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ORCIDJournal of Computational Chemistry, Volume 35
Volume 35, Number 1, January 2014
- Anton Jesser, Martin Rohrmüller, Wolf Gero Schmidt
, Sonja Herres-Pawlis:
Geometrical and optical benchmarking of copper guanidine-quinoline complexes: Insights from TD-DFT and many-body perturbation theory. 1-17 - Franziska D. Hofmann, Michael Devereux, Andreas Pfaltz, Markus Meuwly:
Toward force fields for atomistic simulations of iridium-containing complexes. 18-29 - Francesco Fracchia, Claudia Filippi, Claudio Amovilli:
Multi-level quantum monte Carlo wave functions for complex reactions: The decomposition of α-hydroxy-dimethylnitrosamine. 30-38 - Jinzen Ikebe, Shun Sakuraba, Hidetoshi Kono:
Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules. 39-50 - Soumya Ganguly Neogi, Pinaki Chaudhury:
Structural, spectroscopic aspects, and electronic properties of (TiO2)n clusters: A study based on the use of natural algorithms in association with quantum chemical methods. 51-61 - Pei-Kun Yang:
Incorporating the excluded solvent volume and surface charges for computing solvation free energy. 62-69 - Zhijun Xu, Yang Yang, Ziqiu Wang, Donald Mkhonto, Cheng Shang, Zhi-Pan Liu, Qiang Cui, Nita Sahai:
Small molecule-mediated control of hydroxyapatite growth: Free energy calculations benchmarked to density functional theory. 70-81
- Sébastien Canneaux, Frédéric Bohr, Eric Henon:
KiSThelP: A program to predict thermodynamic properties and rate constants from quantum chemistry results. 82-93
Volume 35, Number 2, January 2014
- Andreas W. Götz, Matthew A. Clark, Ross C. Walker:
An extensible interface for QM/MM molecular dynamics simulations with AMBER. 95-108 - Panwang Zhou, Jianyong Liu, Ke-Li Han, Guo-Zhong He:
The photoisomerization of 11-cis-retinal protonated schiff base in gas phase: Insight from spin-flip density functional theory. 109-120 - Feiwu Chen, Zhihui Fan:
A new size extensive multireference perturbation theory. 121-129 - Fabien Cailliez, Arnaud Bourasseau, Pascal Pernot:
Calibration of forcefields for molecular simulation: Sequential design of computer experiments for building cost-efficient kriging metamodels. 130-149 - Katja Ostermeir, Martin Zacharias:
Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles. 150-158 - Shuai Jiang, Yi-Rong Liu, Teng Huang, Hui Wen, Kang-Ming Xu, Wei-Xiong Zhao, Wei-Jun Zhang, Wei Huang:
Study of Cl-(H2O)n (n = 1-4) using basin-hopping method coupled with density functional theory. 159-165 - Satoshi Maeda, Tetsuya Taketsugu, Keiji Morokuma:
Exploring transition state structures for intramolecular pathways by the artificial force induced reaction method. 166-173 - Wenliang Li, Jingping Zhang:
Multiscale simulation of pollution gases adsorption in porous organic cage CC3. 174-180
Volume 35, Number 3, January 2014
- Ivan D. Welsh, Matthias Lein:
Accurate density functional theory description of binding constants and NMR chemical shifts of weakly interacting complexes of C60 with corannulene-based molecular bowls. 181-191 - Elisabeth Ortega-Carrasco, Agustí Lledós, Jean-Didier Maréchal:
Assessing protein-ligand docking for the binding of organometallic compounds to proteins. 192-198 - Angelika Baranowska-Laczkowska, Berta Fernández:
Basis sets for the evaluation of van der Waals complex interaction energies: Ne-N2 intermolecular potential and microwave spectrum. 199-203 - Edoardo Fertitta, Elena Voloshina, Beate Paulus:
Adsorption of multivalent alkylthiols on Au(111) surface: Insights from DFT. 204-213 - Vishwesh Venkatraman, Per-Olof Åstrand, Bjørn Kåre Alsberg:
Quantitative structure-property relationship modeling of Grätzel solar cell dyes. 214-226 - Maria M. Reif, Chris Oostenbrink:
Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. 227-243 - Mahdi Shirazi, Simon D. Elliott:
Atomistic kinetic Monte Carlo study of atomic layer deposition derived from density functional theory. 244-259
- Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, Erik Lindahl:
An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. 260-269
Volume 35, Number 4, February 2014
- Taro Udagawa, Masanori Tachikawa:
Why is N···Be distance of NH3H+···DBeH shorter than that of NH3D+···HBeH? paradoxical geometrical isotope effects for partially isotope-substituted dihydrogen-bonded isotopomers. 271-274
- Marco Heinen, Elshad Allahyarov, Hartmut Löwen:
Highly asymmetric electrolytes in the primitive model: Hypernetted chain solution in arbitrary spatial dimensions. 275-289 - Otávio Beruski, Luciano N. Vidal:
Algorithms for computer detection of symmetry elements in molecular systems. 290-299 - Pai-Chi Li, Naoyuki Miyashita, Wonpil Im, Satoshi Ishido, Yuji Sugita:
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers. 300-308 - Jorge A. Vila, Yelena A. Arnautova, Osvaldo A. Martin, Harold A. Scheraga:
Are accurate computations of the 13C′ shielding feasible at the DFT level of theory? 309-312 - Vitaly N. Glushkov, Xavier Assfeld:
Multireference space without first solving the configuration interaction problem. 313-323 - Dimas Suárez, Natalia Díaz, Ramón López:
A combined semiempirical and DFT computational protocol for studying bioorganometallic complexes: Application to molybdocene-cysteine complexes. 324-334 - Shide Liang, Chi Zhang, Yaoqi Zhou:
LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains. 335-341
Volume 35, Number 5, February 2014
- Yongna Yuan, Matthew J. L. Mills, Paul L. A. Popelier:
Multipolar electrostatics for proteins: Atom-atom electrostatic energies in crambin. 343-359 - Dina T. Mirijanian, Ranjan V. Mannige, Ronald N. Zuckermann, Stephen Whitelam:
Development and use of an atomistic CHARMM-based forcefield for peptoid simulation. 360-370 - Israel Fernández, Friedrich Matthias Bickelhaupt:
Origin of the "endo rule" in Diels-Alder reactions. 371-376 - David J. Huggins:
Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation. 377-385 - Alessandra Forni, Stefano Pieraccini, Stefano Rendine, Maurizio Sironi:
Halogen bonds with benzene: An assessment of DFT functionals. 386-394 - Andrei V. Bandura, Robert A. Evarestov:
TiS2 and ZrS2 single- and double-wall nanotubes: First-principles study. 395-405
- Antti-Pekka Hynninen, Michael F. Crowley:
New faster CHARMM molecular dynamics engine. 406-413
Volume 35, Number 6, March 2014
- Shu-Shi Li, Cui-Ying Huang, Jiao-Jiao Hao, Chang-Sheng Wang:
A polarizable dipole-dipole interaction model for evaluation of the interaction energies for N‒H···O˭C and C‒H···O˭C hydrogen-bonded complexes. 415-426 - Pablo García-Risueño, Joseba Alberdi-Rodriguez, Micael J. T. Oliveira, Xavier Andrade, Michael Pippig, Javier Muguerza, Agustin Arruabarrena, Angel Rubio:
A survey of the parallel performance and accuracy of Poisson solvers for electronic structure calculations. 427-444 - Jie Chen, Yulong Xu, Dunyou Wang:
A multilayered representation, quantum mechanical and molecular mechanics study of the CH3F + OH- reaction in water. 445-450 - Ol'ha O. Brovarets', Roman O. Zhurakivsky, Dmytro M. Hovorun:
Is the DPT tautomerization of the long A·G Watson-Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question. 451-466 - Tonghao Shen, Neil Qiang Su, Anan Wu, Xin Xu:
Perturbative treatment of anharmonic vibrational effects on bond distances: An extended langevin dynamics method. 467-478 - Eric Van Dornshuld, Gregory S. Tschumper:
Characterization of the potential energy surfaces of two small but challenging noncovalent dimers: (P2)2 and (PCCP)2. 479-487 - Leslie Sánchez, Gonzalo A. Jaña, Eduardo J. Delgado:
A QM/MM study on the reaction pathway leading to 2-Aceto-2-hydroxybutyrate in the catalytic cycle of AHAS. 488-494
- Abdullah Ozkanlar, Aurora E. Clark:
ChemNetworks: A complex network analysis tool for chemical systems. 495-505
Volume 35, Number 7, March 2014
- Luís P. Viegas, António J. C. Varandas:
Coupled-cluster reaction barriers of HO2+H2O+O3: An application of the coupled-cluster//Kohn-Sham density functional theory model chemistry. 507-517 - Mateusz Maciejewski, Paul N. Barlow, Nico Tjandra:
Decoding the components of dynamics in three-domain proteins. 518-525 - Anita K. Nivedha, Spandana Makeneni, Bethany Lachele Foley, Matthew B. Tessier, Robert J. Woods:
Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff. 526-539 - Travis V. Harris, Robert K. Szilagyi:
Iron-sulfur bond covalency from electronic structure calculations for classical iron-sulfur clusters. 540-552 - Katharina Krause, Thomas Bredow:
Conductor-like screening model for relaxed excited states: Implementation in the semiempirical method MSINDO. 553-564 - Alexey I. Baranov:
Electron localizability indicators from spinor wavefunctions. 565-585 - Talapunur Vikramaditya, Kanakamma Sumithra:
Effect of substitutionally boron-doped single-walled semiconducting zigzag carbon nanotubes on ammonia adsorption. 586-594
Volume 35, Number 8, March 2014
- Uppula Purushotham, G. Narahari Sastry:
A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms. 595-610 - Elda Rossi, Stefano Evangelisti, Antonio Laganà, Antonio Monari, Sergio Rampino, Marco Verdicchio, Kim K. Baldridge, Gian Luigi Bendazzoli, Stefano Borini, Renzo Cimiraglia, Celestino Angeli, Peter Kallay, Hans Peter Lüthi, Kenneth Ruud, José Sánchez-Marín, Anthony Scemama, Péter G. Szalay, Attila Tajti:
Code interoperability and standard data formats in quantum chemistry and quantum dynamics: The Q5/D5Cost data model. 611-621 - Magnus Ringholm, Dan Jonsson, Kenneth Ruud:
A general, recursive, and open-ended response code. 622-633 - Tony Anacker, Joachim Friedrich:
New accurate benchmark energies for large water clusters: DFT is better than expected. 634-643 - Kevin J. Maurice:
SSThread: Template-free protein structure prediction by threading pairs of contacting secondary structures followed by assembly of overlapping pairs. 644-656
- Maarten G. Wolf, Gerrit Groenhof:
Explicit proton transfer in classical molecular dynamics simulations. 657-671 - Kliment Olechnovic, Ceslovas Venclovas:
Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls. 672-681
Volume 35, Number 9, April 2014
- Sateesh Bandaru, Niall J. English, J. M. D. MacElroy:
Implicit and explicit solvent models for modeling a bifunctional arene ruthenium hydrogen-storage catalyst: A classical and ab initio molecular simulation study. 683-691 - Hugh S. C. Martin, Shantenu Jha, Peter V. Coveney:
Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force. 692-702 - Kun Liu, Yu-Xue Li, Jia-Ling Su, Bin Wang:
The reliability of DFT methods to predict electronic structures and minimum energy crossing point for [FeIVO](OH)2 models: A comparison study with MCQDPT method. 703-710 - Pablo M. De Biase, Suren Markosyan, Sergei Yu Noskov:
Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials. 711-721 - Alexander Kurnosov, Mario Cacciatore, Antonio Laganà, Fernando Pirani, Massimiliano Bartolomei, Ernesto Garcia:
The effect of the intermolecular potential formulation on the state-selected energy exchange rate coefficients in N2-N2 collisions. 722-736 - Xiangyu Jia, Juan Zeng, John Z. H. Zhang, Ye Mei:
Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis. 737-747 - Chaim Dryzun:
Continuous symmetry measures for complex symmetry group. 748-755
- Bruce M. Allen, Paul K. Predecki, Maciej S. Kumosa:
Integrating open-source software applications to build molecular dynamics systems. 756-764
Volume 35, Number 10, April 2014
- Anna Katharina Hildebrandt, Matthias Dietzen, Thomas Lengauer, Hans-Peter Lenhof, Ernst Althaus, Andreas Hildebrandt:
Efficient computation of root mean square deviations under rigid transformations. 765-771 - José Diogo L. Dutra, Thiago D. Bispo, Ricardo Oliveira Freire:
LUMPAC lanthanide luminescence software: Efficient and user friendly. 772-775 - Tsvetan K. Zahariev, Radomir I. Slavchov, Alia V. Tadjer, Anela N. Ivanova:
Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation. 776-788 - Oliwia M. Szklarczyk, Stephan J. Bachmann, Wilfred F. van Gunsteren:
A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons. 789-801 - Gian Luigi Bendazzoli, Muammar El Khatib, Stefano Evangelisti, Thierry Leininger:
The total Position Spread in mixed-valence compounds: A study on the H4+ model system. 802-808 - Cheng-chau Chiu, Georgi N. Vayssilov, Alexander Genest, Armando Borgna, Notker Rösch:
Predicting adsorption enthalpies on silicalite and HZSM-5: A benchmark study on DFT strategies addressing dispersion interactions. 809-819 - Eric Iván Sánchez-Flores, Rodrigo Chávez-Calvillo, Todd A. Keith, Gabriel Cuevas, Tomás Rocha-Rinza, Fernando Cortés-Guzmán:
Properties of atoms in electronically excited molecules within the formalism of TDDFT. 820-828
Volume 35, Number 11, April 2014
- Panaghiotis Karamanis, Nicolás Otero, Claude Pouchan, Juan José Torres, William Tiznado, Aggelos Avramopoulos, Manthos G. Papadopoulos:
Significant nonlinear-optical switching capacity in atomic clusters built from silicon and lithium: A combined ab initio and density functional study. 829-838 - Michael F. Peintinger, Thomas Bredow:
The cyclic cluster model at hartree-fock level. 839-846 - Toshiaki Kawamura, Minori Abe, Masaichi Saito, Masahiko Hada:
Quantum-chemical analyses of aromaticity, UV spectra, and NMR chemical shifts in plumbacyclopentadienylidenes stabilized by Lewis bases. 847-853 - Arne Lüchow:
Maxima of |Ψ|2: A connection between quantum mechanics and Lewis structures. 854-864 - Kazuaki Z. Takahashi:
Design of a reaction field using a linear-combination-based isotropic periodic sum method. 865-875 - Anita Plazinska, Wojciech Plazinski, Krzysztof Józwiak:
Fast, metadynamics-based method for prediction of the stereochemistry-dependent relative free energies of ligand-receptor interactions. 876-882 - Ana E. Torres, Guadalupe Castro, Ricardo Pablo-Pedro, Fernando Colmenares:
A two-step reaction scheme leading to singlet carbene species that can be detected under matrix conditions for the reaction of Zr(3F) with either CH3F or CH3CN. 883-890
Volume 35, Number 12, May 2014
- Sateesh Bandaru, Niall J. English, Andrew D. Phillips, J. M. D. MacElroy:
Towards the design of novel boron- and nitrogen-substituted ammonia-borane and bifunctional arene ruthenium catalysts for hydrogen storage. 891-903 - Yi-Quan Zhang, Cheng-Lin Luo, Qiang Zhang:
Exchange coupling and magnetic anisotropy in a family of bipyrimidyl radical-bridged dilanthanide complexes: Density functional theory and ab initio calculations. 904-909 - Karunakaran Remya, Cherumuttathu H. Suresh:
Cooperativity and cluster growth patterns in acetonitrile: A DFT study. 910-922 - Xinying Li:
Metalophilic interaction in gold halide: Quantum chemical study of AuX (X = F‒at). 923-931 - Sam Z. Grinter, Xiaoqin Zou:
A Bayesian statistical approach of improving knowledge-based scoring functions for protein-ligand interactions. 932-943 - David Casanova:
How much tetraradical character is present in the Si6Ge9 cluster? 944-949
- Petr Popov, Sergei Grudinin:
Rapid determination of RMSDs corresponding to macromolecular rigid body motions. 950-956 - Jong Cheol Jeong, Sunhwan Jo, Emilia L. Wu, Yifei Qi, Viviana Monje-Galvan, Min Sun Yeom, Lev Gorenstein, Feng Chen, Jeffery B. Klauda, Wonpil Im:
ST-analyzer: A web-based user interface for simulation trajectory analysis. 957-963
Volume 35, Number 13, May 2014
- Dong-Xia Zhao, Zhong-Zhi Yang:
Investigation of the distinction between van der Waals interaction and chemical bonding based on the PAEM-MO diagram. 965-977 - David Ferro-Costas, Ignacio Pérez-Juste, Ricardo A. Mosquera:
Electronegativity estimator built on QTAIM-based domains of the bond electron density. 978-985 - Doreen Mollenhauer, Nicola Gaston:
A balanced procedure for the treatment of cluster-ligand interactions on gold phosphine systems in catalysis. 986-997 - Zhi Sun, Henry F. Schaefer III, Yaoming Xie, Yongdong Liu, Rugang Zhong:
The reactions of Cr(CO)6, Fe(CO)5, and Ni(CO)4 with O2 yield viable oxo-metal carbonyls. 998-1009 - Gennady N. Chuev, Ivan Vyalov, Nikolaj Georgi:
Extraction of site-site bridge functions and effective pair potentials from simulations of polar molecular liquids. 1010-1023 - Georgios C. Boulougouris:
Free energy calculations, enhanced by a gaussian ansatz, for the "chemical work" distribution. 1024-1035
- Paola Gramatica, Stefano Cassani, Nicola Chirico:
QSARINS-chem: Insubria datasets and new QSAR/QSPR models for environmental pollutants in QSARINS. 1036-1044
Volume 35, Number 14, May 2014
- Marc Raupach, Stefanie Dehnen, Ralf Tonner:
Quantitative investigation of bonding characteristics in ternary Zintl anions: Charge and energy analysis of [Sn2E152(ZnPh)]- (E15 = Sb, Bi) and [Sn2Sb5(ZnPh)2]3-. 1045-1057 - Haining Liu, C. Heath Turner:
Oxygen adsorption characteristics on hybrid carbon and boron-nitride nanotubes. 1058-1063 - Jaewoon Jung, Takaharu Mori, Yuji Sugita:
Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations. 1064-1072 - Emine Soydas, Ugur Bozkaya:
Assessment of the orbital-optimized coupled-electron pair theory for thermochemistry and kinetics: Improving on CCSD and CEPA(1). 1073-1081 - Po-Jen Hsu:
A new perspective of shape recognition to discover the phase transition of finite-size clusters. 1082-1092 - Takao Tsuneda, Raman K. Singh:
Reactivity index based on orbital energies. 1093-1100
- Biao Fu, Aleksandr B. Sahakyan, Carlo Camilloni, Gian Gaetano Tartaglia, Emanuele Paci, Amedeo Caflisch, Michele Vendruscolo, Andrea Cavalli:
ALMOST: An all atom molecular simulation toolkit for protein structure determination. 1101-1105
Volume 35, Number 15, June 2014
- Hui Zhu, Zheng-Wang Qu:
Toward product control in ring-opening oligomerization of 9H-9-borafluorenes. 1107-1110
- Fei Xia, Dudu Tong, Lifeng Yang, Dayong Wang, Steven C. H. Hoi, Patrice Koehl, Lanyuan Lu:
Identifying essential pairwise interactions in elastic network model using the alpha shape theory. 1111-1121 - Xin Yan, Jiabo Li, Qiong Gu, Jun Xu:
gWEGA: GPU-accelerated WEGA for molecular superposition and shape comparison. 1122-1130 - Adèle D. Laurent, Vitaly N. Glushkov, Thibaut Very, Xavier Assfeld:
Toward the understanding of the environmental effects on core ionizations. 1131-1139 - Shinichi Yamabe, Guixiang Zeng, Wei Guan, Shigeyoshi Sakaki:
SN1-SN2 and SN2-SN3 mechanistic changes revealed by transition states of the hydrolyses of benzyl chlorides and benzenesulfonyl chlorides. 1140-1148 - Martin Carlsen:
Using operators to expand the block matrices forming the Hessian of a molecular potential. 1149-1158 - Solen Ekesan, Seyit Kale, Judith Herzfeld:
Transferable pseudoclassical electrons for aufbau of atomic ions. 1159-1164
Volume 35, Number 16, June 2014
- Chérif F. Matta:
Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential. 1165-1198
- Nicodemo Di Pasquale, Richard J. Gowers, Paola Carbone:
A multiple time step scheme for multiresolved models of Macromolecules. 1199-1207 - Alexander Mirzoev, Alexander Lyubartsev:
Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids. 1208-1218 - Alexey Savelyev, Alexander D. MacKerell Jr.:
All-atom polarizable force field for DNA based on the classical drude oscillator model. 1219-1239 - Takeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru Shigeta:
On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase. 1240-1247 - Phillip V. Smith, Marian W. Radny, G. Ali Shah:
Surface electronic structure calculations using the MBJLDA potential: Application to Si(111)2 × 1. 1248-1254
- Bingjie Hu, Markus A. Lill:
WATsite: Hydration site prediction program with PyMOL interface. 1255-1260
Volume 35, Number 17, June 2014
- Marcos Mandado, Nicolás Ramos-Berdullas:
Analyzing the electric response of molecular conductors using "electron deformation" orbitals and occupied-virtual electron transfer. 1261-1269 - Olga E. Glukhova, Anna S. Kolesnikova, Michael M. Slepchenkov, Vladislav V. Shunaev:
Moving of fullerene between potential wells in the external icosahedral shell. 1270-1277 - Olivia Wise, Orkid Coskuner:
New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue. 1278-1289 - Alba Campo-Cacharrón, Enrique M. Cabaleiro-Lago, Jorge A. Carrazana-García, Jesús Rodríguez-Otero:
Interaction of aromatic units of amino acids with guanidinium cation: The interplay of π···π, X‒H···π, and M+···π contacts. 1290-1301 - Kin-Yiu Wong, Yuqing Xu, Darrin M. York:
Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models. 1302-1316
- Mikhail Panshenskov, Ilia A. Solov'yov, Andrey V. Solov'yov:
Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics. 1317-1329 - César Mogo, João Brandão:
The READY program: Building a global potential energy surface and reactive dynamic simulations for the hydrogen combustion. 1330-1337
Volume 35, Number 18, July 2014
- Ariadna Blanca Romero, Piotr M. Kowalski, George Beridze, Hartmut Schlenz, Dirk Bosbach:
Performance of DFT+U method for prediction of structural and thermodynamic parameters of monazite-type ceramics. 1339-1346 - Yutaka Maruyama, Norio Yoshida, Hiroto Tadano, Daisuke Takahashi, Mitsuhisa Sato, Fumio Hirata:
Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT. 1347-1355 - Emilio San-Fabián, Federico Moscardó:
Cyclobutadiene automerization and rotation of ethylene: Energetics of the barriers by using Spin-polarized wave functions. 1356-1363 - Song-Ho Chong, Sihyun Ham:
Site-directed analysis on protein hydrophobicity. 1364-1370 - Thomas Gaillard, Thomas Simonson:
Pairwise decomposition of an MMGBSA energy function for computational protein design. 1371-1387 - Gregory K. Pierens:
1H and 13C NMR scaling factors for the calculation of chemical shifts in commonly used solvents using density functional theory. 1388-1394
- César R. García-Jacas, Yovani Marrero-Ponce, Liesner Acevedo-Martínez, Stephen J. Barigye, José R. Valdés-Martiní, Ernesto Contreras-Torres:
QuBiLS-MIDAS: A parallel free-software for molecular descriptors computation based on multilinear algebraic maps. 1395-1409
Volume 35, Number 19, July 2014
- Daniel Roston, Amnon Kohen, Dvir Doron, Dan Thomas Major:
Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer. 1411-1417 - Roberta P. Dias, Lin Li, Thereza A. Soares, Emil Alexov:
Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi. 1418-1429 - Hsin-Lin Chiang, Chun-Jung Chen, Hisashi Okumura, Chin-Kun Hu:
Transformation between α-helix and β-sheet structures of one and two polyglutamine peptides in explicit water molecules by replica-exchange molecular dynamics simulations. 1430-1437 - Steven K. Burger, Paul W. Ayers, Jeremy Schofield:
Efficient parameterization of torsional terms for force fields. 1438-1445 - Zdenek Futera, Jaroslav V. Burda:
Reaction mechanism of Ru(II) piano-stool complexes: Umbrella sampling QM/MM MD study. 1446-1456 - Frans T. I. Marx, Johan H. L. Jordaan, Gerhard Lachmann, Hermanus C. M. Vosloo:
A Molecular modeling study of the changes of some steric properties of the precatalysts during the olefin metathesis reaction. 1457-1463 - Frans T. I. Marx, Johan H. L. Jordaan, Gerhard Lachmann, Hermanus C. M. Vosloo:
A comparison of low and high activity precatalysts: Do the calculated energy barriers during the self-metathesis reaction of 1-Octene correlate with the precatalyst metathesis activity? 1464-1471
Volume 35, Number 20, July 2014
- Masaki Okoshi, Hiromi Nakai:
Acceleration of self-consistent field convergence in ab initio molecular dynamics simulation with multiconfigurational wave function. 1473-1480 - Lewis C. Smeeton, Mark T. Oakley, Roy L. Johnston:
Visualizing energy landscapes with metric disconnectivity graphs. 1481-1490 - Hao Hu, Lin Shen:
In silico concurrent multisite pH titration in proteins. 1491-1498 - Frank Weinhold, Paul von Ragué Schleyer, William Chadwick McKee:
Bay-type H···H "bonding" in cis-2-butene and related species: QTAIM versus NBO description. 1499-1508 - Tobias Risthaus, Marc Steinmetz, Stefan Grimme:
Implementation of nuclear gradients of range-separated hybrid density functionals and benchmarking on rotational constants for organic molecules. 1509-1516 - Masao Hayami, Junji Seino, Hiromi Nakai:
Extension of accompanying coordinate expansion and recurrence relation method for general-contraction basis sets. 1517-1527
- Hung Dien, Charlotte M. Deane, Bernhard Knapp:
Gro2mat: A package to efficiently read gromacs output in MATLAB. 1528-1531
Volume 35, Number 21, August 2014
- Alba Campo-Cacharrón, Enrique M. Cabaleiro-Lago, Jesús Rodríguez-Otero:
Interaction between ions and substituted buckybowls: A comprehensive computational study. 1533-1544 - Ahmed A. K. Mohammed, Steven K. Burger, Paul W. Ayers:
Drug release by pH-responsive molecular tweezers: Atomistic details from molecular modeling. 1545-1551 - Jirí Kessler, Petr Bour:
Molecular dynamics with helical periodic boundary conditions. 1552-1559 - Po-Chun Liu, Wei-Ping Hu:
The MC-DFT approach including the SCS-MP2 energies to the new minnesota-type functionals. 1560-1567 - Gurpreet Kaur, Vikas:
On the mechanism of intramolecular nitrogen-atom hopping in the carbon chain of C6N radical: A Plausible 3c-4e crossover π̂ Long-Bond. 1568-1576 - Michael Devereux, Nohad Gresh, Jean-Philip Piquemal, Markus Meuwly:
A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field. 1577-1591
- Shun Sakuraba, Nobuyuki Matubayasi:
Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions. 1592-1608
Volume 35, Number 22, August 2014
- Pooria Farahani, Daniel Roca-Sanjuán, Francesco Aquilante:
A two-scale approach to electron correlation in multiconfigurational perturbation theory. 1609-1617
- Johannes M. Dieterich, Bernd Hartke:
A graph-based short-cut to low-energy structures. 1618-1620
- Sergio A. Hassan:
Implicit treatment of solvent dispersion forces in protein simulations. 1621-1629 - My-Phuong Pham, Buu Q. Pham, Lam Kim Huynh, Ha Q. Pham, Maurice J. Marks, Thanh N. Truong:
Density functional theory study on mechanisms of epoxy-phenol curing reaction. 1630-1640 - Maxim R. Rizhikov, Vladimir A. Slepkov, Svetlana G. Kozlova, Svyatoslav P. Gabuda:
Evolution of chemical bonding and electron density rearrangements during D3h &[RIGHTWARDS ARROW]; D3d reaction in monolayered TiS2: A QTAIM and ELF study. 1641-1645 - Yunju Zhang, Jingyu Sun, Wanqiao Zhang, Yizhen Tang, Rongshun Wang:
Theoretical study on the gas phase reaction of propargyl alcohol with hydroxyl radical. 1646-1656 - Zhao Pei, Tao Yang, Yi-Jun Guo, Jing-Shuang Dang, Xiang Zhao, Shigeru Nagase:
Dimetallic sulfide endohedral metallofullerene Sc2S@C76: Density functional theory characterization. 1657-1663
- Xinying Li:
Metalophilic interaction in gold halide: Quantum chemical study of AuX (X=F-At). 1664
Volume 35, Number 23, September 2014
- Mariano Spivak, Celestino Angeli, Carmen Jiménez Calzado, Coen de Graaf:
Improving the calculation of magnetic coupling constants in MRPT methods. 1665-1671 - Kirill Zinovjev, Iñaki Tuñón:
Exploring chemical reactivity of complex systems with path-based coordinates: Role of the distance metric. 1672-1681 - Weihong Zhang, Jianhan Chen:
Replica exchange with guided annealing for accelerated sampling of disordered protein conformations. 1682-1689 - Zhong-Zhi Yang, Jian-Jiang Wang, Dong-Xia Zhao:
Valence state parameters of all transition metal atoms in metalloproteins - development of ABEEMσπ fluctuating charge force field. 1690-1706 - Soran Jahangiri, Lemin Cai, Gilles H. Peslherbe:
Performance of density-functional tight-binding models in describing hydrogen-bonded anionic-water clusters. 1707-1715 - Sebastian Höfener:
Coupled-cluster frozen-density embedding using resolution of the identity methods. 1716-1724
- Marcela Hrdá, Tomás Kulich, Michal Repiský, Jozef Noga, Olga L. Malkina, Vladimir G. Malkin:
Implementation of the diagonalization-free algorithm in the self-consistent field procedure within the four-component relativistic scheme. 1725-1737
Volume 35, Number 24, September 2014
- Miroslaw Jablonski:
Red and blue shifted hydridic bonds. 1739-1747 - Laura J. Kingsley, Markus A. Lill:
Including ligand-induced protein flexibility into protein tunnel prediction. 1748-1756 - Sean M. Law, Aaron T. Frank, Charles L. Brooks III:
PCASSO: A fast and efficient Cα-based method for accurately assigning protein secondary structure elements. 1757-1761 - Athanassios C. Tsipis:
DFT assessment of the spectroscopic constants and absorption spectra of neutral and charged diatomic species of group 11 and 14 elements. 1762-1777 - Soroosh Pezeshki, Hai Lin:
Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems. 1778-1788 - Marco Lorenz, Bartolomeo Civalleri, Lorenzo Maschio, Mauro Francesco Sgroi, Daniele Pullini:
Benchmarking dispersion and geometrical counterpoise corrections for cost-effective large-scale DFT calculations of water adsorption on graphene. 1789-1800
- Christoph Grebner, Johannes Becker, Daniel Weber, Daniel Bellinger, Maxim Tafipolski, Charlotte Brückner, Bernd Engels:
CAST: A new program package for the accurate characterization of large and flexible molecular systems. 1801-1807
Volume 35, Number 25, September 2014
- Morten N. Pedersen, Erik D. Hedegård, Jacob Kongsted:
Basis set error estimation for DFT calculations of electronic g-tensors for transition metal complexes. 1809-1814 - Stefano Pelloni, Inmaculada García Cuesta:
CCSD-CTOCD static dipole shielding polarizability for quantification of the chiral NMR effects in oxaziridine derivatives. 1815-1823 - David Ryan Koes, Carlos J. Camacho:
Shape-based virtual screening with volumetric aligned molecular shapes. 1824-1834 - Tatsuki Negami, Kentaro Shimizu, Tohru Terada:
Coarse-grained molecular dynamics simulations of protein-ligand binding. 1835-1845 - Carlos T. Nieto, David Díez, Narciso M. Garrido:
To be or not to be butterfly: New mechanistic insights in the Aza-Michael asymmetric addition of lithium (R)-N-benzyl-N-(α-methylbenzyl)amide. 1846-1853 - Pablo G. Garay, Osvaldo A. Martin, Harold A. Scheraga, Jorge A. Vila:
Factors affecting the computation of the 13C shielding in disaccharides. 1854-1864 - Mirco Zerbetto, Andrea Piserchia, Diego Frezzato:
Looking for some free energy? Call JEFREE (...). 1865-1881
Volume 35, Number 26, October 2014
- Kiamars Eskandari, Christian Van Alsenoy:
Hydrogen-hydrogen interaction in planar biphenyl: A theoretical study based on the interacting quantum atoms and Hirshfeld atomic energy partitioning methods. 1883-1889 - Thong Nguyen-Minh Le, Bin Liu, Lam Kim Huynh:
SurfKin: An ab initio kinetic code for modeling surface reactions. 1890-1899 - Jan Wenzel, Michael Wormit, Andreas Dreuw:
Calculating core-level excitations and x-ray absorption spectra of medium-sized closed-shell molecules with the algebraic-diagrammatic construction scheme for the polarization propagator. 1900-1915 - Mohammad Reza Rezapour, Arunkumar Chitteth Rajan, Kwang S. Kim:
Molecular sensing using armchair graphene nanoribbon. 1916-1920 - Ivana Matanovic, Plamen Atanassov, Boris Kiefer, Fernando H. Garzon, Neil J. Henson:
Applicability of density functional theory in reproducing accurate vibrational spectra of surface bound species. 1921-1929
- José J. Baldoví, Juan M. Clemente-Juan, Eugenio Coronado, Alejandro Gaita-Ariño, Andrew V. Palii:
An updated version of the computational package SIMPRE that uses the standard conventions for Stevens crystal field parameters. 1930-1934 - Miroslaw Karbowiak, Czeslaw Rudowicz:
Software package SIMPRE - Revisited. 1935-1941
Volume 35, Number 27, October 2014
- Alexander Hoffmann, Richard Grunzke, Sonja Herres-Pawlis:
Insights into the influence of dispersion correction in the theoretical treatment of guanidine-quinoline copper(I) complexes. 1943-1950 - Chanin Nantasenamat, Saw Simeon, Wiwat Owasirikul, Napat Songtawee, Maris Lapins, Virapong Prachayasittikul, Jarl E. S. Wikberg:
Illuminating the origins of spectral properties of green fluorescent proteins via proteochemometric and molecular modeling. 1951-1966 - Xiao-Jing Liu, Ian P. Hamilton:
Adsorption of small molecules on helical gold nanorods: A relativistic density functional study. 1967-1976 - Manoj K. Shukla, Frances Hill:
Plane-wave density functional theory investigation of adsorption of 2, 4, 6-trinitrotoluene on al-hydroxylated (0001) surface of (4 × 4) α-alumina. 1977-1985 - Wei Chen, Jana K. Shen:
Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics. 1986-1996
- Emilia L. Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C. Song, Eder M. Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M. Venable, Jeffery B. Klauda, Wonpil Im:
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. 1997-2004 - Alessandro Di Domizio, Alessandro Vitriolo, Giulio Vistoli, Alessandro Pedretti:
SPILLO-PBSS: Detecting hidden binding sites within protein 3D-structures through a flexible structure-based approach. 2005-2017
Volume 35, Number 28, October 2014
- Annia Galano, Juan Raúl Alvarez-Idaboy:
Kinetics of radical-molecule reactions in aqueous solution: A benchmark study of the performance of density functional methods. 2019-2026 - Julia Setzler, Carolin Seith, Martin Brieg, Wolfgang Wenzel:
SLIM: An improved generalized Born implicit membrane model. 2027-2039 - James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, Kuldip K. Paliwal, Abdul Sattar, Yaoqi Zhou, Yuedong Yang:
Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. 2040-2046 - Minhajul Arfeen, Dhilon S. Patel, Sheenu Abbat, Nikhil Taxak, Prasad V. Bharatam:
Importance of cytochromes in cyclization reactions: Quantum chemical study on a model reaction of proguanil to cycloguanil. 2047-2055 - Taweetham Limpanuparb, Josh Milthorpe, Alistair P. Rendell:
Resolutions of the Coulomb operator: VIII. Parallel implementation using the modern programming language X10. 2056-2069 - Martin P. Andersson, Susan L. S. Stipp:
Predicting hydration energies for multivalent ions. 2070-2075
- Saleh Riahi, Christopher N. Rowley:
The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties. 2076-2086
Volume 35, Number 29, November 2014
- Laercio Pol-Fachin, Hugo Verli, Roberto D. Lins:
Extension and validation of the GROMOS 53A6glyc parameter set for glycoproteins. 2087-2095 - Nohad Gresh, Krystel El Hage, David Perahia, Jean-Philip Piquemal, Catherine Berthomieu, Dorothée Berthomieu:
Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters. 2096-2106 - Marta Erminia Alberto, Gloria Mazzone, Angelo Domenico Quartarolo, Flavio Fortes Ramos Sousa, Emilia Sicilia, Nino Russo:
Electronic spectra and intersystem spin-orbit coupling in 1, 2- and 1, 3-squaraines. 2107-2113 - Xavier Lucas, Stefan Günther:
Using chiral molecules as an approach to address low-druggability recognition sites. 2114-2121 - Oliver Sala, Hans Peter Lüthi, Antonio Togni:
The solvent effect on two competing reaction mechanisms involving hypervalent iodine reagents (λ3-iodanes): Facing the limit of the stationary quantum chemical approach. 2122-2131 - Junya Yamagishi, Noriaki Okimoto, Gentaro Morimoto, Makoto Taiji:
A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model. 2132-2139 - Israel Fernández, Lando P. Wolters, Friedrich Matthias Bickelhaupt:
Controlling the oxidative addition of aryl halides to Au(I). 2140-2145 - Alexander Hoffmann, Martin Rohrmüller, Anton Jesser, Ines dos Santos Vieira, Wolf Gero Schmidt, Sonja Herres-Pawlis:
Geometrical and optical benchmarking of copper(II) guanidine-quinoline complexes: Insights from TD-DFT and many-body perturbation theory (part II). 2146-2161
Volume 35, Number 30, November 2014
- Ryoichi Fukuda, Masahiro Ehara:
Efficiency of perturbation-selection and its orbital dependence in the SAC-CI calculations for valence excitations of medium-size molecules. 2163-2176 - Huiying Zhao, Yuedong Yang, Mark von Itzstein, Yaoqi Zhou:
Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. 2177-2183 - Olle Falklöf, Bo Durbeej:
Distinguishing between keto-enol and acid-base forms of firefly oxyluciferin through calculation of excited-state equilibrium constants. 2184-2194 - Shinichi Yamabe, Guixiang Zeng, Wei Guan, Shigeyoshi Sakaki:
A DFT study on proton transfers in hydrolysis reactions of phosphate dianion and sulfate monoanion. 2195-2204 - Yonaton Heit, Gregory J. O. Beran:
Exploiting space-group symmetry in fragment-based molecular crystal calculations. 2205-2214 - Vincent A. Voelz, Guangfeng Zhou:
Bayesian inference of conformational state populations from computational models and sparse experimental observables. 2215-2224 - Dan Berco, Chin-Kun Hu:
A spherical harmonic transform spectral analysis of a localized surface plasmon on a gold nano shell. 2225-2230
Volume 35, Number 31, December 2014
- Bing Fu, Li Chen, Feifei Wang, Yiqun Xie, Xiang Ye:
Melting of icosahedral nickel clusters under hydrostatic pressure. 2231-2238 - Jörg Von Appen, Richard Dronskowski, Aurab Chakrabarty, Tilmann Hickel, Robert Spatschek, Jörg Neugebauer:
Impact of Mn on the solution enthalpy of hydrogen in austenitic Fe-Mn alloys: A first-principles study. 2239-2244 - Adrien B. Larsen, Jeffrey R. Wagner, Saugat Kandel, Romelia Salomón-Ferrer, Nagarajan Vaidehi, Abhinandan Jain:
GneimoSim: A modular internal coordinates molecular dynamics simulation package. 2245-2255 - Fabian Zeller, Martin Zacharias:
Efficient calculation of relative binding free energies by umbrella sampling perturbation. 2256-2262 - Damien J. Carter, Andrew L. Rohl:
van der Waals corrected density functional calculations of the adsorption of benzene on the Cu (111) surface. 2263-2271 - Raymundo Hernández-Esparza, Sol-Milena Mejía-Chica, Andy D. Zapata-Escobar, Alfredo Guevara-García, Apolinar Martínez-Melchor, Julio-M. Hernández-Pérez, Rubicelia Vargas, Jorge Garza:
Grid-based algorithm to search critical points, in the electron density, accelerated by graphics processing units. 2272-2278
Volume 35, Number 32, December 2014
- Charleen G. Don, Sereina Riniker:
Scents and sense: In silico perspectives on olfactory receptors. 2279-2287
- Rafael Grande-Aztatzi, Paulina R. Martínez-Alanis, José Luis Cabellos, Edison Osorio, Ana Martínez, Gabriel Merino:
Structural evolution of small gold clusters doped by one and two boron atoms. 2288-2296 - Aleksandra Karolak, Arjan van der Vaart:
Enhanced sampling simulations of DNA step parameters. 2297-2304 - Tod D. Romo, Nicholas Leioatts, Alan Grossfield:
Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations. 2305-2318 - Maria M. Reif, Chris Oostenbrink:
Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies. 2319-2332 - Natalja Vogt, Jean Demaison, Jürgen Vogt, Heinz Dieter Rudolph:
Why it is sometimes difficult to determine the accurate position of a hydrogen atom by the semiexperimental method: Structure of molecules containing the OH or the CH3 group. 2333-2342
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