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Journal of Computational Chemistry, Volume 37
Volume 37, Number 1, 2016
Full Papers
- Lukas N. Wirz, Ralf Tonner
, Andreas Hermann
, Rebecca Sure
, Peter Schwerdtfeger:
From small fullerenes to the graphene limit: A harmonic force-field method for fullerenes and a comparison to density functional calculations for Goldberg-Coxeter fullerenes up to C980. 10-17 - Andreas J. Achazi, Larissa K. S. von Krbek
, Christoph A. Schalley, Beate Paulus:
Theoretical and experimental investigation of crown/ammonium complexes in solution. 18-24 - Rodrigo A. Cormanich
, Roberto Rittner
, David O'Hagan
, Michael Bühl
:
Inter- and intramolecular CF···c˭o interactions on aliphatic and cyclohexane carbonyl derivatives. 25-33 - Changwei Wang, Liangyu Guan, David Danovich, Sason Shaik, Yirong Mo:
The origins of the directionality of noncovalent intermolecular interactions#. 34-45 - Yunfei Zhou, Xiaoguang Bao, Weston Thatcher Borden:
Nucleus-independent chemical shift analysis of the electronic states of the (CO)4, (CS)4, and (CSe)4 molecules. 46-48 - Amir Karton
, Peter R. Schreiner
, Jan M. L. Martin
:
Heats of formation of platonic hydrocarbon cages by means of high-level thermochemical procedures. 49-58 - Megha Anand
, Israel Fernández
, Henry F. Schaefer III, Judy I-Chia Wu:
Hydrogen bond-aromaticity cooperativity in self-assembling 4-pyridone chains. 59-63 - Alexandru Lupan
, Robert Bruce King:
Molybdatricarbaboranes as examples of isocloso metallaborane deltahedra with three carbon vertices. 64-69 - George A. Olah, G. K. Surya Prakash, Golam Rasul:
Ab initio/GIAO-CCSD(T) 13C NMR study of the rearrangement and dynamic aspects of rapidly equilibrating tertiary carbocations, C6 H13+ and C7 H15+. 70-77 - Ramon Carbó-Dorca:
Aromaticity, quantum multimolecular polyhedra, and quantum QSPR fundamental equation. 78-82 - Riccardo Petraglia, Adrien Nicolaï, Matthew D. Wodrich
, Michele Ceriotti, Clémence Corminboeuf:
Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry. 83-92 - Martin Kaupp, Simon Gückel, Manuel Renz, Sascha Klawohn
, Kolja Theilacker, Matthias Parthey, Christoph Lambert:
Electron transfer pathways in mixed-valence paracyclophane-bridged bis-triarylamine radical cations. 93-102 - Xiaohu Yu
, Artem R. Oganov
, Ivan A. Popov
, Alexander I. Boldyrev
:
d-AO spherical aromaticity in Ce6O8. 103-109 - Klara Edel, Reinhold F. Fink, Holger F. Bettinger
:
Isomerization and fragmentation pathways of 1, 2-azaborine. 110-116 - Brian J. Levandowski, Lufeng Zou, K. N. Houk:
Schleyer hyperconjugative aromaticity and Diels-Alder reactivity of 5-substituted cyclopentadienes. 117-123 - Jenn-Huei Lii, Norman L. Allinger, Ching-Han Hu, Henry F. Schaefer III:
Catenanes: A molecular mechanics analysis of the (C13H26)2 Structure 13-13 D2. 124-129 - Elfi Kraka, Dani Setiawan, Dieter Cremer:
Re-evaluation of the bond length-bond strength rule: The stronger bond is not always the shorter bond. 130-142 - Chérif F. Matta
, Seyed Abdolreza Sadjadi, Dale A. Braden, Gernot Frenking:
The barrier to the methyl rotation in Cis-2-butene and its isomerization energy to Trans-2-butene, revisited. 143-154
Volume 37, Number 2, 2016
Full Papers
- Jose L. Mendoza-Cortes, Qi An, William A. Goddard III, Caichao Ye
, Sergey Zybin:
Prediction of the crystal packing of di-tetrazine-tetroxide (DTTO) energetic material. 163-167 - Haijun Jiao, Kathrin Junge, Elisabetta Alberico, Matthias Beller:
A comparative computationally study about the defined m(II) pincer hydrogenation catalysts (m = fe, ru, os). 168-176 - Guoliang Li, Hui Wang
, Qian-Shu Li, Yaoming Xie, Henry F. Schaefer III:
The Reaction between Bromine and the Water Dimer and the Highly Exothermic Reverse Reaction. 177-182 - Bun Chan
, Lars Goerigk
, Leo Radom
:
On the inclusion of post-MP2 contributions to double-Hybrid density functionals. 183-193 - Habib U. Rehman, Nida A. McKee, Michael L. Mckee:
Saturn Systems. 194-209 - Andrey V. Shernyukov
, Alexander M. Genaev, George E. Salnikov, Henry S. Rzepa, Vyacheslav G. Shubin:
Noncatalytic bromination of benzene: A combined computational and experimental study. 210-225 - Sudip Pan
, Diego Moreno, Sreyan Ghosh, Pratim Kumar Chattaraj
, Gabriel Merino:
Structure and stability of noble gas bound EX3+ compounds (E = C, Ge, Sn, Pb; X = H, F, Cl, Br). 226-236 - Clark R. Landis, Frank Weinhold
:
18-electron rule and the 3c/4e hyperbonding saturation limit. 237-241 - Masahiro Ehara
, Ryoichi Fukuda
, Thomas Sommerfeld:
Projected CAP/SAC-CI method with smooth Voronoi potential for calculating resonance states. 242-249 - Hong-Yan Wang, Hui Wang, Robert Bruce King, Henry F. Schaefer III:
Bis(azulene) "submarine" metal dimer sandwich compounds (C10H8)2M2 (M = Ti, V, Cr, Mn, Fe, Co, Ni): Parallel and opposed orientations. 250-260 - Xue-Feng Zhao, Haixia Li, Caixia Yuan, Yan-Qin Li, Yan-Bo Wu, Zhi-Xiang Wang:
Linear, planar, and tubular molecular structures constructed by double planar tetracoordinate carbon D2h C2(BeH)4 species via hydrogen-bridged -BeH2Be- bonds. 261-269 - Jyothish Joy
, Anex Jose, Eluvathingal D. Jemmis
:
Continuum in the X-Z - Y weak bonds: Z= main group elements. 270-279 - Berit Heggen, Mahendra Patil, Walter Thiel
:
Cyclization of an α, β-Unsaturated hydrazone catalyzed by a BINOL-phosphoric acid: Pericyclic or not? 280-285 - Arkajyoti Sengupta
, Raghunath O. Ramabhadran, Krishnan Raghavachari:
Breaking a bottleneck: Accurate extrapolation to "gold standard" CCSD(T) energies for large open shell organic radicals at reduced computational cost. 286-295 - Xue-Feng Zhao, Caixia Yuan, Xiang Wang, Jia-Jia Li, Yan-Bo Wu, Xiaotai Wang
:
Computational design of organometallic oligomers featuring 1, 3-metal-carbon bonding and planar tetracoordinate carbon atoms. 296-303 - R. Joshua Mulder, Célia Fonseca Guerra
, J. Chris Slootweg, Koop Lammertsma, Friedrich Matthias Bickelhaupt:
Substituent effects on the optical properties of naphthalenediimides: A frontier orbital analysis across the periodic table. 304-313
Volume 37, Number 3, 2016
- Yingdi Jin, Neil Qiang Su
, Xin Xu, Hao Hu:
Self-consistent field for fragmented quantum mechanical model of large molecular systems. 321-326
- Arifin, Maneeporn Puripat, Daisuke Yokogawa, Vudhichai Parasuk
, Stephan Irle:
Glucose transformation to 5-hydroxymethylfurfural in acidic ionic liquid: A quantum mechanical study. 327-335 - Li Rao, Bo Chi, Yanliang Ren, Yongjian Li, Xin Xu, Jian Wan:
DOX: A new computational protocol for accurate prediction of the protein-ligand binding structures. 336-344 - Dilan Yildiz, Ugur Bozkaya
:
Assessment of the extended Koopmans' theorem for the chemical reactivity: Accurate computations of chemical potentials, chemical hardnesses, and electrophilicity indices. 345-353 - Wojciech Plazinski
, Alice Lonardi, Philippe H. Hünenberger
:
Revision of the GROMOS 56A6CARBO force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains. 354-365 - M. Althaf Hussain, Dolly Vijay, G. Narahari Sastry:
Buckybowls as adsorbents for CO2, CH4, and C2H2: Binding and structural insights from computational study. 366-377
- Sheng-Chun Yang, Yong-Lei Wang
, Gui-Sheng Jiao, Hu-Jun Qian
, Zhong-Yuan Lu:
Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non-uniform fast fourier transform. 378-387
Volume 37, Number 4, 2016
- Marzena Jankowska, Teobald Kupka
, Leszek Stobinski, Rasmus Faber
, Evanildo G. Lacerda Jr., Stephan P. A. Sauer
:
Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers. 395-403 - Karen Druart
, Zoltan Palmai
, Eyaz Omarjee, Thomas Simonson
:
Protein: Ligand binding free energies: A stringent test for computational protein design. 404-415 - Sirish Kaushik Lakkaraju
, Justin A. Lemkul
, Jing Huang
, Alexander D. MacKerell Jr.:
DIRECT-ID: An automated method to identify and quantify conformational variations - application to β2-adrenergic GPCR. 416-425 - Ngaam J. Cheung, Xueming Ding, Hong-Bin Shen:
Protein folds recognized by an intelligent predictor based-on evolutionary and structural information. 426-436 - Vincent Zoete, Thierry Schüpbach, Christophe Bovigny, Prasad Chaskar, Antoine Daina, Ute F. Röhrig
, Olivier Michielin:
Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape. 437-447 - Murat Keçeli
, Hong Zhang, Peter Zapol, David A. Dixon, Albert F. Wagner:
Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding. 448-459
Volume 37, Number 5, 2016
- Anna Stachiewicz, Andrzej Molski
:
Diffusive dynamics of DNA unzipping in a nanopore. 467-476 - Rahul V. Pinjari
, Mickaël G. Delcey
, Meiyuan Guo
, Michael Odelius
, Marcus Lundberg:
Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra. 477-486 - Yu Harabuchi, Yuriko Ono
, Satoshi Maeda
, Tetsuya Taketsugu, Kristopher Keipert
, Mark S. Gordon:
Nontotally symmetric trifurcation of an SN2 reaction pathway. 487-493 - Christophe Narth, Louis Lagardère
, Étienne Polack
, Nohad Gresh, Qiantao Wang, David R. Bell, Joshua A. Rackers, Jay W. Ponder, Pengyu Y. Ren
, Jean-Philip Piquemal
:
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. 494-506
- Francesco Aquilante, Jochen Autschbach
, Rebecca K. Carlson
, Liviu F. Chibotaru
, Mickaël G. Delcey, Luca De Vico
, Ignacio Fdez. Galván
, Nicolas Ferré
, Luis Manuel Frutos
, Laura Gagliardi
, Marco Garavelli
, Angelo Giussani, Chad E. Hoyer
, Giovanni Li Manni
, Hans Lischka, Dongxia Ma, Per-Åke Malmqvist, Thomas Müller
, Artur Nenov
, Massimo Olivucci
, Thomas Bondo Pedersen
, Daoling Peng, Felix Plasser, Ben Pritchard, Markus Reiher
, Ivan Rivalta
, Igor Schapiro
, Javier Segarra-Martí
, Michael Stenrup, Donald G. Truhlar
, Liviu Ungur
, Alessio Valentini
, Steven Vancoillie, Valera Veryazov, Victor P. Vysotskiy, Oliver Weingart
, Felipe Zapata
, Roland Lindh:
Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table. 506-541
Volume 37, Number 6, 2016
Editorial
- Wei Yang:
Advanced Sampling for Molecular Simulation is Coming of Age. 549
- Kuo-Hao Lee, Jianhan Chen:
Multiscale enhanced sampling of intrinsically disordered protein conformations. 550-557 - Gregory R. Bowman
:
Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation. 558-566 - Chao Lv, Erick W. Aitchison
, Dongsheng Wu, Lianqing Zheng, Xiaolin Cheng, Wei Yang:
Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling. 567-574 - Davide Branduardi, Fabrizio Marinelli
, José D. Faraldo-Gómez:
Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg2+ through the SOMA string method. 575-586 - Alex Dickson
, Logan S. Ahlstrom, Charles L. Brooks III:
Coupled folding and binding with 2D Window-Exchange Umbrella Sampling. 587-594 - Xiongwu Wu, Bernard R. Brooks, Eric Vanden-Eijnden:
Self-guided Langevin dynamics via generalized Langevin equation. 595-601 - Juan M. Bello-Rivas, Ron Elber:
Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning. 602-613 - Xiangda Peng
, Yuebin Zhang, Huiying Chu, Guohui Li:
Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform. 614-622
Volume 37, Number 7, 2016
- Alexander Cumberworth
, Jennifer M. Bui, Jörg Gsponer:
Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models. 629-640 - Andrei V. Bandura
, Vitaly V. Porsev
, Robert A. Evarestov
:
Application of zone-folding approach to the first-principles estimation of thermodynamic properties of carbon and ZrS2-based nanotubes. 641-652 - Zhao Jin, Chunwei Yang, Fenglei Cao, Feng Li, Zhifeng Jing
, Long Chen, Zhe Shen
, Liang Xin, Sijia Tong, Huai Sun:
Hierarchical atom type definitions and extensible all-atom force fields. 653-664 - Arne Scherrer, Daniel Sebastiani:
Moment expansion of the linear density-density response function. 665-674 - Gessenildo Pereira Rodrigues, Elizete Ventura
, Silmar Andrade do Monte, Mario Barbatti
:
UV-photoexcitation and ultrafast dynamics of HCFC-132b (CF2ClCH2Cl). 675-683 - Haitao Sun, Shian Zhang, Cheng Zhong, Zhenrong Sun:
Theoretical study of excited states of DNA base dimers and tetramers using optimally tuned range-separated density functional theory. 684-693
Volume 37, Number 8, 2016
- Miguel Angelo Fonseca de Souza
, Elizete Ventura
, Silmar Andrade do Monte, José M. Riveros, Ricardo L. Longo:
Revisiting the concept of the (a)synchronicity of diels-alder reactions based on the dynamics of quasiclassical trajectories. 701-711 - Hiraku Oshima
, Masahiro Kinoshita:
A highly efficient hybrid method for calculating the hydration free energy of a protein. 712-723 - Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
:
Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution. 724-738 - Christine-Andrea Roth, Tom Dreyfus, Charles H. Robert
, Frédéric Cazals:
Hybridizing rapidly exploring random trees and basin hopping yields an improved exploration of energy landscapes. 739-752 - Jessica K. Gagnon, Sean M. Law, Charles L. Brooks III:
Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. 753-762 - Simon W. L. Hogan, Tanja Van Mourik
:
Competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems. 763-770 - Julien Racine, Denis Hagebaum-Reignier
, Yannick Carissan
, Stéphane Humbel:
Recasting wave functions into valence bond structures: A simple projection method to describe excited states. 771-779
Volume 37, Number 9, 2016
- Cláudio M. Lousada
, Pavel A. Korzhavyi:
Surface chemistry of oxygen on aluminum - Performance of the density functionals: PBE, PBE0, M06, and M06-L. 787-794 - Min Li, John Z. H. Zhang, Fei Xia:
A new algorithm for construction of coarse-grained sites of large biomolecules. 795-804 - Alain C. Vaucher
, Moritz P. Haag, Markus Reiher
:
Real-time feedback from iterative electronic structure calculations. 805-812 - Xi Chen
, Fu-Quan Bai
, Yongan Tang
, Hong-Xing Zhang:
How the substituents in corannulene and sumanene derivatives alter their molecular assemblings and charge transport properties? - A theoretical study with a dimer model. 813-824 - Bolong Huang
:
4f fine-structure levels as the dominant error in the electronic structures of binary lanthanide oxides. 825-835 - Pin-Chih Su, Michael E. Johnson
:
Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors. 836-847 - Maciej Dziubinski, Bogdan Lesyng
:
Toward the identification of molecular cogs. 848-860 - Davide Presti
, Frédéric Labat
, Alfonso Pedone, Michael J. Frisch, Hrant P. Hratchian, Ilaria Ciofini
, Maria Cristina Menziani
, Carlo Adamo
:
Modeling emission features of salicylidene aniline molecular crystals: A QM/QM' approach. 861-870
Volume 37, Number 10, April 2016
- Hongbo Du
, Xianghong Qian:
The hydration properties of carboxybetaine zwitterion brushes. 877-885 - Yasuhito Ohta:
Possible mechanism of BN fullerene formation from a boron cluster: Density-functional tight-binding molecular dynamics simulations. 886-895 - You Xu, Kenno Vanommeslaeghe
, Alexey Aleksandrov
, Alexander D. MacKerell Jr., Lennart Nilsson
:
Additive CHARMM force field for naturally occurring modified ribonucleotides. 896-912 - Roman Osman, Mihaly Mezei, Stanislav Engel:
The role of protein "Stability patches" in molecular recognition: A case study of the human growth hormone-receptor complex. 913-919 - Leebyn Chong, Fikret Aydin
, Meenakshi Dutt
:
Implicit solvent coarse-grained model of polyamidoamine dendrimers: Role of generation and pH. 920-926 - Evan J. Arthur, Charles L. Brooks III:
Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors. 927-939 - Rodrigo Galindo-Murillo, Luis Enrique Aguilar-Suárez
, Joaquín Barroso-Flores
:
A mixed DFT-MD methodology for the in silico development of drug releasing macrocycles. Calix and thia-calix[N]arenes as carriers for Bosutinib and Sorafenib. 940-946 - Sergi Vela
, Maria Fumanal
, Jordi Ribas-Ariño
, Vincent Robert:
On the zeroth-order hamiltonian for CASPT2 calculations of spin crossover compounds. 947-953
Volume 37, Number 11, April 2016
- Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove
, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda
, Dima Kozakov
:
Focused grid-based resampling for protein docking and mapping. 961-970 - Il Seung Youn, Woo Jong Cho, Kwang S. Kim
:
Effects of an electric field on interaction of aromatic systems. 971-975 - Yuedong Yang
, Yaoqi Zhou
:
Effective protein conformational sampling based on predicted torsion angles. 976-980 - Ingrid G. Prandi
, Lucas Viani, Oliviero Andreussi
, Benedetta Mennucci
:
Combining classical molecular dynamics and quantum mechanical methods for the description of electronic excitations: The case of carotenoids. 981-991 - Bhaskar Sharma, Y. Indra Neela, G. Narahari Sastry:
Structures and energetics of complexation of metal ions with ammonia, water, and benzene: A computational study. 992-1004 - Matthias Witte, Uwe Gerstmann
, Adam Neuba, Gerald Henkel, Wolf Gero Schmidt
:
Density functional theory of the CuA-like Cu2S2 diamond core in Cu 2II(NGuaS)2Cl2. 1005-1018
- Eric G. Kratz, Alice R. Walker
, Louis Lagardère
, Filippo Lipparini
, Jean-Philip Piquemal
, G. Andrés Cisneros
:
LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. 1019-1029 - Stefan Maintz, Volker L. Deringer
, Andreì L. Tchougréeff
, Richard Dronskowski
:
LOBSTER: A tool to extract chemical bonding from plane-wave based DFT. 1030-1035
Volume 37, Number 12, May 2016
- Jiaye Su, Keda Yang:
Temperature dependence of the transport of single-file water molecules through a hydrophobic channel. 1043-1047
- Seydou Traoré, Kyle E. Roberts, David Allouche, Bruce Randall Donald, Isabelle André, Thomas Schiex, Sophie Barbe
:
Fast search algorithms for computational protein design. 1048-1058 - Jiri Brabec
, Chao Yang, Evgeny Epifanovsky, Anna I. Krylov
, Esmond Ng:
Reduced-cost sparsity-exploiting algorithm for solving coupled-cluster equations. 1059-1067 - Daniela E. Ortega
, Quynh Nhu N. Nguyen
, Dean J. Tantillo
, Alejandro Toro-Labbé
:
The catalytic effect of the NH3 base on the chemical events in the caryolene-forming carbocation cascade. 1068-1081 - Emanuele Rossini, Ernst-Walter Knapp:
Proton solvation in protic and aprotic solvents. 1082-1091 - Johannes Heuser, Sebastian Höfener:
Wave-function frozen-density embedding: Approximate analytical nuclear ground-state gradients. 1092-1101 - Bachir Aoun:
Fullrmc, a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence. 1102-1111 - Ronald D. Hills Jr.
, Nicholas McGlinchey:
Model parameters for simulation of physiological lipids. 1112-1118
- Md. Tamjidul Hoque, Yuedong Yang
, Avdesh Mishra, Yaoqi Zhou
:
sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections. 1119-1124 - Yu Takano
, Kazuto Nakata, Yasushige Yonezawa, Haruki Nakamura:
Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions. 1125-1132
Volume 37, Number 13, May 2016
- Yasushige Yonezawa:
A method for predicting protein conformational pathways by using molecular dynamics simulations guided by difference distance matrices. 1139-1146 - Tiziana Ginex
, Jordi Muñoz-Muriedas
, Enric Herrero
, Enric Gibert, Pietro Cozzini, F. Javier Luque
:
Development and validation of hydrophobic molecular fields derived from the quantum mechanical IEF/PCM-MST solvation models in 3D-QSAR. 1147-1162