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ORCIDJournal 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, R. 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 Cardenas, 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 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 - Robert C. Harris, Nan-Jie Deng, Ronald M. Levy, Ryosuke Ishizuka, Nobuyuki Matubayasi:
Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points. 1198-1208 - Leon A. Sakkal, Kyle Z. Rajkowski, Roger S. Armen:
Prediction of consensus binding mode geometries for related chemical series of positive allosteric modulators of adenosine and muscarinic acetylcholine receptors. 1209-1228 - Cen Gao, Jérémy Desaphy, Michal Vieth:
Are induced fit protein conformational changes caused by ligand-binding predictable? A molecular dynamics investigation. 1229-1237 - E. Prabhu Raman, Sirish Kaushik Lakkaraju, Rajiah A. Denny, Alexander D. MacKerell Jr.:
Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches. 1238-1251 - Sam Tonddast-Navaei, Bharath Srinivasan, Jeffrey Skolnick:
On the importance of composite protein multiple ligand interactions in protein pockets. 1252-1259 - Christopher R. Ellis, Cheng-Chieh Tsai, Fang-Yu Lin, Jana Shen:
Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor. 1260-1269 - Shuai Wei, Charles L. Brooks III, Aaron T. Frank:
A rapid solvent accessible surface area estimator for coarse grained molecular simulations. 1270-1274 - Lisa E. Felberg, David H. Brookes, Eng-Hui Yap, Elizabeth Jurrus, Nathan A. Baker, Teresa Head-Gordon:
PB-AM: An open-source, fully analytical linear poisson-boltzmann solver. 1275-1282
Volume 38, Number 16, June 2017
Review
- Garrett B. Goh, Nathan O. Hodas, Abhinav Vishnu:
Deep learning for computational chemistry. 1291-1307
- Bercem Dutagaci, Maryam Sayadi, Michael Feig:
Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices. 1308-1320