All Publications

Bankura, A, Carnevale, V, and Klein, ML (2013).
Hydration structure of salt solutions from ab initio molecular dynamics
The Journal of Chemical Physics, 138(1):014501–014501-10.

Coccia, E, Varsano, D, and Guidoni, L (2013).
Protein Field Effect on the Dark State of 11-cis Retinal in Rhodopsin by Quantum Monte Carlo/Molecular Mechanics
Journal of Chemical Theory and Computation, 9(1):8–12.

Deiana, C, Minella, M, Tabacchi, G, Maurino, V, Fois, E, and Martra, G (2013).
Shape-controlled TiO2 nanoparticles and TiO2 P25 interacting with CO and H2O2 molecular probes: a synergic approach for surface structure recognition and physico-chemical understanding
Physical Chemistry Chemical Physics, 15(1):307.

Durlak, P and Latajka, Z (2013).
Ab Initio Molecular Dynamics Study of the Very Short O–H···O Hydrogen Bonds in the Condensed Phases
Journal of Chemical Theory and Computation, 9(1):65–72.

Guido, CA, Pietrucci, F, Gallet, GA, and Andreoni, W (2013).
The Fate of a Zwitterion in Water from ab Initio Molecular Dynamics: Monoethanolamine (MEA)-CO2
Journal of Chemical Theory and Computation, 9(1):28–32.

Kowalski, PM, Wunder, B, and Jahn, S (2013).
Ab initio prediction of equilibrium boron isotope fractionation between minerals and aqueous fluids at high P and T
Geochimica et Cosmochimica Acta, 101(0):285–301.

Kroes, JM, Pietrucci, F, Curioni, A, Jaafar, R, Gröning, O, and Andreoni, W (2013).
Atomic Oxygen Chemisorption on Carbon Nanotubes Revisited with Theory and Experiment
The Journal of Physical Chemistry C, 117(4):1948-1954.

Morita, M and Takahashi, K (2013).
Multidimensional OH local mode calculations for OH−(H2O)3—Importance of intermode anharmonicity
Physical Chemistry Chemical Physics, 15(1):114.

Niskanen, J, Arul Murugan, N, Rinkevicius, Z, Vahtras, O, Li, C, Monti, S, Carravetta, V, and Ågren, H (2013).
Hybrid density functional–molecular mechanics calculations for core-electron binding energies of glycine in water solution
Physical Chemistry Chemical Physics, 15(1):244.

Pavlova, A, Trinh, TT, van Santen, RA, and Meijer, EJ (2013).
Clarifying the role of sodium in the silica oligomerization reaction
Physical Chemistry Chemical Physics, 15(4):1123.

Penfold, T, Tavernelli, I, Doemer, M, Abela, R, Röthlisberger, U, and Chergui, M (2013).
Solvent rearrangements during the transition from hydrophilic to hydrophobic solvation
Chemical Physics, 410(0):25–30.

Rieth, M, Dudarev, S, Gonzalez de Vicente, S, Aktaa, J, Ahlgren, T, Antusch, S, Armstrong, D, Balden, M, Baluc, N, Barthe, M, Basuki, W, Battabyal, M, Becquart, C, Blagoeva, D, Boldyryeva, H, Brinkmann, J, Celino, M, Ciupinski, L, Correia, J, De Backer, A, Domain, C, Gaganidze, E, García-Rosales, C, Gibson, J, Gilbert, M, Giusepponi, S, Gludovatz, B, Greuner, H, Heinola, K, Höschen, T, Hoffmann, A, Holstein, N, Koch, F, Krauss, W, Li, H, Lindig, S, Linke, J, Linsmeier, C, López-Ruiz, P, Maier, H, Matejicek, J, Mishra, T, Muhammed, M, Muñoz, A, Muzyk, M, Nordlund, K, Nguyen-Manh, D, Opschoor, J, Ordás, N, Palacios, T, Pintsuk, G, Pippan, R, Reiser, J, Riesch, J, Roberts, S, Romaner, L, Rosiński, M, Sanchez, M, Schulmeyer, W, Traxler, H, Ureña, A, van der Laan, J, Veleva, L, Wahlberg, S, Walter, M, Weber, T, Weitkamp, T, Wurster, S, Yar, M, You, J, and Zivelonghi, A (2013).
Recent progress in research on tungsten materials for nuclear fusion applications in Europe
Journal of Nuclear Materials, 432(1–3):482–500.

Sieffert, N, Bühl, M, Gaigeot, M, and Morrison, CA (2013).
Liquid Methanol from DFT and DFT/MM Molecular Dynamics Simulations
Journal of Chemical Theory and Computation, 9(1):106–118.

Sulpizi, M, Salanne, M, Sprik, M, and Gaigeot, M (2013).
Vibrational Sum Frequency Generation Spectroscopy of the Water Liquid–Vapor Interface from Density Functional Theory-Based Molecular Dynamics Simulations
The Journal of Physical Chemistry Letters, 4(1):83–87.

Tuma, C, Laino, T, Martin, E, Stolz, S, and Curioni, A (2013).
Modeling the Impact of Solid Surfaces in Thermal Degradation Processes
ChemPhysChem, 14(1):88–91.

Zhou, X, Wesolowski, TA, Tabacchi, G, Fois, E, Calzaferri, G, and Devaux, A (2013).
First-principles simulation of the absorption bands of fluorenone in zeolite L
Physical Chemistry Chemical Physics, 15(1):159.

Abolfath, RM and Cho, K (2012).
Computational Studies for Reduced Graphene Oxide in Hydrogen-Rich Environment
The Journal of Physical Chemistry A, 116(7):1820–1827.

Abolfath, RM, Biswas, PK, Rajnarayanam, R, Brabec, T, Kodym, R, and Papiez, L (2012).
Multiscale QM/MM Molecular Dynamics Study on the First Steps of Guanine Damage by Free Hydroxyl Radicals in Solution
The Journal of Physical Chemistry A, 116(15):3940–3945.

Agarwal, V, Dauenhauer, PJ, Huber, GW, and Auerbach, SM (2012).
Ab Initio Dynamics of Cellulose Pyrolysis: Nascent Decomposition Pathways at 327 and 600 °C
Journal of the American Chemical Society, 134(36):14958–14972.

Akola, J and Jones, R (2012).
Phase change materials: Density functional / molecular dynamics simulations of Ag/In-doped Sb4Te alloy
In: 2012 12th IEEE Conference on Nanotechnology (IEEE-NANO), pp. 1 –6.

Akola, J and Jones, RO (2012).
Structure and dynamics in amorphous tellurium and Te\_\n\ clusters: A density functional study
Physical Review B, 85(13):134103.

Aktulga, HM, Pandit, SA, van Duin, AC, and Grama, AY (2012).
Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques
SIAM Journal on Scientific Computing, 34(1):C1–C23.

Ali, ME, Nair, NN, Staemmler, V, and Marx, D (2012).
Constrained spin-density dynamics of an iron-sulfur complex: Ferredoxin cofactor
The Journal of Chemical Physics, 136(22):224101–224101-8.

Ambrosetti, A and Silvestrelli, PL (2012).
van der Waals interactions in density functional theory using Wannier functions: Improved C\_\6\ and C\_\3\ coefficients by a different approach
Physical Review B, 85(7):073101.

Andreoni, W, Curioni, A, Kroes, JM, Pietrucci, F, and Gröning, O (2012).
Exohedral Hydrogen Chemisorption on a Carbon Nanotube: The Clustering Effect
The Journal of Physical Chemistry C, 116(1):269–275.

Ashby, JA, McGonigle, IV, Price, KL, Cohen, N, Comitani, F, Dougherty, DA, Molteni, C, and Lummis, SC (2012).
GABA Binding to an Insect GABA Receptor: A Molecular Dynamics and Mutagenesis Study
Biophysical Journal, 103(10):2071–2081.

Bankura, A and Chandra, A (2012).
Hydration structure and dynamics of a hydroxide ion in water clusters of varying size and temperature: Quantum chemical and ab initio molecular dynamics studies
Chemical Physics, 400(0):154–164.

Bankura, A and Chandra, A (2012).
Hydroxide Ion Can Move Faster Than an Excess Proton through One-Dimensional Water Chains in Hydrophobic Narrow Pores
The Journal of Physical Chemistry B, 116(32):9744–9757.

Bankura, A and Chandra, A (2012).
A first principles molecular dynamics study of the solvation structure and migration kinetics of an excess proton and a hydroxide ion in binary water-ammonia mixtures
The Journal of Chemical Physics, 136(11):114509–114509-13.

Bester, G and Han, P (2012).
Ab-initio Calculations of the Vibrational Properties of Nanostructures
In: High Performance Computing in Science and Engineering '11, ed. by Nagel, Wolfgang E. and Kröner, Dietmar B. and Resch, Michael M., pp. 119–129, Springer Berlin Heidelberg, Berlin, Heidelberg.

Bjornsson, R and Bühl, M (2012).
Modeling Molecular Crystals by QM/MM: Self-Consistent Electrostatic Embedding for Geometry Optimizations and Molecular Property Calculations in the Solid
Journal of Chemical Theory and Computation, 8(2):498–508.

Bonhomme, C, Gervais, C, Babonneau, F, Coelho, C, Pourpoint, F, Azaïs, T, Ashbrook, SE, Griffin, JM, Yates, JR, Mauri, F, and Pickard, CJ (2012).
First-Principles Calculation of NMR Parameters Using the Gauge Including Projector Augmented Wave Method: A Chemist’s Point of View
Chemical Reviews, 112(11):5733–5779.

Branduardi, D, Bussi, G, and Parrinello, M (2012).
Metadynamics with Adaptive Gaussians
Journal of Chemical Theory and Computation, 8(7):2247–2254.

Brndiar, J and Štich, I (2012).
van der Waals Interaction Energies of Small Fragments of P, As, Sb, S, Se, and Te: Comparison of Complete Basis Set Limit CCSD(T) and DFT with Approximate Dispersion
Journal of Chemical Theory and Computation, 8(7):2301–2309.

Broqvist, P, Binder, JF, and Pasquarello, A (2012).
First principles study of electronic and structural properties of the Ge/GeO2 interface
Physica B: Condensed Matter, 407(15):2926–2931.

Bucher, D (2012).
Orientational relaxation of water trapped inside C60 fullerenes
Chemical Physics Letters, 534(0):38–42.

Burresi, E and Celino, M (2012).
Methodological approach to study energetic and structural properties of nanostructured cadmium sulfide by using ab-initio molecular dynamics simulations
Solid State Sciences, 14(5):567–573.

Bühl, M, Sieffert, N, Chaumont, A, and Wipff, G (2012).
Water versus Acetonitrile Coordination to Uranyl. Effect of Chloride Ligands
Inorganic Chemistry, 51(3):1943–1952.

Bühl, M, Sieffert, N, Partouche, A, Chaumont, A, and Wipff, G (2012).
Speciation of La(III) Chloride Complexes in Water and Acetonitrile: A Density Functional Study
Inorganic Chemistry, 51(24):13396–13407.

Carbone, M and Caminiti, R (2012).
ADSORPTION STATES AND SITE CONVERSIONS OF PHENYLACETYLENE ON Si(100)2 × 1 CALCULATED BY DFT
Journal of Theoretical and Computational Chemistry, 11(05):1089–1099.

Carvalho, A, Öberg, S, Rayson, MJ, and Briddon, PR (2012).
Electronic properties, doping, and defects in chlorinated silicon nanocrystals
Physical Review B, 86(4):045308.

Casida, ME, Natarajan, B, and Deutsch, T (2012).
Non-Born–Oppenheimer Dynamics and Conical Intersections
In: Fundamentals of Time-Dependent Density Functional Theory, ed. by Marques, Miguel A. L. and Maitra, Neepa T. and Nogueira, Fernando M. S. and Gross, E. K. U. and Rubio, Angel, pp. 279–299, Springer Berlin Heidelberg. Lecture Notes in Physics.

Chen, Y, Doltsinis, NL, Hider, RC, and Barlow, DJ (2012).
Prediction of Absolute Hydroxyl pKa Values for 3-Hydroxypyridin-4-ones
The Journal of Physical Chemistry Letters, 3(20):2980–2985.

Codorniu-Hernández, E and Kusalik, PG (2012).
Hydroxyl radicals in ice: insights into local structure and dynamics
Physical Chemistry Chemical Physics, 14(33):11639–11650.

Curchod, BF, Rothlisberger, U, and Tavernelli, I (2012).
Excited State Dynamics with Quantum Trajectories
CHIMIA, 66(4):174–177.

De Toni, M, Jonchiere, R, Pullumbi, P, Coudert, F, and Fuchs, AH (2012).
How Can a Hydrophobic MOF be Water-Unstable? Insight into the Hydration Mechanism of IRMOFs
ChemPhysChem, 13(15):3497–3503.

Djerdj, I, Popović, J, Stare, J, Ambrožič, G, Škapin, SD, Kozlevčar, B, Pajić, D, Jagličić, Z, and Orel, ZC (2012).
Nanocrystalline hybrid inorganic–organic one-dimensional chain systems tailored with 2- and 3-phenyl ring monocarboxylic acids
Journal of Materials Chemistry, 22(20):10255–10265.

Doemer, M, Tavernelli, I, and Rothlisberger, U (2012).
Intricacies of Describing Weak Interactions Involving Halogen Atoms within Density Functional Theory
Journal of Chemical Theory and Computation.

Domingo, A, Rodríguez-Fortea, A, and de Graaf, C (2012).
The Absorption Spectrum of Cytosine Tautomers: Beyond the Static Approach
Journal of Chemical Theory and Computation, 8(1):235–244.

Dommert, F, Wendler, K, Berger, R, Delle Site, L, and Holm, C (2012).
Force Fields for Studying the Structure and Dynamics of Ionic Liquids: A Critical Review of Recent Developments
ChemPhysChem, 13(7):1625–1637.