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Q-Next: A Fast, Parallel, and Diagonalization-Free Alternative to Direct Inversion of the Iterative Subspace J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-24 Christopher Seidl, Giuseppe M. J. Barca
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DFTB Parameters for the Periodic Table: Part III, Spin-Orbit Coupling J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-23 Gautam Jha, Thomas Heine
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Anharmonic Coupling of Stretching Vibrations in Ice: A Periodic VSCF and VCI Description J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-23 Raymond G. Schireman, Jefferson Maul, Alessandro Erba, Michael T. Ruggiero
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Multireference Approach to Normal and Resonant Auger Spectra Based on the One-Center Approximation J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-23 Bruno Nunes Cabral Tenorio, Torben Arne Voß, Sergey I. Bokarev, Piero Decleva, Sonia Coriani
A methodology to calculate the decay rates of normal and resonant Auger processes in atoms and molecules based on the One-Center Approximation (OCA), using atomic radial Auger integrals, is implemented within the restricted-active-space self-consistent-field (RASSCF) and the multistate restricted-active-space perturbation theory of second order (MS-RASPT2) frameworks, as part of the OpenMolcas project
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Machine Learning Models Predict Calculation Outcomes with the Transferability Necessary for Computational Catalysis J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-23 Chenru Duan, Aditya Nandy, Husain Adamji, Yuriy Roman-Leshkov, Heather J. Kulik
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A Mountaineering Strategy to Excited States: Revising Reference Values with EOM-CC4 J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-23 Pierre-François Loos, Filippo Lipparini, Devin A. Matthews, Aymeric Blondel, Denis Jacquemin
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Tensor Network Path Integral Study of Dynamics in B850 LH2 Ring with Atomistically Derived Vibrations J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-22 Amartya Bose, Peter L. Walters
The recently introduced multisite tensor network path integral (MS-TNPI) allows simulation of extended quantum systems coupled to dissipative media. We use MS-TNPI to simulate the exciton transport and the absorption spectrum of a B850 bacteriochlorophyll (BChl) ring. The MS-TNPI network is extended to account for the ring topology of the B850 system. Accurate molecular-dynamics-based description of
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Coupled Cluster and Perturbation Theories Based on a Cluster Mean-Field Reference Applied to Strongly Correlated Spin Systems J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-21 Athanasios Papastathopoulos-Katsaros, Carlos A. Jiménez-Hoyos, Thomas M. Henderson, Gustavo E. Scuseria
We introduce perturbation and coupled-cluster theories based on a cluster mean-field reference for describing the ground state of strongly correlated spin systems. In cluster mean-field, the ground state wave function is written as a simple tensor product of optimized cluster states. The cluster language and the mean-field nature of the ansatz allow for a straightforward improvement which uses perturbation
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Identifying a Feasible Transition Pathway between Two Conformational States for a Protein J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-20 Yao Li, Haipeng Gong
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Correction to “Noncovalent Interactions by the Quantum Monte Carlo Method: Strong Influence of Isotropic Jastrow Cutoff Radii” J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-17 Roman Fanta, Matúš Dubecký
In the original paper focusing on the unexpected and strong dependency of noncovalent interaction energy differences on isotropic Jastrow cutoff radii (rcut) setting within 1-determinant fixed-node diffusion Monte Carlo (FNDMC) computations involving effective core potentials (ECPs), wrong data and conclusions regarding the determinant localization approximation (DLA) (1) method were presented. The
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Accelerators for Classical Molecular Dynamics Simulations of Biomolecules J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-16 Derek Jones, Jonathan E. Allen, Yue Yang, William F. Drew Bennett, Maya Gokhale, Niema Moshiri, Tajana S. Rosing
Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model biomolecular structures such as proteins and their interactions with drug-like small molecules with greater spatiotemporal resolution than is otherwise possible using experimental methods. MD simulations are notoriously expensive computational endeavors that have traditionally required massive investment in specialized
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Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-16 Timothy J. Giese, Jinzhe Zeng, Şölen Ekesan, Darrin M. York
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Efficient Quantification of Lipid Packing Defect Sensing by Amphipathic Peptides: Comparing Martini 2 and 3 with CHARMM36 J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-16 Niek van Hilten, Kai Steffen Stroh, Herre Jelger Risselada
In biological systems, proteins can be attracted to curved or stretched regions of lipid bilayers by sensing hydrophobic defects in the lipid packing on the membrane surface. Here, we present an efficient end-state free energy calculation method to quantify such sensing in molecular dynamics simulations. We illustrate that lipid packing defect sensing can be defined as the difference in mechanical
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A Hybrid Machine Learning Approach for Structure Stability Prediction in Molecular Co-crystal Screenings J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-16 Simon Wengert, Gábor Csányi, Karsten Reuter, Johannes T. Margraf
Co-crystals are a highly interesting material class as varying their components and stoichiometry in principle allows tuning supramolecular assemblies toward desired physical properties. The in silico prediction of co-crystal structures represents a daunting task, however, as they span a vast search space and usually feature large unit cells. This requires theoretical models that are accurate and fast
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A Unified Approach to Derive Atomic Partial Charges and Polarizabilities of Ionic Liquids J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-14 Menglin Liu, Tianying Yan
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Implementation and Validation of Constrained Density Functional Theory Forces in the CP2K Package J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-14 Christian S. Ahart, Kevin M. Rosso, Jochen Blumberger
Constrained density functional theory (CDFT) is a powerful tool for the prediction of electron transfer parameters in condensed phase simulations at a reasonable computational cost. In this work we present an extension to CDFT in the popular mixed Gaussian/plane wave electronic structure package CP2K, implementing the additional force terms arising from a constraint based on Hirshfeld charge partitioning
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Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-14 Thorben Fröhlking, Vojtěch Mlýnský, Michal Janeček, Petra Kührová, Miroslav Krepl, Pavel Banáš, Jiří Šponer, Giovanni Bussi
The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental data in order to enforce agreement with experiments. Here, we extend an existing framework which allows arbitrarily chosen force-field correction terms to be fitted by quantification of the discrepancy between observables back-calculated from
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Ab Initio Cluster Approach for High Harmonic Generation in Liquids J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-14 Ofer Neufeld, Zahra Nourbakhsh, Nicolas Tancogne-Dejean, Angel Rubio
High harmonic generation (HHG) takes place in all phases of matter. In gaseous atomic and molecular media, it has been extensively studied and is very well understood. In solids, research is ongoing, but a consensus is forming for the dominant microscopic HHG mechanisms. In liquids, on the other hand, no established theory yet exists, and approaches developed for gases and solids are generally inapplicable
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Analytic First-Order Derivatives of (X)MS, XDW, and RMS Variants of the CASPT2 and RASPT2 Methods J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-14 Yoshio Nishimoto, Stefano Battaglia, Roland Lindh
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Symmetric Molecular Dynamics J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-14 Sam Cox, Andrew D. White
We derive a formulation of molecular dynamics that generates only symmetric configurations. We implement it for all 2D planar and 3D space groups. An atlas of 2D Lennard-Jones crystals under all planar groups is created with symmetric molecular dynamics.
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Molecular Conformer Search with Low-Energy Latent Space J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-13 Xiaomi Guo, Lincan Fang, Yong Xu, Wenhui Duan, Patrick Rinke, Milica Todorović, Xi Chen
Identifying low-energy conformers with quantum mechanical accuracy for molecules with many degrees of freedom is challenging. In this work, we use the molecular dihedral angles as features and explore the possibility of performing molecular conformer search in a latent space with a generative model named variational auto-encoder (VAE). We bias the VAE towards low-energy molecular configurations to
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Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of De Novo Designed Glu/Lys Peptides J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-10 Eric J. M. Lang, Emily G. Baker, Derek N. Woolfson, Adrian J. Mulholland
We test a range of standard generalized Born (GB) models and protein force fields for a set of five experimentally characterized, designed peptides comprising alternating blocks of glutamate and lysine, which have been shown to differ significantly in α-helical content. Sixty-five combinations of force fields and GB models are evaluated in >800 μs of molecular dynamics simulations. GB models generally
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Development of OPLS-AA/M Parameters for Simulations of G Protein-Coupled Receptors and Other Membrane Proteins J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-10 Michael J. Robertson, Georgios Skiniotis
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Efficiently Computing NMR 1H and 13C Chemical Shifts of Saccharides in Aqueous Environment J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-10 Vladimír Palivec, Radek Pohl, Jakub Kaminský, Hector Martinez-Seara
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A Hessian-Free Method to Prevent Zero-Point Energy Leakage in Classical Trajectories J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-09 Saikat Mukherjee, Mario Barbatti
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Assessment of Simultaneous Global Optimization of Geometry and Total Spin of Small Iron Clusters J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-09 Luis Ángel Zárate-Hernández, José Manuel Vásquez-Pérez, Julián Cruz-Borbolla
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Localization and Delocalization in Solids from Electron Distribution Functions J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-09 A. Gallo-Bueno, M. Kohout, E. Francisco, Á. Martín Pendás
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Frequency-Dependent Sternheimer Linear-Response Formalism for Strongly Coupled Light–Matter Systems J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-08 Davis M. Welakuh, Johannes Flick, Michael Ruggenthaler, Heiko Appel, Angel Rubio
The rapid progress in quantum-optical experiments, especially in the field of cavity quantum electrodynamics and nanoplasmonics, allows one to substantially modify and control chemical and physical properties of atoms, molecules, and solids by strongly coupling to the quantized field. Alongside such experimental advances has been the recent development of ab initio approaches such as quantum electrodynamical
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Highly Efficient and Accurate Computation of Multiple Orbital Spaces Spanning Fock Matrix Elements on Central and Graphics Processing Units for Application in F12 Theory J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-08 Lars Urban, Henryk Laqua, Christian Ochsenfeld
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Graph Neural Networks for Learning Molecular Excitation Spectra J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-07 Kanishka Singh, Jannes Münchmeyer, Leon Weber, Ulf Leser, Annika Bande
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Atomistic Mechanisms of Binary Alloy Surface Segregation from Nanoseconds to Seconds Using Accelerated Dynamics J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-07 Richard B. Garza, Jiyoung Lee, Mai H. Nguyen, Andrew Garmon, Danny Perez, Meng Li, Judith C. Yang, Graeme Henkelman, Wissam A. Saidi
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Quantum Perturbation Theory Using Tensor Cores and a Deep Neural Network J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-07 Joshua Finkelstein, Emanuel H. Rubensson, Susan M. Mniszewski, Christian F. A. Negre, Anders M. N. Niklasson
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Spin–Orbit Couplings for Nonadiabatic Molecular Dynamics at the ΔSCF Level J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-06 Momir Mališ, Eva Vandaele, Sandra Luber
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Toward Efficient Direct Dynamics Studies of Chemical Reactions: A Novel Matrix Completion Algorithm J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-06 Stephen Jon Quiton, Jeongmin Chae, Selin Bac, Kareesa Kron, Urbashi Mitra, Shaama Mallikarjun Sharada
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Correction to “The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design” J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-06 Rebecca F. Alford, Andrew Leaver-Fay, Jeliazko R. Jeliazkov, Matthew J. O’Meara, Frank P. DiMaio, Hahnbeom Park, Maxim V. Shapovalov, P. Douglas Renfrew, Vikram K. Mulligan, Kalli Kappel, Jason W. Labonte, Michael S. Pacella, Richard Bonneau, Philip Bradley, Roland L. Dunbrack, Jr., Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J. Gray
In the initially published version of this article, the potential for the disulfide dihedral CαCβSS was incorrect in Figure 4E, with a sign error in A_{2,CαCβSS} from equation S11. Here is the corrected figure panel: We thank Claiborne W. Tydings, Dr. Oanh T. Vu, and Prof. Jens Meiler of Vanderbilt University for identifying this error. This article has not yet been cited by other publications.
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Explicitly Correlated Electronic Structure Calculations with Transcorrelated Matrix Product Operators J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-06 Alberto Baiardi, Michał Lesiuk, Markus Reiher
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Enhanced Sampling Simulation Reveals How Solvent Influences Chirogenesis of the Intra-Molecular Diels–Alder Reaction J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-06 Xu Han, Jun Zhang, Yi Isaac Yang, Zhen Zhang, Lijiang Yang, Yi Qin Gao
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Studying the Dynamics of a Complex G-Quadruplex System: Insights into the Comparison of MD and NMR Data J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-06 Matteo Castelli, Filippo Doria, Mauro Freccero, Giorgio Colombo, Elisabetta Moroni
Molecular dynamics (MD) simulations are coming of age in the study of nucleic acids, including specific tertiary structures such as G-quadruplexes. While being precious for providing structural and dynamic information inaccessible to experiments at the atomistic level of resolution, MD simulations in this field may still be limited by several factors. These include the force fields used, different
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ATOMIC-2 Protocol for Thermochemistry J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-03 Dirk Bakowies
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Toward a QUBO-Based Density Matrix Electronic Structure Method J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-03 Christian F. A. Negre, Alejandro Lopez-Bezanilla, Yu Zhang, Prosper D. Akrobotu, Susan M. Mniszewski, Sergei Tretiak, Pavel A. Dub
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Efficient Integral-Direct Methods for Self-Consistent Reduced Density Matrix Functional Theory Calculations on Central and Graphics Processing Units J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-03 Y. Lemke, J. Kussmann, C. Ochsenfeld
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New Framework for Computing a General Local Self-Diffusion Coefficient Using Statistical Mechanics J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-03 Michelle A. Hunter, Baris Demir, Charlotte F. Petersen, Debra J. Searles
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Machine Learning Force Field Aided Cluster Expansion Approach to Configurationally Disordered Materials: Critical Assessment of Training Set Selection and Size Convergence J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-03 Jun-Zhong Xie, Xu-Yuan Zhou, Dong Luan, Hong Jiang
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Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-02 Maria M. Reif, Martin Zacharias
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Combined Deep Learning and Classical Potential Approach for Modeling Diffusion in UiO-66 J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-02 Siddarth K. Achar, Jacob J. Wardzala, Leonardo Bernasconi, Linfeng Zhang, J. Karl Johnson
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Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4 J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-02 Vicky Charitou, Siri C. van Keulen, Alexandre M. J. J. Bonvin
An emerging class of therapeutic molecules are cyclic peptides with over 40 cyclic peptide drugs currently in clinical use. Their mode of action is, however, not fully understood, impeding rational drug design. Computational techniques could positively impact their design, but modeling them and their interactions remains challenging due to their cyclic nature and their flexibility. This study presents
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Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-02 Amirhossein Taghavi, Ivan Riveros, David J. Wales, Ilyas Yildirim
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Tensor-Train Split-Operator KSL (TT-SOKSL) Method for Quantum Dynamics Simulations J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-01 Ningyi Lyu, Micheline B. Soley, Victor S. Batista
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InteraChem: Exploring Excited States in Virtual Reality with Ab Initio Interactive Molecular Dynamics J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-01 Yuanheng Wang, Stefan Seritan, Dean Lahana, Jason E. Ford, Alessio Valentini, Edward G. Hohenstein, Todd J. Martínez
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Green’s Function Formulation of Quantum Defect Embedding Theory J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-01 Nan Sheng, Christian Vorwerk, Marco Govoni, Giulia Galli
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Hydration of Linear Alkanes is Governed by the Small Length-Scale Hydrophobic Effect J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-01 Himanshu Singh, Sumit Sharma
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Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-06-01 Piero Procacci
In the context of advanced hit-to-lead drug design based on atomistic molecular dynamics simulations, we propose a dual topology alchemical approach for calculating the relative binding free energy (RBFE) between two chemically distant compounds. The method (termed NE-RBFE) relies on the enhanced sampling of the end-states in bulk and in the bound state via Hamiltonian Replica Exchange, alchemically
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GronOR: Scalable and Accelerated Nonorthogonal Configuration Interaction for Molecular Fragment Wave Functions J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-05-31 T. P. Straatsma, R. Broer, A. Sánchez-Mansilla, C. Sousa, C. de Graaf
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py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-05-27 Mohammad Soroush Barhaghi, Brad Crawford, Gregory Schwing, David J. Hardy, John E. Stone, Loren Schwiebert, Jeffrey Potoff, Emad Tajkhorshid
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Projected Complex Absorbing Potential Multireference Configuration Interaction Approach for Shape and Feshbach Resonances J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-05-27 Mushir Thodika, Spiridoula Matsika
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Orthogonal State Reduction Variational Eigensolver for the Excited-State Calculations on Quantum Computers J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-05-27 Qing-Xing Xie, Sheng Liu, Yan Zhao
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Slip-Spring Hybrid Particle-Field Molecular Dynamics for Coarse-Graining Branched Polymer Melts: Polystyrene Melts as an Example J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-05-26 Zhenghao Wu, Florian Müller-Plathe
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Exploration vs Convergence Speed in Adaptive-Bias Enhanced Sampling J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-05-26 Michele Invernizzi, Michele Parrinello
In adaptive-bias enhanced sampling methods, a bias potential is added to the system to drive transitions between metastable states. The bias potential is a function of a few collective variables and is gradually modified according to the underlying free energy surface. We show that when the collective variables are suboptimal, there is an exploration–convergence tradeoff, and one must choose between
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Mobility of Polymer Melts in a Regular Array of Carbon Nanotubes J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-05-26 Simon A. N. Alberti, Jurek Schneider, Florian Müller-Plathe
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Learning Efficient, Collective Monte Carlo Moves with Variational Autoencoders J. Chem. Theory Comput. (IF 6.006) Pub Date : 2022-05-25 Jacob I. Monroe, Vincent K. Shen