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ORCIDJournal of Computational Chemistry, Volume 36
Volume 36, Number 1, January 2015
- Lorenzo Rovigatti
, Petr Sulc, István Z. Reguly, Flavio Romano:
A comparison between parallelization approaches in molecular dynamics simulations on GPUs. 1-8 - Chiara Ricca, Armelle Ringuedé, Michel Cassir, Carlo Adamo, Frédéric Labat:
A comprehensive DFT investigation of bulk and low-index surfaces of ZrO2 polymorphs. 9-21 - Qi Song, Zhenyi Jiang, Zhiyong Zhang, Yuqing Hou, Xiaodong Zhang:
From orientation disordered to ordered - An ab initio simulation on ammonia borane phase transition within van der Waals corrections. 22-32 - Hyungjun Kim, Joungwon Park, Yoon Sup Lee:
Prediction of the reduction potential of tris(2, 2′-bipyridinyl)iron(III/II) derivatives. 33-41 - Andrey A. Kirilchuk, Aleksandr A. Yurchenko, Aleksandr N. Kostyuk, Alexander B. Rozhenko:
1, 2-migration in N-phosphano functionalized N-heterocyclic carbenes. 42-48 - Chengfei Yan, Xiaoqin Zou:
Predicting peptide binding sites on protein surfaces by clustering chemical interactions. 49-61
- Iwona E. Weidlich, Yuri Pevzner, Benjamin T. Miller, Igor V. Filippov, H. Lee Woodcock III, Bernard R. Brooks:
Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface. 62-67
Volume 36, Number 2, January 2015
- Gegham Galstyan, Ernst-Walter Knapp:
Computing pKA values of hexa-aqua transition metal complexes. 69-78 - Robin M. Betz, Ross C. Walker:
Paramfit: Automated optimization of force field parameters for molecular dynamics simulations. 79-87 - Rebecca Sure, Ralf Tonner, Peter Schwerdtfeger:
A systematic study of rare gas atoms encapsulated in small fullerenes using dispersion corrected density functional theory. 88-96 - Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta:
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method. 97-102 - Peter Clote:
Expected degree for RNA secondary structure networks. 103-117 - Shabbir Muhammad, Ahmad Irfan, Mohd Shkir, Aijaz R. Chaudhry, Abul Kalam, Salem AlFaify, Abdullah G. Al-Sehemi, A. E. Al-Salami, I. S. Yahia, Hong-Liang Xu, Zhongmin Su:
How does hybrid bridging core modification enhance the nonlinear optical properties in donor-π-acceptor configuration? A case study of dinitrophenol derivatives. 118-128
- Ilya A. Kaliman, Lyudmila V. Slipchenko:
Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library. 129-135
Volume 36, Number 3, January 2015
- Yanliang Ren, Osama Melhem, Yongjian Li, Bo Chi, Xinya Han, Hao Zhu, Lingling Feng, Jian Wan, Xin Xu:
Clarifying and illustrating the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria allophycocyanin within the framework of Förster theory. 137-145 - Timothy J. Fuhrer, Angel M. Lambert:
Isolated pentagon rule violating endohedral metallofullerenes explained using the Hückel rule: A statistical mechanical study of the C84 Isomeric Set. 146-150 - Jing Huang, Likai Du, Deping Hu, Zhenggang Lan:
Theoretical analysis of excited states and energy transfer mechanism in conjugated dendrimers. 151-163 - Takeshi Yoshikawa, Hiromi Nakai:
Linear-scaling self-consistent field calculations based on divide-and-conquer method using resolution-of-identity approximation on graphical processing units. 164-170 - Mariusz Pawel Mitoraj, Goran V. Janjic, Vesna B. Medakovic, Dusan Z. Veljkovic, Artur Michalak, Snezana D. Zaric, Milos K. Milcic:
Nature of the water/aromatic parallel alignment interactions. 171-180 - Nick M. Vandewiele, Ruben Van de Vijver, Kevin M. Van Geem, Marie Françoise Reyniers, Guy B. Marin:
Symmetry calculation for molecules and transition states. 181-192 - Andrii Shyichuk, Marcin Runowski, Stefan Lis, Jakub Kaczkowski, Andrzej Jezierski:
Semiempirical and DFT computations of the influence of Tb(III) dopant on unit cell dimensions of cerium(III) fluoride. 193-199
Volume 36, Number 4, February 2015
- Jonny Proppe, Carmen Herrmann:
Communication through molecular bridges: Different bridge orbital trends result in common property trends. 201-209 - Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard G. Maroun, Nohad Gresh:
Could the "Janus-like" properties of the halobenzene CX bond (X˭Cl, Br) be leveraged to enhance molecular recognition? 210-221 - Emilio Martínez-Núñez:
An automated method to find transition states using chemical dynamics simulations. 222-234 - Marcia O. Fenley, Robert C. Harris, Travis Mackoy, Alexander H. Boschitsch:
Features of CPB: A Poisson-Boltzmann solver that uses an adaptive cartesian grid. 235-243 - Elaine Limé, Per-Ola Norrby:
Improving the Q2MM method for transition state force field modeling. 244-250
- Robert J. Pantazes, Matthew J. Grisewood, Tong Li, Nathanael P. Gifford, Costas D. Maranas:
The Iterative Protein Redesign and Optimization (IPRO) suite of programs. 251-263 - Pablo M. De Biase, Suren Markosyan, Sergei Yu Noskov:
BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials. 264-271
- Alexander Hoffmann, Martin Rohrmüller, Anton Jesser, Ines dos Santos Vieira, Wolf Gero Schmidt, Sonja Herres-Pawlis:
Corrigendum: Geometrical and optical benchmarking of copper(II) guanidine-quinoline complexes: Insights from TD-DFT and many-body perturbation theory (Part II). 272
Volume 36, Number 5, February 2015
- Dmitry Zuev, Eugene Vecharynski, Chao Yang, Natalie Orms, Anna I. Krylov:
New algorithms for iterative matrix-free eigensolvers in quantum chemistry. 273-284 - Todor Dudev, Mike Devereux, Markus Meuwly, Carmay Lim, Jean-Philip Piquemal, Nohad Gresh:
Quantum-chemistry based calibration of the alkali metal cation series (Li+-Cs+) for large-scale polarizable molecular mechanics/dynamics simulations. 285-302 - Yasuhiro Ikabata, Yusuke Tsukamoto, Yutaka Imamura, Hiromi Nakai:
Local response dispersion method in periodic systems: Implementation and assessment. 303-311 - Igor Schapiro, Daniel Roca-Sanjuán, Roland Lindh, Massimo Olivucci:
A surface hopping algorithm for nonadiabatic minimum energy path calculations. 312-320
- Daniele Licari, Alberto Baiardi, Malgorzata Biczysko, Franco Egidi, Camille Latouche, Vincenzo Barone:
Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS-Draw tool. 321-334 - Susi Lehtola:
Automatic algorithms for completeness-optimization of Gaussian basis sets. 335-347 - Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, Bert L. de Groot:
pmx: Automated protein structure and topology generation for alchemical perturbations. 348-354
Volume 36, Number 6, March 2015
- Jing Xu, Yi-Hong Ding:
Pentaatomic planar tetracoordinate silicon with 14 valence electrons: A large-scale global search of SiXnYmq (n + m = 4; q = 0, ±1, -2; X, Y = main group elements from H to Br). 355-360 - Víctor Duarte Alaniz, Tomás Rocha-Rinza, Gabriel Cuevas:
Assessment of hydrophobic interactions and their contributions through the analysis of the methane dimer. 361-375 - Siyan Chen, Shasha Yi, Wenmei Gao, Chuncheng Zuo, Zhonghan Hu:
Force field development for organic molecules: Modifying dihedral and 1-n pair interaction parameters. 376-384 - Iskender Muz, Osman Canko, Murat Atis, Erdem Kamil Yildirim:
Search for the global minimum structures of AlB3H2n (n = 0 - 6) clusters. 385-391 - Tibor Dubaj, Zuzana Cibulková, Peter Simon:
An incremental isoconversional method for kinetic analysis based on the orthogonal distance regression. 392-398 - Maira D'Alessando, Andrea Amadei, Mauro Stener, Massimiliano Aschi:
Essential dynamics for the study of microstructures in liquids. 399-407 - Kelin Xia, Xin Feng, Yiying Tong, Guo-Wei Wei:
Persistent homology for the quantitative prediction of fullerene stability. 408-422
Volume 36, Number 7, March 2015
- Gustavo Pierdominici-Sottile, Juliana Palma:
New insights into the meaning and usefulness of principal component analysis of concatenated trajectories. 424-432 - Hamed Akbarzadeh, Amir Nasser Shamkhali:
H2 adsorption on Ag-nanocluster/single-walled carbon nanotube composites: A molecular dynamics study on the effects of nanocluster size, diameter, and chirality of nanotube. 433-440 - Fang Liu, Likai Du, Jun Gao, Lili Wang, Bo Song, Chengbu Liu:
Application of polarizable ellipsoidal force field model to pnicogen bonds. 441-448 - Wen-Xin Ji, Wei Xu, W. H. Eugen Schwarz, Shu-Guang Wang:
Ionic bonding of lanthanides, as influenced by d- and f-atomic orbitals, by core-shells and by relativity. 449-458 - Yusuke Ootani, Yoshinobu Akinaga, Takahito Nakajima:
Theoretical investigation of enantioselectivity of cage-like supramolecular assembly: The insights into the shape complementarity and host-guest interaction. 459-466
- Stas Bevc, Christoph Junghans, Matej Praprotnik:
STOCK: Structure mapper and online coarse-graining kit for molecular simulations. 467-477 - Hiram Ponce-Espinosa, Pedro Ponce, Arturo Molina:
The development of an artificial organic networks toolkit for LabVIEW. 478-492
Volume 36, Number 8, March 2015
- Abraham Yosipof, Hanoch Senderowitz:
k-Nearest neighbors optimization-based outlier removal. 493-506 - Pin-Kuang Lai, Shiang-Tai Lin:
Internal coordinate density of state from molecular dynamics simulation. 507-517 - Kun Yuan, Jing-Shuang Dang, Yi-Jun Guo, Xiang Zhao:
Theoretical prediction of the host-guest interactions between novel photoresponsive nanorings and C60: A strategy for facile encapsulation and release of fullerene. 518-528 - Bhaskar Sharma, Hemant Kumar Srivastava, Gaddamanugu Gayatri, Garikapati Narahari Sastry:
Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions. 529-538 - Siladitya Padhi, Siddabattula Ramakrishna, U. Deva Priyakumar:
Prediction of the structures of helical membrane proteins based on a minimum unfavorable contacts approach. 539-552 - Martin T. Stiebritz:
MetREx: A protein design approach for the exploration of sequence-reactivity relationships in metalloenzymes. 553-563 - Elixabete Rezabal, Gilles Frison:
Estimating π binding energy of N-Heterocyclic carbenes: The role of polarization. 564-572
- Andrew J. Schultz, David A. Kofke:
Etomica: An object-oriented framework for molecular simulation. 573-583
Volume 36, Number 9, April 2015
- Federico Fogolari, Alessandra Corazza, Gennaro Esposito:
Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes. 585-596 - Caleb Carlin, Mark S. Gordon:
Ab initio calculation of anion proton affinity and ionization potential for energetic ionic liquids. 597-600 - Paul M. Zimmerman:
Single-ended transition state finding with the growing string method. 601-611 - Topi Karilainen, Oana Cramariuc, Mikael Kuisma, Kirsi Tappura, Terttu I. Hukka:
van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads. 612-621 - Amir Karton, Lars Goerigk:
Accurate reaction barrier heights of pericyclic reactions: Surprisingly large deviations for the CBS-QB3 composite method and their consequences in DFT benchmark studies. 622-632 - Letif Mones, Andrew Jones, Andreas W. Götz, Teodoro Laino, Ross C. Walker, Ben Leimkuhler, Gábor Csányi, Noam Bernstein:
The adaptive buffered force QM/MM method in the CP2K and AMBER software packages. 633-648 - Vincent Tognetti, Christophe Morell, Laurent Joubert:
Quantifying electro/nucleophilicity by partitioning the dual descriptor. 649-659 - Simone Morpurgo:
A DFT study on Cu(I) coordination in Cu-ZSM-5: Effects of the functional choice and tuning of the ONIOM approach. 660-669 - Avijit Sen, Sangita Sen, Pradipta Kumar Samanta, Debashis Mukherjee:
Unitary group adapted state specific multireference perturbation theory: Formulation and pilot applications. 670-688
- Alexander A. Kantardjiev:
irGPU.proton.Net: Irregular strong charge interaction networks of protonatable groups in protein molecules - a GPU solver using the fast multipole method and statistical thermodynamics. 689-693
Volume 36, Number 10, 2015
- Jin-Dou Huang, Wen-Liang Li, Shu-Hao Wen, Bin Dong:
Electronic structure and microscopic charge-transport properties of a new-type diketopyrrolopyrrole-based material. 695-706 - Paolo Della Porta, Riccardo Zanasi, Guglielmo Monaco:
Hydrogen-hydrogen bonding: The current density perspective. 707-716 - Xiao Wang, Juan Yang, Ruoming Li, Hong Jiang, Yan Li:
Deformation of single-walled carbon nanotubes by interaction with graphene: A first-principles study. 717-722 - Petr Stepánek, Petr Bour:
Origin-independent sum over states simulations of magnetic and electronic circular dichroism spectra via the localized orbital/local origin method. 723-730 - Haiyan Yuan, Yiying Zheng, Bo Li, Wenliang Li, Jingping Zhang:
The multieffects of DMF and DBU on the [5 + 1] benzannulation of nitroethane and α-alkenoyl ketene-(S, S)-acetals: Hydrogen bonding and electrostatic interactions. 731-738 - Hanne S. Antila, Emppu Salonen:
On combining Thole's induced point dipole model with fixed charge distributions in molecular mechanics force fields. 739-750 - Andrzej Eilmes, Piotr Kubisiak:
Stability of ion triplets in ionic liquid/lithium salt solutions: Insights from implicit and explicit solvent models and molecular dynamics simulations. 751-762 - Ryuhei Harada, Yu Takano, Yasuteru Shigeta:
Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin. 763-772 - Adelene Y. L. Sim, Chandra Verma:
How does a hydrocarbon staple affect peptide hydrophobicity? 773-784
Volume 36, Number 11, 2015
- Oliver Sala, Hans Peter Lüthi, Antonio Togni, Marcella Iannuzzi, Jürg Hutter:
Dividing a complex reaction involving a hypervalent iodine reagent into three limiting mechanisms by ab initio molecular dynamics. 785-794 - Nishamol Kuriakose, Kumar Vanka:
Can substituted allenes be highly efficient leaving groups in catalytic processes? A computational investigation. 795-804 - Nguyen Minh Tam, Tran Dieu Hang, Hung Tan Pham, Huyen Thi Nguyen, My Phuong Pham-Ho, Pablo A. Denis, Minh Tho Nguyen:
Bonding and singlet-triplet gap of silicon trimer: Effects of protonation and attachment of alkali metal cations. 805-815 - Keisuke Nemoto, Minori Abe, Junji Seino, Masahiko Hada:
An ab initio study of nuclear volume effects for isotope fractionations using two-component relativistic methods. 816-820 - Wiktor Zierkiewicz, Dariusz C. Bienko, Danuta Michalska, Thérèse Zeegers-Huyskens:
Theoretical investigation of the halogen bonded complexes between carbonyl bases and molecular chlorine. 821-832 - Marcos Menéndez, Roberto Álvarez Boto, Evelio Francisco, Ángel Martín Pendás:
One-electron images in real space: Natural adaptive orbitals. 833-843 - Wen-Yang Zhao, Jie Yu, Si-Jia Ren, Xi-Guang Wei, Fang-Zhou Qiu, Peng-Hui Li, He Li, Yi-Peng Zhou, Chang-Zhen Yin, An-Pu Chen, Hao Li, Lei Zhang, Jun Zhu, Yi Ren, Kai-Chung Lau:
Probing the reactivity of microhydrated α-nucleophile in the anionic gas-phase SN2 reaction. 844-852 - Nils Middendorf, Katharina Krause, Sebastian Höfener:
Solvatochromic shifts of Br2 and I2 in water cages of type 512, 51262, 51263, and 51264. 853-860 - Alex Domingo, Celestino Angeli, Coen de Graaf, Vincent Robert:
Electronic reorganization triggered by electron transfer: The intervalence charge transfer of a Fe3+/Fe2+ bimetallic complex. 861-869
Volume 36, Number 12, 2015
- Bun Chan, Jong-Won Song, Yukio Kawashima, Kimihiko Hirao:
Toward the complete range separation of non-hybrid exchange-correlation functional. 871-877 - Polina V. Banushkina, Sergei V. Krivov:
Fep1d: A script for the analysis of reaction coordinates. 878-882 - Jan Dillen:
The topology of the Ehrenfest force density revisited. A different perspective based on Slater-type orbitals. 883-890 - Xu Zhang, Xiaodi Yang, Hua Geng, Guangjun Nan, Xingwen Sun, Jinyang Xi, Xin Xu:
Theoretical comparative studies on transport properties of pentacene, pentathienoacene, and 6, 13-dichloropentacene. 891-900 - Yury D. Fomin, Elena N. Tsiok, Valentin N. Ryzhov:
The behavior of benzene confined in a single wall carbon nanotube. 901-906 - Sudip Chattopadhyay, Rajat K. Chaudhuri, Uttam Sinha Mahapatra:
State-specific multireference perturbation theory with improved virtual orbitals: Taming the ground state of F2, Be2, and N2. 907-925 - Russell Thackston, Ryan C. Fortenberry:
The performance of low-cost commercial cloud computing as an alternative in computational chemistry. 926-933 - Matthew Welborn, Jiahao Chen, Lee-Ping Wang, Troy A. Van Voorhis:
Why many semiempirical molecular orbital theories fail for liquid water and how to fix them. 934-939
- Adam K. Sieradzan:
Introduction of periodic boundary conditions into UNRES force field. 940-946
Volume 36, Number 13, 2015
- Anna Stachiewicz, Andrzej Molski:
A coarse-grained MARTINI-like force field for DNA unzipping in nanopores. 947-956 - Robert A. Evarestov, Andrej I. Panin:
Symmetry classification of electron and phonon states in TiO2-based nanowires and nanotubes. 957-969 - Maria T. Panteva, George M. Giambasu, Darrin M. York:
Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations. 970-982 - Antonio Cardone, Aaron Bornstein, Harish C. Pant, Mary Brady, Ram D. Sriram, Sergio A. Hassan:
Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation. 983-995 - Elmar Krieger, Gert Vriend:
New ways to boost molecular dynamics simulations. 996-1007 - Yi Wang, William Yi Wang, Long-Qing Chen, Zi-Kui Liu:
Bonding charge density from atomic perturbations. 1008-1014
- Louis Vanduyfhuys, Steven Vandenbrande, Toon Verstraelen, Rochus Schmid, Michel Waroquier, Veronique Van Speybroeck:
QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input. 1015-1027
Volume 36, Number 14, 2015
- Liudmyla K. Sviatenko, Olexandr Isayev, Leonid Gorb, Frances C. Hill, Danuta Leszczynska, Jerzy Leszczynski:
Are the reduction and oxidation properties of nitrocompounds dissolved in water different from those produced when adsorbed on a silica surface? A DFT M05-2X computational study. 1029-1035 - Hong-Zhi Li, Ziyan Zhong, Lin Li, Rui Gao, Jingxia Cui, Ting Gao, Li Hong Hu, Yinghua Lu, Zhongmin Su, Hui Li:
A cascaded QSAR model for efficient prediction of overall power conversion efficiency of all-organic dye-sensitized solar cells. 1036-1046 - Shenggao Zhou, Li-Tien Cheng, Hui Sun, Jianwei Che, Joachim Dzubiella, Bo Li, James Andrew McCammon:
LS-VISM: A software package for analysis of biomolecular solvation. 1047-1059 - Tirtharaj Dash, Prabhat K. Sahu:
Gradient gravitational search: An efficient metaheuristic algorithm for global optimization. 1060-1068 - Milan Randic, Tomaz Pisanski:
Protein alignment: Exact versus approximate. An illustration. 1069-1074 - Masaki Okoshi, Teruo Atsumi, Hiromi Nakai:
Revisiting the extrapolation of correlation energies to complete basis set limit. 1075-1082 - Kenno Vanommeslaeghe, Mingjun Yang, Alexander D. MacKerell Jr.:
Robustness in the fitting of molecular mechanics parameters. 1083-1101
Volume 36, Number 15, 2015
- Hujun Shen, Yan Li, Peijun Xu, Xiaofang Li, Huiying Chu, Dinglin Zhang, Guohui Li:
An anisotropic coarse-grained model based on Gay-Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model. 1103-1113 - Claudia Loerbroks, Andreas Heimermann, Walter Thiel:
Solvents effects on the mechanism of cellulose hydrolysis: A QM/MM study. 1114-1123