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Journal of Chemical Theory and Computation
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Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-20 Giorgia Ceselin, Vincenzo Barone, Nicola Tasinato
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Fast and Accurate Multidimensional Free Energy Integration J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-19 Jérôme Hénin
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Defect Tolerance Mechanism Revealed! Influence of Polaron Occupied Surface Trap States on CsPbBr3 Nanocrystal Photoluminescence: Ab Initio Excited-State Dynamics J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-19 Aaron Forde, Dmitri Kilin
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SGOOP-d: Estimating Kinetic Distances and Reaction Coordinate Dimensionality for Rare Event Systems from Biased/Unbiased Simulations J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-18 Sun-Ting Tsai, Zachary Smith, Pratyush Tiwary
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TopProperty: Robust Metaprediction of Transmembrane and Globular Protein Features Using Deep Neural Networks J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-18 Daniel Mulnaes, Stephan Schott-Verdugo, Filip Koenig, Holger Gohlke
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Tumuc1: A New Accurate DNA Force Field Consistent with High-Level Quantum Chemistry J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-18 Korbinian Liebl, Martin Zacharias
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Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-15 Nicola Scafuri, Miguel A. Soler, Andrea Spitaleri, Walter Rocchia
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Two Faces of the Two-Phase Thermodynamic Model J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-14 Ádám Madarász, Andrea Hamza, Dávid Ferenc, Imre Bakó
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Simulation of Condensed-Phase Spectroscopy with Near-Term Digital Quantum Computers J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-14 Chee-Kong Lee, Chang-Yu Hsieh, Shengyu Zhang, Liang Shi
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Activation of Abl1 Kinase Explored Using Well-Tempered Metadynamics Simulations on an Essential Dynamics Sampled Path J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-14 Baswanth Oruganti, Ran Friedman
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Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-13 Jinzhe Zeng, Timothy J. Giese, Şölen Ekesan, Darrin M. York
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Machine Learning-Assisted Hybrid ReaxFF Simulations J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-13 Dundar E. Yilmaz, William Hunter Woodward, Adri C. T. van Duin
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Generation of Quantum Configurational Ensembles Using Approximate Potentials J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-13 João Morado, Paul N. Mortenson, J. Willem M. Nissink, Marcel L. Verdonk, Richard A. Ward, Jonathan W. Essex, Chris-Kriton Skylaris
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Dressing of Vertices by Cumulants in Multi-Reference Coupled Cluster J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-13 Ádám Margócsy, Ágnes Szabados
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Do Double-Hybrid Exchange–Correlation Functionals Provide Accurate Chemical Shifts? A Benchmark Assessment for Proton NMR J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-12 Marcelo T. de Oliveira, Júlia M. A. Alves, Ataualpa A. C. Braga, David J. D. Wilson, Cristina A. Barboza
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Molecular Spectra Calculations Using an Optimized Quasi-Regular Gaussian Basis and the Collocation Method J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-12 Shane W. Flynn, Vladimir A. Mandelshtam
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Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-11 Egor S. Kolesnikov, Ivan Yu. Gushchin, Petr A. Zhilyaev, Alexey V. Onufriev
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Nonadiabatic Dynamics with Coupled Trajectories J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-10 Carlotta Pieroni, Federica Agostini
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Investigating the Accuracy of Water Models through the Van Hove Correlation Function J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-13 Ray A. Matsumoto, Matthew W. Thompson, Van Quan Vuong, Weiwei Zhang, Yuya Shinohara, Adri C. T. van Duin, Paul R. C. Kent, Stephan Irle, Takeshi Egami, Peter T. Cummings
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NMR Relaxation Rates of Quadrupolar Aqueous Ions from Classical Molecular Dynamics Using Force-Field Specific Sternheimer Factors J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-27 Iurii Chubak, Laura Scalfi, Antoine Carof, Benjamin Rotenberg
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Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-08 Christopher C. Walker, Garrett A. Meek, Theodore L. Fobe, Michael R. Shirts
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The Sign Problem in Density Matrix Quantum Monte Carlo J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-21 Hayley R. Petras, William Z. Van Benschoten, Sai Kumar Ramadugu, James J. Shepherd
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Machine Learning-Assisted Selection of Active Spaces for Strongly Correlated Transition Metal Systems J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-27 Pavlo Golub, Andrej Antalik, Libor Veis, Jiri Brabec
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Electronic Excitations in Crystalline Solids through the Maximum Overlap Method J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-30 Loredana Edith Daga, Lorenzo Maschio
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Quantitative Account of the Bonding Properties of a Rubredoxin Model Complex [Fe(SCH3)4]q, q = −2, −1, +2, +3 J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-21 Demeter Tzeli, Simone Raugei, Sotiris S. Xantheas
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Fixed- and Partial-Node Approximations in Slater Determinant Space for Molecules J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-22 Nick S. Blunt
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Protein Response Effects on Cofactor Excitation Energies from First Principles: Augmenting Subsystem Time-Dependent Density-Functional Theory with Many-Body Expansion Techniques J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-15 Linus Scholz, Johannes Neugebauer
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Analytical Gradient Theory for Resolvent-Fitted Second-Order Extended Multiconfiguration Perturbation Theory (XMCQDPT2) J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-28 Jae Woo Park
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Assessing Density Functional Theory for Chemically Relevant Open-Shell Transition Metal Reactions J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-21 Leonard R. Maurer, Markus Bursch, Stefan Grimme, Andreas Hansen
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Multireference Algebraic Diagrammatic Construction Theory for Excited States: Extended Second-Order Implementation and Benchmark J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-23 Ilia M. Mazin, Alexander Yu. Sokolov
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Theoretical Prediction and Interpretation of 237Np Mössbauer Isomer Shifts J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-22 Laura C. Motta, Jochen Autschbach
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Quantum-Based Molecular Dynamics Simulations Using Tensor Cores J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-10-01 Joshua Finkelstein, Justin S. Smith, Susan M. Mniszewski, Kipton Barros, Christian F. A. Negre, Emanuel H. Rubensson, Anders M. N. Niklasson
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Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-24 Sander Roet, Christopher D. Daub, Enrico Riccardi
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Machine Learning to Predict Diels–Alder Reaction Barriers from the Reactant State Electron Density J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-03 Santiago Vargas, Matthew R. Hennefarth, Zhihao Liu, Anastassia N. Alexandrova
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Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-13 Haixin Wei, Zekai Zhao, Ray Luo
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Does Explicit Polarizability Improve Simulations of Phase Behavior of Ionic Liquids? J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-14 Martin Klajmon, Ctirad Červinka
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Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-13 Esam A. Orabi, Tuǧba N. Öztürk, Nathan Bernhardt, José D. Faraldo-Gómez
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Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-22 Yudong Qiu, Daniel G. A. Smith, Simon Boothroyd, Hyesu Jang, David F. Hahn, Jeffrey Wagner, Caitlin C. Bannan, Trevor Gokey, Victoria T. Lim, Chaya D. Stern, Andrea Rizzi, Bryon Tjanaka, Gary Tresadern, Xavier Lucas, Michael R. Shirts, Michael K. Gilson, John D. Chodera, Christopher I. Bayly, David L. Mobley, Lee-Ping Wang
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gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-29 Mario S. Valdés-Tresanco, Mario E. Valdés-Tresanco, Pedro A. Valiente, Ernesto Moreno
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Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-28 Marie Zgarbová, Jiří Šponer, Petr Jurečka
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Time-Resolved Excited-State Analysis of Molecular Electron Dynamics by TDDFT and Bethe–Salpeter Equation Formalisms J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-06 P. Grobas Illobre, M. Marsili, S. Corni, M. Stener, D. Toffoli, E. Coccia
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Molecular-Frame Photoelectron Angular Distributions of CO in the Vicinity of Feshbach Resonances: An XCHEM Approach J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-16 Vicent J. Borràs, Jesús González-Vázquez, Luca Argenti, Fernando Martín
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Multiscale Modeling of Electronic Spectra Including Nuclear Quantum Effects J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-28 Péter P. Fehér, Ádám Madarász, András Stirling
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Machine Learning Approach for Describing Water OH Stretch Vibrations J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-09 Kijeong Kwac, Holly Freedman, Minhaeng Cho
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A Joint Venture of Ab Initio Molecular Dynamics, Coupled Cluster Electronic Structure Methods, and Liquid-State Theory to Compute Accurate Isotropic Hyperfine Constants of Nitroxide Probes in Water J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-13 Bikramjit Sharma, Van Anh Tran, Tim Pongratz, Laura Galazzo, Irina Zhurko, Enrica Bordignon, Stefan M. Kast, Frank Neese, Dominik Marx
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Absorption Spectra of Solids from Periodic Equation-of-Motion Coupled-Cluster Theory J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-24 Xiao Wang, Timothy C. Berkelbach
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Optimal Representation of the Nuclear Ensemble: Application to Electronic Spectroscopy J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-20 Štěpán Sršeň, Petr Slavíček
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Assessment of the Accuracy of Density Functionals for Calculating Oxygen Reduction Reaction on Nitrogen-Doped Graphene J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-22 Björn Kirchhoff, Aleksei Ivanov, Egill Skúlason, Timo Jacob, Donato Fantauzzi, Hannes Jónsson
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De Novo Simulation of Charge Transport through Organic Single-Carrier Devices J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-30 Simon Kaiser, Naresh B. Kotadiya, Roland Rohloff, Artem Fediai, Franz Symalla, Tobias Neumann, Gert-Jan A. H. Wetzelaer, Paul W. M. Blom, Wolfgang Wenzel
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Subsystem Density Functional Theory Augmented by a Delta Learning Approach to Achieve Kohn–Sham Accuracy J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-10 Michela Pauletti, Vladimir V. Rybkin, Marcella Iannuzzi
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Generalizing Continuum Solvation in Crystal to Nonaqueous Solvents: Implementation, Parametrization, and Application to Molecules and Surfaces J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-06 Dario Vassetti, Ismail Can Oǧuz, Frédéric Labat
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An Exact Algorithm to Detect the Percolation Transition in Molecular Dynamics Simulations of Cross-Linking Polymer Networks J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-09 Mattia Livraghi, Kevin Höllring, Christian R. Wick, David M. Smith, Ana-Sunčana Smith
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Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of PHF6 Peptide of Tau Protein J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-07 Viet Hoang Man, Xibing He, Jie Gao, Junmei Wang
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CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-07 Owen N. Vickery, Phillip J. Stansfeld
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Computational Study on the Function of Palmitoylation on the Envelope Protein in SARS-CoV-2 J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-13 Shengjie Sun, Chitra Karki, Javier Aguilera, Alan E. Lopez Hernandez, Jianjun Sun, Lin Li
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Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-10 Lily Wang, Megan L. O’Mara
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Biasing RNA Coarse-Grained Folding Simulations with Small-Angle X-ray Scattering Data J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-10 Liuba Mazzanti, Lina Alferkh, Elisa Frezza, Samuela Pasquali
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Contact Map Fingerprints of Protein–Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-08 Marc Bianciotto, Paraskevi Gkeka, Daria B. Kokh, Rebecca C. Wade, Hervé Minoux
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Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-13 Si Zhang, David F. Hahn, Michael R. Shirts, Vincent A. Voelz
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Relative Affinities of Protein–Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations J. Chem. Theory Comput. (IF 6.006) Pub Date : 2021-09-15 T. Bertie Ansell, Luke Curran, Michael R. Horrell, Tanadet Pipatpolkai, Suzanne C. Letham, Wanling Song, Christian Siebold, Phillip J. Stansfeld, Mark S. P. Sansom, Robin A. Corey
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