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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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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
The spin‐orbit coupling corrected absorption spectra of osmium complexes, [Os(bpy)] and [Os(phen)], were calculated by using ab initio multireference perturbation method (NEVPT2) with relativistic effects taken into account throughout ZORA approximation and corresponding all‐electron basis sets. For the same purpose, the time‐dependent DFT techniques were used. A very good agreement between NEVPT2
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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
Protein–ligand binding prediction typically relies on docking methodologies and associated scoring functions to propose the binding mode of a ligand in a biological target. Significant challenges are associated with this approach, including the flexibility of the protein–ligand system, solvent‐mediated interactions, and associated entropy changes. In addition, scoring functions are only weakly accurate
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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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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
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Stepping-Stone CBH: Benchmark and Application of a Multilayered Isodesmic-Based Correction Scheme J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-17 Eric M. Collins, Krishnan Raghavachari
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Protein Engineering with Lightweight Graph Denoising Neural Networks J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-17 Bingxin Zhou, Lirong Zheng, Banghao Wu, Yang Tan, Outongyi Lv, Kai Yi, Guisheng Fan, Liang Hong
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Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-17 Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiří Šponer, Petr Stadlbauer
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Quantum Algorithmic Approach to Multiconfigurational Valence Bond Theory: Insights from Interpretable Circuit Design J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-16 Jakob S. Kottmann, Francesco Scala
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Projected Atomic Orbitals As Optimal Virtual Space for Excited State Projection-Based Embedding Calculations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-16 Ádám B. Szirmai, Bence Hégely, Attila Tajti, Mihály Kállay, Péter G. Szalay
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Secondary Conformational Checkpoint in CRISPR-Cas9 J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-16 Shuxin Zhao, Jin Liu, Zhicheng Zuo
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Efficient Exploitation of Numerical Quadrature with Distance-Dependent Integral Screening in Explicitly Correlated F12 Theory: Linear Scaling Evaluation of the Most Expensive RI-MP2-F12 Term J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-16 Lars Urban, Henryk Laqua, Travis H. Thompson, Christian Ochsenfeld
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AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-16 Boyang Ni, Haoying Wang, Huda Kadhim Salem Khalaf, Vincent Blay, Douglas R. Houston
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Analytical Gradient Using Cluster-in-Molecule RI-MP2 Method for the Geometry Optimizations of Large Systems J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-16 Yang Zheng, Zhigang Ni, Yuqi Wang, Wei Li, Shuhua Li
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Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-16 Marzieh Saeedimasine, Roja Rahmani, Alexander P. Lyubartsev
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Understanding the Modulatory Role of E2012 on the γ-Secretase–Substrate Interaction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-16 Dulce C. Guzmán-Ocampo, Rodrigo Aguayo-Ortiz, Laura Dominguez
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Unlocking enhanced thermal conductivity in polymer blends through active learning npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-16 Jiaxin Xu, Tengfei Luo
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Classification of substances by health hazard using deep neural networks and molecular electron densities J. Cheminfom. (IF 8.6) Pub Date : 2024-04-16 Satnam Singh, Gina Zeh, Jessica Freiherr, Thilo Bauer, Isik Türkmen, Andreas T. Grasskamp
In this paper we present a method that allows leveraging 3D electron density information to train a deep neural network pipeline to segment regions of high, medium and low electronegativity and classify substances as health hazardous or non-hazardous. We show that this can be used for use-cases such as cosmetics and food products. For this purpose, we first generate 3D electron density cubes using
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Meta-learning-based Inductive logistic matrix completion for prediction of kinase inhibitors J. Cheminfom. (IF 8.6) Pub Date : 2024-04-16 Ming Du, XingRan Xie, Jing Luo, Jin Li
Protein kinases become an important source of potential drug targets. Developing new, efficient, and safe small-molecule kinase inhibitors has become an important topic in the field of drug research and development. In contrast with traditional wet experiments which are time-consuming and expensive, machine learning-based approaches for predicting small molecule inhibitors for protein kinases are time-saving
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Solvate Suite: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-15 Otávio L. Santana, Daniel G. Silva, Sidney R. Santana
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Intramolecular and Water Mediated Tautomerism of Solvated Glycine J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-15 Pengchao Zhang, Axel Tosello Gardini, Xuefei Xu, Michele Parrinello
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Modifying electronic and optical properties of violet phosphorus through variable fluorine coverage J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-16 Suen Wang, Xiaoyu Liu, Yang Zhang, Shasha Li, Xiangyan Bo, Lujun Wei, Wei Niu, Hong Wu, Yong Pu, Feng Li
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Theoretical study of PdNi and PdCu clusters embedded on graphene modified by monovacancy and nitrogen doping J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-16 E. A. Ortiz‐Vázquez, F. Montejo‐Alvaro, H. Cruz‐Martínez, P. Calaminici
The stability and reactivity of Pd4Ni4 and Pd4Cu4 clusters embedded on graphene modified by monovacancy and nitrogen doping were investigated using auxiliary density functional theory (ADFT) calculations. The most stable structure of the Pd4Ni4 cluster is found in high spin multiplicity, whereas the lowest stable energy structure of the Pd4Cu4 cluster is a close shell system. The interaction energies
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Mind your prevalence! J. Cheminfom. (IF 8.6) Pub Date : 2024-04-15 Sébastien J. J. Guesné, Thierry Hanser, Stéphane Werner, Samuel Boobier, Shaylyn Scott
Multiple metrics are used when assessing and validating the performance of quantitative structure–activity relationship (QSAR) models. In the case of binary classification, balanced accuracy is a metric to assess the global performance of such models. In contrast to accuracy, balanced accuracy does not depend on the respective prevalence of the two categories in the test set that is used to validate
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Zombie cheminformatics: extraction and conversion of Wiswesser Line Notation (WLN) from chemical documents J. Cheminfom. (IF 8.6) Pub Date : 2024-04-15 Michael Blakey, Samantha Pearman-Kanza, Jeremy G. Frey
Wiswesser Line Notation (WLN) is a old line notation for encoding chemical compounds for storage and processing by computers. Whilst the notation itself has long since been surpassed by SMILES and InChI, distribution of WLN during its active years was extensive. In the context of modernising chemical data, we present a comprehensive WLN parser developed using the OpenBabel toolkit, capable of translating
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PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction J. Cheminfom. (IF 8.6) Pub Date : 2024-04-15 Xinwei Zhao, Junqing Xu, Youyuan Shui, Mengdie Xu, Jie Hu, Xiaoyan Liu, Kai Che, Junjie Wang, Yun Liu
Drug combination therapies have shown promise in clinical cancer treatments. However, it is hard to experimentally identify all drug combinations for synergistic interaction even with high-throughput screening due to the vast space of potential combinations. Although a number of computational methods for drug synergy prediction have proven successful in narrowing down this space, fusing drug pairs
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Leveraging Bidirectional Nature of Allostery To Inhibit Protein–Protein Interactions (PPIs): A Case Study of PCSK9–LDLR Interaction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-14 Krishnendu Sinha, Ipsita Basu, Zacharia Shah, Salim Shah, Suman Chakrabarty
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Data-Driven Path Collective Variables J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-04-15 Arthur France-Lanord, Hadrien Vroylandt, Mathieu Salanne, Benjamin Rotenberg, A. Marco Saitta, Fabio Pietrucci
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The rule of four: anomalous distributions in the stoichiometries of inorganic compounds npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-12 Elena Gazzarrini, Rose K. Cersonsky, Marnik Bercx, Carl S. Adorf, Nicola Marzari
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Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-12 Dhiman Ray, Sudip Das, Umberto Raucci
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Deciphering S100B Allosteric Signaling: The Role of a Peptide Target, TRTK-12, as an Ensemble Modulator J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-11 Riya Samanta, Xinhao Zhuang, Kristen M. Varney, David J. Weber, Silvina Matysiak
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Computed entropy spectra for grain boundary segregation in polycrystals npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-12 Nutth Tuchinda, Christopher A. Schuh
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Central role of d-band energy level in Cu-based intermetallic alloys npj Comput. Mater. (IF 9.7) Pub Date : 2024-04-11 Jing Zhao, Wenming Xia, Zhi Zeng, Xianlong Wang