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Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-26 Tianlong Jiang; Kenta Moriwaki; Osamu Kobayashi; Kazuya Ishimura; Sebastian O. Danielache; Shinkoh Nanbu
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Monte Carlo simulation and thermodynamic integration applied to protein charge transfer J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-25 Jan Kaiser; Mike Castellano; David Gnandt; Thorsten Koslowski
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Three‐site and five‐site fixed‐charge water models compatible with AMOEBA force field J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-24 Cong Pan; Chengwen Liu; Junhui Peng; Pengyu Ren; Xuhui Huang
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Calculation of the inner‐shell contribution to the correlation energy through DLPNO‐CEPA/1 and scaled same‐spin second‐order Møller–Plesset perturbation theory J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-23 Hernán R. Sánchez
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Amorphous polymerization of nitrogen in compressed cupric azide J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-22 Yujia Xu; Weijing Zhang; Tonglai Zhang; Wei Guo; Yongjun Lü
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Excited‐state intramolecular proton transfer driven by conical intersection in hydroxychromones J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-22 Neethu Anand; Sai Vamsi Krishna Isukapalli; Sivaranjana Reddy Vennapusa
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Improving the predictive quality of time‐dependent density functional theory calculations of the X‐ray emission spectroscopy of organic molecules J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-22 Adam A. E. Fouda; Nicholas A. Besley
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Complexes of helium with neutral molecules: Progress toward a quantitative scale of bonding character J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-21 Stefano Borocci; Felice Grandinetti; Nico Sanna; Paola Antoniotti; Francesca Nunzi
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Semiempirical methods do Fukui functions: Unlocking a modeling framework for biosystems J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-20 Igor Barden Grillo; Gabriel A. Urquiza‐Carvalho; Elton José Ferreira Chaves; Gerd Bruno Rocha
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Dual‐hybrid direct random phase approximation and second‐order screened exchange with nonlocal van der Waals correlations for noncovalent interactions J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-17 Feng Yu; Yaoting Wang
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Fast multipole method for three‐dimensional systems with periodic boundary condition in two directions J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-12 Noriyuki Yoshii; Yoshimichi Andoh; Susumu Okazaki
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Correcting electrostatic artifacts due to net‐charge changes in the calculation of ligand binding free energies J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-12 Christoph Öhlknecht; Bettina Lier; Drazen Petrov; Julian Fuchs; Chris Oostenbrink
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Anisotropic charge carrier transport of optoelectronic functional selenium‐containing organic semiconductor materials J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-11 Daoyuan Zheng; Yurong Guo; Mingxing Zhang; Xia Feng; Lina Zhu; Lijuan Qiu; Xiaoning Jin; Guangjiu Zhao
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Evaluation of Chemical Reactivity and Stability of Ionic Liquids Using Ab Initio and COSMO‐RS model J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-10 Rajadurai Vijayalakshmi; Ramalingam Anantharaj; Anguraj Brinda Lakshmi
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Calibration of the dianionic phosphate group: Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-07 Marion Devillers; Jean‐Philip Piquemal; Laurent Salmon; Nohad Gresh
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fromage: A library for the study of molecular crystal excited states at the aggregate scale J. Comput. Chem. (IF 3.194) Pub Date : 2020-01-07 Miguel Rivera; Michael Dommett; Amir Sidat; Warda Rahim; Rachel Crespo‐Otero
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Domain‐based local pair natural orbital methods within the correlation consistent composite approach J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-31 Prajay Patel; Angela K. Wilson
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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 J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-31 Zahra Ghalami; Vanik Ghoulipour; Ali Reza Khanchi
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Effect of the Solute Cavity on the Solvation Energy and its Derivatives within the Framework of the Gaussian Charge Scheme J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-30 Miquel Garcia‐Ratés; Frank Neese
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FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-30 Anmol Kumar; Ozge Yoluk; Alexander D. MacKerell
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Dimerization energetics of the G‐protein coupled bile acid receptor TGR5 from all‐atom simulations J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-27 Lucas Wäschenbach; Christoph G. W. Gertzen; Verena Keitel; Holger Gohlke
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Next‐generation QTAIM for scoring molecular wires in E‐fields for molecular electronic devices J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-27 Alireza Azizi; Roya Momen; Herbert Früchtl; Tanja van Mourik; Steven R. Kirk; Samantha Jenkins
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Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-24 Xiping Gong; Mara Chiricotto; Xiaorong Liu; Erik Nordquist; Michael Feig; Charles L. Brooks; Jianhan Chen
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Computations of Colorings 7D‐Hypercube's Hyperplanes for All Irreducible Representations J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-22 Krishnan Balasubramanian
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Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-20 Mingwei Wan; Junjie Song; Wenli Li; Lianghui Gao; Weihai Fang
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BAND NN: A Deep Learning Framework for Energy Prediction and Geometry Optimization of Organic Small Molecules J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-17 Siddhartha Laghuvarapu; Yashaswi Pathak; U. Deva Priyakumar
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SPOT‐Fold: Fragment‐Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-17 Yufeng Cai; Xiongjun Li; Zhe Sun; Yutong Lu; Huiying Zhao; Jack Hanson; Kuldip Paliwal; Thomas Litfin; Yaoqi Zhou; Yuedong Yang
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Oversampling Free Energy Perturbation Simulation in Determination of the Ligand‐Binding Free Energy J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-16 Son Tung Ngo; Trung Hai Nguyen; Nguyen Thanh Tung; Pham Cam Nam; Khanh B. Vu; Van V. Vu
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Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-16 Thomas M. Griffiths; Aaron J. Oakley; Haibo Yu
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State‐of‐the‐art computations of dipole moments using analytic gradients of high‐level density‐fitted coupled‐cluster methods with focal‐point approximations J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-14 Uğur Bozkaya; Emine Soydaş; Bahar Filiz
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A dispersion‐corrected density functional theory study of the noncovalent interactions between nucleobases and carbon nanotube models containing stone–wales defects J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-14 Flavio F. Contreras‐Torres; Elena V. Basiuk; Vladimir A. Basiuk
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First‐Principles Calculations of Phonons and Thermodynamic Properties of Zr(Hf)S2‐Based Nanotubes J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-11 Anton V. Domnin; Andrei V. Bandura; Robert A. Evarestov
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Atomistic Simulation of Structural and Mechanical Properties of the AMgF3 (A = K, Rb, and Cs) Compounds Under Hydrostatic Pressure J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-11 Afranio Sousa; Heveson Lima
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On Restraints in End‐Point Protein–Ligand Binding Free Energy Calculations J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-10 William M. Menzer, Bing Xie, David D. L. Minh
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A Validation of Cluster Modeling in the Description of Matrix Isolation Spectroscopy J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-05 Frederik Bader, Tilen Lindic, Beate Paulus
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Role of the N‐Terminal Transmembrane Helix Contacts in the Activation of FGFR3 J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-05 Daisuke Matsuoka, Motoshi Kamiya, Takeshi Sato, Yuji Sugita
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Coordination bonding in dicopper and dichromium tetrakis(μ‐acetato)‐diaqua complexes: Nature, strength, length, and topology J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-05 Michal Malček, Barbora Vénosová, Ingrid Puškárová, Jozef Kožíšek, Marián Gall, Lukáš Bučinský
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Quantum Chemical Exploration of Intermolecular Reactions of Acetylene J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-02 Koichi Ohno, Takuto Oki, Hideo Yamakado
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Some Mathematical Reasoning on the Artificial Force Induced Reaction Method J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-02 Wolfgang Quapp, Josep Maria Bofill
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PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide–Protein Computational Docking J. Comput. Chem. (IF 3.194) Pub Date : 2019-12-02 Xianjin Xu, Xiaoqin Zou
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Investigating Protein–Protein Allosteric Network using Current‐Flow Scheme J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-28 Wesley M. Botello‐Smith, Yun Luo
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Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-25 Shashank Pant, Emad Tajkhorshid
The pleckstrin homology (PH) domain of general receptor for phosphoionositides 1 (GRP1‐PHD) binds specifically to phosphatidylinositol (3,4,5)‐triphosphate (PIP3), and acts as a second messenger. Using an extensive array of molecular dynamics (MD) simulations employing highly mobile membrane mimetic (HMMM) model as well as complementary full membrane simulations, we capture differentiable binding and dynamics of GRP1‐PHD in the presence of membranes containing PC, PS, and PIP3 lipids in varying compositions. While GRP1‐PHD forms only transient interactions with pure PC membranes, incorporation of anionic lipids resulted in stable membrane‐bound configurations. We report the first observation of two distinct PIP3 binding modes on GRP1‐PHD, involving PIP3 interactions at a “canonical” and at an “alternate” site, suggesting the possibility of simultaneous binding of multiple anionic lipids. The full membrane simulations confirmed the stability of the membrane bound pose of GRP1‐PHD as captured from our HMMM membrane binding simulations. By performing additional steered membrane unbinding simulations and calculating nonequilibrium work associated with the process, as well as metadynamics simulations, on the protein bound to full membranes, allowing for more quantitative examination of the binding strength of the GRP1‐PHD to the membrane, we demonstrate that along with the bound PIP3, surrounding anionic PS lipids increase the energetic cost of unbinding of GRP1‐PHD from the canonical mode, causing them to dissociate more slowly than the alternate mode. Our results demonstrate that concurrent binding of multiple anionic lipids by GRP1‐PHD contributes to its membrane affinity, which in turn control its signaling activity. © 2019 Wiley Periodicals, Inc.
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Martini Force Field for Protonated Polyethyleneimine J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-25 Titus Adrian Beu, Andrada‐Elena Ailenei, Răzvan‐Ioan Costinaş
Polyethyleneimine (PEI), one of the most widely used nonviral gene carriers, was investigated in the presented work at coarse‐grained (CG) level. The main focus was on elaborating a realistic CG force field (FF) aimed to reproduce dynamic structural features of protonated PEI chains and, furthermore, to enable massive simulations of DNA–PEI complex formation and condensation. We parametrized CG Martini FF models for PEI in polarizable and nonpolarizable water by applying Boltzmann inversion techniques to all‐atom (AA) probability distributions for distances, angles, and dihedrals of entire monomers. The fine‐tuning of the FFs was achieved by fitting simulated CG gyration radii and end‐to‐end distances to their AA counterparts. The developed Martini FF models are shown to be well suited for realistic large‐scale simulations of size/protonation‐dependent behavior of solvated PEI chains, either individually or as part of DNA–PEI systems. © 2019 Wiley Periodicals, Inc.
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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 J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-21 Cameron D. Smith, Amir Karton
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Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-21 George Khelashvili, Xiaolu Cheng, Maria E. Falzone, Milka Doktorova, Alessio Accardi, Harel Weinstein
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A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-20 Zak E. Hughes, Emmanuel Ren, Joseph C. R. Thacker, Benjamin C. B. Symons, Arnaldo F. Silva, Paul L. A. Popelier
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Simulating ion channel activation mechanisms using swarms of trajectories J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-19 Bogdan Lev, Toby W. Allen
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PyRETIS 2: An improbability drive for rare events J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-19 Enrico Riccardi, Anders Lervik, Sander Roet, Ola Aarøen, Titus S. van Erp
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Record Atomistic Simulation of Crystalline Silicon: Bridging Microscale Structures and Macroscale Properties J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-19 Chaofeng Hou, Chenglong Zhang, Wei Ge, Lei Wang, Lin Han, Jianmin Pang
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Functional and Basis Set Dependence for Time‐Dependent Density Functional Theory Trajectory Surface Hopping Molecular Dynamics: Cis‐Azobenzene Photoisomerization J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-19 Linfeng Ye, Chao Xu, Feng Long Gu, Chaoyuan Zhu
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CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations J. Comput. Chem. (IF 3.194) Pub Date : 2019-07-22 Yifei Qi, Jumin Lee, Xi Cheng, Rong Shen, Shahidul M. Islam, Benoît Roux, Wonpil Im
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The Mechanism of Cholesterol Modification of Hedgehog Ligand J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-14 Nilesh K. Banavali
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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 J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-14 Khalid A. H. Alzahrani, Robert J. Deeth
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A size‐modified poisson–boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage‐dependent anion channel J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-14 Dexuan Xie, Said H. Audi, Ranjan K. Dash
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A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-13 Hyea Hwang, Anthony Hazel, Peng Lian, Jeremy C. Smith, James C. Gumbart, Jerry M. Parks
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Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-13 Qingyi Yang, Woodrow Burchett, Gregory S. Steeno, Shuai Liu, Mingjun Yang, David L. Mobley, Xinjun Hou
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Performance of Range Separated Density Functional in Solvent Continuum: Tuning Long‐range Hartree–Fock Exchange for Improved Orbital Energies J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-11 Abhijit Boruah, Manash Protim Borpuzari, Rahul Kar
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Critical Assessment of the DFT + U Approach for the Prediction of Vanadium Dioxide Properties J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-11 Berenike Stahl, Thomas Bredow
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Activation Strain Analyses of Counterion and Solvent Effects on the Ion‐Pair SN2 Reaction of and CH3Cl J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-11 Nandini Savoo, Jalal Z. A. Laloo, Lydia Rhyman, Ponnadurai Ramasami, F. Matthias Bickelhaupt, Jordi Poater
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Mechanistic Study of Unprecedented Highly Regioselective Hydrocyanation of Terminal Alkynes: Insight into the Origins of the Regioselectivity and Ligand Effects J. Comput. Chem. (IF 3.194) Pub Date : 2019-11-11 Dandan Jiang, Mingxing Fu, Yajun Zhang, Qianqian Li, Kai Guo, Yanhui Yang, Lili Zhao
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