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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, 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, José Antonio Reyes-Suárez, 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 - 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 Aldrin 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 - Andrea Bazzoli, John Karanicolas:
"Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics. 1321-1331 - Kuo-Hao Lee, Jianhan Chen:
Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria. 1332-1341 - Mark A. Olson, Michael S. Lee, In-Chul Yeh:
Membrane insertion of fusion peptides from Ebola and Marburg viruses studied by replica-exchange molecular dynamics simulations. 1342-1352 - Bin Song, Nathaniel Charest, Herbert Alexander Morriss-Andrews, Valeria Molinero, Joan-Emma Shea:
Systematic derivation of implicit solvent models for the study of polymer collapse. 1353-1361 - Fouad S. Husseini, David Robinson, Neil T. Hunt, Anthony W. Parker, Jonathan D. Hirst:
Computing infrared spectra of proteins using the exciton model. 1362-1375 - Fiona L. Kearns, Phillip S. Hudson, Henry L. Woodcock, Stefan Boresch:
Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities. 1376-1388 - Sudipta Kumar Sinha, Mohit Mehta, Sandeep Patel:
A charge equilibration formalism for treating charge transfer effects in MD simulations: Application to water clusters. 1389-1409 - Jaewoon Jung, Yuji Sugita:
Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems. 1410-1418 - Travis Johnston, Boyu Zhang, Adam Liwo, Silvia Crivelli, Michela Taufer:
In situ data analytics and indexing of protein trajectories. 1419-1430 - Catherine A. Hurd, Nicholas A. Besley, David Robinson:
A QM/MM study of the nature of the entatic state in plastocyanin. 1431-1437 - Cathy Ng, Padmavathy Nandha Premnath, Olgun Guvench:
Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation. 1438-1446 - Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, Florence Tama:
Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. 1447-1461 - Michael D. Ward, Shivangi Nangia, Eric R. May:
Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides. 1462-1471 - Greg Starek, J. Alfredo Freites, Simon Bernèche, Douglas J. Tobias:
Gating energetics of a voltage-dependent K+ channel pore domain. 1472-1478 - Asanga Bandara, Afra Panahi, George A. Pantelopulos, John E. Straub:
Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers. 1479-1488
Volume 38, Number 17, June 2017
- Christian J. Suess, Jonathan D. Hirst, Nicholas A. Besley:
Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin. 1495-1502 - Hiroto Tachikawa:
Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization. 1503-1508 - Juan Carlos Sancho-García, Ángel J. Pérez-Jiménez, Marika Savarese, Éric Brémond, Carlo Adamo:
Determining the role of the underlying orbital-dependence of PBE0-DH and PBE-QIDH double-hybrid density functionals. 1509-1514 - Vincent Pohl, Gunter Hermann, Jean Christophe Tremblay:
An open-source framework for analyzing N-electron dynamics. I. Multideterminantal wave functions. 1515-1527 - Chong Yang, Andreas Dreuw:
Evaluation of the restricted virtual space approximation in the algebraic-diagrammatic construction scheme for the polarization propagator to speed-up excited-state calculations. 1528-1537 - Sjoerd Jacob de Vries, Martin Zacharias:
Fast and accurate grid representations for atom-based docking with partner flexibility. 1538-1546 - George Opletal, Timothy C. Petersen, Amanda S. Barnard, Salvy P. Russo:
On reverse Monte Carlo constraints and model reproduction. 1547-1551
- Johannes M. Dieterich, William C. Witt, Emily A. Carter:
libKEDF: An accelerated library of kinetic energy density functionals. 1552-1559
Volume 38, Number 18, July 2017
- Kenji Hirano, Hiroshi Nakano, Yoshihide Nakao, Hirofumi Sato, Shigeyoshi Sakaki:
Photo absorption of p-coumaric acid in aqueous solution: RISM-SCF-SEDD theory approach. 1567-1573 - Zhifeng Lin, Tian Lu, Xun-Lei Ding:
A theoretical investigation on doping superalkali for triggering considerable nonlinear optical properties of Si12C12 nanostructure. 1574-1582 - Andrew L. Ferguson:
BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method. 1583-1605 - Anand Kumar, Miquel Duran, Miquel Solà:
Is coronene better described by Clar's aromatic π-sextet model or by the AdNDP representation? 1606-1611 - Natacha Gillet, Bernard Lévy, Vicent Moliner, Isabelle Demachy, Aurélien de la Lande:
Theoretical estimation of redox potential of biological quinone cofactors. 1612-1621 - Swapnil Mahajan, Yves-Henri Sanejouand:
Jumping between protein conformers using normal modes. 1622-1630 - Teerapong Pirojsirikul, Andreas W. Götz, John H. Weare, Ross C. Walker, Karol Kowalski, Marat Valiev:
Combined quantum-mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution. 1631-1639 - Dariusz W. Szczepanik, Miquel Solà, Marcin Andrzejak, Barbara Pawelek, Justyna Dominikowska, Mercedes Kukulka, Karol Dyduch, Tadeusz M. Krygowski, Halina Szatylowicz:
The role of the long-range exchange corrections in the description of electron delocalization in aromatic species. 1640-1654
Volume 38, Number 19, July 2017
- Alvaro Muñoz-Castro, Robert Bruce King:
On the formation of smaller p-block endohedral fullerenes: Bonding analysis in the E@C20 (E = Si, Ge, Sn, Pb) series from relativistic DFT calculations. 1661-1667 - Osvaldo Yañez, Alejandro Vásquez-Espinal, Diego Inostroza, Lina Ruiz, Ricardo Pino-Rios, William Tiznado:
A Fukui function-guided genetic algorithm. Assessment on structural prediction of Sin (n = 12-20) clusters. 1668-1677 - Kuan-Yu Liu, Jie Liu, John M. Herbert:
Accuracy of finite-difference harmonic frequencies in density functional theory. 1678-1684 - Daijiro Nozaki, Wolf Gero Schmidt:
Current density analysis of electron transport through molecular wires in open quantum systems. 1685-1692 - Nils Schieschke, Roberto Di Remigio, Luca Frediani, Johannes Heuser, Sebastian Höfener:
Combining frozen-density embedding with the conductor-like screening model using Lagrangian techniques for response properties. 1693-1703 - Premaja R. Remya, Cherumuttathu H. Suresh:
Theoretical evidence for bond stretch isomerism in Grubbs olefin metathesis. 1704-1711 - Tamara Papp, László E. Kollár, Tamás Kégl:
Theoretical insights into the nature of Pt‒Sn bond: Reevaluating the bonding/back-bonding properties of trichlorostannate with comparison to the cyano ligand. 1712-1726
- Jindal K. Shah, Eliseo Marin-Rimoldi, Ryan Gotchy Mullen, Brian P. Keene, Sandip Khan, Andrew S. Paluch, Neeraj Rai, Lucienne L. Romanielo, Thomas W. Rosch, Brian Yoo, Edward J. Maginn:
Cassandra: An open source Monte Carlo package for molecular simulation. 1727-1739
Volume 38, Number 20, July 2017
- José A. Gámez, Markus Hölscher, Walter Leitner:
On the applicability of density functional theory to manganese-based complexes with catalytic activity toward water oxidation. 1747-1751
- Matthias Witte, Martin Rohrmüller, Uwe Gerstmann, Gerald Henkel, Wolf Gero Schmidt, Sonja Herres-Pawlis:
[Cu6(NGuaS)6]2+ and its oxidized and reduced derivatives: Confining electrons on a torus. 1752-1761 - Dóra Papp, Petra Rovó, Imre Jákli, Attila G. Császár, András Perczel:
Four faces of the interaction between ions and aromatic rings. 1762-1773 - Paul G. Mezey, Zoltan Antal:
An alternative to the "Star Path" enhancement of the ADMA linear scaling method for protein modeling. 1774-1779 - Athanassios C. Tsipis:
Exploring possible reaction pathways for the o-atom transfer reactions to unsaturated substrates catalyzed by a [Ni-NO2] ↔ [Ni-NO] redox couple using DFT methods. 1780-1788 - Ian L. Rogers, Kevin J. Naidoo:
Producing DFT/MM enzyme reaction trajectories from SCC-DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction. 1789-1798 - Borys Szefczyk, Dawid Grabarek, Elzbieta Walczak, Tadeusz Andruniów:
Excited-state minima and emission energies of retinal chromophore analogues: Performance of CASSCF and CC2 methods as compared with CASPT2. 1799-1810 - Jeroen Rombouts, Andreas W. Ehlers, Koop Lammertsma:
A quantitative analysis of light-driven charge transfer processes using voronoi partitioning of time dependent DFT-derived electron densities. 1811-1818
Volume 38, Number 21, August 2017
- Shigeru Yamaguchi, Takahiro Nishimura, Yuta Hibe, Masaki Nagai, Hirofumi Sato, Ian Johnston:
Regularized regression analysis of digitized molecular structures in organic reactions for quantification of steric effects. 1825-1833 - Matteo Masetti, Francesco Musiani, Mattia Bernetti, Federico Falchi, Andrea Cavalli, Stefano Ciurli, Maurizio Recanatini:
Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data. 1834-1843 - Talapunur Vikramaditya, Shiang-Tai Lin:
Assessing the role of Hartree-Fock exchange, correlation energy and long range corrections in evaluating ionization potential, and electron affinity in density functional theory. 1844-1852 - Martin Krupicka, Kantharuban Sivalingam, Lee Huntington, Alexander A. Auer, Frank Neese:
A toolchain for the automatic generation of computer codes for correlated wavefunction calculations. 1853-1868 - Joaquín Calbo, Juan Carlos Sancho-García, Enrique Ortí, Juan Aragó:
DLPNO-CCSD(T) scaled methods for the accurate treatment of large supramolecular complexes. 1869-1878
- Seonghoon Kim, Jumin Lee, Sunhwan Jo, Charles L. Brooks III, Hui Sun Lee, Wonpil Im:
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. 1879-1886 - Jean-Baptiste Chéron, Martin Zacharias, Serge Antonczak, Sébastien Fiorucci:
Update of the ATTRACT force field for the prediction of protein-protein binding affinity. 1887-1890
Volume 38, Number 22, August 2017
- Lea El-Khoury, Sehr Naseem-Khan, Karolina Kwapien, Zeina Hobaika, Richard G. Maroun, Jean-Philip Piquemal, Nohad Gresh:
Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions. 1897-1920 - Ryuhei Harada, Yasuteru Shigeta:
Structural dissimilarity sampling with dynamically self-guiding selection. 1921-1929 - Hernán R. Sánchez:
Revisiting the thermochemistry of chlorine fluorides. 1930-1940 - Nicolas Chéron, Eugene I. Shakhnovich:
Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations. 1941-1951 - Anis Ghazouani, Jalel M'halla:
Simple computing of the viscosity of water-dioxane mixtures, according to a fluctuating SPC/E-Ih interstitial model. 1952-1965 - Andrés G. Algarra:
Computational insights into the S3 transfer reaction: A special case of double group transfer reaction featuring bicyclically delocalized aromatic transition state geometries. 1966-1973
- Zhe Jia, Lin Li, Arghya Chakravorty, Emil Alexov:
Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. 1974-1979
Volume 38, Number 23, September 2017
- Iñaki Morao, Dmitri G. Fedorov, Roger Robinson, Michelle Southey, Andrea Townsend-Nicholson, Michael J. Bodkin, Alexander Heifetz:
Rapid and accurate assessment of GPCR-ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method. 1987-1990
- Lei Sun, Li Yang, Ya-dong Zhang, Qi Shi, Rui-Feng Lu, Wei-Qiao Deng:
Accurate van der Waals force field for gas adsorption in porous materials. 1991-1999 - Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou:
Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins. 2000-2006 - Ming Huang, Wenjun Huang, Fei Wen, Ronald G. Larson:
Efficient estimation of binding free energies between peptides and an MHC class II molecule using coarse-grained molecular dynamics simulations with a weighted histogram analysis method. 2007-2019 - Takao Tsuneda, Raman K. Singh, Ayako Nakata:
On low-lying excited states of extended nanographenes. 2020-2029 - Rei Matsuzaki, Satoshi Yabushita:
Calculation of photoionization differential cross sections using complex Gauss-type orbitals. 2030-2040 - I-Hsiang Lin, Yu-Huan Lu, Hsin-Tsung Chen:
Nitrogen-doped C60 as a robust catalyst for CO oxidation. 2041-2046 - Matthew Harger, Daniel Li, Zhi Wang, Kevin N. Dalby, Louis Lagardère, Jean-Philip Piquemal, Jay W. Ponder, Pengyu Y. Ren:
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. 2047-2055
Volume 38, Number 24, September 2017
- Amir Karton, Nitai Sylvetsky, Jan M. L. Martin:
W4-17: A diverse and high-confidence dataset of atomization energies for benchmarking high-level electronic structure methods. 2063-2075 - Silvia Díaz, Mateusz Z. Brela, Soledad Gutiérrez-Oliva, Alejandro Toro-Labbé, Artur Michalak:
ETS-NOCV Decomposition of the Reaction Force: The HCN/CNH Isomerization Reaction Assisted by Water. 2076-2087 - Robert A. Evarestov, Andrei V. Bandura, Vitaly V. Porsev, Alexey V. Kovalenko:
First-principles modeling of hafnia-based nanotubes. 2088-2099 - Yujia Pang, Wenliang Li, Jingping Zhang:
Gas adsorption in Mg-porphyrin-based porous organic frameworks: A computational simulation by first-principles derived force field. 2100-2107 - Dalibor Hrsak, Jógvan Magnus H. Olsen, Jacob Kongsted:
Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model. 2108-2117
- Jaime Rodríguez-Guerra Pedregal, Giuseppe Sciortino, Jordi Guasp, Martí Municoy, Jean-Didier Maréchal:
GaudiMM: A modular multi-objective platform for molecular modeling. 2118-2126
- Stephan N. Steinmann, Paul Fleurat-Lessard, Andreas W. Götz, Carine Michel, Rodrigo Ferreira de Morais, Philippe Sautet:
Molecular mechanics models for the image charge, a comment on "including image charge effects in the molecular dynamics simulations of molecules on metal surfaces". 2127-2129 - Stefano Corni:
Reply to "Molecular mechanics models for the image charge". 2130-2133
Volume 38, Number 25, September 2017
- Fabian Weber, Emad F. Aziz, Annika Bande:
Interdependence of ICD rates in paired quantum dots on geometry. 2141-2150 - Marco Campetella, Federica Maschietto, Mike J. Frisch, Giovanni Scalmani, Ilaria Ciofini, Carlo Adamo:
Charge transfer excitations in TDDFT: A ghost-hunter index. 2151-2156 - Per E. M. Siegbahn, Xichen Li:
Cluster size convergence for the energetics of the oxygen evolving complex in PSII. 2157-2160 - Sadanandam Namsani, Bhasker Gahtori, Sushil Auluck, Jayant K. Singh:
An interaction potential to study the thermal structure evolution of a thermoelectric material: β-Cu2Se. 2161-2170 - Maja Gruden, Ljubica Andjeklovic, Akkarapattiakal Kuriappan Jissy, Stepan Stepanovic, Matija Zlatar, Qiang Cui, Marcus Elstner:
Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules. 2171-2185 - Lakshmanan Sandhiya, Hendrik Zipse:
O‒O bond homolysis in hydrogen peroxide. 2186-2192
- Chigusa Kobayashi, Jaewoon Jung, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya, Yuji Sugita:
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms. 2193-2206
Volume 38, Number 26, October 2017
- Kimichi Suzuki, Keiji Morokuma, Satoshi Maeda:
Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems. 2213-2221 - Shi Deng, Qiantao Wang, Pengyu Y. Ren:
Estimating and modeling charge transfer from the SAPT induction energy. 2222-2231 - Ramachandran Rakhi, Cherumuttathu H. Suresh:
A DFT study on 1, 4-dihydro-1, 4-azaborinine annulated linear polyacenes: Absorption spectra, singlet-triplet energy gap, aromaticity, and HOMO-LUMO energy modulation. 2232-2240 - Jing-Shuang Dang, Weiwei Wang, Jia-Jia Zheng, Shigeru Nagase, Xiang Zhao:
Formation of Stone-Wales edge: Multistep reconstruction and growth mechanisms of zigzag nanographene. 2241-2247 - Samik Bose, Debashree Ghosh:
An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase. 2248-2257 - Manash Protim Borpuzari, Rahul Kar:
A new nonempirical tuning scheme with single self-consistent field calculation: Comparison with global and IP-tuned range-separated functional. 2258-2267 - Shanshan Cao, Haiyan Yuan, Yang Yang, Mang Wang, Xiaoying Zhang, Jingping Zhang:
Mechanistic investigation inspired "on water" reaction for hydrobromic acid-catalyzed Friedel-Crafts-type reaction of β-naphthol and formaldehyde. 2268-2275 - Andreas Lücke, Uwe Gerstmann, Thomas D. Kühne, Wolf Gero Schmidt:
Efficient PAW-based bond strength analysis for understanding the In/Si(111)(8 × 2) - (4 × 1) phase transition. 2276-2282
Volume 38, Number 27, October 2017
- Haiyan Yuan, Pin Xiao, Yiying Zheng, Jingping Zhang:
DFT studies on the mechanism of Ag2CO3-catalyzed hydroazidation of unactivated terminal alkynes with TMS-N3: An insight into the silver(I) activation mode. 2289-2297 - Changjun Chen:
Constructing a multidimensional free energy surface like a spider weaving a web. 2298-2306 - Bun Chan, Yukio Kawashima, Kimihiko Hirao:
Correlation functional in screened-exchange density functional theory procedures. 2307-2315 - Johannes Heuser, Sebastian Höfener:
Analytical nuclear excited-state gradients for the Tamm-Dancoff approximation using uncoupled frozen-density embedding. 2316-2325 - Jun Chen, Neil Qiang Su, Xin Xu, Dong H. Zhang:
Accurate potential energy surfaces for hydrogen abstraction reactions: A benchmark study on the XYG3 doubly hybrid density functional. 2326-2334 - Titus Adrian Beu, Alexandra Farcas:
CHARMM force field and molecular dynamics simulations of protonated polyethylenimine. 2335-2348 - Carolin Hühn, Andreas Erlebach, Dorothea Mey, Lothar Wondraczek, Marek Sierka:
Ab Initio energetics of Si‒O bond cleavage. 2349-2353
- Pin-Chia Hsu, Bart M. H. Bruininks, Damien Jefferies, Paulo Cesar Telles de Souza, Jumin Lee, Dhilon S. Patel, Siewert J. Marrink, Yifei Qi, Syma Khalid, Wonpil Im:
CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. 2354-2363
Volume 38, Number 28, October 2017
- Vitor H. Menezes da Silva, Ana Paula de Lima Batista, Oscar Navarro, Ataualpa A. C. Braga:
Theoretical study on selectivity trends in (N-heterocyclic carbene)-Pd catalyzed mizoroki-heck reactions: Exploring density functionals methods and molecular models. 2371-2377 - Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay:
An open-source framework for analyzing N-electron dynamics. II. Hybrid density functional theory/configuration interaction methodology. 2378-2387 - Xiang-Yang Liu, Pin Xiao, Wei-Hai Fang, Ganglong Cui:
Theoretical studies of spin state-specific [2 + 2] and [5 + 2] photocycloaddition reactions of n-(1-penten-5-yl)maleimide. 2388-2395 - Francesco Villa, David Mignon, Savvas Polydorides, Thomas Simonson:
Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design. 2396-2410 - Yuichi Tanaka, Yukio Kawashima, Norio Yoshida, Haruyuki Nakano:
Solvatochromism and preferential solvation of Brooker's merocyanine in water-methanol mixtures. 2411-2419 - Mateusz Snamina, Grzegorz Mazur, Piotr Petelenz:
Partial atomic multipoles for internally consistent microelectrostatic calculations. 2420-2429 - Guangchao Liang, Nathan J. DeYonker, Xuan Zhao, Charles Edwin Webster:
Prediction of the reduction potential in transition-metal containing complexes: How expensive? For what accuracy? 2430-2438
- Anders Lervik, Enrico Riccardi, Titus S. van Erp:
PyRETIS: A well-done, medium-sized python library for rare events. 2439-2451
Volume 38, Number 29, November 2017
- Peter Maxwell, Paul L. A. Popelier:
Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective. 2459-2474 - Ismail A. M. Ibrahim:
Electronic structure, magnetic properties, and mixed valence character of Ce2Ni3Si5 from first principles calculations. 2475-2480 - Chao Huang, Wenjian Liu, Yunlong Xiao, Mark R. Hoffmann:
iVI: An iterative vector interaction method for large eigenvalue problems. 2481-2499 - Oinam Romesh Meitei, Andreas Hesselmann:
Intramolecular interactions in sterically crowded hydrocarbon molecules. 2500-2508 - Eleni Michael, Savvas Polydorides, Thomas Simonson, Georgios Archontis:
Simple models for nonpolar solvation: Parameterization and testing. 2509-2519 - Masahiko Nakano, Takeshi Yoshikawa, So Hirata, Junji Seino, Hiromi Nakai:
Computerized implementation of higher-order electron-correlation methods and their linear-scaling divide-and-conquer extensions. 2520-2527 - Rahul Chakraborty, Samik Bose, Debashree Ghosh:
Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study. 2528-2537
- Matthew J. L. Mills, Kenneth L. Sale, Blake A. Simmons, Paul L. A. Popelier:
Rhorix: An interface between quantum chemical topology and the 3D graphics program blender. 2538-2552
Volume 38, Number 30, November 2017
- Ryosuke Ishizuka, Nobuyuki Matubayasi:
Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory. 2559-2569 - Sean McConnell, Johannes Kästner:
Instanton rate constant calculations close to and above the crossover temperature. 2570-2580 - Robert A. Evarestov, Andrei V. Bandura, Vitaly V. Porsev, Alexey V. Kovalenko:
Phonon spectra, electronic, and thermodynamic properties of WS2 nanotubes. 2581-2593 - Nickolas D. Charistos, Anastasios G. Papadopoulos, Thomas A. Nikopoulos, Alvaro Muñoz-Castro, Michael P. Sigalas:
Canonical orbital contributions to the magnetic fields induced by global and local diatropic and paratropic ring currents. 2594-2604 - Jayangika N. Dahanayake, Chandana Kasireddy, Jonathan M. Ellis, Derek Hildebrandt, Olivia A. Hull, Joseph P. Karnes, Dylan Morlan, Katie R. Mitchell-Koch:
Evaluating electronic structure methods for accurate calculation of 19F chemical shifts in fluorinated amino acids. 2605-2617 - Philipp Pracht, Christoph Alexander Bauer, Stefan Grimme:
Automated and efficient quantum chemical determination and energetic ranking of molecular protonation sites. 2618-2631 - Kuo-Hao Lee, Jianhan Chen:
Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins. 2632-2640 - William J. Allen, Brian C. Fochtman, Trent E. Balius, Robert C. Rizzo:
Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. 2641-2663
Volume 38, Number 31, December 2017
- Ryuhei Harada, Yasuteru Shigeta:
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. 2671-2674
- Gabriel R. Schleder, Adalberto Fazzio, Jeverson T. Arantes:
Dynamic covalent bond from first principles: Diarylbibenzofuranone structural, electronic, and oxidation studies. 2675-2679 - Filip Sebesta, Mateusz Z. Brela, Silvia Díaz, Sebastian Miranda, Jane S. Murray, Soledad Gutiérrez-Oliva, Alejandro Toro-Labbé, Artur Michalak, Jaroslav V. Burda:
The influence of the metal cations and microhydration on the reaction trajectory of the N3 [LEFT RIGHT ARROW] O2 thymine proton transfer: Quantum mechanical study. 2680-2692 - Andreas J. Achazi, Dirk Andrae, Hans-Ulrich Reissig, Beate Paulus:
A computational study of samarium diiodide-induced cyclizations of N-oxoalkyl-substituted methyl indole-3-carboxylates - A rationale of the diastereoselectivity. 2693-2700 - Jeremy P. Coe, Nuno M. S. Almeida, Martin J. Paterson:
Investigation of challenging spin systems using Monte Carlo configuration interaction and the density matrix renormalization group. 2701-2712 - Dario Ghersi, Abhishek Parakh, Mihaly Mezei:
Comparison of a quantum random number generator with pseudorandom number generators for their use in molecular Monte Carlo simulations. 2713-2720 - Neda Khanjari, Hossein Eslami, Florian Müller-Plathe:
Adaptive-numerical-bias metadynamics. 2721-2729 - Agnieszka S. Karczynska, Cezary Czaplewski, Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Adam Liwo:
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins. 2730-2746
Volume 38, Number 32, December 2017
- Mohamed Amaouch, Dumitru-Claudiu Sergentu, David Steinmetz, Rémi Maurice, Nicolas Galland, Julien Pilmé:
The bonding picture in hypervalent XF3 (X = Cl, Br, I, At) fluorides revisited with quantum chemical topology. 2753-2762 - Olaseni Sode, Jasmine N. Cherry:
Development of a Flexible-Monomer Two-Body Carbon Dioxide Potential and Its Application to Clusters up to (CO2)13. 2763-2774 - Matteo Piccardo, Alessandro Soncini:
A full-pivoting algorithm for the Cholesky decomposition of two-electron repulsion and spin-orbit coupling integrals. 2775-2783 - Lizé-Mari Ferreira, Alan Eaby, Jan Dillen:
The topology of the Coulomb potential density. A comparison with the electron density, the virial energy density, and the Ehrenfest force density. 2784-2790 - Debarati DasGupta, Varun Mandalaparthy, Bhyravabhotla Jayaram:
A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level. 2791-2801 - Arpita Varadwaj, Pradeep R. Varadwaj, Koichi Yamashita:
Hybrid organic-inorganic CH3NH3PbI3 perovskite building blocks: Revealing ultra-strong hydrogen bonding and mulliken inner complexes and their implications in materials design. 2802-2818 - Miquel Torrent-Sucarrat, Sara Navarro, Fernando P. Cossío, Josep M. Anglada, Josep M. Luis:
Relevance of the DFT method to study expanded porphyrins with different topologies. 2819-2828
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