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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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Research Progresses and Applications of Knowledge Graph Embedding Technique in Chemistry J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-20 Chuanghui Wang, Yunqing Yang, Jinshuai Song, Xiaofei Nan
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Prediction of Acrylonitrile–Butadiene–Styrene Mechanical Properties through Compressed-Sensing Techniques J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-19 Jonah Poort, Milad Golkaram, Pieter Janssen, Jan Harm Urbanus
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ResiDEM: Analytical Tool for Isomorphous Difference Electron Density Maps Utilizing Dynamic Residue Identification via Density Clustering J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-19 Sriram Srinivasa Raghavan, Osamu Miyashita
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Modeling the effect of substituents on the electronically excited states of indole derivatives J. Comput. Chem. (IF 3.4) Pub Date : 2024-09-20 Jordan Howe, Salsabil Abou-Hatab, Spiridoula Matsika
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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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Machine-Learning Predictions of Critical Temperatures from Chemical Compositions of Superconductors J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-17 Son Gyo Jung, Guwon Jung, Jacqueline M. Cole
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Atomistic Insights into the Stabilization of TDP-43 Protofibrils by ATP J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-18 Zhengdong Xu, Jiaxing Tang, Yehong Gong, Jianxin Zhang, Yu Zou
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Combining Data-Driven and Structure-Based Approaches in Designing Dual PARP1-BRD4 Inhibitors for Breast Cancer Treatment J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-18 Bo Feng, Hui Yu, Xu Dong, Alejandro Díaz-Holguín, Albert A. Antolin, Huabin Hu
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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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MHIPM: Accurate Prediction of Microbe-Host Interactions Using Multiview Features from a Heterogeneous Microbial Network J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-17 Jie Pan, Guangming Zhang, Yong Yang, Wenli Yang, Ning Mao, Zhuhong You, Jie Feng, Shiwei Wang, Yanmei Sun
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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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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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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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MEPO-ML: a robust graph attention network model for rapid generation of partial atomic charges in metal-organic frameworks npj Comput. Mater. (IF 9.4) Pub Date : 2024-09-18 Jun Luo, Omar Ben Said, Peigen Xie, Marco Gibaldi, Jake Burner, Cécile Pereira, Tom K. Woo
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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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In Silico Insights: QSAR Modeling of TBK1 Kinase Inhibitors for Enhanced Drug Discovery J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-17 Julian M. Ivanov, Rumiana Tenchov, Krittika Ralhan, Kavita A. Iyer, Shivangi Agarwal, Qiongqiong Angela Zhou
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Transfer Learning Approach to Multitarget QSRR Modeling in RPLC J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-16 Priyanka Kumari, Madureira Sanches Ribeiro Guilherme, Pratyush Choudhary, Thomas Van Laethem, Marianne Fillet, Phillipe Hubert, Pierre Yves Sacre, Cedric Hubert
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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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Efficient acceleration of the convergence of the minimum free energy path via a path‐planning generated initial guess J. Comput. Chem. (IF 3.4) Pub Date : 2024-09-18 Yi Sun
We demonstrate that combining a shifted clustering algorithm with a fast‐marching‐based algorithm can generate accurate approximations of the minimum energy path (MEP) given a free energy landscape (FEL). Using this approximation as the initial guess for the MEP, followed by further refinement with the string method (referred to as the fast marching tree (FMT)‐string combined approach), significantly
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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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An influence of electronic structure theory method, thermodynamic and implicit solvation corrections on the organic carbonates conformational and binding energies J. Comput. Chem. (IF 3.4) Pub Date : 2024-09-17 Alexander S. Ryzhako, Anna A. Tuma, Arseniy A. Otlyotov, Yury Minenkov
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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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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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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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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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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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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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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