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Publications related to CPMD

This folder holds the following references to publications, sorted by year and author.

There are 1429 references in this bibliography folder.

Schwörer, M, Wichmann, C, and Tavan, P (2016).
A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water
The Journal of Chemical Physics, 144(11).

Martínez-Suárez, L, Siemer, N, Frenzel, J, and Marx, D (2015).
Reaction network of methanol synthesis over Cu/ZnO Nanocatalysts
ACS Catalysis, 0(ja):null.

Schwörer, M, Lorenzen, K, Mathias, G, and Tavan, P (2015).
Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations
The Journal of Chemical Physics, 142(10):104108.

Bolze, CS, Helbling, RE, Owen, RL, Pearson, AR, Pompidor, G, Dworkowski, F, Fuchs, MR, Furrer, J, Golczak, M, Palczewski, K, Cascella, M, and Stocker, A (2014).
Human Cellular Retinaldehyde-Binding Protein Has Secondary Thermal 9-cis-Retinal Isomerase Activity
Journal of the American Chemical Society, 136(1):137–146.

Chan, KS, Miller, MA, Liang, W, and Ellis-Terrell, C (2014).
Computational Design and Synthesis of Nitrogen-Substituted Carbon and Silicon Clathrates
Materials Research Letters, 2(2):70–75.

Chan, KS, Miller, MA, Liang, W, Ellis-Terrell, C, and Peng, X (2014).
First-principles computational design and synthesis of hybrid carbon–silicon clathrates
Journal of Materials Science.

Doemer, M, Maurer, P, Campomanes, P, Tavernelli, I, and Rothlisberger, U (2014).
Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin
Journal of Chemical Theory and Computation, 10(1):412–422.

Frenzel, J and Marx, D (2014).
Methanol synthesis on ZnO(0001¯). IV. Reaction mechanisms and electronic structure
The Journal of Chemical Physics, 141(12):-.

Korsun, OM, Kalugin, ON, and Prezhdo, OV (2014).
Control of Carbon Nanotube Electronic Properties by Lithium Cation Intercalation
The Journal of Physical Chemistry Letters, 5(23):4129-4133.

Martelli, F, Jeanvoine, Y, Vercouter, T, Beuchat, C, Vuilleumier, R, and Spezia, R (2014).
Hydration properties of lanthanoid(III) carbonate complexes in liquid water determined by polarizable molecular dynamics simulations
Physical Chemistry Chemical Physics.

Martinez-Suarez, L, Frenzel, J, and Marx, D (2014).
Cu/ZnO nanocatalysts in response to environmental conditions: surface morphology, electronic structure, redox state and CO2 activation
Phys. Chem. Chem. Phys., 16:26119-26136.

Momany, F and Schnupf, U (2014).
DFT optimization and DFT-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO
Computational and Theoretical Chemistry, 1029:57–67.

Akimov, AV and Prezhdo, OV (2013).
The PYXAID Program for Non-Adiabatic Molecular Dynamics in Condensed Matter Systems
Journal of Chemical Theory and Computation, 9(11):4959–4972.

Alam, S, Bekas, C, Boettiger, H, Curioni, A, Fourestey, G, Homberg, W, Knobloch, M, Laino, T, Maurer, T, Mohr, B, Pleiter, D, Schiller, A, Schulthess, T, and Weber, V (2013).
Early experiences with scientific applications on the IBM Blue Gene/Q supercomputer
IBM Journal of Research and Development, 57(1/2):14:1–14:9.

Assary, RS, Lau, KC, Amine, K, Sun, Y, and Curtiss, LA (2013).
Interactions of Dimethoxy Ethane with Li2O2 Clusters and Likely Decomposition Mechanisms for Li–O2 Batteries
The Journal of Physical Chemistry C, 117(16):8041–8049.

Atta-Fynn, R, Bylaska, EJ, and de Jong, WA (2013).
Importance of Counteranions on the Hydration Structure of the Curium Ion
The Journal of Physical Chemistry Letters, 4(13):2166–2170.

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.

Bao, X, Nie, X, Deak, D, Biddinger, EJ, Luo, W, Asthagiri, A, Ozkan, US, and Hadad, CM (2013).
A First-Principles Study of the Role of Quaternary-N Doping on the Oxygen Reduction Reaction Activity and Selectivity of Graphene Edge Sites
Topics in Catalysis, 56(18-20):1623–1633.

Bauchy, M, Micoulaut, M, Boero, M, and Massobrio, C (2013).
Compositional Thresholds and Anomalies in Connection with Stiffness Transitions in Network Glasses
Physical Review Letters, 110(16):165501.

Bester, G and Han, P (2013).
Ab-Initio Calculations of the Vibrational Properties of Nanostructures
In: High Performance Computing in Science and Engineering ‘12, ed. by Nagel, Wolfgang E. and Kröner, Dietmar H. and Resch, Michael M., pp. 145–156, Springer Berlin Heidelberg, Berlin, Heidelberg.

Bodo, E, Sferrazza, A, Caminiti, R, Mangialardo, S, and Postorino, P (2013).
A prototypical ionic liquid explored by ab initio molecular dynamics and Raman spectroscopy
The Journal of Chemical Physics, 139(14):144309.

Celino, M, Le Roux, S, Ori, G, Coasne, B, Bouzid, A, Boero, M, and Massobrio, C (2013).
First-principles molecular dynamics study of glassy GeS2: Atomic structure and bonding properties
Physical Review B, 88(17):174201.

Ceriotti, M, Cuny, J, Parrinello, M, and Manolopoulos, DE (2013).
Nuclear quantum effects and hydrogen bond fluctuations in water
Proceedings of the National Academy of Sciences, 110(39):15591–15596.

Chakraborty, S, Levenson, AS, and Biswas, PK (2013).
Structural insights into Resveratrol’s antagonist and partial agonist actions on estrogen receptor alpha
BMC Structural Biology, 13(1):27.

Chang, J, Zhou, X, Zhao, G, and Wang, L (2013).
A first-principles study of the structural, electronic and elastic properties of solid nitromethane under pressure
Science China Physics, Mechanics and Astronomy, 56(10):1874–1881.

Chatterjee, A, Dixit, MK, and Tembe, BL (2013).
Solvation Structures and Dynamics of the Magnesium Chloride (Mg2+–Cl–) Ion Pair in Water–Ethanol Mixtures
The Journal of Physical Chemistry A, 117(36):8703–8709.

Chou, C and Hwang, GS (2013).
Lithiation Behavior of Silicon-Rich Oxide (SiO1/3): A First-Principles Study
Chemistry of Materials, 25(17):3435–3440.

Choudhary, V, Mushrif, SH, Ho, C, Anderko, A, Nikolakis, V, Marinkovic, NS, Frenkel, AI, Sandler, SI, and Vlachos, DG (2013).
Insights into the Interplay of Lewis and Brønsted Acid Catalysts in Glucose and Fructose Conversion to 5-(Hydroxymethyl)furfural and Levulinic Acid in Aqueous Media
Journal of the American Chemical Society, 135(10):3997–4006.

Choudhuri, JR, Yadav, VK, Karmakar, A, Mallik, BS, and Chandra, A (2013).
A first-principles theoretical study of hydrogen‑bond dynamics and vibrational spectral diffusion in aqueous ionic solution: Water in the hydration shell of a fluoride ion
Pure and Applied Chemistry, 85(1):27–40.

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.

Codorniu-Hernández, E, Boese, AD, and Kusalik, PG (2013).
The hemibond as an alternative condensed phase structure for the hydroxyl radical
Canadian Journal of Chemistry, 91(7):544-551.

Coghlan, S, Kumaran, K, Loy, RM, Messina, P, Morozov, V, Osborn, JC, Parker, S, Riley, KM, Romero, NA, and Williams, TJ (2013).
Argonne applications for the IBM Blue Gene/Q, Mira
IBM Journal of Research and Development, 57(1/2):12:1–12:11.

Costanzo, F, Silvestrelli, PL, Gleria, M, and Boscoletto, AB (2013).
The Thermally-Induced Bulk Polymerization of Hexachlorocyclotriphosphazene to Polydichlorophosphazene by First-Principles Simulations
Journal of Inorganic and Organometallic Polymers and Materials, 23(6):1397–1408.

Curchod, BF, Penfold, TJ, Rothlisberger, U, and Tavernelli, I (2013).
Nonadiabatic ab initio molecular dynamics using linear-response time-dependent density functional theory
Central European Journal of Physics, 11(9):1059–1065.

Curchod, BF, Rothlisberger, U, and Tavernelli, I (2013).
Trajectory-Based Nonadiabatic Dynamics with Time-Dependent Density Functional Theory
ChemPhysChem, 14(7):1314–1340.

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.

Deiana, C, Tabacchi, G, Maurino, V, Coluccia, S, Martra, G, and Fois, E (2013).
Surface features of TiO2 nanoparticles: combination modes of adsorbed CO probe the stepping of (101) facets
Physical Chemistry Chemical Physics, 15(32):13391–13399.

Demontis, P, Masia, M, and Suffritti, GB (2013).
Water Nanoconfined in Clays: The Structure of Na Vermiculite Revisited by Ab Initio Simulations
The Journal of Physical Chemistry C, 117(30):15583–15592.

Doemer, M, Liberatore, E, Knaup, JM, Tavernelli, I, and Rothlisberger, U (2013).
In situ parameterisation of SCC-DFTB repulsive potentials by iterative Boltzmann inversion
Molecular Physics, 111(22-23):3595–3607.

Domene, C, Portius, P, Fowler, PW, and Bernasconi, L (2013).
Simulating the Pyrolysis of Polyazides: a Mechanistic Case Study of the [P(N3)6]− Anion
Inorganic Chemistry, 52(4):1747–1754.

Dommert, F, Wendler, K, Qiao, B, Delle Site, L, and Holm, C (2013).
Generic force fields for ionic liquids
Journal of Molecular Liquids.

Dopieralski, P, Ribas-Arino, J, Anjukandi, P, Krupicka, M, Kiss, J, and Marx, D (2013).
The Janus-faced role of external forces in mechanochemical disulfide bond cleavage
Nature Chemistry, n/a(n/a):n/a–n/a.

Draguta, S, Fonari, MS, Masunov, AE, Zazueta, J, Sullivan, S, Antipin, MY, and Timofeeva, TV (2013).
New acentric materials constructed from aminopyridines and 4-nitrophenol
CrystEngComm, 15(23):4700–4710.

Dreyer, J, Zhang, C, Ippoliti, E, and Carloni, P (2013).
Role of the Membrane Dipole Potential for Proton Transport in Gramicidin A Embedded in a DMPC Bilayer
Journal of Chemical Theory and Computation, 9(8):3826–3831.

Du, P, Lu, J, Lau, KC, Luo, X, Bareño, J, Zhang, X, Ren, Y, Zhang, Z, Curtiss, LA, Sun, Y, and Amine, K (2013).
Compatibility of lithium salts with solvent of the non-aqueous electrolyte in Li–O2 batteries
Physical Chemistry Chemical Physics, 15(15):5572–5581.

Dudenko, DV, Yates, JR, Harris, KD, and Brown, SP (2013).
An NMR crystallography DFT-D approach to analyse the role of intermolecular hydrogen bonding and π–π interactions in driving cocrystallisation of indomethacin and nicotinamide
CrystEngComm, 15(43):8797.

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.

Dutta, B, Tanaka, T, Banerjee, A, and Chowdhury, J (2013).
Conformational Preferences of Ethyl Propionate Molecule: Raman, Temperature Dependent FTIR Spectroscopic Study Aided by ab Initio Quantum Chemical and Car–Parrinello Molecular Dynamics Simulation Studies
The Journal of Physical Chemistry A, 117(23):4838–4850.

Eisenmayer, TJ, Lasave, JA, Monti, A, de Groot, HJ, and Buda, F (2013).
Proton Displacements Coupled to Primary Electron Transfer in the Rhodobacter sphaeroides Reaction Center
The Journal of Physical Chemistry B, 117(38):11162–11168.

Elenewski, JE and Hackett, JC (2013).
Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)–oxo porphyrin
Journal of Computational Chemistry, 34(19):1647–1660.

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