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Issue Information J. Comput. Chem. (IF 3.4) Pub Date : 2025-06-04
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Effect of Iodine, and Polar Group Substitutions at α,β, and meso-Positions on Some Photophysical Properties of BODIPY-Based Photosensitizers Relevant to Photodynamic Therapy J. Comput. Chem. (IF 3.4) Pub Date : 2025-06-04
Neelam Chandravanshi, Tejendra Banana, Samarth Razdan, Swati Singh Rajput, Avantika, Md Mehboob Alam -
First‐Principles Study of Tuneable Electrochemical Performance of Zr‐Based Bimetallic Mxenes as Anode Materials for Li and Na‐Ion Batteries: Exploring the Synergistic Effect of Transition Metals J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-30
K. P. Aswathi, Baskaran Natesan -
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Parametrization of Zirconium for DFTB3/3OB: A Pathway to Study Complex Zr‐Compounds for Biomedical and Material Science Applications J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-26
Armin Penz, Jakob Gamper, Josef M. Gallmetzer, Felix R. S. Purtscher, Thomas S. HoferThis work presents the extension of the semi‐empirical density functional tight binding method, DFTB3, to include zirconium for biomedical and material science applications. The parametrization of Zr has been carried out in consistency with already established 3OB parameters including the elements C, H, N, O, S, P, Mg, Zn, Na, K, Ca, F, Cl, Br, and I. Zirconium‐ligand association and reaction energies
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Organodichalcogenide Structure and Stability: Hierarchical Ab Initio Benchmark and DFT Performance Study J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-26
Steven E. Beutick, Francesco Lambertini, Trevor A. Hamlin, F. Matthias Bickelhaupt, Laura OrianWe conducted a double‐hierarchical ab initio benchmark and DFT performance study of the organodichalcogenide bonding motif CH3Ch1Ch2(O)nCH3 with Ch1, Ch2 = S, Se and n = 0, 1, 2. The organodichalcogenide model systems were optimized at ZORA‐CCSD(T)/ma‐ZORA‐def2‐TZVPP. Our ab initio benchmark involved a hierarchical series of all‐electron relativistically contracted variants of the Karlsruhe basis
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Electronic Structure and Vibrational Properties of Indenotetracene‐Based Crystal J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-24
Federico Coppola, Raoul Carfora, Nadia Rega -
Parallelization of Particle‐Based Reaction–Diffusion Simulations Using MPI J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-23
Sikao Guo, Nenad Korolija, Kent Milfeld, Adip Jhaveri, Mankun Sang, Yue Moon Ying, Margaret E. Johnson -
AI‐Assisted Protein–Peptide Complex Prediction in a Practical Setting J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-22
Darren Y. Wang, Luxuan Wang, Andrew Mi, Junmei WangAccurate prediction of protein–peptide complex structures plays a critical role in structure‐based drug design, including antibody design. Most peptide‐docking benchmark studies were conducted using crystal structures of protein–peptide complexes; as such, the performance of the current peptide docking tools in the practical setting is unknown. Here, the practical setting implies there are no crystal
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Exploring Monomer‐Amino Acid Interactions in Mimicking Mips for PSA Detection—Using the Novel MBASM Approach J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-21
Lariel Chagas da Silva Neres, Johnatan Mucelini, Gabriel Augusto Pinheiro, Helen Luiza Brandão Silva Ambrósio, Albérico Borges Ferreira da Silva, Maria Del Pilar Taboada Sotomayor, Karla Furtado Andriani -
Development and Validation of Atomic Group Descriptors for Substituent Effects J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-20
Kevin Lefrancois‐Gagnon, Robert Mawhinney -
Quantifying the Cooperativity of Backbone Hydrogen Bonding J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-19
You Xu, Jing Huang -
Rate Constants and Energetics of the H2SiO + H Reaction System: RP‐VTST/MT and VRC Calculations J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-19
Marcelo André Petry Pontes, Edson Firmino Viana de Carvalho, Luiz Fernando de Araujo Ferrão, Francisco Bolivar Correto Machado, Orlando Roberto‐Neto -
Comparative Study of Predicting Radical CH Functionalization Sites in Nitrogen Heteroarenes Using a Radical General‐Purpose Reactivity Indicator and the Radical Fukui Function J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-19
Yoshio Barrera, James S. M. Anderson -
Issue Information J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-16
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Non‐Covalent Molecular Interaction Rules to Define Internal Dimer Coordinates for Quantum Mechanical Potential Energy Scans J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-16
Suliman Sharif, Anmol Kumar, Alexander D. MacKerell -
Analyzing Many‐Body Charge Transfer Effects With the Fragment Molecular Orbital Method J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-15
Dmitri G. Fedorov -
Evaluating the Functional Importance of Conformer‐Dependent Atomic Partial Charge Assignment J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-15
Meghan Osato, Hannah M. Baumann, Jennifer Huang, Irfan Alibay, David L. MobleyPhysics‐based methods such as protein‐ligand binding free energy calculations have been increasingly adopted in early‐stage drug discovery to prioritize promising compounds for synthesis. However, the accuracy of these methods is highly dependent on the details of the calculation and choices made while preparing the ligands and protein ahead of running calculations. During ligand preparation, researchers
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Modulation of the Product Upon the Reaction of CO2 With Dimethylamine Cluster: A Topological Analysis of the Reaction Mechanism J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-15
Mohammad Esmaïl Alikhani, Bernard SilviThe capture, activation, and reaction of carbon dioxide with dimethylamine (DMA) clusters have been investigated theoretically in the gas phase. The electronic structure of various compounds has been obtained using the density functional theory approach. The partitioning of the reaction path into different domains of structural stability has been done within the framework of the electron localization
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Issue Information J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-14
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Graph Neural Network for 3‐Dimensional Structures Including Dihedral Angles for Molecular Property Prediction J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-14
Sri Abhirath Reddy Sangala, Shampa Raghunathan -
PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-14
Piero Procacci -
Practical Machine Learning Strategies. 2. Accurate Prediction of ωB97X‐V/6‐311+G(2df,2p), ωB97M‐V/6‐311+G(2df,2p) and ωB97M(2)/6‐311+G(2df,2p) Energies From Neural Networks Trained From ωB97X‐D/6‐31G* Equilibrium Geometries and Energies J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-14
Philip Klunzinger, Thomas Hehre, Bernard Deppmeier, William Ohlinger, Warren Hehre -
GPU Accelerated Hybrid Particle‐Field Molecular Dynamics: Multi‐Node/Multi‐GPU Implementation and Large‐Scale Benchmarks of the OCCAM Code J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-14
Rosario Esposito, Giuseppe Mensitieri, You‐Liang Zhou, Zhong‐Yuan Lu, Ying Zhao, Toshihiro Kawakatsu, Giuseppe Milano -
Effects of Probe‐Related Correlations on Local Electrostatic Potentials Around DNA J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-14
Chuanying Chen, Binhan Yu, Xi Wang, Junji Iwahara, B. Montgomery Pettitt -
Unveiling the Hypervalent Electronic Structure of Main Group Zwitterions: Ylides or Ylenes? A DFT Study J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-14
Mathew Saumini, Cherumuttathu H. Suresh -
Adaptive Restraints to Accelerate Geometry Optimizations of Large Biomolecular Systems J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-04
Mark A. Hix, Alice R. Walker -
Vibrational Spectroscopy Through Time Averaged Fourier Transform of Autocorrelated Molecular Dynamics Data: Introducing the Free SEMISOFT Web‐Platform J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-03
Riccardo Conte, Michele Gandolfi, Davide Moscato, Chiara Aieta, Stefano Valtolina, Michele Ceotto -
Issue Information J. Comput. Chem. (IF 3.4) Pub Date : 2025-05-03
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The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-30
Holden Paz, Silvan Beck, Richmond Lee, Junming Ho, Haibo Yu -
Through‐Space/Through‐Bond Energy Decomposition Analysis Clarifies the Mechanism of Transition Mutation in DNA Containing O6‐Methylguanine Lesion J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-30
Mariia V. Ivonina, Yuuichi Orimoto, Yuriko Aoki -
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Beyond ST‐246: Unveiling Potential Inhibitors Targeting VP37 Protein in Silico From Herb and Marine Databases J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-24
Runhua Zhang, Xin Zhang, Shulin Zhao, Quan Zou, Yijie Ding, Xiaoyi Guo, Hongjie Wu -
Analytical First Derivatives of the SCF Energy for the Conductor‐Like Polarizable Continuum Model With Non‐Static Radii J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-24
Lukas Wittmann, Miquel Garcia‐Ratés, Christoph Riplinger -
The Role of Gold in Modifying the Structural Stabilities, Superhalogen Properties, and Double Aromaticity of Cyclic Carbon Clusters: Insights From AuC20− and AuC20 J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-24
Sheng‐Jie Lu, Guo‐Jin Cao, Zhao‐Ou Gao -
Assessment of Free Energies From Electrostatic Embedding Density Functional Tight Binding‐Based/Molecular Mechanics in Periodic Boundary Conditions J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-22
Simone Bonfrate, Woojin Park, Dulce Trejo‐Zamora, Nicolas Ferré, Cheol Ho Choi, Miquel Huix‐Rotllant -
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Computational Study of Complexation in LiH:nNH3 (n = 1–4) Clusters: An Interplay Among Hydrogen, Dihydrogen, and Lithium Bonds J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-19
Krishna, Lalit Kumar Saini, Mukesh Pandey -
On the Use of PDB X‐Ray Crystal Structures as Force Field Target and Validation Data for Pyranose Ring Puckering J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-19
Olgun Guvench, Andrew L. Straffin -
Giant Dipole Moments: Remarkable Effects Mono‐, Di‐, and Tri‐ Hydrated 5,6‐Diaminobenzene‐1,2,3,4‐Tetracarbonnitrile J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-19
Katherine Stanley, R. Houston Givhan, Justin M. Turney, Henry F. Schaefer -
Collisional Dynamics of Newly Detected Protonated Dicyanoacetylene (NC4NH+$$ {\mathrm{NC}}_4{\mathrm{NH}}^{+} $$) With He at Low Interstellar Temperatures J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-19
Pooja Chahal, T. J. Dhilip Kumar -
IMPACT‐4CCS: Integrated Modeling and Prediction Using Ab Initio and Trained Potentials for Collision Cross Sections J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-19
Carson Farmer, Hector Medina -
Atomic Neural Network for Calculation of Solvation Free Energies in Organic Solvents J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-19
Sergei F. Vyboishchikov -
Substrates (Acyl‐CoA and Diacylglycerol) Entry and Products (CoA and Triacylglycerol) Egress Pathways in DGAT1 J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-19
Hwayoung Lee, Wonpil Im -
Front Cover J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-18
Tatsuhiro Nakanishi, Takuro Tsutsumi, Yuriko Ono, Kazuki Sada, Tetsuya Taketsugu -
Issue Information J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-18
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Studying the Protein Thermostabilities and Folding Rates by the Interaction Energy Network in Solvent J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-18
Jun Liao, Mincong Wu, Fanjun Meng, Changjun Chen -
Unraveling Reaction Path Bifurcation: Insights Into Electron Movement via Natural Reaction Orbitals J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-11
Tatsuhiro Nakanishi, Takuro Tsutsumi, Yuriko Ono, Kazuki Sada, Tetsuya Taketsugu -
MolRWKV: Conditional Molecular Generation Model Using Local Enhancement and Graph Enhancement J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-10
Xihan Li, Kuanping Gong, Yongquan Jiang, Yan Yang, Tianrui Li -
Docking Survey, ADME, Toxicological Insights, and Mechanistic Exploration of the Diels–Alder Reaction Between Hexachlorocyclopentadiene and Dichloroethylene J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-09
Agnieszka Kącka‐Zych, Abdellah Zeroual, Asad Syed, Ali H. Bahkali -
Enhancing MM/P(G)BSA Methods: Integration of Formulaic Entropy for Improved Binding Free Energy Calculations J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-08
Lina Dong, Pengfei Li, Binju Wang -
The Relation Between the Excited Electronic States of Acene Radical Cations and Neutrals—A Computational Analysis J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-08
Anna M. Weidlich, Andreas Dreuw -
Issue Information J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-07
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Can Water Trigger Room‐Temperature Formation of Benzofuran‐2(3H)‐one Scaffolds From Vinyldiazene Derivatives? Computational Insights Into an Unusual Cyclization J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-07
Ulviyya Askerova, Yusif Abdullayev, Namiq Shikhaliyev, Avtandil Talybov, Jochen Autschbach -
Computational Probing of Schleyer's Hyperconjugative Aromaticity in a Novel Designed Anion Acceptor J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-04
Lawen Mohammed Rasul, Morteza Rouhani, Zohreh Mirjafary -
CCPE: A Tool to Quickly Extract, Format, and Present the Outputs From Gaussian and VEDA Computational Chemistry Programs J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-03
Mehmet Bozuyla, Alpaslan Bayrakdar, Yusuf Sert, Hasan Huseyin Kart, Sevgi Ozdemir Kart, Prasath Manivannan, Mehmet Hakkı Alma -
Issue Information J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-03
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DFT Insights Into the Structural, Stability, Elastic, and Optoelectronic Characteristics of Na2LiZF6 (Z = Ir and Rh) Double Perovskites for Sustainable Energy J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-02
Adil Es‐Smairi, Samah Al‐Qaisi, N. Sfina, Abderrazak Boutramine, Hamad Rahman Jappor, Hind Saeed Alzahrani, Amani H. Alfaifi, Habib Rached, Ajay Singh Verma, Marouane Archi, Md. Ferdous Rahman -
UV Absorption Spectra of TAMRA and TAMRA Labeled Peptides: A Combined Density Functional Theory and Classical Molecular Dynamics Study J. Comput. Chem. (IF 3.4) Pub Date : 2025-04-01
Mercedes Kukulka, Barbara Pem, Katarina Vazdar, Lukasz Cwiklik, Mario Vazdar
更新日期：2025-05-03
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