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ORCIDJournal 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, Kendall 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