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Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-20 Mingyuan Zhang, Hao Wu, Yong Wang
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Two-Tier Modular Anharmonic Small Matrix Path Integral with Composite Spin-Boson Baths J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-20 Nancy Makri
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pyMSER─An Open-Source Library for Automatic Equilibration Detection in Molecular Simulations J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-18 Felipe L. Oliveira, Binquan Luan, Pierre M. Esteves, Mathias Steiner, Rodrigo Neumann Barros Ferreira
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Parallel Implementation of the Density Matrix Renormalization Group Method Achieving a Quarter petaFLOPS Performance on a Single DGX-H100 GPU Node J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-19 Andor Menczer, Maarten van Damme, Alan Rask, Lee Huntington, Jeff Hammond, Sotiris S. Xantheas, Martin Ganahl, Örs Legeza
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Theoretical Insight into the Fluorescence Spectral Tuning Mechanism: A Case Study of Flavin-Dependent Bacterial Luciferase J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-19 Xiaodi Fu, Wenwen Diao, Yanling Luo, Yajun Liu, Zhanfeng Wang
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Halogen Bonding on Water─A Drop in the Ocean? J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-18 Marc U. Engelhardt, Markus O. Zimmermann, Marcel Dammann, Jason Stahlecker, Antti Poso, Thales Kronenberger, Conrad Kunick, Thilo Stehle, Frank M. Boeckler
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Pursuing Extreme Descriptive Power and Generality in Chemical Bond Theories: A Method to Decipher “Interatomic Genomes” from Interatomic Electron Structures J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-16 Xinxu Zhang, Jiahao Wei, Hui Jia, Jiamin Liu, Guo Li, Ling Liu, Yulong Wu, Changlong Liu, Xiao-Dong Zhang, Yonghui Li
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Configuration Interaction in Frontier Molecular Orbital Basis for Screening the Spin-Correlated, Spatially Separated Triplet Pair State 1(T···T) Formation J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-18 Anurag Singh, Merle I. S. Röhr
In the theoretical screening of Singlet Fission rates in molecular aggregates, often the frontier molecular orbital model for dimers is employed. However, the dimer approach fails to account for recent experimental findings that suggest singlet fission progresses through a further intermediate state featuring two spatially separated, spin-correlated triplets, specifically a 1(T···T) state. We address
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Excited-State Forces with the Gaussian and Augmented Plane Wave Method for the Tamm–Dancoff Approximation of Time-Dependent Density Functional Theory J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-18 Beliz Sertcan Gökmen, Jürg Hutter, Anna-Sophia Hehn
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From Many-Body Ab Initio to Effective Excitonic Models: A Versatile Mapping Approach Including Environmental Embedding Effects J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-18 Mauricio Rodriguez-Mayorga, Xavier Blase, Ivan Duchemin, Gabriele D’Avino
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Exploring Ground and Excited States Via Single Reference Coupled-Cluster Theory and Algebraic Geometry J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-17 Svala Sverrisdóttir, Fabian M. Faulstich
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Capturing Correlation Effects in Positron Binding to Atoms and Molecules J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-17 Shiv Upadhyay, Anouar Benali, Kenneth D. Jordan
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A Mode Evolution Metric to Extract Reaction Coordinates for Biomolecular Conformational Transitions J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-17 Mitradip Das, Ravindra Venkatramani
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Completely Multipolar Model as a General Framework for Many-Body Interactions as Illustrated for Water J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-17 Joseph P. Heindel, Selim Sami, Teresa Head-Gordon
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Reconciling Accuracy and Feasibility for Barrierless Reaction Steps by the PCS/DDCI/MC-PDFT Protocol: Methane and Ethylene Dissociations as Case Studies J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-17 Luigi Crisci, Vincenzo Barone
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Correction to “BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations” J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-17 Germano Heinzelmann, David J. Huggins, Michael K. Gilson
The current published version did not include a few supporting files, namely, two tables containing detailed results of the calculations (Table S1 and Table S2) and also the input files needed to reproduce the paper results. The two tables are inside the tables.zip file, and the input files are inside input-files.zip, both uploaded as Supporting Information in this addition submission. The Supporting
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Excitonic Approach for Nonadiabatic Dynamics: Extending Beyond the Frenkel Exciton Model J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-16 Eduarda Sangiogo Gil, Andrea Giustini, Davide Accomasso, Giovanni Granucci
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Spin Dynamics of Radical Pairs Using the Stochastic Schrödinger Equation in MolSpin J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-16 Gediminas Jurgis Pažėra, Thomas P. Fay, Ilia A. Solov’yov, P. J. Hore, Luca Gerhards
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Machine Learning a Simple Interpretable Short-Range Potential for Silica J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-16 Aditya Koneru, Henry Chan, Sukriti Manna, Suvo Banik, Valeria Molinero, Subramanian K. R. S. Sankaranarayanan
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Particle–Particle Random Phase Approximation for Predicting Correlated Excited States of Point Defects J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-16 Jiachen Li, Yu Jin, Jincheng Yu, Weitao Yang, Tianyu Zhu
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Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-16 Egor S. Kolesnikov, Yeyue Xiong, Alexey V. Onufriev
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Toward Reliable Conformational Energies of Amino Acids and Dipeptides─The DipCONFS Benchmark and DipCONL Datasets J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-11 Christoph Plett, Stefan Grimme, Andreas Hansen
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State Interaction for Relativistic Four-Component Methods: Choose the Right Zeroth-Order Hamiltonian for Late-Row Elements J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-10 Chad E. Hoyer, Can Liao, Kirill D. Shumilov, Tianyuan Zhang, Xiaosong Li
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MMFA-DTA: Multimodal Feature Attention Fusion Network for Drug-Target Affinity Prediction for Drug Repurposing Against SARS-CoV-2 J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-13 Guanxing Chen, Haohuai He, Qiujie Lv, Lu Zhao, Calvin Yu-Chian Chen
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Tuning Two-Photon Absorption in Rhodopsin Chromophore via Backbone Modification: The Story Told by CC2 and TD-DFT J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-13 Saruti Sirimatayanant, Tadeusz Andruniów
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Benchmark Study of Core-Ionization Energies with the Generalized Active Space-Driven Similarity Renormalization Group J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-13 Meng Huang, Francesco A. Evangelista
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Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-12 Jakub Rydzewski
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Synergistic Integration of Physical Embedding and Machine Learning Enabling Precise and Reliable Force Field J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-12 Lifeng Xu, Jian Jiang
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Singlet–Triplet Inversion in Triangular Boron Carbon Nitrides J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-12 Matteo Bedogni, Francesco Di Maiolo
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Physics-Informed Active Learning for Accelerating Quantum Chemical Simulations J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-12 Yi-Fan Hou, Lina Zhang, Quanhao Zhang, Fuchun Ge, Pavlo O. Dral
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Stability and Dynamics of Zeolite-Confined Gold Nanoclusters J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-12 Siddharth Sonti, Chenghan Sun, Zekun Chen, Robert Michael Kowalski, Joseph S. Kowalski, Davide Donadio, Surl-Hee Ahn, Ambarish R. Kulkarni
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Direct Unconstrained Optimization of Molecular Orbital Coefficients in Density Functional Theory J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-11 Hanh D. M. Pham, Rustam Z. Khaliullin
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Internal Conversion Cascade in a Carbon Nanobelt: A Multiconfigurational Quantum Dynamical Study J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-11 James A. Green, Dominik Brey, Leyla P. Razgatlioglu, Badria Ali, Bartosz Błasiak, Irene Burghardt
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Is Quantum Above-Barrier Reflection Important for Molecular Barrier Crossing Rates? J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-11 Chiara Aieta, Michele Ceotto, Eli Pollak
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The Localized Active Space Method with Unitary Selective Coupled Cluster J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-10 Abhishek Mitra, Ruhee D’Cunha, Qiaohong Wang, Matthew R. Hermes, Yuri Alexeev, Stephen K. Gray, Matthew Otten, Laura Gagliardi
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Effect of Protein-Polarized Ligand Charges on Relative Protein Ligand Binding Affinities J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-11 Suliman Adam, Itamar Kass, Dana Krepel-Zussman, Gal Masarati, Dorit Shemesh, Avital Sharir-Ivry
A major challenge in computer-aided drug design is predicting relative binding energies of different molecules to a target protein using fast and accurate free-energy calculation methods. Free-energy calculations are primarily computed by utilizing classical molecular dynamics simulations based on all-atom force fields (FF) to model the interactions in the system. The present standard classical all-atom
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Numerical Investigation of the Quantum Inverse Algorithm on Small Molecules J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-11 Mauro Cainelli, Reo Baba, Yuki Kurashige
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Coarse-Graining Conformational Dynamics with Multidimensional Generalized Langevin Equation: How, When, and Why J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-11 Pinchen Xie, Weinan E
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Nonadiabatic Hydrogen Tunneling Dynamics for Multiple Proton Transfer Processes with Generalized Nuclear-Electronic Orbital Multistate Density Functional Theory J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-11 Joseph A. Dickinson, Sharon Hammes-Schiffer
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Production of Distinct Fibrillar, Oligomeric, and Other Aggregation States from Network Models of Multibody Interaction J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-11 Elizabeth M. Diessner, Loring J. Thomas, Carter T. Butts
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Hybrid Quantum Mechanical, Molecular Mechanical, and Machine Learning Potential for Computing Aqueous-Phase Adsorption Free Energies on Metal Surfaces J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-10 Mehdi Zare, Dia Sahsah, Mohammad Saleheen, Jörg Behler, Andreas Heyden
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Partial to Total Generation of 3D Transition-Metal Complexes J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-09 Hongni Jin, Kenneth M. Merz, Jr.
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Theory of Magnetic Properties in Quantum Electrodynamics Environments: Application to Molecular Aromaticity J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-10 Alberto Barlini, Andrea Bianchi, Enrico Ronca, Henrik Koch
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Range Separation of the Interaction Potential in Intermolecular and Intramolecular Symmetry-Adapted Perturbation Theory J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-10 Du Luu, Clemence Corminboeuf, Konrad Patkowski
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Automated Adaptive Absolute Binding Free Energy Calculations J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-10 Finlay Clark, Graeme R. Robb, Daniel J. Cole, Julien Michel
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Static Subspace Approximation for Random Phase Approximation Correlation Energies: Implementation and Performance J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-10 Daniel Weinberg, Olivia A. Hull, Jacob M. Clary, Ravishankar Sundararaman, Derek Vigil-Fowler, Mauro Del Ben
Developing theoretical understanding of complex reactions and processes at interfaces requires using methods that go beyond semilocal density functional theory to accurately describe the interactions between solvent, reactants and substrates. Methods based on many-body perturbation theory, such as the random phase approximation (RPA), have previously been limited due to their computational complexity
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Driven Self-Assembly of Patchy Particles Overcoming Equilibrium Limitations J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-10 Shubhadeep Nag, Gili Bisker
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Modified Activation-Relaxation Technique (ARTn) Method Tuned for Efficient Identification of Transition States in Surface Reactions J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-06 Jisu Jung, Hyungmin An, Jinhee Lee, Seungwu Han
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Reference CC3 Excitation Energies for Organic Chromophores: Benchmarking TD-DFT, BSE/GW, and Wave Function Methods J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-05 Iryna Knysh, Filippo Lipparini, Aymeric Blondel, Ivan Duchemin, Xavier Blase, Pierre-François Loos, Denis Jacquemin
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Grand Canonical Ensemble Approaches in CP2K for Modeling Electrochemistry at Constant Electrode Potentials J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-06 Ziwei Chai, Sandra Luber
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OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-05 Kasper B. Pedersen, Luís Borges-Araújo, Amanda D. Stange, Paulo C. T. Souza, Siewert J. Marrink, Birgit Schiøtt
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Quantum Dynamics from Classical Trajectories J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-05 Rafael S. Mattos, Saikat Mukherjee, Mario Barbatti
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Reaction Networks Resemble Low-Dimensional Regular Lattices J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-05 Miko M. Stulajter, Dmitrij Rappoport
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Melting Point and Crystal Growth Kinetics of Metals and Metal Oxides Using Reactive Force Fields: The Case of Aluminum and Alumina J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-05 Hao Zhao, Fernando Bresme
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Convergence-Adaptive Roundtrip Method Enables Rapid and Accurate FEP Calculations J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-05 Yufen Yao, Runduo Liu, Wenchao Li, Wanyi Huang, Yijun Lai, Hai-Bin Luo, Zhe Li
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Accelerating Relativistic Exact-Two-Component Density Functional Theory Calculations with Graphical Processing Units J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-03 Mikael Kovtun, Eleftherios Lambros, Aodong Liu, Diandong Tang, David B. Williams-Young, Xiaosong Li
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Kernel-Based Minimal Distributed Charges: A Conformationally Dependent ESP-Model for Molecular Simulations J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-04 Eric Boittier, Kai Töpfer, Mike Devereux, Markus Meuwly
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Ab Initio Multiple Spawning Nonadiabatic Dynamics with Different CASPT2 Flavors: A Fully Open-Source PySpawn/OpenMolcas Interface J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-04 Lea M. Ibele, Arshad Memhood, Benjamin G. Levine, Davide Avagliano
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Contact-Map-Driven Exploration of Heterogeneous Protein-Folding Paths J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-04 Ziad Fakhoury, Gabriele C. Sosso, Scott Habershon
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Beyond Catalysts: Exploring Discharge Product Growth and Intrinsic Overpotential in Lithium–Oxygen Batteries J. Chem. Theory Comput. (IF 5.7) Pub Date : 2024-09-03 Zhengxuan Yin, Lixin Xiong, Neil Qiang Su