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Journal of Computational Chemistry, Volume 38
Volume 38, Number 1, January 2017
- Hiromi Nakai
, Takeshi Yoshikawa
, Yutaro Nonaka:
Efficient pole-search algorithm for dynamic polarizability: Toward alternative excited-state calculation for large systems. 7-14 - Axel Wuttke, Ricardo A. Mata:
Visualizing dispersion interactions through the use of local orbital spaces. 15-23 - Duc Duy Nguyen
, Guo-Wei Wei:
The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling. 24-36 - Jacek Koput
:
Ab initio potential energy surface and vibration-rotation energy levels of beryllium monohydroxide. 37-43 - Alvaro Muñoz-Castro
, Robert Bruce King:
Evaluation of bonding, electron affinity, and optical properties of M@C28 (M = Zr, Hf, Th, and U): Role of d- and f-orbitals in endohedral fullerenes from relativistic DFT calculations. 44-50
- Sebastian Dohm, Eckhard Spohr, Martin Korth:
Developing adaptive QM/MM computer simulations for electrochemistry. 51-58
Volume 38, Number 2, January 2017
- Ity Sharma, George A. Kaminski:
Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pKa shifts of protein residues. 65-80 - James S. M. Anderson, Juan I. Rodríguez, Paul W. Ayers, Andreas W. Götz
:
Relativistic (SR-ZORA) quantum theory of atoms in molecules properties. 81-86 - Enrico Benassi:
Benchmarking of density functionals for a soft but accurate prediction and assignment of 1H and 13C NMR chemical shifts in organic and biological molecules. 87-92 - Charles C. Kirkpatrick, John N. Truong, Bruce A. Kowert:
d-electron count, ion-pairing and diagonal twist angles in metallo-bis(dithiolene) complexes. 93-100 - Yosuke Sumiya, Tetsuya Taketsugu, Satoshi Maeda
:
Full rate constant matrix contraction method for obtaining branching ratio of unimolecular decomposition. 101-109 - Peter L. Walters, Thomas C. Allen, Nancy Makri:
Direct determination of discrete harmonic bath parameters from molecular dynamics simulations. 110-115 - Christopher Ehlert, Tillmann Klamroth:
The quest for best suited references for configuration interaction singles calculations of core excited states. 116-126
Volume 38, Number 3, January 2017
- Bastien Belzunces, Sophie Hoyau, Magali Benoit
, Nathalie Tarrat, Fabienne Bessac
:
Theoretical study of the atrazine pesticide interaction with pyrophyllite and Ca2+-montmorillonite clay surfaces. 133-143 - Li-Hua Gan, Rui Wu, Jian-Lei Tian, Joseph Clarke, Christopher Gibson, Patrick W. Fowler:
From C58 to C62 and back: Stability, structural similarity, and ring current. 144-151 - Song Liu, Lizhe Zhu
, Fu Kit Sheong
, Wei Wang
, Xuhui Huang
:
Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories. 152-160 - John P. Cvitkovic, George A. Kaminski:
Developing multisite empirical force field models for Pt(II) and cisplatin. 161-168 - Cheng Wang, Yingkai Zhang:
Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. 169-177 - Valter H. Carvalho-Silva
, Vincenzo Aquilanti, Heibbe C. B. de Oliveira, Kleber C. Mundim:
Deformed transition-state theory: Deviation from Arrhenius behavior and application to bimolecular hydrogen transfer reaction rates in the tunneling regime. 178-188
Volume 38, Number 4, February 2017
- Fahimeh Ghasemi, Afshin Fassihi
, Horacio Pérez Sánchez
, Alireza Mehri Dehnavi:
The role of different sampling methods in improving biological activity prediction using deep belief network. 195-203 - Julien Pilmé:
Electron localization function from density components. 204-210 - Yuta Kajiwara
, Satoshi Yasuda
, Yuuki Takamuku, Takeshi Murata
, Masahiro Kinoshita:
Identification of thermostabilizing mutations for a membrane protein whose three-dimensional structure is unknown. 211-223 - Salvador Cardona-Serra
, Stefano Sanvito
:
Influence of the dipolar interactions on the relative stability in spin crossover systems. 224-227 - Dmytro Bykov
, Thomas Kjærgaard:
The GPU-enabled divide-expand-consolidate RI-MP2 method (DEC-RI-MP2). 228-237
- Danny Schlüns, Mirko Franchini, Andreas W. Götz
, Johannes Neugebauer
, Christoph R. Jacob
, Lucas Visscher
:
Analytical gradients for subsystem density functional theory within the slater-function-based amsterdam density functional program. 238-249
Volume 38, Number 5, February 2017
- Alessandro Erba
, Dominique Caglioti, Claudio Marcelo Zicovich-Wilson, Roberto Dovesi:
Nuclear-relaxed elastic and piezoelectric constants of materials: Computational aspects of two quantum-mechanical approaches. 257-264 - Peter P. Passler, Thomas S. Hofer
:
Conserving the linear momentum in stochastic dynamics: Dissipative particle dynamics as a general strategy to achieve local thermostatization in molecular dynamics simulations. 265-275 - Jason W. Labonte
, Jared Adolf-Bryfogle, William R. Schief, Jeffrey J. Gray
:
Residue-centric modeling and design of saccharide and glycoconjugate structures. 276-287 - Marek Szczepaniak, Jerzy Moc
:
Anomerization reaction of bare and microhydrated d-erythrose via explicitly correlated coupled cluster approach. Two water molecules are optimal. 288-303 - Xiaoling Zhan, Hu Shi
, Hongguang Liu
, Jin Yong Lee:
Applying strong external electric field to thiophene-based oligomers: A promising approach to upgrade semiconducting performance. 304-311
Volume 38, Number 6, March 2017
- Marco Pagliai
, Giordano Mancini, Ivan Carnimeo, Nicola De Mitri
, Vincenzo Barone
:
Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach. 319-335 - Timothy L. Fletcher, Paul L. A. Popelier:
Toward amino acid typing for proteins in FFLUX. 336-345 - Miguel Jorge
, Nuno M. Garrido, Carlos J. V. Simões, Cândida G. Silva, Rui M. M. Brito
:
Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models. 346-358 - Miguel Jorge
:
Predicting hydrophobic solvation by molecular simulation: 2. New united-atom model for alkanes, alkenes, and alkynes. 359-369 - Amir Karton
:
How reliable is DFT in predicting relative energies of polycyclic aromatic hydrocarbon isomers? comparison of functionals from different rungs of jacob's ladder. 370-382
- Katharina Krause, Wim Klopper
:
Implementation of the Bethe-Salpeter equation in the TURBOMOLE program. 383-388 - Ingo Heimbach, Florian Rhiem
, Fabian Beule, David Knodt, Josef Heinen, Robert O. Jones
:
pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter and molecules. 389-394
Volume 38, Number 7, March 2017
- Elena I. Davydova
, Anna S. Lisovenko
, Alexey Y. Timoshkin
:
Complex beryllium amidoboranes: Structures, stability, and evaluation of their potential as hydrogen storage materials. 401-405 - Yoshio Nishimoto
, Dmitri G. Fedorov:
Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding. 406-418 - Antoni Oliver
, Christopher A. Hunter, Rafel Prohens, Josep L. Rosselló
:
A surface site interaction point methodology for macromolecules and huge molecular databases. 419-426 - Martina Rubesová, Veronika Jurásková
, Petr Slavícek:
Efficient modeling of liquid phase photoemission spectra and reorganization energies: Difficult case of multiply charged anions. 427-437 - Haiyan Yuan, Jingping Zhang
:
Mechanistic insights on DBU catalyzed β-amination of nbs to chalcone driving by water: Multiple roles of water. 438-445
- Beibei Liu, Bao Wang, Rundong Zhao, Yiying Tong, Guo-Wei Wei:
ESES: Software for Eulerian solvent excluded surface. 446-466 - Braulio Valdebenito-Maturana
, Jose Antonio Reyes-Suarez, Jaime Henriquez, David S. Holmes
, Raquel Quatrini, Ehmke Pohl
, Mauricio Arenas-Salinas:
Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins. 467-474
Volume 38, Number 8, March 2017
- Ricardo Pino-Rios
, Osvaldo Yañez
, Diego Inostroza
, Lina Ruiz, Carlos Cárdenas, Patricio Fuentealba, William Tiznado:
Proposal of a simple and effective local reactivity descriptor through a topological analysis of an orbital-weighted fukui function. 481-488 - Michio Katouda
, Takahito Nakajima:
MPI/OpenMP hybrid parallel algorithm for resolution of identity second-order Møller-Plesset perturbation calculation of analytical energy gradient for massively parallel multicore supercomputers. 489-507 - Koen Visscher, C. Ruben Vosmeer, Rosa A. Luirink, Daan P. Geerke
:
A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols. 508-517 - Noèlia Pueyo Bellafont, Francesc Viñes, Wolfgang Hieringer, Francesc Illas:
Predicting core level binding energies shifts: Suitability of the projector augmented wave approach as implemented in VASP. 518-522 - Francesc Viñes, Francesc Illas:
Electronic structure of stoichiometric and reduced ZnO from periodic relativistic all electron hybrid density functional calculations using numeric atom-centered orbitals. 523-529 - Isabel Lage-Estebanez, Lourdes del Olmo, Rafael López, José Manuel García de la Vega:
The role of errors related to DFT methods in calculations involving ion pairs of ionic liquids. 530-540
- Yang Xie, Jinyong Ying, Dexuan Xie:
SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation. 541-552 - Adam K. Sieradzan
, Rafal Jakubowski
:
Introduction of steered molecular dynamics into UNRES coarse-grained simulations package. 553-562
Volume 38, Number 9, April 2017
- Zhubin Hu, Bin Zhou, Zhenrong Sun, Haitao Sun
:
Prediction of excited-state properties of oligoacene crystals using polarizable continuum model-tuned range-separated hybrid functional approach. 569-575 - Guido Falk von Rudorff
, Tobias Watermann, Xiangyang Guo, Daniel Sebastiani:
Conformational Space of a Polyphilic Molecule with a Fluorophilic Side Chain Integrated in a DPPC Bilayer. 576-583 - Lin Li, Arghya Chakravorty
, Emil Alexov:
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. 584-593 - Chao Wang
, Yizhong Yuan, Xiaohui Tian:
Assessment of range-separated exchange functionals and nonempirical functional tuning for calculating the static second hyperpolarizabilities of streptocyanines. 594-600 - Sarah Witzke, Nanna Holmgaard List, Jógvan Magnus H. Olsen
, Casper Steinmann
, Michael Petersen
, Maarten T. P. Beerepoot, Jacob Kongsted
:
An averaged polarizable potential for multiscale modeling in phospholipid membranes. 601-611 - Jingyuan Gao, Wenliang Li
, Jingping Zhang
:
Theoretical simulation of CO2 capture in organic cage impregnated with polyoxometalates. 612-619 - Marc Esser, Stefan Maintz, Richard Dronskowski
:
Automated first-principles mapping for phase-change materials. 620-628
- Volker Lesch, Diddo Diddens, Carlos E. S. Bernardes, Benjamin Golub
, Alain Dequidt, Veronika Zeindlhofer, Marcello Sega, Christian Schröder
:
ForConX: A forcefield conversion tool based on XML. 629-638
Volume 38, Number 10, April 2017
- Mina Jafari
, Paul M. Zimmerman:
Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method. 645-658 - Marilia T. C. Martins-Costa, Manuel F. Ruiz-López
:
Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling. 659-668 - Koichi Ohno
, Naoki Kishimoto
, Takeaki Iwamoto, Hiroko Satoh
:
Global exploration of isomers and isomerization channels on the quantum chemical potential energy surface of H3CNO3. 669-687 - Vijay Madhav Miriyala, Jan Rezác
:
Description of non-covalent interactions in SCC-DFTB methods. 688-697 - Pouya Partovi-Azar, Payam Kaghazchi
:
Time-dependent density functional theory study on direction-dependent electron and hole transfer processes in molecular systems. 698-703 - Yoshimichi Andoh
, Noriyuki Yoshii, Atsushi Yamada
, Susumu Okazaki:
Evaluation of atomic pressure in the multiple time-step integration algorithm. 704-713 - Christian Margreitter
, Maria M. Reif
, Chris Oostenbrink
:
Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field. 714-720 - Xiaojuan Yu, Hua Hou, Baoshan Wang
:
Prediction on dielectric strength and boiling point of gaseous molecules for replacement of SF6. 721-729 - Kun Yuan, Rui-Sheng Zhao, Jia-Jia Zheng
, Hong Zheng, Shigeru Nagase, Sheng-Dun Zhao, Yan-Zhi Liu, Xiang Zhao
:
Van Der Waals heterogeneous layer-layer carbon nanostructures involving π···H-C-C-H···π···H-C-C-H stacking based on graphene and graphane sheets. 730-739 - Baofeng Zhang, Denise Kilburg, Peter K. Eastman, Vijay S. Pande, Emilio Gallicchio
:
Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units. 740-752
- Carlos E. S. Bernardes
:
AGGREGATES: Finding structures in simulation results of solutions. 753-765
Volume 38, Number 11, April 2017
- Sirous Yourdkhani
, Miroslaw Jablonski
:
Revealing the physical nature and the strength of charge-inverted hydrogen bonds by SAPT(DFT), MP2, SCS-MP2, MP2C, and CCSD(T) methods. 773-780 - Francesc Viñes, Oriol Lamiel-García, Kyoung Chul Ko
, Jin Yong Lee, Francesc Illas:
Systematic study of the effect of HSE functional internal parameters on the electronic structure and band gap of a representative set of metal oxides. 781-789 - Ryuhei Harada
, Yu Takano
, Yasuteru Shigeta
:
Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. 790-797 - Xiaojun Zhou
, Fan Wang:
Barrier heights of hydrogen-transfer reactions with diffusion quantum monte carlo method. 798-806 - Álvaro Vega-Vega, Carmen Barrientos
, Antonio Largo
:
Metallic monoboronyl compounds: Prediction of their structure and comparison with the cyanide analogues. 807-815 - Evelio Francisco, Daniel Menéndez Crespo, Aurora Costales, Ángel Martín Pendás
:
A multipolar approach to the interatomic covalent interaction energy. 816-829 - Ellie Fought
, Vaibhav Sundriyal, Masha Sosonkina, Theresa L. Windus
:
Saving time and energy with oversubscription and semi-direct Møller-Plesset second order perturbation methods. 830-841
- Ilya A. Kaliman, Anna I. Krylov
:
New algorithm for tensor contractions on multi-core CPUs, GPUs, and accelerators enables CCSD and EOM-CCSD calculations with over 1000 basis functions on a single compute node. 842-853
Volume 38, Number 12, May 2017
- Lynn Groß, Marc Philipp Bahlke, Torben Steenbock, Christian Klinke
, Carmen Herrmann
:
Modeling adsorbate-induced property changes of carbon nanotubes. 861-868 - Saswata Dasgupta
, John M. Herbert
:
Standard grids for high-precision integration of modern density functionals: SG-2 and SG-3. 869-882 - Renato Pereira Orenha
, Régis Tadeu Santiago, Roberto Luiz Andrade Haiduke
, Sérgio Emanuel Galembeck
:
How computational methods and relativistic effects influence the study of chemical reactions involving Ru-NO complexes? 883-891 - Jacek Koput
:
Ab initio potential energy surface and vibration-rotation energy levels of sulfur dioxide. 892-900 - Yaowarat Surakhot, Viktor Laszlo, Chirawat Chitpakdee, Vinich Promarak
, Taweesak Sudyoadsuk
, Nawee Kungwan
, Tim Kowalczyk, Stephan Irle, Siriporn Jungsuttiwong
:
Theoretical rationalization for reduced charge recombination in bulky carbazole-based sensitizers in solar cells. 901-909 - Rei Matsuzaki, Satoshi Yabushita
:
Optimization of complex slater-type functions with analytic derivative methods for describing photoionization differential cross sections. 910-925
- Anton A. Raskovalov
:
A new extension of classical molecular dynamics: An electron transfer algorithm. 926-932
- Simon W. L. Hogan, Tanja Van Mourik
:
Corrigendum: Competition between Hydrogen and Halogen Bonding in Halogenated 1-Methyluracil: Water Systems. 933
Volume 38, Number 13, May 2017
- Duc Duy Nguyen
, Bao Wang, Guo-Wei Wei
:
Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies. 941-948 - Sean T. Holmes
, Shi Bai, Robbie J. Iuliucci, Karl T. Mueller, Cecil Dybowski:
Calculations of solid-state 43Ca NMR parameters: A comparison of periodic and cluster approaches and an evaluation of DFT functionals. 949-956 - Jesús Jara-Cortés
, José Manuel Guevara-Vela
, Ángel Martín Pendás
, Jesús Hernández-Trujillo
:
Chemical bonding in excited states: Energy transfer and charge redistribution from a real space perspective. 957-970 - Hujun Shen
, Mingsen Deng
, Yachao Zhang
:
Extension of CAVS coarse-grained model to phospholipid membranes: The importance of electrostatics. 971-980 - Jurgens Hendrik de Lange, Ignacy Cukrowski
:
Toward deformation densities for intramolecular interactions without radical reference states using the fragment, atom, localized, delocalized, and interatomic (FALDI) charge density decomposition scheme. 981-997 - Stefania Di Tommaso, Diane Bousquet, Delphine Moulin, Frédéric Baltenneck, Priscilla Riva, Hervé David, Aziz Fadli, Jérôme Gomar, Ilaria Ciofini
, Carlo Adamo
:
Theoretical approaches for predicting the color of rigid dyes in solution. 998-1004 - Timothy L. Fletcher, Paul L. A. Popelier
:
FFLUX: Transferability of polarizable machine-learned electrostatics in peptide chains. 1005-1014
Volume 38, Number 14, May 2017
- Florian Krausbeck, Jan-Grimo Sobez, Markus Reiher
:
Stabilization of activated fragments by shell-wise construction of an embedding environment. 1023-1038 - Riccardo Volpi
, Mathieu Linares
:
Study of the cold charge transfer state separation at the TQ1/PC71BM interface. 1039-1048 - Jihène Jerbi
, Michael Springborg:
Computational study of the reactivity of cytosine derivatives. 1049-1056 - Changhao Wang, Li Xiao, Ray Luo
:
Numerical interpretation of molecular surface field in dielectric modeling of solvation. 1057-1070 - Gaëtan Rubez, Jean-Matthieu Etancelin, Xavier Vigouroux, Michaël Krajecki
, Jean-Charles Boisson, Eric Henon
:
GPU accelerated implementation of NCI calculations using promolecular density. 1071-1083 - Marika Savarese
, Umberto Raucci
, Ryoichi Fukuda
, Carlo Adamo
, Masahiro Ehara
, Nadia Rega
, Ilaria Ciofini
:
Comparing the performance of TD-DFT and SAC-CI methods in the description of excited states potential energy surfaces: An excited state proton transfer reaction as case study. 1084-1092 - Uyen Q. Ly, My-Phuong Pham, Maurice J. Marks, Thanh N. Truong
:
Density functional theory study of mechanism of epoxy-carboxylic acid curing reaction. 1093-1102
Volume 38, Number 15, June 2017
Introduction
- Jonathan D. Hirst, Wonpil Im, Joan-Emma Shea:
Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III. 1111-1113
- Sunhwan Jo, Xi Cheng, Jumin Lee, Seonghoon Kim, Sang-Jun Park, Dhilon S. Patel, Andrew H. Beaven, Kyu Il Lee, Huan Rui, Soohyung Park
, Hui Sun Lee, Benoît Roux, Alexander D. MacKerell Jr., Jeffrey B. Klauda, Yifei Qi, Wonpil Im:
CHARMM-GUI 10 years for biomolecular modeling and simulation. 1114-1124
- Ester Sesmero, Jodian A. Brown, Ian F. Thorpe:
Molecular simulations to delineate functional conformational transitions in the HCV polymerase. 1125-1137 - Alex Dickson
, Christopher T. Bailey, John Karanicolas:
Optimal allosteric stabilization sites using contact stabilization analysis. 1138-1146 - You Xu, Alessandra Villa
, Lennart Nilsson:
The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid. 1147-1157 - Hossein Mohammadiarani
, Harish Vashisth
:
Insulin mimetic peptide S371 folds into a helical structure. 1158-1166 - Yoshiharu Mori, Yuko Okamoto
:
Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study. 1167-1173 - Qi Huang, Jocelyn M. Rodgers, Russell J. Hemley, Toshiko Ichiye:
Extreme biophysics: Enzymes under pressure. 1174-1182 - Zhe Jia, Christine Ackroyd, Tingting Han, Vibhor Agrawal, Yinling Liu, Kenneth Christensen, Brian N. Dominy
:
Effects from metal ion in tumor endothelial marker 8 and anthrax protective antigen: BioLayer Interferometry experiment and molecular dynamics simulation study. 1183-1190 - Christopher G. Myers, B. Montgomery Pettitt
:
Phage-like packing structures with mean field sequence dependence. 1191-1197