MOLDRAW: a program to display and manipulate molecular and crystalline structures

by Piero UGLIENGO  University of Torino - Dipartimento Chimica. Via P. Giuria 7 -10125 Torino. ITALY

MS Windows (Linux & Mac OS X) - http://www.moldraw.unito.it  

 Piero Ugliengo

 University of Torino

 Dipartimento Chimica

 Via P. Giuria 7

 10125 Torino - ITALY

 piero.ugliengo@unito.it

Main research interests:

• Computer graphics
• H-bond interactions
• ab-initio simulation of crystalline materials
• ab-initio modeling of adsorption at inorganic surfaces
• ab-initio modeling of biomaterials
• prebiotic and astro chemistry

Academic position:

• Associate professor of physical chemistry at the Dipartimento di Chimica  of the University of Torino

Selected recent publications:

• Rimola, A.; Costa, D.; Sodupe, M.; Lambert, J.-F.; Ugliengo, P. Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments. Chem. Rev. 2013, 10.1021/cr3003054.

• Delle Piane, M.; Corno, M.; Ugliengo, P. Does dispersion dominate over H-bonds in drug-surface interactions? The case of silica-based materials as excipients and drug-delivery agents. J. Chem. Theory Comput. 2013, 10.1021/ct400073s.

• Rimola, A.; Sodupe, M.; Ugliengo, P. COMPUTATIONAL STUDY OF INTERSTELLAR GLYCINE FORMATION OCCURRING AT RADICAL SURFACES OF WATER-ICE DUST PARTICLES. Astrophysical Journal 2012, 754.

• Rimola, A.; Aschi, M.; Orlando, R.; Ugliengo, P. Does Adsorption at Hydroxyapatite Surfaces Induce Peptide Folding? Insights from Large-Scale B3LYP Calculations. J. Am. Chem. Soc. 2012, 134, 10899.

• Orlando, R.; Delle Piane, M.; Bush, I. J.; Ugliengo, P.; Ferrabone, M.; Dovesi, R. A new massively parallel version of CRYSTAL for large systems on high performance computing architectures. J. Comput. Chem. 2012, 33, 2276.

• Musso, F.; Mignon, P.; Ugliengo, P.; Sodupe, M. Cooperative effects at water-crystalline silica interfaces strengthen surface silanol hydrogen bonding. An ab initio molecular dynamics study. Phys. Chem. Chem. Phys. 2012, 14, 10507.

• Lambert, J.-F.; Sodupe, M.; Ugliengo, P. Prebiotic chemistry. Chem. Soc. Rev. 2012, 41, 5373.

• Jimenez-Izal, E.; Chiatti, F.; Corno, M.; Rimola, A.; Ugliengo, P. Glycine Adsorption at Nonstoichiometric (010) Hydroxyapatite Surfaces: A B3LYP Study. J. Phys. Chem. C 2012, 116, 14561.

• Coasne, B.; Ugliengo, P. Atomistic model of micelle-templated mesoporous silicas: structural, morphological, and adsorption properties. Langmuir 2012, 28, 11131.

• Chiatti, F.; Corno, M.; Ugliengo, P. Stability of the Dipolar (001) Surface of Hydroxyapatite. J. Phys. Chem. C 2012, 116, 6108.

• Canepa, P.; Ugliengo, P.; Alfredsson, M. Elastic and Vibrational Properties of alpha- and beta-PbO. J. Phys. Chem. C 2012, 116, 21514.

• Bolis, V.; Busco, C.; Martra, G.; Bertinetti, L.; Sakhno, Y.; Ugliengo, P.; Chiatti, F.; Corno, M.; Roveri, N. Coordination chemistry of Ca sites at the surface of nanosized hydroxyapatite: interaction with H2O and CO. Philos. Trans. R. Soc. A 2012, 370, 1313.

• Rimola, A.; Sakhno, Y.; Bertinetti, L.; Lelli, M.; Martra, G.; Ugliengo, P. Toward a Surface Science Model for Biology: Glycine Adsorption on Nanohydroxyapatite with Well-Defined Surfaces. J. Phys. Chem. Lett. 2011, 2, 1390.

• Musso, F.; Ugliengo, P.; Sodupe, M. Do H-Bond Features of Silica Surfaces Affect the H2O and NH3 Adsorption? Insights from Periodic B3LYP Calculations. J. Phys. Chem. A 2011, 115, 11221.

• Maschio, L.; Civalleri, B.; Ugliengo, P.; Gavezzotti, A. Intermolecular Interaction Energies in Molecular Crystals: Comparison and Agreement of Localized Moller-Plesset 2, Dispersion-Corrected Density Functional, and Classical Empirical Two-Body Calculations. J. Phys. Chem. A 2011, 115, 11179.

• Canepa, P.; Hanson, R. M.; Ugliengo, P.; Alfredsson, M. J-ICE: a new Jmol interface for handling and visualizing crystallographic and electronic properties. J. Appl. Crystallogr. 2011, 44, 225.

• Armandi, M.; Bolis, V.; Bonelli, B.; Arean, C. O.; Ugliengo, P.; Garrone, E. Silanol-Related and Unspecific Adsorption of Molecular Ammonia on Highly Dehydrated Silica. J. Phys. Chem. C 2011, 115, 23344.

• Tosoni, S.; Civalleri, B.; Ugliengo, P. Hydrophobic Behavior of Dehydroxylated Silica Surfaces: A B3LYP Periodic Study. J. Phys. Chem. C 2010, 114, 19984.

• Rimola, A.; Sodupe, M.; Ugliengo, P. Deep-space glycine formation via Strecker-type reactions activated by ice water dust mantles. A computational approach. Phys. Chem. Chem. Phys. 2010, 12, 5285.

• Rimola, A.; Civalleri, B.; Ugliengo, P. Physisorption of aromatic organic contaminants at the surface of hydrophobic/hydrophilic silica geosorbents: a B3LYP-D modeling study. Phys. Chem. Chem. Phys. 2010, 12, 6357.

• Musso, F.; Ugliengo, P.; Solans-Monfort, X.; Sodupe, M. Periodic DFT Study of Radical Species on Crystalline Silica Surfaces. J. Phys. Chem. C 2010, 114, 16430.

• Mignon, P.; Ugliengo, P.; Sodupe, M.; Hernandez, E. R. Ab initio molecular dynamics study of the hydration of Li+, Na+ and K+ in a montmorillonite model. Influence of isomorphic substitution. Phys. Chem. Chem. Phys. 2010, 12, 688.

• Haworth, R.; Mountjoy, G.; Corno, M.; Ugliengo, P.; Newport, R. J. Probing vibrational modes in silica glass using inelastic neutron scattering with mass contrast. Phys. Rev. B 2010, 81.

• Corno, M.; Rimola, A.; Bolis, V.; Ugliengo, P. Hydroxyapatite as a key biomaterial: quantum-mechanical simulation of its surfaces in interaction with biomolecules. Phys. Chem. Chem. Phys. 2010, 12, 6309.

• Civalleri, B.; Maschio, L.; Ugliengo, P.; Zicovich-Wilson, C. M. Role of dispersive interactions in the CO adsorption on MgO(001): periodic B3LYP calculations augmented with an empirical dispersion term. Phys. Chem. Chem. Phys. 2010, 12, 6382.

• Ugliengo, P.; Zicovich-Wilson, C. M.; Tosoni, S.; Civalleri, B. Role of dispersive interactions in layered materials: a periodic B3LYP and B3LYP-D* study of Mg(OH)(2), Ca(OH)(2) and kaolinite. J. Mater. Chem. 2009, 19, 2564.

• Rimola, A.; Ugliengo, P.; Sodupe, M. Formation versus Hydrolysis of the Peptide Bond from a Quantum-mechanical Viewpoint: The Role of Mineral Surfaces and Implications for the Origin of Life. International Journal of Molecular Sciences 2009, 10, 746.

• Rimola, A.; Ugliengo, P. The role of defective silica surfaces in exogenous delivery of prebiotic compounds: clues from first principles calculations. Phys. Chem. Chem. Phys. 2009, 11, 2497.

• Rimola, A.; Sodupe, M.; Ugliengo, P. Affinity Scale for the Interaction of Amino Acids with Silica Surfaces. J. Phys. Chem. C 2009, 113, 5741.

• Rimola, A.; Corno, M.; Zicovich-Wilson, C. M.; Ugliengo, P. Ab initio modeling of protein/biomaterial interactions: competitive adsorption between glycine and water onto hydroxyapatite surfaces. Phys. Chem. Chem. Phys. 2009, 11, 9005.

• Musso, F.; Sodupe, M.; Corno, M.; Ugliengo, P. H-Bond Features of Fully Hydroxylated Surfaces of Crystalline Silica Polymorphs: A Periodic B3LYP Study. J. Phys. Chem. C 2009, 113, 17876.

• Mignon, P.; Ugliengo, P.; Sodupe, M. Theoretical Study of the Adsorption of RNA/DNA Bases on the External Surfaces of Na+-Montmorillonite. J. Phys. Chem. C 2009, 113, 13741.

• Corno, M.; Busco, C.; Bolis, V.; Tosoni, S.; Ugliengo, P. Water Adsorption on the Stoichiometric (001) and (010) Surfaces of Hydroxyapatite: A Periodic B3LYP Study. Langmuir 2009, 25, 2188.

• Civalleri, B.; Ugliengo, P.; Zicovich-Wilson, C. M.; Dovesi, R. Ab initio modeling of layered materials with the CRYSTAL code: an overview. Z. Kristallogr. 2009, 224, 241.

• Ugliengo, P.; Sodupe, M.; Musso, F.; Bush, I. J.; Orlando, R.; Dovesi, R. Realistic Models of Hydroxylated Amorphous Silica Surfaces and MCM-41 Mesoporous Material Simulated by Large-scale Periodic B3LYP Calculations. Adv. Mater. 2008, 20, 4579.

• Tosoni, S.; Civalleri, B.; Pascale, F.; Ugliengo, P. Hydroxylated crystalline edingtonite silica faces as models for the amorphous silica surface - art. no. 012026. Ab Initio Simulation of Crystalline Solids: History and Prospects - Contributions in Honor of Cesare Pisani 2008, 117, 12026.

• Rimola, A.; Ugliengo, P. A quantum mechanical study of the reactivity of (SiO)(2)-defective silica surfaces. J. Chem. Phys. 2008, 128.

• Rimola, A.; Corno, M.; Zicovich-Wilson, C. M.; Ugliengo, P. Ab Initio Modeling of Protein/Biomaterial Interactions: Glycine Adsorption at Hydroxyapatite Surfaces. J. Am. Chem. Soc. 2008, 130, 16181.

• Rimola, A.; Civalleri, B.; Ugliengo, P. Neutral vs Zwitterionic Glycine Forms at the Water/Silica Interface: Structure, Energies, and Vibrational Features from B3LYP Periodic Simulations. Langmuir 2008, 24, 14027.

• Pedone, A.; Malavasi, G.; Menziani, M. C.; Segre, U.; Musso, F.; Corno, M.; Civalleri, B.; Ugliengo, P. FFSiOH: a new force field for silica polymorphs and their hydroxylated surfaces based on periodic B3LYP calculations. Chem. Mater. 2008, 20, 2522.

• Corno, M.; Pedone, A.; Dovesi, R.; Ugliengo, P. B3LYP simulation of the full vibrational spectrum of 45S5 bioactive silicate glass compared to nu-silica. Chem. Mater. 2008, 20, 5610.

• Civalleri, B.; Zicovich-Wilson, C. M.; Valenzano, L.; Ugliengo, P. B3LYP augmented with an empirical dispersion term (B3LYP-D*) as applied to molecular crystals. Crystengcomm 2008, 10, 405.

• Camarota, B.; Ugliengo, P.; Garrone, E.; Arean, C. O.; Delgado, M. R.; Inagaki, S.; Onida, B. IR and Computational Characterization of CO Adsorption on a Model Surface, the Phenylene Periodic Mesoporous Organosilca with Crystalline Walls. J. Phys. Chem. C 2008, 112, 19560.

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