pisa
Emilia
[email protected]
Dipartimento di
Chimica
Università
della Calabria
Stener
Mauro
[email protected]
Suffritti
Giuseppe B.
[email protected]
Tantardini
Gian Franco
[email protected]
Dipartimento di
Chimica
Tarantelli
Francesco
[email protected]
Dipartimento di
Chimica
Toffoli
Daniele
[email protected]
Department of
Chemistry
Torsello
Mauro
[email protected]
Dipartimento di
Scienze Chimiche
Viani
Lucas
[email protected]
Dipartimento di
chimica e chimica
industriale
Università di
Pisa
[email protected]
Dipartimetno di
Scienze
Università
degli Studi
della
Basilicata
Segado
Centellas
Mireia
Sicilia
Villani
Vittadini
Zaccaron
Zerbetto
Vincenzo
Andrea
Sara
Mirco
[email protected]
[email protected]
[email protected]
127
Dipartimento di
Scienze Chimiche
e Farmaceutche
Dipartimento di
Chimica e
Farmacia
Istituto di Scienze
e Tecnologie
Molecolari
Dipartimento di
Scienze
Molecolari e
Nanosistemi
Dipartimento di
Scienze Chimiche
Università di
Trieste
Università
degli studi di
Sassari
Università
degli Studi di
Milano
Università di
Perugia
Middle East
Technical
University
Università
degli studi di
Padova
CNR
Università
Ca' Foscari
Venezia
Università
degli Studi di
Padova

DCTC13 II Congresso Nazionale della Divisione di Chimica Teorica

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