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Unsupervised machine learning and cepstral analysis with 4D-STEM for characterizing complex microstructures of metallic alloys npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-18 Timothy Yoo, Eitan Hershkovitz, Yang Yang, Flávia da Cruz Gallo, Michele V. Manuel, Honggyu Kim
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Quantum embedding method with transformer neural network quantum states for strongly correlated materials npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-17 Huan Ma, Honghui Shang, Jinlong Yang
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Theoretical approaches for the description of plasmon generated hot carriers phenomena npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-17 Mirko Vanzan, Margherita Marsili
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Prediction of the Cu oxidation state from EELS and XAS spectra using supervised machine learning npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-17 Samuel P. Gleason, Deyu Lu, Jim Ciston
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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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MolPipeline: A Python Package for Processing Molecules with RDKit in Scikit-learn J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-17 Jochen Sieg, Christian W. Feldmann, Jennifer Hemmerich, Conrad Stork, Frederik Sandfort, Philipp Eiden, Miriam Mathea
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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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Effect of Direct and Water-Mediated Interactions on the Identification of Hotspots in Biomolecular Complexes with Multiple Subsystems J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-16 Vladimir Sladek, Polina V. Artiushenko, Dmitri G. Fedorov
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Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-16 Erik B. Nordquist, Mingtian Zhao, Anmol Kumar, Alexander D. MacKerell, Jr.
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Discovering Dually Active Anti-cancer Compounds with a Hybrid AI-structure-based Approach J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-14 Michele Roggia, Benito Natale, Giorgio Amendola, Nicola Grasso, Salvatore Di Maro, Sabrina Taliani, Sabrina Castellano, Serena Concetta Rita Reina, Erica Salvati, Jussara Amato, Sandro Cosconati
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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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RNAfcg: RNA Flexibility Prediction Based on Topological Centrality and Global Features J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-14 Fubin Chang, Lamei Liu, Fangrui Hu, Xiaohan Sun, Yingchun Zhao, Na Zhang, Chunhua Li
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A Machine Learning Method for RNA–Small Molecule Binding Preference Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-12 Chen Zhuo, Jiaming Gao, Anbang Li, Xuefeng Liu, Yunjie Zhao
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Data-driven modeling of dislocation mobility from atomistics using physics-informed machine learning npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-14 Yifeng Tian, Soumendu Bagchi, Liam Myhill, Giacomo Po, Enrique Martinez, Yen Ting Lin, Nithin Mathew, Danny Perez
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A unified moment tensor potential for silicon, oxygen, and silica npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-13 Karim Zongo, Hao Sun, Claudiane Ouellet-Plamondon, Laurent Karim Béland
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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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Unraveling the Interplay between Stability and Flexibility in the Design of Polyethylene Terephthalate (PET) Hydrolases J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-13 Shiqinrui Xu, Chengze Huo, Xiakun Chu
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Target-Specific De Novo Peptide Binder Design with DiffPepBuilder J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-12 Fanhao Wang, Yuzhe Wang, Laiyi Feng, Changsheng Zhang, Luhua Lai
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Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-11 Goran Giudetti, Madhubani Mukherjee, Samprita Nandi, Sraddha Agrawal, Oleg V. Prezhdo, Aiichiro Nakano
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Hidden magnetism and split off flat bands in the insulator metal transition in VO2 npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-13 Xiuwen Zhang, Jia-Xin Xiong, Alex Zunger
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Emergence and transformation of polar skyrmion lattices via flexoelectricity npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-13 Jianhua Ren, Linjie Liu, Fei Sun, Qian He, Mengjun Wu, Weijin Chen, Yue Zheng
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Chemical-motif characterization of short-range order with E(3)-equivariant graph neural networks npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-13 Killian Sheriff, Yifan Cao, Rodrigo Freitas
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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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Small Molecule NS11021 Promotes BK Channel Activation by Increasing Inner Pore Hydration J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-12 Erik B. Nordquist, Zhiguang Jia, Jianhan Chen
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Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-12 Shayantan Chaudhuri, David M. Rogers, Christopher J. Hayes, Katherine Inzani, Jonathan D. Hirst
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Decomposition of Forces in Protein: Methodology and General Properties J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-11 Pengbo Song, Qiaojing Huang, Wenyu Li, Maodong Li, Zhirong Liu
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CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-11 Xiu Li, Yuan He, Yuxuan Wang, Kaidong Lin, Xubo Lin
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Accelerating multiscale electronic stopping power predictions with time-dependent density functional theory and machine learning npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-12 Logan Ward, Ben Blaiszik, Cheng-Wei Lee, Troy Martin, Ian Foster, André Schleife
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Construction frontier molecular orbital prediction model with transfer learning for organic materials npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-11 Xinyu Peng, Jiaojiao Liang, Kuo Wang, Xiaojie Zhao, Zhiyan Peng, Zhennan Li, Jinhui Zeng, Zheng Lan, Min Lei, Di Huang
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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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Novel Combination Therapy for Heart Failure: Trimebutine–Methoxsalen Identified through Synergistic Network Virtual Screening and Experimental Validation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-11 Yunyuan Huang, Xin Chen, Jin Yang, Yue Yao, Manjiong Wang, Taotao Lu, Xiao Li, Jiqun Wang, Sicong Qiao, Donglei Shi, Xiaokang Li, Jian Li, Yixiang Xu
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MPNTEXT: An Interactive Platform for Automatically Extracting Metal-Polyphenol Networks and Their Applications from Scientific Literature J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-11 Zihui Huang, Xinyi Li, Andi Li, Yuhang Yang, Liqiang He, Zhiwen Zhang, Siwei Wu, Yang Wang, Shuting Cai, Yan He, Xujie Liu
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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
更新日期：2024-09-17
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