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Journal of Computational Chemistry, Volume 41
Volume 41, Number 1, January 2020
- Cover Image, Volume 41, Issue 1. C1
- Jia Wang, Xiaoyan Li
, Shijun Zheng, Lingpeng Meng:
Mechanism and Stereoselectivity of the Elementometalation Process of Activated Alkyne RCCR(RCO2Me) by Cp2TaH3. 6-13 - Zhenliang Wu, Yuwei Zhang, John Z. H. Zhang, Kelin Xia
, Fei Xia
:
Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes. 14-20 - Alhadji Malloum
, Jean Jules Fifen
, Jeanet Conradie
:
Large-Sized Ammonia Clusters and Solvation Energies of the Proton in Ammonia. 21-30 - Miyu Kusumoto, Kaori Ueno-Noto
, Keiko Takano
:
Systematic Interaction Analysis of Anti-Human Immunodeficiency Virus Type-1 Neutralizing Antibodies with High Mannose Glycans Using Fragment Molecular Orbital and Molecular Dynamics Methods. 31-42 - Pi A. B. Haase
, Rasmus Faber
, Patricio F. Provasi, Stephan P. A. Sauer
:
Noniterative Doubles Corrections to the Random Phase and Higher Random Phase Approximations: Singlet and Triplet Excitation Energies. 43-55 - Yoshitake Sakae
, Bin W. Zhang, Ronald M. Levy, Nan-Jie Deng:
Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses. 56-68
- Amauri Duarte da Silva
, Gabriela Bitencourt-Ferreira
, Walter F. de Azevedo Jr.
:
Taba: A Tool to Analyze the Binding Affinity. 69-73 - Thijs Stuyver
, Jing Huang, Dibyendu Mallick
, David Danovich
, Sason Shaik
:
TITAN: A Code for Modeling and Generating Electric Fields - Features and Applications to Enzymatic Reactivity. 74-82
Volume 41, Number 2, January 2020
- Cover Image, Volume 41, Issue 2. C1
- Jingbai Li, Andrey Yu Rogachev
:
Homolytic Versus Heterolytic Bond Breaking in Functionalized [R-C20H10]+ Systems. 88-96 - Kalaiarasi Chinnasamy
, Manjula Saravanan, Kumaradhas Poomani
:
Investigation of binding mechanism and downregulation of elacestrant for wild and L536S mutant estrogen receptor-α through molecular dynamics simulation and binding free energy analysis. 97-109 - Xiuzhen Hu, Riletu Ge, Zhenxing Feng
:
Recognizing five molecular ligand-binding sites with similar chemical structure. 110-118 - Hai-Feng Zheng, Jing Xu
, Yi-Hong Ding
:
Mono-silicon isoelectronic replacement in CAl4: van't hoff/le bel carbon or not? 119-128 - Ron L. Shepard
, Scott R. Brozell, Gergely Gidofalvi
:
Representations of Shavitt Graphs Within the Graphical Unitary Group Approach. 129-135 - Ximena Zarate
, Angela Rodriguez-Serrano
, Eduardo Schott
, Jörg Tatchen:
DFT/MRCI assessment of the excited-state interplay in a coumarin-schiff Mg2+ fluorescent sensor. 136-146
- Peng Lian
, Luanjing Guo
, Deepa Devarajan
, Jerry M. Parks
, Scott L. Painter
, Scott C. Brooks
, Jeremy C. Smith
:
The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation. 147-155 - Haomiao Zhang, Qiankun Gong
, Haozhe Zhang, Changjun Chen
:
FSATOOL: A useful tool to do the conformational sampling and trajectory analysis work for biomolecules. 156-164
Volume 41, Number 3, January 2020
- Cover Image, Volume 41, Issue 3. C1
- Prajay Patel
, Jiaqi Wang, Angela K. Wilson
:
Prediction of pKas of Late Transition-Metal Hydrides via a QM/QM Approach. 171-183 - Duncan W. Stuart, Nicholas J. Mosey
:
Pseudodiagonalization-based wavefunction optimization with contracted planewave basis functions. 184-193 - Jemal Yimer Damte
, Zhan-Jun Zhu, Pin-Jun Lin, Chen-Hao Yeh
, Jyh-Chiang Jiang
:
B, N-co-doped graphene-supported Ir and Pt clusters for methane activation and C─C coupling: A density functional theory study. 194-202 - César R. García-Jacas
, Yovani Marrero-Ponce
, Carlos A. Brizuela
, José Suárez-Lezcano, Felix Martinez-Rios
:
Smoothed Spherical Truncation based on Fuzzy Membership Functions: Application to the Molecular Encoding. 203-217 - Dexuan Xie
, Said H. Audi, Ranjan K. Dash:
A size-modified poisson-boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage-dependent anion channel. 218-230 - Edson F. V. de Carvalho, Guilherme D. Vicentini
, Tiago Vinicius Alves
, Orlando Roberto-Neto
:
Variational transition state theory rate constants and H/D kinetic isotope effects for CH3 + CH3OCOH reactions. 231-239 - Roma Mukhopadhyay
, Marat R. Talipov
:
Efficient newton-raphson/singular value decomposition-based optimization scheme with dynamically updated critical condition number for rapid convergence of weighted histogram analysis method equations. 240-246 - Qingyi Yang
, Woodrow Burchett, Gregory S. Steeno, Shuai Liu, Mingjun Yang, David L. Mobley
, Xinjun Hou:
Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability. 247-257 - Berenike Stahl
, Thomas Bredow:
Critical Assessment of the DFT + U Approach for the Prediction of Vanadium Dioxide Properties. 258-265
- Szymon Zaczek
:
MDMS: Software Facilitating Performing Molecular Dynamics Simulations. 266-271
Volume 41, Number 4, February 2020
- Cover Image, Volume 41, Issue 4. C1
- Dandan Jiang, Mingxing Fu, Yajun Zhang, Qianqian Li, Kai Guo
, Yanhui Yang, Lili Zhao
:
Mechanistic Study of Unprecedented Highly Regioselective Hydrocyanation of Terminal Alkynes: Insight into the Origins of the Regioselectivity and Ligand Effects. 279-289 - Fortuna Ponte
, GiovanniMaria Piccini
, Emilia Sicilia
, Michele Parrinello:
A metadynamics perspective on the reduction mechanism of the Pt(IV) asplatin prodrug. 290-294 - Abhijit Boruah
, Manash Protim Borpuzari
, Rahul Kar:
Performance of Range Separated Density Functional in Solvent Continuum: Tuning Long-range Hartree-Fock Exchange for Improved Orbital Energies. 295-304 - Xiaoyan Cao
, Liangliang Wu
, Jun Zhang, Michael Dolg:
Density Functional Studies of Coenzyme NADPH and Its Oxidized Form NADP+: Structures, UV-Vis Spectra, and the Oxidation Mechanism of NADPH. 305-316 - Nandini Savoo
, Jalal Z. A. Laloo
, Lydia Rhyman
, Ponnadurai Ramasami
, Friedrich Matthias Bickelhaupt
, Jordi Poater
:
Activation Strain Analyses of Counterion and Solvent Effects on the Ion-Pair SN2 Reaction of and CH3Cl. 317-327 - Cameron D. Smith, Amir Karton
:
Kinetics and Thermodynamics of Reactions Involving Criegee Intermediates: An Assessment of Density Functional Theory and Ab Initio Methods Through Comparison with CCSDT(Q)/CBS Data. 328-339 - Khalid A. H. Alzahrani
, Robert J. Deeth:
A Computational Analysis of the Intrinsic Plasticity of Five-Coordinate Cu(II) Complexes and the Factors Leading to the Breakdown of the Orbital Directing Effect in Paddlewheel Secondary Building Units. 340-348 - Titus Adrian Beu
, Andrada-Elena Ailenei
, Razvan-Ioan Costinas:
Martini Force Field for Protonated Polyethyleneimine. 349-361 - Xianjin Xu
, Xiaoqin Zou
:
PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking. 362-369
- Enrico Riccardi
, Anders Lervik
, Sander Roet
, Ola Aarøen
, Titus S. van Erp
:
PyRETIS 2: An improbability drive for rare events. 370-377
Volume 41, Number 5, February 2020
Cover Image
- Cover Image, Volume 41, Issue 5. C1
- Wonpil Im, Nilesh K. Banavali, Yun Lyna Luo:
Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane. 385-386
- Bogdan Lev
, Toby W. Allen
:
Simulating ion channel activation mechanisms using swarms of trajectories. 387-401
- Kendra Marcus
, Carla Mattos
:
Water in Ras Superfamily Evolution. 402-414 - Yifei Qi, Jumin Lee, Xi Cheng, Rong Shen, Shahidul M. Islam
, Benoît Roux, Wonpil Im
:
CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations. 415-420 - Hong Zhang, Xueguang Shao, François Dehez
, Wensheng Cai, Christophe Chipot
:
Modulation of membrane permeability by carbon dioxide. 421-426 - Ernest Awoonor-Williams
, William C. Isley III, Stephen G. Dale
, Erin R. Johnson
, Haibo Yu
, Axel D. Becke, Benoît Roux, Christopher N. Rowley
:
Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. 427-438 - Fang-Yu Lin, Alexander D. MacKerell Jr.
:
Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins. 439-448 - Giacomo Fiorin
, Fabrizio Marinelli
, José D. Faraldo-Gómez
:
Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics. 449-459 - Apurba Bhattarai, Jinan Wang
, Yinglong Miao
:
G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State. 460-471 - Esam A. Orabi
, Rebecca L. Davis
, Guillaume Lamoureux
:
Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains. 472-481
Volume 41, Number 6, March 2020
- Cover Image, Volume 41, Issue 6. C1
- Shashank Pant
, Emad Tajkhorshid
:
Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes. 489-499 - Neha Verma
, Peter Dollinger, Filip Kovacic, Karl-Erich Jaeger
, Holger Gohlke
:
The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A. 500-512 - Zhi Wang
, Jessica M. J. Swanson
, Gregory A. Voth
:
Local conformational dynamics regulating transport properties of a Cl-/H+ antiporter. 513-519 - Hyea Hwang, Anthony Hazel
, Peng Lian, Jeremy C. Smith, James C. Gumbart
, Jerry M. Parks
:
A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. 528-537 - George Khelashvili, Xiaolu Cheng, Maria E. Falzone
, Milka Doktorova, Alessio Accardi, Harel Weinstein
:
Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins. 538-551 - Wesley M. Botello-Smith, Yun Lyna Luo
:
Investigating Protein-Protein Allosteric Network using Current-Flow Scheme. 552-560 - Daisuke Matsuoka, Motoshi Kamiya, Takeshi Sato, Yuji Sugita
:
Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3. 561-572 - William M. Menzer, Bing Xie
, David D. L. Minh
:
On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations. 573-586 - Thomas M. Griffiths
, Aaron J. Oakley
, Haibo Yu
:
Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin. 587-603
Volume 41, Number 7, March 2020
- Cover Image, Volume 41, Issue 7. C1
- Son Tung Ngo
, Trung Hai Nguyen
, Nguyen Thanh Tung, Pham Cam Nam
, Khanh B. Vu
, Van V. Vu
:
Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy. 611-618 - Zak E. Hughes
, Emmanuel Ren
, Joseph C. R. Thacker, Benjamin C. B. Symons
, Arnaldo F. Silva
, Paul L. A. Popelier
:
A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics. 619-628 - Wolfgang Quapp
, Josep Maria Bofill:
Some Mathematical Reasoning on the Artificial Force Induced Reaction Method. 629-634 - Linfeng Ye, Chao Xu, Feng Long Gu
, Chaoyuan Zhu
:
Functional and Basis Set Dependence for Time-Dependent Density Functional Theory Trajectory Surface Hopping Molecular Dynamics: Cis-Azobenzene Photoisomerization. 635-645 - Afranio Sousa
, Heveson Lima
:
Atomistic Simulation of Structural and Mechanical Properties of the AMgF3 (A = K, Rb, and Cs) Compounds Under Hydrostatic Pressure. 646-652 - Krishnan Balasubramanian
:
Computations of Colorings 7D-Hypercube's Hyperplanes for All Irreducible Representations. 653-686 - Koichi Ohno
, Takuto Oki, Hideo Yamakado
:
Quantum Chemical Exploration of Intermolecular Reactions of Acetylene. 687-697 - Michal Malcek
, Barbora Vénosová
, Ingrid Puskárová, Jozef Kozísek, Marián Gall
, Lukás Bucinský
:
Coordination bonding in dicopper and dichromium tetrakis(μ-acetato)-diaqua complexes: Nature, strength, length, and topology. 698-714
- David D. L. Minh
:
Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors. 715-730 - Chaofeng Hou
, Chenglong Zhang, Wei Ge, Lei Wang, Lin Han, Jianmin Pang:
Record Atomistic Simulation of Crystalline Silicon: Bridging Microscale Structures and Macroscale Properties. 731-738
Volume 41, Number 8, March 2020
- Cover Image, Volume 41, Issue 8. C1
- Yufeng Cai, Xiongjun Li
, Zhe Sun, Yutong Lu, Huiying Zhao, Jack Hanson
, Kuldip K. Paliwal
, Thomas Litfin
, Yaoqi Zhou
, Yuedong Yang
:
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. 745-750 - Frederik Bader
, Tilen Lindic
, Beate Paulus:
A Validation of Cluster Modeling in the Description of Matrix Isolation Spectroscopy. 751-758 - Anton V. Domnin, Andrei V. Bandura
, Robert A. Evarestov
:
First-Principles Calculations of Phonons and Thermodynamic Properties of Zr(Hf)S2-Based Nanotubes. 759-768 - Ugur Bozkaya
, Emine Soydas, Bahar Filiz:
State-of-the-art computations of dipole moments using analytic gradients of high-level density-fitted coupled-cluster methods with focal-point approximations. 769-779 - Flavio F. Contreras-Torres
, Elena V. Basiuk
, Vladimir A. Basiuk
:
A dispersion-corrected density functional theory study of the noncovalent interactions between nucleobases and carbon nanotube models containing stone-wales defects. 780-789 - Siddhartha Laghuvarapu
, Yashaswi Pathak, U. Deva Priyakumar
:
BAND NN: A Deep Learning Framework for Energy Prediction and Geometry Optimization of Organic Small Molecules. 790-799 - Prajay Patel
, Angela K. Wilson
:
Domain-based local pair natural orbital methods within the correlation consistent composite approach. 800-813 - Mingwei Wan, Junjie Song
, Wenli Li, Lianghui Gao
, Wei-Hai Fang
:
Development of Coarse-Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm. 814-829 - Xiping Gong, Mara Chiricotto, Xiaorong Liu
, Erik B. Nordquist
, Michael Feig, Charles L. Brooks III, Jianhan Chen
:
Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units. 830-838 - Marion Devillers, Jean-Philip Piquemal
, Laurent Salmon
, Nohad Gresh
:
Calibration of the dianionic phosphate group: Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase. 839-854
- Hai-Feng Zheng, Jing Xu
, Yi-Hong Ding
:
Mono-silicon Isoelectronic Replacement in CAI4: van't Hoff/Le Bel Carbon or Not? 855
Volume 41, Number 9, April 2020
- Cover Image, Volume 41, Issue 9. C1
- Igor Barden Grillo, Gabriel Aires Urquiza-Carvalho
, Elton José Ferreira Chaves
, Gerd Bruno Rocha
:
Semiempirical methods do Fukui functions: Unlocking a modeling framework for biosystems. 862-873 - Lucas Wäschenbach
, Christoph G. W. Gertzen, Verena Keitel
, Holger Gohlke
:
Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations. 874-884 - Rajadurai Vijayalakshmi, Ramalingam Anantharaj
, Anguraj Brinda Lakshmi:
Evaluation of Chemical Reactivity and Stability of Ionic Liquids Using Ab Initio and COSMO-RS model. 885-912 - Alireza Azizi
, Roya Momen
, Herbert Früchtl
, Tanja Van Mourik
, Steven R. Kirk
, Samantha Jenkins
:
Next-generation QTAIM for scoring molecular wires in E-fields for molecular electronic devices. 913-921 - Miquel Garcia-Ratés
, Frank Neese:
Effect of the Solute Cavity on the Solvation Energy and its Derivatives within the Framework of the Gaussian Charge Scheme. 922-939 - Noriyuki Yoshii
, Yoshimichi Andoh
, Susumu Okazaki:
Fast multipole method for three-dimensional systems with periodic boundary condition in two directions. 940-948 - Zahra Ghalami, Vanik Ghoulipour, Ali Reza Khanchi
:
Adsorption and sequential thermal release of F2, Cl2, and Br2 molecules by a porous organic cage material (CC3-R): Molecular dynamics and grand-canonical Monte Carlo simulations. 949-957
- Anmol Kumar
, Ozge Yoluk, Alexander D. MacKerell Jr.
:
FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules. 958-970
Volume 41, Number 10, April 2020
- Daoyuan Zheng, Yurong Guo, Mingxing Zhang, Xia Feng, Lina Zhu, Lijuan Qiu, Xiaoning Jin, Guang-Jiu Zhao
:
Anisotropic charge carrier transport of optoelectronic functional selenium-containing organic semiconductor materials. 976-985 - Christoph Öhlknecht
, Bettina Lier
, Drazen Petrov
, Julian Fuchs, Chris Oostenbrink
:
Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies. 986-999 - Stefano Borocci, Felice Grandinetti
, Nico Sanna
, Paola Antoniotti, Francesca Nunzi:
Complexes of helium with neutral molecules: Progress toward a quantitative scale of bonding character. 1000-1011 - Hernán R. Sánchez
:
Calculation of the inner-shell contribution to the correlation energy through DLPNO-CEPA/1 and scaled same-spin second-order Møller-Plesset perturbation theory. 1012-1017 - Feng Yu
, Yaoting Wang:
Dual-hybrid direct random phase approximation and second-order screened exchange with nonlocal van der Waals correlations for noncovalent interactions. 1018-1025 - Yujia Xu, Weijing Zhang
, Tonglai Zhang, Wei Guo
, Yongjun Lü
:
Amorphous polymerization of nitrogen in compressed cupric azide. 1026-1033 - Cong Pan
, Chengwen Liu
, Junhui Peng
, Pengyu Y. Ren, Xuhui Huang
:
Three-site and five-site fixed-charge water models compatible with AMOEBA force field. 1034-1044
- Miguel Rivera
, Michael Dommett, Amir Sidat, Warda Rahim
, Rachel Crespo-Otero
:
fromage: A library for the study of molecular crystal excited states at the aggregate scale. 1045-1058
Volume 41, Number 11, April 2020
- Cover Image, Volume 41, Issue 11. C1
- Wenhong Yang
, Timothy Tizhe Fidelis
, Wen-Hua Sun
:
Prediction of catalytic activities of bis(imino)pyridine metal complexes by machine learning. 1064-1067 - Neethu Anand, Sai Vamsi Krishna Isukapalli
, Sivaranjana Reddy Vennapusa
:
Excited-state intramolecular proton transfer driven by conical intersection in hydroxychromones. 1068-1080 - Adam A. E. Fouda, Nicholas A. Besley
:
Improving the predictive quality of time-dependent density functional theory calculations of the X-ray emission spectroscopy of organic molecules. 1081-1090 - Kader Sahin
, Emin Saripinar
:
A novel hybrid method named electron conformational genetic algorithm as a 4D QSAR investigation to calculate the biological activity of the tetrahydrodibenzazosines. 1091-1104 - Jan Kaiser
, Mike Castellano
, David Gnandt
, Thorsten Koslowski
:
Monte Carlo simulation and thermodynamic integration applied to protein charge transfer. 1105-1115 - Tianlong Jiang
, Kenta Moriwaki, Osamu Kobayashi, Kazuya Ishimura
, Sebastian O. Danielache
, Shinkoh Nanbu
:
Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO. 1116-1123 - Enric Petrus
, Carles Bo
:
Performance of group additivity methods for predicting the stability of uranyl complexes. 1124-1129 - Kohei Saito, Yuya Watabe, Takashi Fujihara
, Toshiyuki Takayanagi
, Jun-Ya Hasegawa
:
Spin-inversion mechanisms in O2 binding to a model heme complex revisited by density function theory calculations. 1130-1138