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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 Dias 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-