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ORCIDJournal of Computational Chemistry, Volume 34
Volume 34, Number 1, January 2013
- Charles L. Brooks III, Masahiro Ehara
, Gernot Frenking, Peter R. Schreiner:
New paint and a new engine. 1
- Mark Pinsky, Amir Zait, Maayan Bonjack, David Avnir:
Continuous symmetry analyses: Cnv and Dn measures of molecules, complexes, and proteins. 2-9 - Susanne Pape, Franziska Hoffgaard, Mirjam Dür, Kay Hamacher:
Distance dependency and minimum amino acid alphabets for decoy scoring potentials. 10-20 - Toru Matsui, Yasutaka Kitagawa, Mitsutaka Okumura, Yasuteru Shigeta, Shigeyoshi Sakaki:
Consistent scheme for computing standard hydrogen electrode and redox potentials. 21-26 - Andriy Samsonyuk, Christoph Scheurer:
Configuration space partitioning and matrix buildup scaling for the vibrational configuration interaction method. 27-37 - Jinshuai Song, Zhenhua Chen, Sason Shaik, Wei Wu:
An efficient algorithm for complete active space valence bond self-consistent field calculation. 38-48 - J. Drujon, Yannick Carissan:
Pseudopotentials for hybridized carbon atoms. 49-59 - Jin Yang, Paul J. Dauenhauer, Ashwin Ramasubramaniam:
The role of water in the adsorption of oxygenated aromatics on Pt and Pd. 60-66 - Yu Liu, Lei Zhao, Wentao Li, Dongyu Zhao, Miao Song, Yongliang Yang:
FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm. 67-75
Volume 34, Number 2, January 2013
- Milan Randic:
Very efficient search for nucleotide alignments. 77-82 - Yutaka Uejima, Ryo Maezono:
GPGPU for orbital function evaluation with a new updating scheme. 83-94 - Yutong Zhao, Fu Kit Sheong, Jian Sun, Pedro V. Sander, Xuhui Huang:
A fast parallel clustering algorithm for molecular simulation trajectories. 95-104 - Paul Mach, Patrice Koehl:
An analytical method for computing atomic contact areas in biomolecules. 105-120 - Yuan Liu, Jijun Zhao, Fengyu Li, Zhongfang Chen:
Appropriate description of intermolecular interactions in the methane hydrates: An assessment of DFT methods. 121-131 - Yannick G. Spill, Guillaume Bouvier, Michael Nilges:
A convective replica-exchange method for sampling new energy basins. 132-140 - Eric A. C. Bushnell, James W. Gauld:
An assessment of pure, hybrid, meta, and hybrid-meta GGA density functional theory methods for open-shell systems: The case of the nonheme iron enzyme 8R-LOX. 141-148 - Kenta Yamada, Nobuaki Koga:
Variationally determined electronic states for the theoretical analysis of intramolecular interaction. II. Qualitative nature of the P‒O bond in phosphine oxides. 149-161
Volume 34, Number 3, January 2013
- Yang Zhong, Sandeep Patel:
Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field. 163-174 - Robert A. Evarestov, Andrei V. Bandura, Dmitrii D. Kuruch:
BaTiO3-based nanolayers and nanotubes: First-principles calculations. 175-186 - Joakim P. M. Jämbeck, Francesca Mocci, Alexander Lyubartsev, Aatto Laaksonen:
Partial atomic charges and their impact on the free energy of solvation. 187-197 - Hiroshi C. Watanabe, Marcus Elstner, Thomas Steinbrecher:
Rotamer decomposition and protein dynamics: Efficiently analyzing dihedral populations from molecular dynamics. 198-205 - Pavel M. Polestshuk:
Accurate integration over atomic regions bounded by zero-flux surfaces. 206-219 - Christopher Pfleger, Sebastian Radestock, Elena Schmidt, Holger Gohlke:
Global and local indices for characterizing biomolecular flexibility and rigidity. 220-233 - Josep M. Porta, Leonard Jaillet:
Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation. 234-244 - Elijah Roberts, John E. Stone, Zaida Luthey-Schulten:
Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. 245-255
- Christopher J. R. Illingworth, Sree V. Chintapalli, Stefano A. Serapian, Andrew D. Miller, Vaclav Veverka, Mark D. Carr, Christopher A. Reynolds:
The statistical significance of selected sense-antisense peptide interactions [J. Comp. Chem. 33, 1440-1447]. 256 - Paola Antoniotti, Elena Bottizzo, Stefano Borocci, Maria Giordani, Felice Grandinetti:
Gas-phase reactions of SiHn+ (n = 1, 2) with NF3: A computational investigation on the detailed mechanistic aspects [J. Comp. Chem. 33, 1918-1926]. 257
Volume 34, Number 4, February 2013
- Stephen J. Barigye, Yovani Marrero-Ponce, Yoan Martínez López, Francisco Torrens, Luis Manuel Artiles-Martínez, Ricardo W. Pino-Urias, Oscar Martínez Santiago:
Relations frequency hypermatrices in mutual, conditional and joint entropy-based information indices. 259-274 - Angelika Baranowska-Laczkowska, Berta Fernández, Robert Zalesny:
New basis sets for the evaluation of interaction-induced electric properties in hydrogen-bonded complexes. 275-283 - Li Yang, Alauddin Ahmed, Stanley I. Sandler:
Comparison of two simulation methods to compute solvation free energies and partition coefficients. 284-293 - Lukasz Piekos, Mariusz Pawel Mitoraj:
Theoretical description of dihydrogen/hydride and trihydride molybdocene complexes: An insight from static and molecular dynamics simulations. 294-304 - Hongguang Liu, Jin Yong Lee:
Electric field assisted oxygen removal from the basal plane of the graphitic material. 305-310 - Sheng-You Huang, Xiaoqin Zou:
A nonredundant structure dataset for benchmarking protein-RNA computational docking. 311-318
- Alexander V. Popov, Yury N. Vorobjev, Dmitry O. Zharkov:
MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface. 319-325 - Xuchang Ouyang, Shuo Zhou, Chinh Tran To Su, Zemei Ge, Runtao Li, Chee Keong Kwoh:
CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints. 326-336
Volume 34, Number 5, February 2013
- Pawel Malyszek, Jacek Koput:
Accurate Ab initio potential energy surface and vibration-rotation energy levels of hydrogen peroxide. 337-345 - Alessandro Erba, Matteo Ferrabone, Roberto Orlando, Roberto Dovesi:
Accurate dynamical structure factors from ab initio lattice dynamics: The case of crystalline silicon. 346-354 - Gonzalo Astray, Juan F. Gálvez, Juan C. Mejuto, Oscar A. Moldes, Iago Montoya:
Esters flash point prediction using artificial neural networks. 355-359 - Hongmei Liu, Hongbo Wang, Jianwei Zhao, Manabu Kiguchi:
Molecular rectification in triangularly shaped graphene nanoribbons. 360-365 - Jirí Kessler, Martin Dracínský, Petr Bour:
Parallel variable selection of molecular dynamics clusters as a tool for calculation of spectroscopic properties. 366-371 - Binju Wang, Zexing Cao:
How water molecules modulate the hydration of CO2 in water solution: Insight from the cluster-continuum model calculations. 372-378 - Raman K. Singh, Takao Tsuneda:
Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions. 379-386 - Zhixiong Lin, Wilfred F. van Gunsteren:
On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment. 387-393 - Shantanu Kadam, Kumar Vanka:
Solving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approach. 394-404 - Danny E. P. Vanpoucke, Patrick Bultinck, Isabel Van Driessche:
Extending Hirshfeld-I to bulk and periodic materials. 405-417
- Thomas A. Manz:
Comment on "Extending hirshfeld-i to bulk and periodic materials". 418-421 - Danny E. P. Vanpoucke, Isabel Van Driessche, Patrick Bultinck:
Reply to 'comment on "extending hirshfeld-I to bulk and periodic materials"'. 422-427
Volume 34, Number 6, March 2013
- Louis P. Lee, Daniel J. Cole, Mike C. Payne, Chris-Kriton Skylaris:
Natural bond orbital analysis in the ONETEP code: Applications to large protein systems. 429-444 - Mohsen Chitsaz, Stephen L. Mayo:
GRID: A high-resolution protein structure refinement algorithm. 445-450 - Michael F. Peintinger, Daniel Vilela Oliveira, Thomas Bredow:
Consistent gaussian basis sets of Triple-Zeta valence with polarization quality for solid-State Calculations. 451-459 - János Pipek, Szilvia Nagy:
An economic prediction of refinement coefficients in wavelet-based adaptive methods for electron structure calculations. 460-465 - Jack Yang, Mark P. Waller:
Revealing noncovalent interactions in quantum crystallography: Taurine revisited. 466-470 - Soumya Ganguly Neogi, Pinaki Chaudhury:
Structure and spectroscopic aspects of water-halide ion clusters: A study based on a conjunction of stochastic and quantum chemical methods. 471-491 - Maël Bosson, Sergei Grudinin, Stephane Redon:
Block-adaptive quantum mechanics: An adaptive divide-and-conquer approach to interactive quantum chemistry. 492-504 - Jorge M. C. Marques, Francisco Baptista Pereira:
A detailed investigation on the global minimum structures of mixed rare-gas clusters: Geometry, energetics, and site occupancy. 505-517
- David D. Jenkins, Jason B. Harris, Elizabeth E. Howell, Robert J. Hinde, Jérôme Baudry:
STAAR: Statistical analysis of aromatic rings. 518-522
Volume 34, Number 7, March 2013
- Ananth P. Kaushik, Paulette Clancy:
Solvent-driven symmetry of self-assembled nanocrystal superlattices - A computational study. 523-532 - Vladimir V. Rybkin, Anton O. Simakov, Vebjørn Bakken, Simen Reine, Thomas Kjærgaard, Trygve Helgaker, Einar Uggerud:
Insights into the dynamics of evaporation and proton migration in protonated water clusters from large-scale born-oppenheimer direct dynamics. 533-544 - Maggie Ng, Daniel K. W. Mok, Edmond P. F. Lee, John M. Dyke:
Rate coefficients of the CF3CHFCF3 + H → CF3CFCF3 + H2 reaction at different temperatures calculated by transition state theory with ab initio and DFT reaction paths. 545-557 - Shelley A. Smith, Karen E. Hand, Melissa L. Love, Glake Hill, David H. Magers:
Conventional strain energies of azetidine and phosphetane: Can density functional theory yield reliable results? 558-565 - Jianan Wang, Jun-Ling Jin, Yun Geng, Shiling Sun, Hong-Liang Xu, Ying-Hua Lu, Zhongmin Su:
An accurate and efficient method to predict the electronic excitation energies of BODIPY fluorescent dyes. 566-575 - Bradley Scott Perrin Jr., Shuqiang Niu, Toshiko Ichiye:
Calculating standard reduction potentials of [4Fe-4S] proteins. 576-582 - Mingyue Zheng, Yanlian Li, Bing Xiong, Hualiang Jiang, Jingkang Shen:
Water PMF for predicting the properties of water molecules in protein binding site. 583-592 - Jihyun Shim, Xiao Zhu, Robert B. Best, Alexander D. MacKerell Jr.:
(Ala)4-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters. 593-603
- Yuye He, Chin Yee Liew, Nitin Sharma, Sze Kwang Woo, Yi Ting Chau, Chun Wei Yap:
PaDEL-DDPredictor: Open-source software for PD-PK-T prediction. 604-610
Volume 34, Number 8, March 2013
- Marcus V. P. dos Santos, Eduardo C. Aguiar, João Bosco P. Da Silva, Ricardo L. Longo:
PICVib: An accurate, fast, and simple procedure to investigate selected vibrational modes at high theoretical levels. 611-621 - Satoru G. Itoh, Hisashi Okumura:
Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules. 622-639
- Ning Ma, Ying-Hua Chung, Arjan van der Vaart:
Free energy simulation of helical transitions. 640-645
- Goran Kovacevic, Aleksandar Sabljic:
Theoretical study on the mechanism and kinetics of addition of hydroxyl radicals to fluorobenzene. 646-655 - Drahomír Hnyk, Elambalassery G. Jayasree:
Cationic Closo-carboranes 2. Do computed 11B and 13C NMR chemical shifts support their experimental availability? 656-661 - Soumen Saha, Rituparna Bhattacharjee, Ram Kinkar Roy:
Hardness potential derivatives and their relation to fukui indices. 662-672 - Jian-Dong Zhang, Shu-Jin Li, Fu-Ming Tao:
Ab initio calculations of the Ar-ethane intermolecular potential energy surface using bond function basis sets. 673-680 - Juan I. Rodríguez:
An efficient method for computing the QTAIM topology of a scalar field: The electron density case. 681-686 - Dennis G. Thomas, Jaehun Chun, Zhan Chen, Guowei Wei, Nathan A. Baker:
Parameterization of a geometric flow implicit solvation model. 687-695 - Halina Szatylowicz, Tadeusz Marek Krygowski, Célia Fonseca Guerra, Friedrich Matthias Bickelhaupt:
Complexes of 4-substituted phenolates with HF and HCN: Energy decomposition and electronic structure analyses of hydrogen bonding. 696-705
Volume 34, Number 9, April 2013
- Florent Réal, Michael Trumm, Bernd Schimmelpfennig, Michel Masella, Valérie Vallet:
Further insights in the ability of classical nonadditive potentials to model actinide ion-water interactions. 707-719 - David Casanova:
Efficient implementation of restricted active space configuration interaction with the hole and particle approximation. 720-730 - Olga Yuzlenko, Themis Lazaridis:
Membrane protein native state discrimination by implicit membrane models. 731-738 - Jin Yu Xiang, Jay W. Ponder:
A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field. 739-749 - Marcin Nowosielski, Marcin Hoffmann, Aneta Kuron, Malgorzata Korycka-Machala, Jaroslaw Dziadek:
The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics. 750-756 - Jia-Lin Chang, Cyong-Huei Huang, Sue-Chang Chen, Tsung-Hao Yin, Yi-Tsung Chen:
An analytical approach for computing franck-condon integrals of harmonic oscillators with arbitrary dimensions. 757-765 - Ramon Carbó-Dorca:
Notes on quantitative structure-property relationships (QSPR), part 3: Density functions origin shift as a source of quantum QSPR algorithms in molecular spaces. 766-779 - Ignacio Viciano, Slawomir Berski, Sergio Martí, Juan Andrés:
New insight into the electronic structure of iron(IV)-oxo porphyrin compound I. A quantum chemical topological analysis. 780-789 - Nikola Minovski, Andrej Perdih, Marjana Novic, Tomaz Solmajer:
Cluster-based molecular docking study for in silico identification of novel 6-fluoroquinolones as potential inhibitors against mycobacterium tuberculosis. 790-801
Volume 34, Number 10, April 2013
- Ardita Shkurti, Mario Orsi, Enrico Macii, Elisa Ficarra, Andrea Acquaviva:
Acceleration of coarse grain molecular dynamics on GPU architectures. 803-818 - Angelika Baranowska-Laczkowska, Wojciech Bartkowiak, Robert W. Góra, Filip Pawlowski, Robert Zalesny:
On the performance of long-range-corrected density functional theory and reduced-size polarized LPol-n basis sets in computations of electric dipole (hyper)polarizabilities of π-conjugated molecules. 819-826 - Ole Schütt, Daniel Sebastiani:
Spectroscopic fingerprints of toroidal nuclear quantum delocalization via Ab Initio path integral simulations. 827-835 - Thomas Simonson, Priyadarshi Satpati:
Simulating GTP: Mg and GDP: Mg with a simple force field: A structural and thermodynamic analysis. 836-846 - Juan Zeng, LiLi Duan, John Z. H. Zhang, Ye Mei:
A numerically stable restrained electrostatic potential charge fitting method. 847-853 - György G. Ferenczy:
Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation. 854-861 - György G. Ferenczy:
Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation. 862-869 - Andranik Kazaryan, Evert Jan Baerends:
Assessment of density functional methods for reaction energetics: Iridium-catalyzed water oxidation as case study. 870-878 - Yoonjoo Choi, Karl E. Griswold, Chris Bailey-Kellogg:
Structure-based redesign of proteins for minimal T-cell epitope content. 879-891
Volume 34, Number 11, April 2013
- Jennifer L. Knight, Joseph D. Yesselman, Charles L. Brooks III:
Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. 893-903 - Jeffrey R. Wagner, Gouthaman S. Balaraman, Michiel J. M. Niesen, Adrien B. Larsen, Abhinandan Jain, Nagarajan Vaidehi:
Advanced techniques for constrained internal coordinate molecular dynamics. 904-914 - Xiaohua Zhang, Sergio Ernesto Wong, Felice C. Lightstone:
Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines. 915-927 - Robert J. Buenker, Heinz-Peter Liebermann, Yu Zhang, Yong Wu, Lingling Yan, Chunhua Liu, Yizhi Qu, Jianguo Wang:
Adjustment of born-oppenheimer electronic wave functions to simplify close coupling calculations. 928-937 - Anthony Scemama, Michel Caffarel, Emmanuel Oseret, William Jalby:
Quantum monte carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond. 938-951 - Heng-Qing Wu, Rong-Lin Zhong, Yu-He Kan, Shiling Sun, Min Zhang, Hong-Liang Xu, Zhongmin Su:
After the electronic field: Structure, bonding, and the first hyperpolarizability of HArF. 952-957 - Rahul Kar, Jong-Won Song, Kimihiko Hirao:
Long-range corrected functionals satisfy Koopmans' theorem: Calculation of correlation and relaxation energies. 958-964
- Nadine Homeyer, Holger Gohlke:
FEW: A workflow tool for free energy calculations of ligand binding. 965-973 - Dong-Jun Yu, Jun Hu, Yan Huang, Hong-Bin Shen, Yong Qi, Zhenmin Tang, Jing-Yu Yang:
TargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble. 974-985
Volume 34, Number 12, May 2013
- Karina Kornobis, Neeraj Kumar, Piotr Lodowski, Maria Jaworska, Piotr Piecuch, Jesse J. Lutz, Bryan M. Wong, Pawel M. Kozlowski:
Electronic structure of the S1 state in methylcobalamin: Insight from CASSCF/MC-XQDPT2, EOM-CCSD, and TD-DFT calculations. 987-1004 - Yanliang Ren, Bo Chi, Osama Melhem, Ke Wei, Lingling Feng, Yongjian Li, Xinya Han, Ding Li, Ying Zhang, Jian Wan, Xin Xu, Minghui Yang:
Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of förster theory. 1005-1012 - Terutaka Yoshizawa, Shigeyoshi Sakaki:
NMR shielding constants of CuX, AgX, and AuX (X = F, Cl, Br, and I) investigated by density functional theory based on the douglas-kroll-hess hamiltonian. 1013-1023 - Anita de Ruiter, Stefan Boresch, Chris Oostenbrink:
Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies. 1024-1034 - Martin Rohrmüller, Sonja Herres-Pawlis, Matthias Witte, Wolf Gero Schmidt:
Bis-μ-oxo and μ-η2: η2-peroxo dicopper complexes studied within (time-dependent) density-functional and many-body perturbation theory. 1035-1045 - Zhanghui Chen, Xiangwei Jiang, Jingbo Li, Shu-Shen Li, Linwang Wang:
PDECO: Parallel differential evolution for clusters optimization. 1046-1059 - Debashree Ghosh, Dmytro Kosenkov, Vitalii Vanovschi, Joanna Flick, Ilya Kaliman, Yihan Shao, Andrew T. B. Gilbert, Anna I. Krylov, Lyudmila V. Slipchenko:
Effective fragment potential method in Q-CHEM: A guide for users and developers. 1060-1070
- Kunal Roy, Pratim Chakraborty, Indrani Mitra, Probir Kumar Ojha, Supratik Kar, Rudra Narayan Das:
Some case studies on application of "rm2" metrics for judging quality of quantitative structure-activity relationship predictions: Emphasis on scaling of response data. 1071-1082
Volume 34, Number 13, May 2013
- Jeremy P. Coe, Daniel J. Taylor, Martin J. Paterson:
Monte carlo configuration interaction applied to multipole moments, ionisation energies and electron affinities. 1083-1093 - Liudmyla K. Sviatenko, Leonid Gorb, Frances Hill, Jerzy Leszczynski:
Theoretical study of ionization and one-electron oxidation potentials of N-heterocyclic compounds. 1094-1100 - Rui Yang, Alistair P. Rendell:
First principles study of gallium cleaning for hydrogen-contaminated α-Al2O3(0001) surfaces. 1101-1111 - Michel Masella, Daniel Borgis, Philippe Cuniasse:
A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics. 1112-1124 - Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard G. Maroun, Nohad Gresh:
Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds? 1125-1135 - Xue X. Yao, Chang G. Ji, Dai Q. Xie, John Z. H. Zhang:
Molecular dynamics study of DNA binding by INT-DBD under a polarized force field. 1136-1142 - Eldhose Iype, Markus Hütter, A. P. J. Jansen, Silvia V. Nedea, C. C. M. Rindt:
Parameterization of a reactive force field using a monte carlo algorithm. 1143-1154
- Torsten Kerber, Rachel Nathaniel Kerber, Xavier Rozanska, Philippe Sautet, Paul Fleurat-Lessard:
QMX: A versatile environment for hybrid calculations applied to the grafting of Al2Cl3Me3 on a silica surface. 1155-1163
- Nicholas F. Chilton, Russell P. Anderson, Lincoln D. Turner, Alessandro Soncini, Keith S. Murray:
PHI: A powerful new program for the analysis of anisotropic monomeric and exchange-coupled polynuclear d- and f-block complexes. 1164-1175
Volume 34, Number 14, May 2013
- Claudia R. Herbers, Chunli Li, Nico F. A. van der Vegt:
Grand challenges in quantum-classical modeling of molecule-surface interactions. 1177-1188
- Jenna A. Bilbrey, Arianna H. Kazez, Jason Locklin, Wesley D. Allen:
Exact ligand cone angles. 1189-1197 - Sandra C. C. Nunes, P. Pinto, A. A. C. C. Pais:
Nonrandom adsorption of polyelectrolyte chains on finite regularly charged surfaces. 1198-1209 - Daniel Strobusch, Mathias Nest, Christoph Scheurer:
The adaptive hierarchical expansion of the kinetic energy operator. 1210-1217 - Yutaka Imamura, Rie Kobayashi, Hiromi Nakai:
Linearity condition for orbital energies in density functional theory (III): Benchmark of total energies. 1218-1225 - Trent E. Balius, William J. Allen, Sudipto Mukherjee, Robert C. Rizzo:
Grid-based molecular footprint comparison method for docking and de novo design: Application to HIVgp41. 1226-1240 - Xinbi Li, Sergei Y. Ponomarev, Qina Sa, Daniel L. Sigalovsky, George A. Kaminski:
Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side-chain analogues. 1241-1250 - Le Chang, Takeshi Ishikawa, Kazuo Kuwata, Shoji Takada:
Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions. 1251-1257 - Marcel Schumann, Roger S. Armen:
Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure. 1258-1269
Volume 34, Number 15, June 2013
- Yao Wu, Xiaodong Dai, Niu Huang, Lifeng Zhao:
A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space. 1271-1282 - Maria Ana Castro, Adrian E. Roitberg, Fabio D. Cukiernik:
Simulation of mesogenic diruthenium tetracarboxylates: Development of a force field for coordination polymers of the MMX type. 1283-1290 - Kalipada Adhikari, Sudip Chattopadhyay, Barin Kumar De, Amitava Sharma, Ranendu Kumar Nath, Dhiman Sinha:
Search of truncation of (N-1) electron basis containing full connected triple excitations in computing main and satellite ionization potentials via fock-space coupled cluster approach. 1291-1310 - Ida-Marie Høyvik, Branislav Jansik, Kasper Kristensen, Poul Jørgensen:
Local hartree-fock orbitals using a three-level optimization strategy for the energy. 1311-1320 - David Casanova, Pere Alemany, Andrés Falceto, Abel Carreras, Santiago Alvarez:
Pseudosymmetry analysis of molecular orbitals. 1321-1331 - Sven Jakobtorweihen, Thomas Ingram, Irina Smirnova:
Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients. 1332-1340 - Karunakaran Remya, Cherumuttathu H. Suresh:
Which density functional is close to CCSD accuracy to describe geometry and interaction energy of small non-covalent dimers? A benchmark study using gaussian09. 1341-1353 - Silvia A. Martins, Sergio F. Sousa:
Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules. 1354-1362
Volume 34, Number 16, June 2013
- Olle Falklöf, Bo Durbeej:
Modeling of phytochrome absorption spectra. 1363-1374 - Tetsuya Morishita, Satoru G. Itoh, Hisashi Okumura, Masuhiro Mikami:
On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics. 1375-1384 - Paul M. Zimmerman:
Automated discovery of chemically reasonable elementary reaction steps. 1385-1392 - Axel Schild, Beate Paulus:
Multireference calculations for ring inversion and double bond shifting in cyclooctatetraene. 1393-1397 - José Antonio Garate, Chris Oostenbrink:
Free-energy differences between states with different conformational ensembles. 1398-1408 - Milan Randic, Marjana Novic, Dejan Plavsic:
Common vertex matrix: A novel characterization of molecular graphs by counting. 1409-1419
- Mark P. Waller, Thomas Dresselhaus, Jack Yang:
JACOB: An enterprise framework for computational chemistry. 1420-1428 - Eric D. Glendening, Clark R. Landis, Frank Weinhold:
NBO 6.0: Natural bond orbital analysis program. 1429-1437
Volume 34, Number 17, June 2013
- Ivana Antol:
Photodeactivation paths in norbornadiene. 1439-1445 - Aggelos Avramopoulos, Heribert Reis, Josep M. Luis, Manthos G. Papadopoulos:
On the Vibrational linear and nonlinear optical properties of compounds involving noble gas atoms: HXeOXeH, HXeOXeF, and FXeOXeF. 1446-1455 - Ida-Marie Høyvik, Branislav Jansik, Poul Jørgensen:
Pipek-Mezey localization of occupied and virtual orbitals. 1456-1462 - Yi He, Lidia Prieto, Themis Lazaridis:
Modeling peptide binding to anionic membrane pores. 1463-1475 - Marco De La Pierre, Cédric Carteret, Roberto Orlando, Roberto Dovesi:
Use of ab initio methods for the interpretation of the experimental IR reflectance spectra of crystalline compounds. 1476-1485 - Patrick Merlot, Thomas Kjærgaard, Trygve Helgaker, Roland Lindh, Francesco Aquilante, Simen Reine, Thomas Bondo Pedersen:
Attractive electron-electron interactions within robust local fitting approximations. 1486-1496 - Ahmed A. K. Mohammed, Peter A. Limacher, Benoît Champagne:
Finding optimal finite field strengths allowing for a maximum of precision in the calculation of polarizabilities and hyperpolarizabilities. 1497-1507
- Peter Schwerdtfeger, Lukas Wirz, James Avery:
Program fullerene - a software package for constructing and analyzing structures of regular fullerenes. 1508-1526
Volume 34, Number 18, July 2013
- Marat R. Talipov, Dmitry G. Khomyakov, Ming Xian, Qadir K. Timerghazin:
Computational design of S-nitrosothiol "Click" reactions. 1527-1530
- Petr Stepánek, Petr Bour:
Computation of magnetic circular dichroism by sum-over-states summations. 1531-1539 - Alexandra T. P. Carvalho, Ana F. S. Teixeira, Maria João Ramos:
Parameters for molecular dynamics simulations of iron-sulfur proteins. 1540-1548 - Azaria Solomon Eisenberg, Laura J. Juszczak:
Relating Trp-Glu dipeptide fluorescence to molecular conformation: The role of the discrete chi 1 and chi 2 angles. 1549-1560 - Paolo Nicolini, Diego Frezzato, Cristina Gellini, Marco Bizzarri, Riccardo Chelli:
Toward quantitative estimates of binding affinities for protein-ligand systems involving large inhibitor compounds: A steered molecular dynamics simulation route. 1561-1576 - Sonam Bhatia, Yogesh J. Malkhede, Prasad V. Bharatam:
Existence of dynamic tautomerism and divalent N(I) character in N-(pyridin-2-yl)thiazol-2-amine. 1577-1588 - Han Myoung Lee, Kwang S. Kim:
Dynamics and structural changes of small water clusters on ionization. 1589-1597 - Peter Comba, Bodo Martin, Avik Sanyal:
An efficient fluctuating charge model for transition metal complexes. 1598-1608
- Yannick G. Spill, Guillaume Bouvier, Michael Nilges:
Erratum: A convective replica-exchange method for sampling new energy basins. 1609
Volume 34, Number 19, July 2013
- Yu-Ai Duan, Yun Geng, Hai-Bin Li, Jun-Ling Jin, Yong Wu, Zhongmin Su:
Theoretical characterization and design of small molecule donor material containing naphthodithiophene central unit for efficient organic solar cells. 1611-1619 - Xueqin Pang, Ke-Li Han, Qiang Cui:
A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB family. 1620-1635 - Li Rao, Igor Ying Zhang, Wenping Guo, Li Feng, Eric Meggers, Xin Xu:
Nonfitting protein-ligand interaction scoring function based on first-principles theoretical chemistry methods: Development and application on kinase inhibitors. 1636-1646 - Justin E. Elenewski, John C. Hackett:
Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin. 1647-1660 - Brajesh K. Rai, Gregory A. Bakken:
Fast and accurate generation of ab initio quality atomic charges using nonparametric statistical regression. 1661-1671 - Rebecca Sure, Stefan Grimme:
Corrected small basis set Hartree-Fock method for large systems. 1672-1685 - Yongqing Li, Jiuchuang Yuan, Maodu Chen, Fengcai Ma, Mengtao Sun:
Accurate double many-body expansion potential energy surface by extrapolation to the complete basis set limit and dynamics calculations for ground state of NH2. 1686-1696
- Wouter Boomsma, Jes Frellsen, Tim Harder, Sandro Bottaro, Kristoffer E. Johansson, Pengfei Tian, Kasper Stovgaard, Christian Andreetta, Simon Olsson, Jan B. Valentin, Lubomir D. Antonov, Anders S. Christensen, Mikael Borg, Jan H. Jensen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Thomas Hamelryck:
PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure. 1697-1705
Volume 34, Number 20, July 2013
- Ranieri V. de Carvalho, Daniel Lopez-Ferrer, Katia S. Guimarães, Roberto D. Lins:
IMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol. 1707-1718 - Christiane Regina Soares Brasil, Alexandre Cláudio Botazzo Delbem, Fernando Luís Barroso da Silva:
Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction. 1719-1734 - Ruifeng Lu, Yunhui Wang, Kaiming Deng:
Quantum wave packet and quasiclassical trajectory studies of the reaction H(2S) + CH(X2Π; v = 0, j = 1) → C(1D) + H2(X1Σg+): Coriolis coupling effects and stereodynamics. 1735-1742 - Victoria A. Roberts, Elaine E. Thompson, Michael E. Pique, Martin S. Perez, Lynn F. Ten Eyck:
DOT2: Macromolecular docking with improved biophysical models. 1743-1758 - Neil Qiang Su, Igor Ying Zhang, Xin Xu:
Analytic derivatives for the XYG3 type of doubly hybrid density functionals: Theory, implementation, and assessment. 1759-1774 - Ireneusz W. Bulik, Robert Zalesny, Wojciech Bartkowiak, Josep M. Luis, Bernard Kirtman, Gustavo E. Scuseria, Aggelos Avramopoulos, Heribert Reis, Manthos G. Papadopoulos:
Performance of density functional theory in computing nonresonant vibrational (hyper)polarizabilities. 1775-1784 - Mark A. Olson, Michael S. Lee:
Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models. 1785-1793
- Sierra Rayne:
Comment on "QSAR model reproducibility and applicability: A case study of rate constants of hydroxyl radical reaction models applied to polybrominated diphenyl ethers and (Benzo-)triazoles". 1794-1795 - Paola Gramatica, Simona Kovarich, Partha Pratim Roy:
Reply to the comment of S. Rayne on "QSAR model reproducibility and applicability: A case study of rate constants of hydroxyl radical reaction models applied to polybrominated diphenyl ethers and (Benzo-)triazoles". 1796
Volume 34, Number 21, August 2013
- Wiktor Beker, Karol M. Langner, Edyta Dyguda-Kazimierowicz, Mikolaj Feliks, W. Andrzej Sokalski:
Low cost prediction of relative stabilities of hydrogen bonded complexes from atomic multipole moments for overly short intermolecular distances. 1797-1799
- Rafael López, Guillermo Ramírez, Ignacio Ema, Jaime Fernández Rico:
Improved partition-expansion of two-center distributions involving slater functions. 1800-1809 - Christoph Grebner, Lukas P. Pason, Bernd Engels:
PathOpt - A global transition state search approach: Outline of algorithm. 1810-1818 - Mirko Franchini, Pierre Herman Theodoor Philipsen, Lucas Visscher:
The Becke Fuzzy Cells Integration Scheme in the Amsterdam Density Functional Program Suite. 1819-1827 - Atsushi Ishikawa, Hiroshi Nakatsuji:
XPS of oxygen atoms on Ag(111) and Ag(110) surfaces: Accurate study with SAC/SAC-CI combined with dipped adcluster model. 1828-1834 - Arnim Hellweg:
Heuristic control of kinetic energy in dynamic reaction coordinate calculations. 1835-1841 - Vladimir V. Rybkin, Ulf Ekström, Trygve Helgaker:
Internal-to-cartesian back transformation of molecular geometry steps using high-order geometric derivatives. 1842-1849 - Shaun M. Kandathil, Timothy L. Fletcher, Yongna Yuan, Joshua D. Knowles, Paul L. A. Popelier:
Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine. 1850-1861
- Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl-Binder, Wolfgang Schreiner, Bernhard Knapp:
Differential geometric analysis of alterations in MH α-helices. 1862-1879
Volume 34, Number 22, August 2013
- Benjamin L. Moore, Lawrence A. Kelley, James Barber, James W. Murray, James T. MacDonald:
High-quality protein backbone reconstruction from alpha carbons using gaussian mixture models. 1881-1889 - Stanislav Standara, Petr Kulhánek, Radek Marek, Michal Straka:
129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent. 1890-1898 - Zhixiong Lin, Wilfred F. van Gunsteren:
Influence of variation of a side chain on the folding equilibrium of a β-peptide: Limitations of one-step perturbation. 1899-1906 - Chandan Sahu, Kaushik Sen, Srimanta Pakhira, Bhaskar Mondal, Abhijit K. Das:
Binding affinity of substituted ureido-benzenesulfonamide ligands to the carbonic anhydrase receptor: A theoretical study of enzyme inhibition. 1907-1916 - Anton S. Nizovtsev:
Activation of C-H bond in methane by Pd atom from the bonding evolution theory perspective. 1917-1924 - Priyanka Dhingra, Bhyravabhotla Jayaram:
A homology/ab initio hybrid algorithm for sampling near-native protein conformations. 1925-1936 - Steven Vancoillie, Mickaël G. Delcey, Roland Lindh, Victor Vysotskiy, Per-Åke Malmqvist, Valera Veryazov:
Parallelization of a multiconfigurational perturbation theory. 1937-1948 - Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov:
Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi. 1949-1960
- José J. Baldoví, Salvador Cardona-Serra, Juan M. Clemente-Juan, Eugenio Coronado, Alejandro Gaita-Ariño, Andrew V. Palii:
SIMPRE: A software package to calculate crystal field parameters, energy levels, and magnetic properties on mononuclear lanthanoid complexes based on charge distributions. 1961-1967
Volume 34, Number 23, September 2013
- Yuichi Harano, Roland Roth, Shuntaro Chiba:
A morphometric approach for the accurate solvation thermodynamics of proteins and ligands. 1969-1974 - Daniel A. Götz, Rolf Schäfer, Peter Schwerdtfeger:
The performance of density functional and wavefunction-based methods for 2D and 3D structures of Au10. 1975-1981 - Takahiro Yamada, Donald K. Phelps, Adri C. T. van Duin:
First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface. 1982-1996 - Yi Ren, Xi-Guang Wei, Si-Jia Ren, Kai-Chung Lau, Ning-Bew Wong, Wai-Kee Li:
The α-effect exhibited in gas-phase SN2@N and SN2@C reactions. 1997-2005 - Angelika Baranowska-Laczkowska, Krzysztof Z. Laczkowski:
The ORP basis set designed for optical rotation calculations. 2006-2013 - Alexander V. Mitin:
Polarization functions for the modified m6-31G basis sets for atoms Ga through Kr. 2014-2019 - Ringo Rey-Villaverde, Hubert Cybulski, Jesús R. Flores, Berta Fernández:
A high-accuracy theoretical study of the CHnP Systems n = 1-3. 2020-2031 - Likai Du, Jun Gao, Fuzhen Bi, Lili Wang, Chengbu Liu:
A polarizable ellipsoidal force field for halogen bonds. 2032-2040
- Ernesto Suárez, Natalia Díaz, Jefferson Méndez, Dimas Suárez:
CENCALC: A computational tool for conformational entropy calculations from molecular simulations. 2041-2054
Volume 34, Number 24, September 2013
- Ge-Fei Hao, Sheng-Gang Yang, Guangfu Yang, Chang-Guo Zhan:
Computational gibberellin-binding channel discovery unraveling the unexpected perception mechanism of hormone signal by gibberellin receptor. 2055-2064 - Bin Tu, Minxin Chen, Yan Xie, Linbo Zhang, Bob Eisenberg, Benzhuo Lu:
A parallel finite element simulator for ion transport through three-dimensional ion channel systems. 2065-2078 - Sérgio Filipe Sousa, Gaspar R. P. Pinto, António J. M. Ribeiro, João T. S. Coimbra, Pedro Alexandrino Fernandes, Maria João Ramos:
Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes. 2079-2090 - Riadh Dardouri, Héla Habli, Brahim Oujia, Florent Xavier Gadéa:
Ab Initio Diabatic energies and dipole moments of the electronic states of RbLi molecule. 2091-2099 - Xin Feng, Kelin Xia, Zhan Chen, Yiying Tong, Guo-Wei Wei:
Multiscale geometric modeling of macromolecules II: Lagrangian representation. 2100-2120
- Paola Gramatica, Nicola Chirico, Ester Papa, Stefano Cassani, Simona Kovarich:
QSARINS: A new software for the development, analysis, and validation of QSAR MLR models. 2121-2132
- Kalipada Adhikari, Sudip Chattopadhyay, Barin Kumar De, Amitava Sharma, Ranendu Kumar Nath, Dhiman Sinha:
Erratum: Search of truncation of (N-1) electron basis containing full connected triple excitations in computing main and satellite ionization potentials via fock space coupled cluster approach. 2133 - Eric D. Glendening, Clark R. Landis, Frank Weinhold:
Erratum: NBO 6.0: Natural bond orbital analysis program. 2134
Volume 34, Number 25, September 2013
- Jing Huang, Alexander D. MacKerell Jr.:
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. 2135-2145 - Betsy M. Rice, Edward F. C. Byrd:
Evaluation of electrostatic descriptors for predicting crystalline density. 2146-2151 - Shigeki Yamamoto, Petr Bour:
Transition polarizability model of induced resonance Raman optical activity. 2152-2158 - Henry A. Boateng, Robert Krasny:
Comparison of treecodes for computing electrostatic potentials in charged particle systems with disjoint targets and sources. 2159-2167 - J. Grant Hill:
Auxiliary basis sets for density-fitting second-order Møller-Plesset perturbation theory: Weighted core-valence correlation consistent basis sets for the 4d elements Y-Pd. 2168-2177 - Henrik R. Larsson, Adri C. T. van Duin, Bernd Hartke:
Global optimization of parameters in the reactive force field ReaxFF for SiOH. 2178-2189
- José Fernando R. Bachega, Luís Fernando S. M. Timmers, Lucas Assirati, Leonardo R. Bachega, Martin J. Field, Troy Wymore:
GTKDynamo: A PyMOL plug-in for QC/MM hybrid potential simulations. 2190-2196 - You-Liang Zhu, Hong Liu, Zhan-Wei Li, Hu-Jun Qian, Giuseppe Milano, Zhong-Yuan Lu:
GALAMOST: GPU-accelerated large-scale molecular simulation toolkit. 2197-2211 - Sally R. Ellingson, Jeremy C. Smith, Jérôme Baudry:
VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers. 2212-2221
Volume 34, Number 26, October 2013
- Tao Yang, Xiang Zhao, Shigeru Nagase:
1, 3-Dipolar cycloadditions of Stone-Wales defective single-walled carbon nanotubes: A theoretical study. 2223-2232 - Hyungjun Kim, Joungwon Park, Yoon Sup Lee:
A protocol to evaluate one electron redox potential for iron complexes. 2233-2241 - Laetitia Bomble, Stephan N. Steinmann, Nancy Perez-Peralta, Gabriel Merino, Clémence Corminboeuf:
Bonding analysis of planar hypercoordinate atoms via the generalized BLW-LOL. 2242-2248 - Athanasios Anthopoulos, Ian J. Grimstead, Andrea Brancale:
GPU-accelerated molecular mechanics computations. 2249-2260 - Anna Stachowicz, Jacek Korchowiec:
Bond detectors for molecular dynamics simulations, Part I: Hydrogen bonds. 2261-2269 - Subha Kalyaanamoorthy, Yi-Ping Phoebe Chen:
Ligand release mechanisms and channels in histone deacetylases. 2270-2283
- Ilya Kaliman, Lyudmila V. Slipchenko:
LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library. 2284-2292 - Evgeny Epifanovsky, Michael Wormit, Tomasz Kus, Arie Landau, Dmitry Zuev, Kirill Khistyaev, Prashant Manohar, Ilya Kaliman, Andreas Dreuw, Anna I. Krylov:
New implementation of high-level correlated methods using a general block tensor library for high-performance electronic structure calculations. 2293-2309 - Panagiotis I. Koukos, Nicholas M. Glykos:
Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories. 2310-2312
Volume 34, Number 27, October 2013
- Steven K. Burger, G. Andrés Cisneros:
Efficient optimization of van der Waals parameters from bulk properties. 2313-2319 - Volker L. Deringer, Marck Lumeij, Ralf P. Stoffel, Richard Dronskowski:
Ab initio study of the high-temperature phase transition in crystalline GeO2. 2320-2326 - Sebastian Kozuch, Jan M. L. Martin:
Spin-component-scaled double hybrids: An extensive search for the best fifth-rung functionals blending DFT and perturbation theory. 2327-2344 - Tomoya Inui, Yasuteru Shigeta, Katsuki Okuno, Takeshi Baba, Ryohei Kishi, Masayoshi Nakano:
Finite-field method with unbiased polarizable continuum model for evaluation of the second hyperpolarizability of an open-shell singlet molecule in solvents. 2345-2352 - Rahul Kar, Jong-Won Song, Takeshi Sato, Kimihiko Hirao:
Long-range corrected density functionals combined with local response dispersion: A promising method for weak interactions. 2353-2359 - Camilo Velez-Vega, Michael K. Gilson:
Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. 2360-2371 - Tiago Quevedo Teodoro, Roberto Luiz Andrade Haiduke:
Accurate relativistic adapted gaussian basis sets for francium through ununoctium without variational prolapse and to be used with both uniform sphere and gaussian nucleus models. 2372-2379 - Yingdi Jin, Erin R. Johnson, Xiangqian Hu, Weitao Yang, Hao Hu:
Contributions of pauli repulsions to the energetics and physical properties computed in QM/MM methods. 2380-2388 - Rong-Zhen Liao, Walter Thiel:
Convergence in the QM-only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase. 2389-2397
- Neil Qiang Su, Igor Ying Zhang, Xin Xu:
Erratum: analytic derivatives for the XYG3 type of doubly hybrid density functionals: Theory, implementation, and assessment. 2398-2399 - M. E. Chen, W. Yang:
Erratum: On-the-path random walk sampling for efficient optimization of minimum free energy path. 2400
- Marcel Swart, Miquel Solà, Friedrich Matthias Bickelhaupt:
Corrigendum: Inter- and intramolecular dispersion interactions. 2401-2402
Volume 34, Number 28, October 2013
- Masashi Daido, Yukio Kawashima, Masanori Tachikawa:
Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of base pairs. 2403-2411 - Jaewoon Jung, Takaharu Mori, Yuji Sugita:
Efficient lookup table using a linear function of inverse distance squared. 2412-2420 - Patrick Bultinck, Sofie Van Damme, Andrés Cedillo:
Bond fukui indices: Comparison of frozen molecular orbital and finite differences through mulliken populations. 2421-2429 - Annia Galano, J. Raúl Alvarez-Idaboy:
A computational methodology for accurate predictions of rate constants in solution: Application to the assessment of primary antioxidant activity. 2430-2445 - Karl A. Wilkinson, Chris-Kriton Skylaris:
Porting ONETEP to graphical processing unit-based coprocessors. 1. FFT box operations. 2446-2459 - Erix Wiliam Hernández-Rodríguez, Ana Lilian Montero-Alejo, Rafael López, Elsa Sánchez-García, Luis Alberto Montero-Cabrera, José Manuel García de la Vega:
Electron density deformations provide new insights into the spectral shift of rhodopsins. 2460-2471 - Thomas Simonson, Thomas Gaillard, David Mignon, Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Savvas Polydorides, Audrey Sedano, Karen Druart, Georgios Archontis:
Computational protein design: The proteus software and selected applications. 2472-2484
- Thorsten Will, Michael C. Hutter, Johann Jauch, Volkhard Helms:
Batch tautomer generation with MolTPC. 2485-2492
Volume 34, Number 29, November 2013
- Satoru G. Itoh, Hisashi Okumura:
Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides. 2493-2497 - Masahiro Ehara, Ryoichi Fukuda, Carlo Adamo, Ilaria Ciofini:
Chemically intuitive indices for charge-transfer excitation based on SAC-CI and TD-DFT calculations. 2498-2501
- Carlos Campañá, Ronald E. Miller:
Transiting the molecular potential energy surface along low energy pathways: The TRREAT algorithm. 2502-2513 - Milan Randic, Marjana Novic, Marjan Vracko, Dejan Plavsic:
On the centrality of vertices of molecular graphs. 2514-2523 - Liang Xu, Xiaojuan Wang, Shengsheng Shan, Xicheng Wang:
Characterization of the polymorphic states of copper(II)-bound Aβ(1-16) peptides by computational simulations. 2524-2536 - Otilia Mó, Al Mokhtar Lamsabhi, Manuel Yáñez, Gavin S. Heverly-Coulson, Russell J. Boyd:
Dramatic substituent effects on the mechanisms of nucleophilic attack on Se - S bridges. 2537-2547 - José Rogan, Alejandro Varas, Juan Alejandro Valdivia, Miguel Kiwi:
A strategy to find minimal energy nanocluster structures. 2548-2556 - Stefan Maintz, Volker L. Deringer, Andreì L. Tchougréeff, Richard Dronskowski:
Analytic projection from plane-wave and PAW wavefunctions and application to chemical-bonding analysis in solids. 2557-2567 - Masato Tanaka, Michio Katouda, Shigeru Nagase:
Optimization of RI-MP2 Auxiliary Basis Functions for 6-31G** and 6-311G** Basis Sets for First-, Second-, and Third-Row Elements. 2568-2575
Volume 34, Number 30, November 2013
- Ol'ha O. Brovarets', Dmytro M. Hovorun:
Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches. 2577-2590 - Matthew A. Addicoat, Syou Fukuoka, Alister J. Page, Stephan Irle:
Stochastic structure determination for conformationally flexible heterogenous molecular clusters: Application to ionic liquids. 2591-2600 - Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto:
Two-dimensional replica-exchange method for predicting protein-ligand binding structures. 2601-2614 - Yu. D. Fomin:
Molecular dynamics simulation of benzene in graphite and amorphous carbon slit pores. 2615-2624 - David Robinson:
Splitting multiple bonds: A comparison of methodologies on the accuracy of bond dissociation energies. 2625-2634 - Mahesh R. Borkar, Raghuvir R. S. Pissurlenkar, Evans C. Coutinho:
HomoSAR: Bridging comparative protein modeling with quantitative structural activity relationship to design new peptides. 2635-2646 - Woong-Hee Shin, Jae-Kwan Kim, Deok-Soo Kim, Chaok Seok:
GalaxyDock2: Protein-ligand docking using beta-complex and global optimization. 2647-2656
- Victor Vysotskiy, Jonas Boström, Valera Veryazov:
A new module for constrained multi-fragment geometry optimization in internal coordinates implemented in the MOLCAS package. 2657-2665
Volume 34, Number 31, December 2013
- Pekka Pyykkö:
The RTAM electronic bibliography, version 17.0, on relativistic theory of atoms and molecules. 2667
- Leonardo Pacifici, Marco Verdicchio, Noelia Faginas Lago, Andrea Lombardi, Alessandro Costantini:
A high-level ab initio study of the N2 + N2 reaction channel. 2668-2676 - Juan Zeng, Xiangyu Jia, John Z. H. Zhang, Ye Mei:
The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect. 2677-2686 - Marina Cendic, Zoran D. Matovic, Robert J. Deeth:
Molecular modeling for Cu(II)-aminopolycarboxylate complexes: Structures, conformational energies, and ligand binding affinities. 2687-2696 - Yung-Ting Lee, Jyh Shing Lin:
Ab Initio molecular dynamics study of ethylene adsorption onto Si(001) surface: Short-time fourier transform analysis of structural coordinate autocorrelation function. 2697-2706 - Stella Nickerson, Denzil S. Frost, Harrison Phelan, Lenore L. Dai:
Comparison of the capillary wave method and pressure tensor route for calculation of interfacial tension in molecular dynamics simulations. 2707-2715 - Tobias Neumann, Denis Danilov, Christian Lennartz, Wolfgang Wenzel:
Modeling disordered morphologies in organic semiconductors. 2716-2725 - Gevorg Grigoryan:
Absolute free energies of biomolecules from unperturbed ensembles. 2726-2741 - Savvas Polydorides, Thomas Simonson:
Monte carlo simulations of proteins at constant pH with generalized born solvent, flexible sidechains, and an effective dielectric boundary. 2742-2756
Volume 34, Number 32, December 2013
- Christopher G. Mayne, Jan Saam, Klaus Schulten, Emad Tajkhorshid, James C. Gumbart:
Rapid parameterization of small molecules using the force field toolkit. 2757-2770 - David Schmidling:
A new set of bending Td symmetry coordinates for MX4 molecules. 2771-2773 - Vincent Austin Hall, Anthony Nash, Evor L. Hines, Alison Rodger:
Elucidating protein secondary structure with circular dichroism and a neural network. 2774-2786 - Yutaka Imamura, Jun Suzuki, Hiromi Nakai:
Kinetic energy decomposition scheme based on information theory. 2787-2795 - Zhixiong Lin, Wilfred F. van Gunsteren:
Refinement of the application of the GROMOS 54A7 force field to β-peptides. 2796-2805 - Jen-Ping Su, Yung-Ting Lee, Shao-Yu Lu, Jyh Shing Lin:
Chemical mechanism of surface-enhanced raman scattering spectrum of pyridine adsorbed on Ag cluster: Ab initio molecular dynamics approach. 2806-2815
- Nandun M. Thellamurege, Dejun Si, Fengchao Cui, Hongbo Zhu, Rui Lai, Hui Li:
QuanPol: A full spectrum and seamless QM/MM program. 2816-2833
- Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl-Binder, Wolfgang Schreiner, Bernhard Knapp:
Corrigendum: Differential geometric analysis of alterations in MH α-helices. 2834
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