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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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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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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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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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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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COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-26 Maksim Kuznetsov, Fedor Ryabov, Roman Schutski, Rim Shayakhmetov, Yen-Chu Lin, Alex Aliper, Daniil Polykovskiy
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Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-26 Carlos Sequeiros-Borja, Bartlomiej Surpeta, Aravind Selvaram Thirunavukarasu, Cedrix J. Dongmo Foumthuim, Igor Marchlewski, Jan Brezovsky
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dMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-25 Haopeng Ai, Deyin Wu, Huihao Zhou, Jun Xu, Qiong Gu
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DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-24 Sergey Gorelov, Anatoly Titov, Olga Tolicheva, Andrey Konevega, Alexey Shvetsov
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Dynamic Simulations of Interaction of the PEG-DPPE Micelle-Encapsulated Short-Chain Ceramides with the Raft-Included Membrane J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-23 Lina Zhao, Yanjiao Wang, Yi Zhang, Hao Chen, Fude Sun
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Early Aggregation Mechanism of SOD128–38 Based on Force Field Parameter of 5-Cyano-Tryptophan J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-23 Mueed Ur Rahman, Saira Bano, Xiaokun Hong, Ruo-Xu Gu, Hai-Feng Chen
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Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-22 Paige E. Bowling, Saswata Dasgupta, John M. Herbert
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FraHMT: A Fragment-Oriented Heterogeneous Graph Molecular Generation Model for Target Proteins J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-22 Shuang Wang, Dingming Liang, Jianmin Wang, Kaiyu Dong, Yunjing Zhang, Huicong Liang, Ximing Xu, Tao Song
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ORDerly: Data Sets and Benchmarks for Chemical Reaction Data J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-22 Daniel S. Wigh, Joe Arrowsmith, Alexander Pomberger, Kobi C. Felton, Alexei A. Lapkin
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Enhancing Coarse-Grained Models through Machine Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-22 Tarak Karmakar, Thereza A. Soares, Kenneth M. Merz, Jr.
Computer simulations, particularly molecular dynamics (MD) simulations, are effective tools for studying microscopic and dynamic details of complex systems governing various physicochemical and biological processes. Recent advancements in computer hardware and algorithms have significantly improved the efficiency of MD methods and expanded their applicability to the treatment of large macromolecular
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Group IV topological quantum alloy and the role of short-range order: the case of Ge-rich Ge1–xPbx npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-25 Yunfan Liang, Shunda Chen, Xiaochen Jin, Damien West, Shui-Qing Yu, Tianshu Li, Shengbai Zhang
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Classification of battery compounds using structure-free Mendeleev encodings J. Cheminfom. (IF 8.6) Pub Date : 2024-04-26 Zixin Zhuang, Amanda S. Barnard
Machine learning is a valuable tool that can accelerate the discovery and design of materials occupying combinatorial chemical spaces. However, the prerequisite need for vast amounts of training data can be prohibitive when significant resources are needed to characterize or simulate candidate structures. Recent results have shown that structure-free encoding of complex materials, based entirely on
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Do electrostatic interactions make a difference in physics‐based AutoDock4 scoring function? J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-25 Arslan R. Shaimardanov, Dmitry A. Shulga, Vladimir A. Palyulin
Physics‐based scoring function AutoDock4 is one of the most successfully applied tools in the area of structure‐based drug design. However, current scoring functions are still far from being perfect. In a recent work highlighting the strengths and deficiencies of current scoring functions, we discovered that the residual error of ΔGbind predictions made by AutoDock4 is highly correlated to the presence
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A mountaineering strategy to excited states: Accurate vertical transition energies and benchmarks for substituted benzenes J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-25 Pierre‐François Loos, Denis Jacquemin
In an effort to expand the existing QUEST database of accurate vertical transition energies [Véril et al. WIREs Comput. Mol. Sci. 2021, 11, e1517], we have modeled more than 100 electronic excited states of different natures (local, charge‐transfer, Rydberg, singlet, and triplet) in a dozen of mono‐ and di‐substituted benzenes, including aniline, benzonitrile, chlorobenzene, fluorobenzene, nitrobenzene
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Improving the reliability of machine learned potentials for modeling inhomogeneous liquids J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-25 Kamron Fazel, Nima Karimitari, Tanooj Shah, Christopher Sutton, Ravishankar Sundararaman
The atomic‐scale response of inhomogeneous fluids at interfaces and surrounding solute particles plays a critical role in governing chemical, electrochemical, and biological processes. Classical molecular dynamics simulations have been applied extensively to simulate the response of fluids to inhomogeneities directly, but are limited by the accuracy of the underlying interatomic potentials. Here, we
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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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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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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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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
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From Latent Dynamics to Meaningful Representations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-22 Dedi Wang, Yihang Wang, Luke Evans, Pratyush Tiwary
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From Chemical Drawing to Electronic Properties of Semiconducting Polymers in Bulk: A Tool for Chemical Discovery J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-20 Colm Burke, Hesam Makki, Alessandro Troisi
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Analytic Nuclear Gradients for Complete Active Space Linearized Pair-Density Functional Theory J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-19 Matthew R. Hennefarth, Matthew R. Hermes, Donald G. Truhlar, Laura Gagliardi
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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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Efficient and Robust Parameter Optimization of the Unitary Coupled-Cluster Ansatz J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-19 Weitang Li, Yufei Ge, Shi-Xin Zhang, Yu-Qin Chen, Shengyu Zhang
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Quantitative Prediction of Dissociation Rates of PYK2 Ligands Using Umbrella Sampling and Milestoning J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-19 Justin Spiriti, Chung F. Wong
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Selected Nonorthogonal Configuration Interaction with Compressed Single and Double Excitations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-19 Chong Sun, Fei Gao, Gustavo E. Scuseria
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Giant piezoelectricity driven by Thouless pump in conjugated polymers npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-23 Stefano Paolo Villani, Marco Campetella, Paolo Barone, Francesco Mauri
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Neural graph distance embedding for molecular geometry generation J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-24 Johannes T. Margraf
This article introduces neural graph distance embedding (nGDE), a method for generating 3D molecular geometries. Leveraging a graph neural network trained on the OE62 dataset of molecular geometries, nGDE predicts interatomic distances based on molecular graphs. These distances are then used in multidimensional scaling to produce 3D geometries, subsequently refined with standard bioorganic forcefields
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Towards atom-level understanding of metal oxide catalysts for the oxygen evolution reaction with machine learning npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-22 Jaclyn R. Lunger, Jessica Karaguesian, Hoje Chun, Jiayu Peng, Yitong Tseo, Chung Hsuan Shan, Byungchan Han, Yang Shao-Horn, Rafael Gómez-Bombarelli
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Learning symmetry-aware atom mapping in chemical reactions through deep graph matching J. Cheminfom. (IF 8.6) Pub Date : 2024-04-22 Maryam Astero, Juho Rousu
Accurate atom mapping, which establishes correspondences between atoms in reactants and products, is a crucial step in analyzing chemical reactions. In this paper, we present a novel end-to-end approach that formulates the atom mapping problem as a deep graph matching task. Our proposed model, AMNet (Atom Matching Network), utilizes molecular graph representations and employs various atom and bond
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High-throughput approach to explore cold metals for electronic and thermoelectric devices npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-22 Ligong Zhang, Fei Liu
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Giant and controllable nonlinear magneto-optical effects in two-dimensional magnets npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-22 Dezhao Wu, Meng Ye, Haowei Chen, Yong Xu, Wenhui Duan
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Ab initio multireference calculation of electronic spectra of the osmium complexes, [Os(bpy)3$$ {}_3 $$]2+$$ {}^{2+} $$ and [Os(phen)3$$ {}_3 $$]2+$$ {}^{2+} $$ J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-22 Saša Terek, Milan Milovanović
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Accurate prediction of dynamic protein–ligand binding using P‐score ranking J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-22 Peter E. G. F. Ibrahim, Fabio Zuccotto, Ulrich Zachariae, Ian Gilbert, Mike Bodkin
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Prevention of Leakage in Machine Learning Prediction for Polymer Composite Properties J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-20 Hajime Shimakawa, Akiko Kumada, Masahiro Sato
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On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-19 Stefan Boresch
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Critical assessment of G0W0 calculations for 2D materials: the example of monolayer MoS2 npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-18 Ronaldo Rodrigues Pela, Cecilia Vona, Sven Lubeck, Ben Alex, Ignacio Gonzalez Oliva, Claudia Draxl
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Calculating Binding Free Energies in Model Host–Guest Systems with Unrestrained Advanced Sampling J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-18 Andrew V. Marquardt, Mohsen Farshad, Jonathan K. Whitmer
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Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-18 Sankar Maity, Somdev Pahari, Santanu Santra, Madhurima Jana
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Managing Expectations and Imbalanced Training Data in Reactive Force Field Development: An Application to Water Adsorption on Alumina J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-19 Loïc Dumortier, Céline Chizallet, Benoit Creton, Theodorus de Bruin, Toon Verstraelen
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Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-18 Gonzalo Díaz Mirón, Carlos R. Lien-Medrano, Debarshi Banerjee, Uriel N. Morzan, Michael A. Sentef, Ralph Gebauer, Ali Hassanali
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Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-18 Kriti Shukla, Kelvin Idanwekhai, Martin Naradikian, Stephanie Ting, Stephen P. Schoenberger, Elizabeth Brunk
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Combined study of phase transitions in the P2-type NaXNi1/3Mn2/3O2 cathode material: experimental, ab-initio and multiphase-field results npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-18 Simon Daubner, Manuel Dillenz, Lukas Fridolin Pfeiffer, Cornelius Gauckler, Maxim Rosin, Nora Burgard, Jan Martin, Peter Axmann, Mohsen Sotoudeh, Axel Groß, Daniel Schneider, Britta Nestler
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Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-17 Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huanxiang Liu, Tingjun Hou, Yu Kang