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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 - Robert Zalesny, Guangjun Tian, Christof Hättig, Wojciech Bartkowiak, Hans Ågren:
Toward assessment of density functionals for vibronic coupling in two-photon absorption: A case study of 4-nitroaniline. 1124-1131 - William J. Allen, Trent E. Balius, Sudipto Mukherjee, Scott R. Brozell, Demetri Moustakas, P. Therese Lang, David A. Case, Irwin D. Kuntz, Robert C. Rizzo:
DOCK 6: Impact of new features and current docking performance. 1132-1156 - Adam B. Birkholz, H. Bernhard Schlegel:
Using bonding to guide transition state optimization. 1157-1166 - Benoit de Courcy, Etienne Derat, Jean-Philip Piquemal:
Bridging organometallics and quantum chemical topology: Understanding electronic relocalisation during palladium-catalyzed reductive elimination. 1167-1175 - Sadanandam Namsani, Nisanth N. Nair, Jayant K. Singh:
Interaction potential models for bulk Zns, Zns nanoparticle, and Zns nanoparticle-PMMA from first-principles. 1176-1186
Volume 36, Number 16, 2015
- David Z. Gao, Filippo Federici Canova, Matthew B. Watkins, Alexander L. Shluger:
Efficient parametrization of complex molecule-surface force fields. 1187-1195 - Shuching Ou, Di Cui, Matthew Wezowicz, Michela Taufer, Sandeep Patel:
Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations. 1196-1212 - Frédéric Cazals, Tom Dreyfus, Dorian Mazauric, Christine-Andrea Roth, Charles H. Robert:
Conformational ensembles and sampled energy landscapes: Analysis and comparison. 1213-1231 - Xun Zhu, Yuriko Aoki:
Development of minimized mixing molecular orbital method for designing organic ferromagnets. 1232-1239 - Hiroo Nozaki, Yuji Ikeda, Kazuhide Ichikawa, Akitomo Tachibana:
Electronic stress tensor analysis of molecules in gas phase of CVD process for gesbte alloy. 1240-1251 - Ayman Farhat, Saleh N. Abdul-Al:
Ab initio calculations of the ground and excited states of the ZrN molecule including spin-orbit effects. 1252-1258
- Rescic Jurij, Per Linse:
MOLSIM: A modular molecular simulation software. 1259-1274
Volume 36, Number 17, 2015
- Justin A. Drake, B. Montgomery Pettitt:
Force field-dependent solution properties of glycine oligomers. 1275-1285 - Jacek Koput:
Ab initio ground-state potential energy function and vibration-rotation energy levels of imidogen, NH. 1286-1294 - Haiyan Yuan, Jingping Zhang:
[DBU-H]+ and H2o as effective catalyst form for 2, 3-dihydropyrido[2, 3-d]pyrimidin-4(1H)-ones: A DFT Study. 1295-1303 - Thomas Long, Owen M. McDougal, Timothy L. Andersen:
GAMPMS: Genetic algorithm managed peptide mutant screening. 1304-1310 - Oliwia M. Szklarczyk, Eirini Arvaniti, Wilfred F. van Gunsteren:
Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane. 1311-1321 - Sandro Marmitt, Paulo Fernando Bruno Gonçalves:
A DFT study on the insertion of CO2 into styrene oxide catalyzed by 1-butyl-3-methyl-Imidazolium bromide ionic liquid. 1322-1333 - Athanassios C. Tsipis, Alexandros V. Stalikas:
Electronic, bonding, and optical properties of 1d [CuCN]n (n = 1-10) chains, 2d [CuCN]n (n = 2-10) nanorings, and 3d [Cun(CN)n]m (n = 4, m = 2, 3; n = 10, m = 2) tubes studied by DFT/TD-DFT methods. 1334-1347
Volume 36, Number 18, 2015
- Wei Li, Yanli Zeng, Xiaoyan Li, Zheng Sun, Lingpeng Meng:
The competition of Y⋯o and X⋯n halogen bonds to enhance the group V σ-hole interaction in the NCY⋯o˭PH3⋯NCX and O˭PH3⋯NCX⋯NCY (X, Y˭F, Cl, and Br) complexes. 1349-1358 - Tomonari Sumi, Ayori Mitsutake, Yutaka Maruyama:
A solvation-free-energy functional: A reference-modified density functional formulation. 1359-1369 - Ming Huang, Timothy J. Giese, Darrin M. York:
Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models. 1370-1389 - Alexander K. H. Weiss, Christian Ochsenfeld:
A rigorous and optimized strategy for the evaluation of the Boys function kernel in molecular electronic structure theory. 1390-1398 - Kyle D. Fernandes, C. Alicia Renison, Kevin J. Naidoo:
Quantum supercharger library: Hyper-parallelism of the Hartree-Fock method. 1399-1409 - C. Alicia Renison, Kyle D. Fernandes, Kevin J. Naidoo:
Quantum supercharger library: Hyper-parallel integral derivatives algorithms for ab initio QM/MM dynamics. 1410-1419 - Carsten Müller, Daniel Spångberg:
Calculation of the stability of nonperiodic solids using classical force fields and the method of increments: N2o as an example. 1420-1427
Volume 36, Number 19, 2015
- Maike Bergeler, Carmen Herrmann, Markus Reiher:
Mode-tracking based stationary-point optimization. 1429-1438 - Raffaella Demichelis, Marco Bruno, Francesco R. Massaro, Mauro Prencipe, Marco De La Pierre, Fabrizio Nestola:
First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets. 1439-1445 - Raimondas Galvelis, Yuji Sugita:
Replica state exchange metadynamics for improving the convergence of free energy estimates. 1446-1455 - Alonso Ramirez-Manzanares, Joaquín Peña, Jon M. Azpiroz, Gabriel Merino:
A hierarchical algorithm for molecular similarity (H-FORMS). 1456-1466 - Kim Julia Hintze, Arne Lützen, Thomas Bredow:
Structure and stability of supramolecular crown ether complexes. 1467-1472
- Justin A. Lemkul, Benoît Roux, David van der Spoel, Alexander D. MacKerell Jr.:
Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. 1473-1479 - Semen O. Yesylevskyy:
Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python. 1480-1488
Volume 36, Number 20, 2015
- Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura:
Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. 1489-1501 - Kelin Xia, Guo-Wei Wei:
Multidimensional persistence in biomolecular data. 1502-1520 - Lukás Grajciar:
Low-memory iterative density fitting. 1521-1535 - Yinglong Miao, Ferran Feixas, Changsun Eun, James Andrew McCammon:
Accelerated molecular dynamics simulations of protein folding. 1536-1549 - Mark Dittner, Julian Müller, Hasan Metin Aktulga, Bernd Hartke:
Efficient global optimization of reactive force-field parameters. 1550-1561 - Sudhir K. Sahoo, Nisanth N. Nair:
A potential with low point charges for pure siliceous zeolites. 1562-1567
- Bing Xia, Artem B. Mamonov, Seppe Leysen, Karen N. Allen, Sergei V. Strelkov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov:
Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. 1568-1572
Volume 36, Number 21, 2015
- Joseelyne G. Hernández-Lima, Jose E. Barquera-Lozada, Gabriel Cuevas, Fernando Cortés-Guzmán:
The role of induced current density in Steroelectronic effects: Perlin effect. 1573-1578 - Sandra C. C. Nunes, Marie Skepö, Alberto A. C. C. Pais:
Confined polyelectrolytes: The complexity of a simple system. 1579-1586 - Benjamin D. Jensen, Kristopher E. Wise, Gregory M. Odegard:
The effect of time step, thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond, graphene, and carbon nanotube. 1587-1596 - Jakub Gunera, Peter Kolb:
Fragment-based similarity searching with infinite color space. 1597-1608 - Felix Plasser, Benjamin Thomitzni, Stefanie A. Bäppler, Jan Wenzel, Dirk R. Rehn, Michael Wormit, Andreas Dreuw:
Statistical analysis of electronic excitation processes: Spatial location, compactness, charge transfer, and electron-hole correlation. 1609-1620 - Tatiana Vasilevskaya, Maria G. Khrenova, Alexander V. Nemukhin, Walter Thiel:
Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling. 1621-1630
- Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter, Rebecca C. Wade:
SDA 7: A modular and parallel implementation of the simulation of diffusional association software. 1631-1645
Volume 36, Number 22, 2015
- Taro Udagawa, Masanori Tachikawa:
H/D isotope effect on charge-inverted hydrogen-bonded systems: Systematic classification of three different types in H3XH...YH3 (X = C, Si, or Ge, and Y = B, Al, or Ga) with multicomponent calculation. 1647-1654 - Yuichi Tanaka, Norio Yoshida, Haruyuki Nakano:
Three-dimensional reference interaction site model self-consistent field analysis of solvent and substituent effects on the absorption spectra of Brooker's merocyanine. 1655-1663 - Qiming Sun:
Libcint: An efficient general integral library for Gaussian basis functions. 1664-1671 - Martin Rohrmüller, Alexander Hoffmann, Christian Thierfelder, Sonja Herres-Pawlis, Wolf Gero Schmidt:
The Cu2O2 torture track for a real-life system: [Cu2(btmgp)2O2]2+ oxo and peroxo species in density functional calculations. 1672-1685 - Noah S. Bieler, Philippe H. Hünenberger:
Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI versus λ-LEUS. 1686-1697 - Michael Stenrup, Roland Lindh, Ignacio Fdez. Galván:
Constrained numerical gradients and composite gradients: Practical tools for geometry optimization and potential energy surface navigation. 1698-1708 - Takakazu Ishikura, Yuki Iwata, Tatsuro Hatano, Takahisa Yamato:
Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study. 1709-1718
Volume 36, Number 23, 2015
- X. W. Zhou, D. K. Ward, Michael E. Foster:
An analytical bond-order potential for carbon. 1719-1735 - Ignacio Viciano, Raquel Castillo, Sergio Martí:
QM/MM modeling of the hydroxylation of the androstenedione substrate catalyzed by cytochrome P450 aromatase (CYP19A1). 1736-1747 - Stephen J. Barigye, Matheus P. Freitas:
Is molecular alignment an indispensable requirement in the MIA-QSAR method? 1748-1755 - Yury Yu. Rusakov, Leonid B. Krivdin:
Four-component relativistic DFT calculations of 77Se NMR chemical shifts: A gateway to a reliable computational scheme for the medium-sized organoselenium molecules. 1756-1762 - Weizhou Wang, Tao Sun, Yu Zhang, Yi-Bo Wang:
Benchmark calculations of the adsorption of aromatic molecules on graphene. 1763-1771 - Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, Ronald M. Levy:
Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. 1772-1785
Volume 36, Number 24, 2015
- Sergey Kazachenko, Mark Giovinazzo, Kyle Wm. Hall, Natalie M. Cann:
Algorithms for GPU-based molecular dynamics simulations of complex fluids: Applications to water, mixtures, and liquid crystals. 1787-1804 - Manuel Hochheim, Thomas Bredow:
Adsorption-induced changes of intramolecular optical transitions: PTCDA/NaCl and PTCDA/KCl. 1805-1811 - Norah Heinz, Michael Dolg, Albrecht Berkessel:
A theoretical study of imine hydrocyanation catalyzed by halogen-bonding. 1812-1817 - Murugesan Thenraj, Ashoka G. Samuelson:
Contrasting electronic requirements for C-H binding and C-H activation in d6 half-sandwich complexes of rhenium and tungsten. 1818-1830 - Nicolás Otero, Christian Van Alsenoy, Claude Pouchan, Panaghiotis Karamanis:
Hirshfeld-based intrinsic polarizability density representations as a tool to analyze molecular polarizability. 1831-1843 - Timothy J. Hughes, Salvatore Cardamone, Paul L. A. Popelier:
Realistic sampling of amino acid geometries for a multipolar polarizable force field. 1844-1857
- Jing Huang, Likai Du, Deping Hu, Zhenggang Lan:
Theoretical analysis of excited states and energy transfer mechanism in conjugated dendrimers. 1858
Volume 36, Number 25, 2015
- Pin-Chih Su, Cheng-Chieh Tsai, Shahila Mehboob, Kirk E. Hevener, Michael E. Johnson:
Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI). 1859-1873 - Marie Zgarbová, Andreana M. Rosnik, F. Javier Luque, Carles Curutchet, Petr Jurecka:
Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields. 1874-1884 - Rui Duan, Raudah Lazim, Dawei Zhang:
Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field. 1885-1892 - M. Luz Sánchez, José C. Corchado, M. Elena Martín, Ignacio Fdez. Galván, Rute Barata-Morgado, Manuel A. Aguilar:
A new QM/MM method oriented to the study of ionic liquids. 1893-1901 - Liangxiao Zhang, Peiwu Li, Jin Mao, Fei Ma, Xiaoxia Ding, Qi Zhang:
An enhanced Monte Carlo outlier detection method. 1902-1906 - Italo Curvelo Anjos, Gerd Bruno Rocha:
A topological assessment of the electronic structure of mesoionic compounds. 1907-1918 - Haisheng Li, Weiguang Chen, Xiaoyu Han, Liben Li, Qiang Sun, Zhengxiao Guo, Yu Jia:
Van der Waals Effects on semiconductor clusters. 1919-1927
Volume 36, Number 26, 2015
- Manuel Hitzenberger, Thomas S. Hofer:
Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds. 1929-1939 - Silvia Casassa, Alessandro Erba, Jacopo Baima, Roberto Orlando:
Electron density analysis of large (molecular and periodic) systems: A parallel implementation. 1940-1946 - Joshua J. Eller, Karen Downey:
Computational assessment of electron density in metallo-organic nickel pincer complexes for formation of P-C bonds. 1947-1953 - Anirban Ghosh, Rajat K. Chaudhuri, Sudip Chattopadhyay, Uttam Sinha Mahapatra:
Relativistic state-specific multireference perturbation theory incorporating improved virtual orbitals: Application to the ground state single-bond dissociation. 1954-1972
- Arina Afanasyeva, Sergey Izmailov, Michel Grigoriev, Michael Petukhov:
AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites. 1973-1977 - Tomás Kubar, Kai Welke, Gerrit Groenhof:
New QM/MM implementation of the DFTB3 method in the gromacs package. 1978-1989 - Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller:
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. 1990-2008
- Tomonari Sumi, Ayori Mitsutake, Yutaka Maruyama:
Erratum: "A solvation-free-energy functional: A reference-modified density functional formulation" [J. Comput. Chem 36, 1359-1369]. 2009-2011
Volume 36, Number 27, 2015
- Yun Ding, Ye Fang, Wei Pan Feinstein, Jagannathan Ramanujam, David M. Koppelman, Juana Moreno, Michal Brylinski, Mark Jarrell:
GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. 2013-2026 - Railton Barbosa de Andrade, Ezequiel Fragoso Vieira Leitão, Miguel Angelo Fonseca de Souza, Elizete Ventura, Silmar Andrade do Monte:
Effect of methylation on relative energies of tautomers and on the intramolecular proton transfer barriers of protonated nitrosamine: A MR-CISD study. 2027-2036 - Sergei F. Vyboishchikov:
Modeling exact exchange potential in spherically confined atoms. 2037-2043 - Guillaume Chevrot, Eudes Eterno Fileti, Vitaly V. Chaban:
Enhanced stability of the model mini-protein in amino acid ionic liquids and their aqueous solutions. 2044-2051 - Anna Pavlova, James C. Gumbart:
Parametrization of macrolide antibiotics using the force field toolkit. 2052-2063 - Jonah Z. Vilseck, Jakub Kostal, Julian Tirado-Rives, William L. Jorgensen:
Application of a BOSS - Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions. 2064-2074 - Arnaud Fihey, Christian Hettich, Jérémy Touzeau, François Maurel, Aurélie Perrier, Christof Köhler, Bálint Aradi, Thomas Frauenheim:
SCC-DFTB parameters for simulating hybrid gold-thiolates compounds. 2075-2087
Volume 36, Number 28, 2015
- Holger Vach, Lena V. Ivanova, Qadir K. Timerghazin, Fatme Jardali, Ha-Linh Thi Le:
A deeper insight into strain for the sila-bi[6]prismane ( Si18H12) cluster with its endohedrally trapped silicon atom, Si19H12. 2089-2094 - Grygoriy A. Dolgonos, Koshka Mekalka:
Strain in nonclassical silicon hydrides: An insight into the "ultrastability" of sila-bi[6]prismane (Si18H12) cluster with the endohedrally trapped silicon atom, Si19H12. 2095-2102 - Yuuichi Orimoto, Kai Liu, Yuriko Aoki:
Elongation method for electronic structure calculations of random DNA sequences. 2103-2113 - Samuel Genheden, Ulf Ryde, Pär Söderhjelm:
Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. 2114-2124 - Régis Tadeu Santiago, Roberto Luiz Andrade Haiduke:
New density functional parameterizations to accurate calculations of electric field gradient variations among compounds. 2125-2130 - Maxim R. Ryzhikov, Vladimir A. Slepkov, Svetlana G. Kozlova, Svyatoslav P. Gabuda, Vladimir E. Fedorov:
Solid-state reaction as a mechanism of 1T &[LEFT RIGHT ARROW]; 2H transformation in MoS2 monolayers. 2131-2134 - Al Mokhtar Lamsabhi, Soledad Gutiérrez-Oliva, Otilia Mó, Alejandro Toro-Labbé, Manuel Yáñez:
Effects of the ionization in the tautomerism of uracil: A reaction electronic flux perspective. 2135-2145
Volume 36, Number 29, 2015
- Ilkay Sakalli, Ernst-Walter Knapp:
pKA in proteins solving the Poisson-Boltzmann equation with finite elements. 2147-2157 - Kestutis Aidas, Kiril Lanevskij, Rytis Kubilius, Liutauras Juska, Daumantas Petkevicius, Pranas Japertas:
Aqueous acidities of primary benzenesulfonamides: Quantum chemical predictions based on density functional theory and SMD. 2158-2167 - Sudip Pan, Ashutosh Gupta, Ranajit Saha, Gabriel Merino, Pratim Kumar Chattaraj:
A coupled-cluster study on the noble gas binding ability of metal cyanides versus metal halides (metal = Cu, Ag, Au). 2168-2176 - Krishnakanta Mondal, Arup Banerjee, Alessandro Fortunelli, Tapan K. Ghanty:
Does enhanced oxygen activation always facilitate CO oxidation on gold clusters? 2177-2187 - Pouya Partovi-Azar, Thomas D. Kühne:
Efficient "On-the-Fly" calculation of Raman Spectra from Ab-Initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water. 2188-2192 - Olga A. Gapurenko, Andrey G. Starikov, Ruslan M. Minyaev, Vladimir I. Minkin:
Germanium, carbon-germanium, and silicon-germanium triangulenes. 2193-2199
- Marat Sibaev, Deborah L. Crittenden:
The PyPES library of high quality semi-global potential energy surfaces. 2200-2207
- Jing Huang, Likai Du, Deping Hu, Zhenggang Lan:
Erratum: Theoretical analysis of excited states and energy transfer mechanism in conjugated dendrimers. 2208
Volume 36, Number 30, 2015
- Takao Otsuka, Noriaki Okimoto, Makoto Taiji:
Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method. 2209-2218 - Jacek Koput:
Ab Initio spectroscopic characterization of borane, BH, in its X1Σ+ electronic state. 2219-2227 - Wenjing Gong, Ruibo Wu, Yingkai Zhang:
Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An Ab initio QM/MM molecular dynamics study. 2228-2235 - Tobias Neumann, Denis Danilov, Wolfgang Wenzel:
Multiparticle moves in acceptance rate optimized monte carlo. 2236-2245 - Roberto Cammi:
A new extension of the polarizable continuum model: Toward a quantum chemical description of chemical reactions at extreme high pressure. 2246-2259 - Lucas Modesto-Costa, Elmar Uhl, Itamar Borges Jr.:
Water solvent effects using continuum and discrete models: The nitromethane molecule, CH3NO2. 2260-2269
Volume 36, Number 31, 2015
- Ivan Carnimeo, Chiara Cappelli, Vincenzo Barone:
Analytical gradients for MP2, double hybrid functionals, and TD-DFT with polarizable embedding described by fluctuating charges. 2271-2290 - Massimiliano Bartolomei, Fernando Pirani, Jorge M. C. Marques:
Low-energy structures of benzene clusters with a novel accurate potential surface. 2291-2301 - Dan Fraenkel:
Ion strength limit of computed excess functions based on the linearized Poisson-Boltzmann equation. 2302-2316 - Guo-Liang Fan, Xiao-Yan Zhang, Yan-Ling Liu, Yi Nang, Hui Wang:
DSPMP: Discriminating secretory proteins of malaria parasite by hybridizing different descriptors of Chou's pseudo amino acid patterns. 2317-2327 - Pradeep R. Varadwaj, Arpita Varadwaj, Bih-Yaw Jin:
Hexahalogenated and their mixed benzene derivatives as prototypes for the understanding of halogen···halogen intramolecular interactions: New insights from combined DFT, QTAIM-, and RDG-based NCI analyses. 2328-2343 - Yoshiharu Mori, Hisashi Okumura:
Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms. 2344-2349
- Anmol Kumar, Sachin D. Yeole, Shridhar R. Gadre, Rafael López, Jaime Fernández Rico, Guillermo Ramírez, Ignacio Ema, David Zorrilla:
DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules. 2350-2359
Volume 36, Number 32, 2015
- Salvatore Cardamone, Paul L. A. Popelier:
Prediction of conformationally dependent atomic multipole moments in carbohydrates. 2361-2373 - Yuanyuan Li, Li Wang, Xugeng Guo, Jinglai Zhang:
A CASSCF/CASPT2 insight into excited-state intramolecular proton transfer of four imidazole derivatives. 2374-2380 - Marharyta Petukh, Min Zhang, Emil Alexov:
Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence. 2381-2393 - Matti Hellström, Daniel Spångberg, Kersti Hermansson:
Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10 1¯0). 2394-2405 - Takuma Nozawa, Kazuaki Z. Takahashi, Tetsu Narumi, Kenji Yasuoka:
Comparison of the accuracy of periodic reaction field methods in molecular dynamics simulations of a model liquid crystal system. 2406-2411 - Sirous Yourdkhani, Tatiana Korona, Nasser L. Hadipour:
Interplay between tetrel and triel bonds in RC6H4CN⋯MF3CN⋯BX3 complexes: A combined symmetry-adapted perturbation theory, Møller-Plesset, and quantum theory of atoms-in-molecules study. 2412-2428
- Eric Iván Sánchez-Flores, Rodrigo Chávez-Calvillo, Todd A. Keith, Gabriel Cuevas, Tomás Rocha-Rinza, Fernando Cortés-Guzmán:
Erratum: Properties of atoms in electronically excited molecules within the formalism of TDDFT [J. Comput Chem. 2014, 35, 820-828]. 2429
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