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ORCIDJournal 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 - Nilesh K. Banavali:
The Mechanism of Cholesterol Modification of Hedgehog Ligand. 520-527 - 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
Volume 41, Number 12, May 2020
- Cover Image, Volume 41, Issue 12. C1