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Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Xudong Yang, Chengwen Liu, Pengyu Ren
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Electronic Couplings for Triplet–Triplet Annihilation Upconversion in Crystal Rubrene J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Aitor Diaz-Andres, Claire Tonnelé, David Casanova
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LigandDiff: de Novo Ligand Design for 3D Transition Metal Complexes with Diffusion Models J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Hongni Jin, Kenneth M. Merz, Jr.
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TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Raul P. Pelaez, Guillem Simeon, Raimondas Galvelis, Antonio Mirarchi, Peter Eastman, Stefan Doerr, Philipp Thölke, Thomas E. Markland, Gianni De Fabritiis
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Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Candide Champion, Philippe H. Hünenberger, Sereina Riniker
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Modulating Efficiency and Color of Thermally Activated Delayed Fluorescence by Rationalizing the Substitution Effect J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-13 Alejandro Jodra, Marco Marazzi, Luis Manuel Frutos, Cristina García-Iriepa
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PointGAT: A Quantum Chemical Property Prediction Model Integrating Graph Attention and 3D Geometry J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 Rong Zhang, Rongqing Yuan, Boxue Tian
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Water Solvent Reorganization upon Ultrafast Resonant Stimulated X-ray Raman Excitation of a Metalloporphyrin Dimer J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 Mayank Dodia, Jérémy R. Rouxel, Daeheum Cho, Yu Zhang, Daniel Keefer, Mischa Bonn, Yuki Nagata, Shaul Mukamel
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2-in-1 Phase Space Sampling for Calculating the Absorption Spectrum of the Hydrated Electron J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 László Turi, Bence Baranyi, Ádám Madarász
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Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 Ivan Isaac Riveros, Ilyas Yildirim
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GradNav: Accelerated Exploration of Potential Energy Surfaces with Gradient-Based Navigation J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 Janghoon Ock, Parisa Mollaei, Amir Barati Farimani
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Toward Real Chemical Accuracy on Current Quantum Hardware Through the Transcorrelated Method J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-09 Werner Dobrautz, Igor O. Sokolov, Ke Liao, Pablo López Ríos, Martin Rahm, Ali Alavi, Ivano Tavernelli
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Evaluating Polarizable Biomembrane Simulations against Experiments J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Hanne S. Antila, Sneha Dixit, Batuhan Kav, Jesper J. Madsen, Markus S. Miettinen, O. H. Samuli Ollila
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Decarboxylation Mechanism of iso-Orotate Decarboxylase Revisited J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Jing Xiong, Dingguo Xu
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Fully Quantum Simulation of Polaritonic Vibrational Spectra of Large Cavity-Molecule System J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Qi Yu, Joel M. Bowman
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QM/MM Free Energy Calculations of Long-Range Biological Protonation Dynamics by Adaptive and Focused Sampling J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Maximilian C. Pöverlein, Andreas Hulm, Johannes C. B. Dietschreit, Jörg Kussmann, Christian Ochsenfeld, Ville R. I. Kaila
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Binding of Phosphate Species to Ca2+ and Mg2+ in Aqueous Solution J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Basak Koca Fındık, Majid Jafari, Lin Frank Song, Zhen Li, Viktorya Aviyente, Kenneth M. Merz, Jr.
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Physical Prior Mean Function-Driven Gaussian Processes Search for Minimum-Energy Reaction Paths with a Climbing-Image Nudged Elastic Band: A General Method for Gas-Phase, Interfacial, and Bulk-Phase Reactions J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Chong Teng, Yang Wang, Junwei Lucas Bao
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Quantum Mechanical Versus Polarizable Embedding Schemes: A Study of the Xray Absorption Spectra of Aqueous Ammonia and Ammonium J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-07 Sarai Dery Folkestad, Alexander C. Paul, Regina Paul née Matveeva, Peter Reinholdt, Sonia Coriani, Michael Odelius, Henrik Koch
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Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-07 Simone Bonfrate, Nicolas Ferré, Miquel Huix-Rotllant
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Sparse-Stochastic Fragmented Exchange for Large-Scale Hybrid Time-Dependent Density Functional Theory Calculations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-07 Mykola Sereda, Tucker Allen, Nadine C. Bradbury, Khaled Z. Ibrahim, Daniel Neuhauser
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Benchmark Investigation of SCC-DFTB against Standard and Hybrid DFT to Model Electronic Properties in Two-Dimensional MOFs for Thermoelectric Applications J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-06 Masoumeh Mahmoudi Gahrouei, Nikiphoros Vlastos, Ransell D’Souza, Emmanuel C. Odogwu, Laura de Sousa Oliveira
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Robust Gaussian Process Regression Method for Efficient Tunneling Pathway Optimization: Application to Surface Processes J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-06 Wei Fang, Yu-Cheng Zhu, Yihan Cheng, Yi-Ping Hao, Jeremy O. Richardson
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A Perspective on Protein Structure Prediction Using Quantum Computers J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-04 Hakan Doga, Bryan Raubenolt, Fabio Cumbo, Jayadev Joshi, Frank P. DiFilippo, Jun Qin, Daniel Blankenberg, Omar Shehab
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Scalable Quantum Monte Carlo with Direct-Product Trial Wave Functions J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-03 Hung Q. Pham, Runsheng Ouyang, Dingshun Lv
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Quantum Equation of Motion with Orbital Optimization for Computing Molecular Properties in Near-Term Quantum Computing J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-03 Phillip W. K. Jensen, Erik Rosendahl Kjellgren, Peter Reinholdt, Karl Michael Ziems, Sonia Coriani, Jacob Kongsted, Stephan P. A. Sauer
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Concentration Fluctuation/Microheterogeneity Duality Illustrated with Aqueous 1,4-Dioxane Mixtures J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-30 Alena Kolaříková, Aurélien Perera
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Orbital-Optimized Versus Time-Dependent Density Functional Calculations of Intramolecular Charge Transfer Excited States J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-02 Elli Selenius, Alec Elías Sigurdarson, Yorick L. A. Schmerwitz, Gianluca Levi
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FSSH-2: Fewest Switches Surface Hopping with Robust Switching Probability J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-02 Leonardo Araujo, Caroline Lasser, Burkhard Schmidt
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Linear Combinations of Cluster Mean-Field States Applied to Spin Systems J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-02 Athanasios Papastathopoulos-Katsaros, Thomas M. Henderson, Gustavo E. Scuseria
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Many-Body Excited States with a Contracted Quantum Eigensolver J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-01 Scott E. Smart, Davis M. Welakuh, Prineha Narang
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DFTB Simulation of Charged Clusters Using Machine Learning Charge Inference J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-01 Paul Guibourg, Léo Dontot, Pierre-Matthieu Anglade, Benoit Gervais
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Development of the Time-Independent Methods for the Cl + H2/F + HD Reaction Using Hyper-Spherical Coordinates Including (Full) Spin–Orbit Characteristics J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-01 Ransheng Wang, Zhigang Sun, Millard H. Alexander
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Subspace Methods for the Simulation of Molecular Response Properties on a Quantum Computer J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-01 Peter Reinholdt, Erik Rosendahl Kjellgren, Juliane Holst Fuglsbjerg, Karl Michael Ziems, Sonia Coriani, Stephan P. A. Sauer, Jacob Kongsted
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Linear Vibronic Coupling Approach for Surface-Enhanced Raman Scattering: Quantifying the Charge-Transfer Enhancement Mechanism J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-30 Francisco García-González, Juan Carlos Otero, Francisco J. Ávila Ferrer, Fabrizio Santoro, Daniel Aranda
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Simulating X-ray Absorption Spectroscopy in Challenging Environments: Methodological Insights from Water-Solvated Ammonia and Ammonium Systems J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-30 Ernst Dennis Larsson, Frederik Kamper Jørgensen, Peter Reinholdt, Erik Donovan Hedegård, Jacob Kongsted
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Accurate Scaling Functions of the Scaled Schrödinger Equation. II. Variational Examination of the Correct Scaling Functions with the Free Complement Theory Applied to the Helium Atom J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-29 Hiroshi Nakatsuji, Hiroyuki Nakashima
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Reshaping the QM Region On-the-Fly: Adaptive-Shape QM/MM Dynamic Simulations of a Hydrated Proton in Bulk Water J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-26 Shengheng Yan, Binju Wang, Hai Lin
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Multireference Correlated Oscillator Strengths from Adiabatic Connection Approaches Based on Extended Random Phase Approximation J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-26 Daria Drwal, Katarzyna Pernal, Ewa Pastorczak
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Short-Time Infrequent Metadynamics for Improved Kinetics Inference J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-26 Ofir Blumer, Shlomi Reuveni, Barak Hirshberg
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Exploiting the Hessian for a Better Convergence of the SCF-RDMFT Procedure J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-26 Nicolas G. Cartier, Klaas J. H. Giesbertz
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100 Years of the Lennard-Jones Potential J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-26 Peter Schwerdtfeger, David J. Wales
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Alchemical Enhanced Sampling with Optimized Phase Space Overlap J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-26 Shi Zhang, Timothy J. Giese, Tai-Sung Lee, Darrin M. York
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Efficient Generation of Conformer Ensembles Using Internal Coordinates and a Generative Directional Graph Convolution Neural Network J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-26 Eugene Raush, Ruben Abagyan, Maxim Totrov
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Which Options Exist for NISQ-Friendly Linear Response Formulations? J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-25 Karl Michael Ziems, Erik Rosendahl Kjellgren, Peter Reinholdt, Phillip W. K. Jensen, Stephan P. A. Sauer, Jacob Kongsted, Sonia Coriani
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Tucker Tensor Approach for Accelerating Fock Exchange Computations in a Real-Space Finite-Element Discretization of Generalized Kohn–Sham Density Functional Theory J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-25 Vishal Subramanian, Sambit Das, Vikram Gavini
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Fast Emulation of Fermionic Circuits with Matrix Product States J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-25 Justin Provazza, Klaas Gunst, Huanchen Zhai, Garnet K.-L. Chan, Toru Shiozaki, Nicholas C. Rubin, Alec F. White
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Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-25 Subarna Sasmal, Triasha Pal, Glen M. Hocky, Martin McCullagh
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Chiral Spectroscopy of Bulk Systems with Propagated Localized Orbitals J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-25 Lukas Schreder, Sandra Luber
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Nuclear Quantum Effects on Nonadiabatic Dynamics of a Green Fluorescent Protein Chromophore Analogue: Ring-Polymer Surface-Hopping Simulation J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-24 Xiang-Yang Liu, Sheng-Rui Wang, Wei-Hai Fang, Ganglong Cui
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Understanding and Predicting the Spatially Resolved Adsorption Properties of Nanoporous Materials J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-19 Yangzesheng Sun, J. Ilja Siepmann
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Natural Orbitals and Sparsity of Quantum Mutual Information J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-24 Leonardo Ratini, Chiara Capecci, Leonardo Guidoni
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All-Atom Photoinduced Charge Transfer Dynamics in Condensed Phase via Multistate Nonlinear-Response Instantaneous Marcus Theory J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-24 Zengkui Liu, Zailing Song, Xiang Sun
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XMECP: Reaching State-of-the-Art MECP Optimization in Multiscale Complex Systems J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-23 Jiawei Xu, Jian Hao, Caijie Bu, Yajie Meng, Han Xiao, Minyi Zhang, Chunsen Li
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Beyond Explored Functionals: A Computational Journey of Two-Photon Absorption J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-22 Ismael A. Elayan, Laura Rib, Rodrigo A. Mendes, Alex Brown
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Born–Oppenheimer Molecular Dynamics with a Linear Combination of Atomic Orbitals and Hybrid Functionals for Condensed Matter Simulations Made Possible. Theory and Performance for the Microcanonical and Canonical Ensembles J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-22 Chiara Ribaldone, Silvia Casassa
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Computational Protocol for the Spectral Assignment of NMR Resonances in Covalent Organic Frameworks J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-22 Siebe Vanlommel, Sander Borgmans, C. Vinod Chandran, Sambhu Radhakrishnan, Pascal Van Der Voort, Eric Breynaert, Veronique Van Speybroeck
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Time-Dependent Multilevel Density Functional Theory J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-22 Tommaso Giovannini, Marco Scavino, Henrik Koch
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Encoding a Many-Body Potential Energy Surface into a Grid-Based Matrix Product Operator J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-22 Kentaro Hino, Yuki Kurashige
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Unveiling Interactions of Tumor-Targeting Nanoparticles with Lipid Bilayers Using a Titratable Martini Model J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-22 Yu Cao, Jin Zhu, Jianlong Kou, D. Peter Tieleman, Qing Liang