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ORCIDJournal of Computational Chemistry, Volume 46
Volume 46, Number 1, 2025
Short Communication
- Yi Sun
:
Efficient acceleration of the convergence of the minimum free energy path via a path-planning generated initial guess.
Research Article
- Jordan Howe, Salsabil Abou-Hatab, Spiridoula Matsika:
Modeling the effect of substituents on the electronically excited states of indole derivatives. - Anna V. Pomogaeva, Anna S. Lisovenko, Alexey Y. Timoshkin:
Facile heterolytic bond splitting of molecular chlorine upon reactions with Lewis bases: Comparison with ICl and I2. - Jinhui Meng, Li Zhang, Zhe He, Mengfeng Hu, Jinhan Liu, Wenzhuo Bao, Qifeng Tian, Huawei Feng, Hongsheng Liu:
Development of a machine learning-based target-specific scoring function for structure-based binding affinity prediction for human dihydroorotate dehydrogenase inhibitors. - Huixue Li, Yvhua Wang, Sujuan Pan, Changqing Wang, Yanzhi Liu, Kun Yuan, Lingling Lv, Zhifeng Li:
Theoretical study on the luminescent and reaction mechanism of dansyl-based fluorescence probe for detecting hydrogen sulfide. - Manuel Yáñez, Otilia Mó, M. Merced Montero-Campillo, Ibon Alkorta, José Elguero:
Hydride and halide abstraction reactions behind the enhanced basicity of Be and Mg clusters with nitrogen bases. - Cai-Yue Gao, Bin-Bin Pei, Si-Dian Li:
Fluxional halogen bonds in linear complexes of tetrafluorodiiodobenzene with dinitrobenzene. - Josefredo R. Pliego Jr.:
Theoretical design of new ligands to boost reaction rate and selectivity in palladium-catalyzed aromatic fluorination. - Francois Berenger, Koji Tsuda:
An ANI-2 enabled open-source protocol to estimate ligand strain after docking. - Victor Ovchinnikov, Martin Karplus:
High-throughput molecular simulations of SARS-CoV-2 receptor binding domain mutants quantify correlations between dynamic fluctuations and protein expression. - Piotr Matczak, Philipp Buday, Stephan Kupfer, Helmar Görls, Grzegorz Mloston, Wolfgang Weigand:
Probing the performance of DFT in the structural characterization of [FeFe] hydrogenase models. - John D. Bickel, Brock T. Boysan, Robert C. Rizzo:
Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK. - Kajjana Boonpalit, Hathaichanok Chuntakaruk, Jiramet Kinchagawat, Peter Wolschann, Supot Hannongbua, Thanyada Rungrotmongkol, Sarana Nutanong:
Pre-training strategy for antiviral drug screening with low-data graph neural network: A case study in HIV-1 K103N reverse transcriptase. - Dusan Cocic, Liu Yang, Ralph Puchta, Tiesheng Shi, Rudi van Eldik:
Investigation of the complete encapsulation process of the noble gases by cryptophanes. - Qiancheng Xia, Qiuyu Fu, Cheng Shen, Ruth Brenk, Niu Huang:
Assessing small molecule conformational sampling methods in molecular docking. - Shailesh Kumar Panday, Arghya Chakravorty, Shan Zhao, Emil Alexov:
On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model. - Nabajyoti Patra, Astha Gupta, Prasad V. Bharatam:
Stable, aromatic, and electrophilic azepinium ions: Design using quantum chemical methods. - Danillo Valverde, Roiney Beal, Paulo Fernando Bruno Gonçalves, Antonio Carlos Borin:
Excited state relaxation mechanisms of paracetamol and acetanilide. - Dayou Zhang, Yinan Shu, Donald G. Truhlar:
DC24: A new density coherence functional for multiconfiguration density-coherence functional theory. - Carlos Vital dos Santos Júnior, Elfi Kraka, Renaldo T. Moura Jr.:
Chemical Bond Overlap Descriptors From Multiconfiguration Wavefunctions. - Kai Wang, Shuai Xu, Yan Zhang:
Unveiling the Antiferromagnetic Properties of Cr2Pbn (n = 3-20) Clusters.
Software note
- Semen O. Yesylevskyy:
MolAR: Memory-Safe Library for Analysis of MD Simulations Written in Rust.
Research Article
- Mohamed Boubchir, Zeyneb Bordjiba, Rabie Amraoui, Rachid Boubchir, Hafid Aourag:
A First-Principle Study Investigating the Half-Metallic and Mechanical Properties of Double Halide Perovskites Rb2OsX6 (X = cl, Br, and I) for Spintronic Applications. - Suranjan Shil:
Assessment of DFT Functionals for Predicting the Magnetic Exchange Coupling Constants of Nonalternant Hydrocarbon Diradicals: The Role of Hartree-Fock Exchange. - Rayene Gara, Ángel Morales-García, Youssef Arfaoui, Francesc Illas:
Density Functional Theory (DFT) and Time-Dependent DFT (TDDFT) Studies of Porphyrin Adsorption on Graphene: Insights on the Effect of Substituents and Central Metal on Adsorption Energies. - Ozlen Balta, Ercument Yilmaz, Gizem Tatar Yilmaz:
Exploring Inhibition Mechanisms in Wildtype and T315I BCR-ABL1: An In Silico Approach Integrating Virtual Screening, MD Simulations, and MM-GBSA Analysis. - Bhrigu Chakraborty, Pratim Kumar Chattaraj:
Exploring the Possibility of a Planar Tetracoordinate Boron in BXY3 (X = B, Al, Ga; Y = C, Si, Ge) Clusters: A Theoretical Study. - Airan F. S. Brito, Adélia J. A. Aquino, José Roberto dos Santos Politi, João B. L. Martins:
Infrared Spectroscopy of Ethanethiol Monomers and Dimers at MP2 Level: Characterizing the Dimer Formation and Hydrogen Bond. - Rui Lai, Hui Li:
Mechanism of Ampicillin Hydrolysis by New Delhi Metallo-β-Lactamase 1: Insight From QM/MM MP2 Calculation. - Shuang Meng, Wenhui Li, Jia Zhou:
Single-Walled ZnSe Nanotubes for High-Performance Photodetectors: A Computational Prediction. - Yuheng Luo, Komal Yadav, Ralf Kaiser, Rui Sun:
Theoretical Study of the Subsequent Decomposition Mechanisms of 1,1-Diamino-2,2-dinitroethene (FOX-7). - Sebastian Ovalle, Cecile Malardier-Jugroot:
Modulating the oxygen affinity of porphyrins with metals, ligands, and functional groups: A DFT study. - Vinay Priy Mishra, Yogendra Narain Singh, Feroz Khan, Malay Kishore Dutta:
SeqDPI: A 1D-CNN approach for predicting binding affinity of kinase inhibitors. - Lipika Oopkaew, Yuwanda Injongkol, Nawee Kungwan, Thanyada Rungrotmongkol:
Theoretical investigation of structure and electronic properties in Cisplatin-citrate complexes. - Qing Fan, Yingxu Liu, Simeng Zhang, Xiangzhen Ning, Chengcheng Xu, Weijie Han, Yanmin Zhang, Yadong Chen, Jun Shen, Haichun Liu:
CGPDTA: An Explainable Transfer Learning-Based Predictor With Molecule Substructure Graph for Drug-Target Binding Affinity. - Michal Janecek, Petra Kührová, Vojtech Mlýnský, Petr Stadlbauer, Michal Otyepka, Giovanni Bussi, Jirí Sponer, Pavel Banás:
Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space. - Simon Ghysbrecht, Luca Donati, Bettina G. Keller:
Accuracy of Reaction Coordinate Based Rate Theories for Modelling Chemical Reactions: Insights From the Thermal Isomerization in Retinal. - Pauline Colinet, Frank Neese, Benjamin Helmich-Paris:
Improving the Efficiency of Electrostatic Embedding Using the Fast Multipole Method. - Jonathan W. Zheng, Emad Al Ibrahim, Ivari Kaljurand, Ivo Leito, William H. Green Jr.:
pKa prediction in non-aqueous solvents. - Anna V. Pomogaeva, Anna S. Lisovenko, Alexey Y. Timoshkin:
The Influence of the Solvation on the Bonding of Molecular Complexes of Diatomic Halogens With Nitrogen-Containing Donors and Their Stability With Respect to the Heterolytic Halogen-Halogen Bond Splitting. - Ali Al-Jaaidi, Josene M. Toldo, Mario Barbatti:
Ultrafast Dynamics of Diketopyrrolopyrrole Dimers. - Oliver J. Conquest, Yijiao Jiang, Catherine Stampfl:
CoTCNQ as a Catalyst for CO2 Electroreduction: A First Principles r2SCAN Meta-GGA Investigation.
Software note
- Ruichen Liu, Li Wang, Xiangwen Zhang, Guozhu Li:
Groupy: An Open-Source Toolkit for Molecular Simulation and Property Calculation.
Research Article
- Laura Alfonso-Hernandez, Victor M. Freixas, Tammie Gibson, Sergei Tretiak, Sebastian Fernandez Alberti:
Tuning Electronic Relaxation of Nanorings Through Their Interlocking. - Ala'a A. A. Azzam, Jonathan Tennyson, Sergei N. Yurchenko, Tibor Furtenbacher, Attila G. Császár:
MARVEL Analysis of High-Resolution Rovibrational Spectra of 16O13C18O. - Elsa Balduzzi, Wenlu Yin, Jean-Christophe Lambry, Hannu Myllykallio, Alexey Aleksandrov:
Additive CHARMM Force Field for Pterins and Folates. - C. Zachary Palmer, Rebecca A. Firth, Ryan C. Fortenberry:
Computing Accurate & Reliable Rovibrational Spectral Data for Aluminum-Bearing Molecules. - Tommaso Nottoli, Mattia Bondanza, Filippo Lipparini, Benedetta Mennucci:
A Polarizable CASSCF/MM Approach Using the Interface Between OpenMMPol Library and Cfour. - Liam Jemison, Matthew Stahl, Ranjan K. Dash, Dexuan Xie:
VDAC Solvation Free Energy Calculation by a Nonuniform Size Modified Poisson-Boltzmann Ion Channel Model. - Junaid Khan, Matiullah Khan, Tanvi Sharma, Imed Boukhris, M. S. Al-Buriahi:
Advanced Computational Insights Into Cs₂NaScX₆ (X = Cl, Br) ₆ Double Perovskites: Structural Stability, Elastic Properties, and Optical Characteristics for Next-Generation Photovoltaics. - Taro Udagawa, Yusuke Kanematsu, Takayoshi Ishimoto, Masanori Tachikawa:
Comprehensive Analysis of Deuterium Isotope Effects on Ionic H3O+...π Interactions Using Multi-Component Quantum Mechanics Methods. - Vladimir Fishman, Emmanouil Semidalas, Margarita Shepelenko, Jan M. L. Martin:
Does Basis Set Superposition Error Significantly Affect Post-CCSD(T) Corrections? - Umut Ozuguzel, Serzat Safaltin, S. Pamir Alpay, Kenda Alkadry, Reed Nieman, Carol Korzeniewski, Adélia J. A. Aquino:
Influence of Ligand Complexity on the Spectroscopic Properties of Type 1 Copper Sites: A Theoretical Study. - Debojyoti Das, Debdutta Chakraborty:
Machine Learning Prediction of Physicochemical Properties in Lithium-Ion Battery Electrolytes With Active Learning Applied to Graph Neural Networks. - Kevin Curtis, Samuel O. Odoh:
Machine Learning-Corrected Simplified Time-Dependent DFT for Systems With Inverted Single-t-o-Triplet Gaps of Interest for Photocatalytic Water Splitting. - Marek Freindorf, Elfi Kraka:
A Closer Look at the FeS Heme Bonds in Azotobacter vinelandii Bacterioferritin: QM/MM and Local Mode Analysis. - Vaibhav Khanna, Bikash Kanungo, Vikram Gavini, Ambuj Tewari, Paul M. Zimmerman:
Examining the Impact of Local Constraint Violations on Energy Computations in DFT. - João Gabriel Farias Romeu, Fernando R. Ornellas:
Thermodynamic Stability in Transition Metal-Hydrogen Dications: Potential Energy Curves, Spectroscopic Parameters, and Bonding for VH2+. - Bharti Dehariya, Mini Bharati Ahirwar, Ayush Shivhare, Milind M. Deshmukh:
Appraisal of the Fragments-In-Fragments Method for the Energetics of Individual Hydrogen Bonds in Molecular Crystals. - Thomas Hehre, Philip E. Klunzinger, Bernard Deppmeier, William Ohlinger, Warren Hehre:
Practical Machine Learning Strategies. I. Correcting the MMFF Molecular Mechanics Model to More Accurately Provide Conformational Energy Differences in Flexible Organic Molecules.
Volume 46, Number 2, 2025
Research Article
- Powsali Ghosh, Ashok Kumar, Sushil Kumar Singh:
COX-2 Inhibitor Prediction With KNIME: A Codeless Automated Machine Learning-Based Virtual Screening Workflow. - Gustavo Gomes de Sousa, João B. L. Martins, José Roberto dos Santos Politi:
Exploring Mechanism and Kinetics of 1,4-Dioxane Oxidative Degradation by OH Radical: A Computational Quantum Chemistry Investigation. - Bartosz Ciborowski, Morgane Vacher:
Photodissociation of Cr(CO) 4 bpy $$ \mathrm{Cr}{\left(\mathrm{CO}\right)}_4\mathrm{bpy} $$ : A Non-Adiabatic Dynamics Investigation. - Kunal Bhattacharya, Atanu Bhattacharjee, Manodeep Chakraborty, Dibyajyoti Das, Keshav Raj Paudel:
From Antipsychotic to Neuroprotective: Computational Repurposing of Fluspirilene as a Potential PDE5 Inhibitor for Alzheimer's Disease. - Renato D. Cunha, S. Romero-Téllez, Filippo Lipparini, F. Javier Luque, Carles Curutchet:
Extending the MST Model to Large Biomolecular Systems: Parametrization of the ddCOSMO-MST Continuum Solvation Model.
Software note
- Moisés Domínguez, Verónica A. Jiménez, Gökcen Savasci, Rocío Araya-Osorio, Janne Pesonen, Raúl Mera-Adasme:
goChem: A Composable Library for Multi-Scale Computational Chemistry Data Analysis.
Research Article
- Raoul Carfora, Federico Coppola, Paola Cimino, Alessio Petrone, Nadia Rega:
A Cost-Effective Computational Strategy for the Electronic Layout Characterization of a Second Generation Light-Driven Molecular Rotary Motor in Solution. - Thierry Tran, Graham A. Worth, Michael A. Robb:
Coherent Excitation of the CH Stretching Vibrations in C2H4+: The Role of the Derivative Coupling Studied by the Quantum Ehrenfest Method. - Oleksandr Gurbych, Petro Pavliuk, Dmytro Krasnienkov, Oleksandr Liashuk, Kostiantyn Melnykov, Oleksandr O. Grygorenko:
Filling the Gap in LogP $$ LogP $$ and pK a $$ {pK}_a $$ Evaluation for Saturated Fluorine-Containing Derivatives With Machine Learning. - A. Karolyna M. S. Gomes, Ricardo R. Oliveira, Thiago M. Cardozo, Felipe Fantuzzi:
Linear or Cyclic? Theoretical Investigation of Astrophysically Relevant Magnesium-Bearing MgCnH Carbon Chains and Related Isomers. - Lucca Blois, Renaldo T. Moura Jr., Ricardo L. Longo, Oscar L. Malta, Hermi F. Brito, Albano N. Carneiro Neto:
Assessment of DFT Functionals for Structural Determination of Lanthanide(III) Complexes Using Ligand Field Splitting. - Marcin Mazdziarz:
Suitability of Available Interatomic Potentials for Sn to Model Its 2D Allotropes. - Donghui Li, Faiza Fayyaz, Wensheng Bian:
A Theoretical Study on Crossings Among Electronically Excited States and Laser Cooling of Group VIA (S, Se, and Te) Hydrides.
Volume 46, Number 3, 2025
Research Article
- Guillermo Goode-Romero, Laura Dominguez:
Scaled and Weighted Laplacian Matrices as Functional Descriptors for GPCR Ligands. - Luan G. F. dos Santos, Julio C. V. Chagas, Luiz F. A. Ferrão, Adélia J. A. Aquino, Reed Nieman, Hans Lischka, Francisco B. C. Machado:
Tuning Aromaticity, Stability and Radicaloid Character of Periacenes by Chemical BN Doping. - Alexander Waigum, Sarah Suchaneck, Andreas Köhn:
Simplified Multireference Coupled-Cluster Methods: Hybrid Approaches With Averaged Coupled Pair Theories. - Weiting Ye, Jingcheng Li, Xianfa Cai:
Mfgnn: Multi-Scale Feature-Attentive Graph Neural Networks for Molecular Property Prediction. - Mauricio Guerrero-Montero, Michal Bosy, Christopher D. Cooper:
Some Challenges of Diffused Interfaces in Implicit-Solvent Models. - Joshua Pandian, Khanh Vu, Jules Tshishimbi Muya, Anna Parker, Christine Mae F. Ancajas, Diomedes Saldana-Greco, Tabitha Yewer, Carol A. Parish:
A Highly Correlated, Multireference Study of the Lowest Lying Singlet and Triplet States of the Four Thiophene Diradicals. - Weina Zhao, Chang Shen, Anil Kumar Tummanapelli, Ming Wah Wong:
Computational Insights Into Corrosion Inhibition Mechanism: Dissociation of Imidazole on Iron Surface. - Aboulfazl Soufi, Sadegh Salehzadeh:
The Degree and Origin of the Cooperativity of the Chalcogen (Ch···N) and Dihydrogen (H···H) Bonds in Some Triad Systems.
Software note
- Masato Sumita, Kei Terayama, Shoichi Ishida, Kensuke Suga, Shohei Saito, Koji Tsuda:
Qcforever2: Advanced Automation of Quantum Chemistry Computations.
Research Article
- Jonas Bentrup, Rahel Weiß, Felix Zeller, Tim Neudecker:
Achieving Pressure Consistency in Mechanochemical Simulations of Chemical Reactions Under Pressure. - Andrea Nedelníková, Petr Stadlbauer, Michal Otyepka, Petra Kührová, Markéta Paloncýová:
Atomistic Insights Into Interaction of Doxorubicin With DNA: From Duplex to Nucleosome. - Gabriel H. L. Munguba, Mateus F. da Silva, Frederico T. Silva, Gabriel A. Urquiza-Carvalho, Alfredo M. Simas:
Decision Trees for the Recognition of Metal-Centered Chirality in Coordination Complexes. - Arpan Choudhury, Debashree Ghosh:
Hybrid Unsupervised/Supervised Machine Learning for Identifying Molecular Structural Fingerprints From Ensemble Property.
Software note
- Denis V. Petrovskiy, Kirill S. Nikolsky, Liudmila I. Kulikova, Vladimir R. Rudnev, Tatyana V. Butkova, Kristina A. Malsagova, Valeriya I. Nakhod, Arthur T. Kopylov, Anna L. Kaysheva:
PSSKB: A Web Application to Study Protein Structures.
Research Article
- Sourav Majumdar, Robin Grotjahn, Ahmadreza Rajabi, Bibo Feng, Luke Nambi Mohanam, Gabriel S. Phun, Nicolas Lutfi, Mohammad Khan, Dmitrij Rappoport, Filipp Furche:
Mechanism of the Non-Kasha Fluorescence in Pyrene. - Daniel Tunega, Martin H. Gerzabek, Leonard Böhm:
Theoretical Study on Adsorption of Halogenated Benzenes on Montmorillonites Modified With M(I)/M(II) Cations. - Jonathan M. Waldrop, Ajay Panyala, Daniel Mejia-Rodriguez, Theresa L. Windus, Niranjan Govind:
Projector-Based Quantum Embedding Study of Iron Complexes.
Volume 46, Number 4, 2025
Short Communication
- Hideo Doi, Tatsuya Nakano, Kota Sakakura, Kazuki Akisawa, Koji Okuwaki, Yoshinori Hirano, Eiji Yamamoto, Kenji Yasuoka, Satoshi Ohshima, Takahiro Katagiri, Yuji Mochizuki:
Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model.
Research Article
- Michel V. Heinz, Emma Gorgas, Nicole Maser, Arne Lüchow:
Probability Density Analysis Reveals Substantial Differences Between the Dinitrogen and Acetylene Triple Bonds. - Zoran Glasovac, Davor Margetic, Ivana Antol:
Molecular and Electronic Structure and Properties of the Single Benzene-Based Fluorophores Containing Guanidine Subunit. - Ayokanmi Joseph Aremu, Phiphob Naweephattana, Ismail Dwi Putra, Borwornlak Toopradab, Phornphimon Maitarad, Thanyada Rungrotmongkol:
Rational Design for Antioxidant Diphenylamine Derivatives Using Quantitative Structure-Activity Relationships and Quantum Mechanics Calculations. - Khaled E. El-Kelany, Alexander Platonenko, Klaus Doll, Roberto Dovesi:
The Structural, Electronic and Vibrational Properties of LaCrO 3 $$ {}_3 $$ . A Quantum Mechanical Investigation by Using an All Electron Gaussian Type Basis Set and a Full Range Hybrid Functional. - Goran Giudetti, Shaama Mallikarjun Sharada, Anna I. Krylov:
AIMD-Based Protocols for Modeling Exciplex Fluorescence Spectra and Inter-System Crossing in Photocatalytic Chromophores.
Volume 46, Number 5, 2025
Research Article
- Peter Poliak, Patrick Bleiziffer, Felix Pultar, Sereina Riniker, Chris Oostenbrink:
A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS. - Shichen Lin, Yuuichi Orimoto, Yuriko Aoki:
Elongation Method-Based Alternating Multi-Directional Automated Property Optimization Process and Its Application.
Short Communication
- Lou Massa:
Book Review: "Electron Localization-Delocalization Matrices" by Chérif F. Matta, Paul W. Ayers, and Ronald Cook.
Software note
- D. D. Raenko, Andreì L. Tchougréeff:
Highly Efficient Numerical Method for Modeling Mofs Containing Transition Metal Ions.
Research Article
- Heriberto Cruz-Martínez, Hugo Rojas-Chávez, L. Santiago-Silva, Luis López-Sosa, Patrizia Calaminici:
Metal Dimers-Doped h-BN Structures as Novel Toxic Gases Sensors With Enhanced Sensitivity Properties: An ADFT Study. - Debojyoti Das, Erico S. Teixeira, Jorge Alberto Morales:
Recurrent Neural Network/Machine Learning Predictions of Reactive Channels in H+ + C2H4 at ELab = 30 eV: A Prototype of Ion Cancer Therapy Reactions. - Richard M. Venable, Anthony J. Pane, Amy Rice, Richard W. Pastor:
Effects of a Polarizable Force Field on Membrane Dynamics: Surface Viscosity, Lipid Diffusion, and Peptide Induced Pore Formation.
Software note
- Carsten Kutzner, Vedran Miletic, Karen Palacio Rodríguez, Markus Rampp, Gerhard Hummer, Bert L. de Groot, Helmut Grubmüller:
Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster.
Research Article
- Abir Jendoubi, Mohamed Oussama Zouaghi, Youssef Arfaoui, Frédéric Guégan, Muneerah Mogren Al-Mogren, Majdi Hochlaf:
Mechanistic Study of the Carbonylation of Aziridines to β-Lactams: Alkylation, Solvent and Molecular NaBr and MgO Clusters Catalysts Effects. - Tyler Walker, Quan Van Vuong, Stephan Irle, Jihong Ma:
Evaluation of Density-Functional Tight-Binding Methods for Simulation of Protic Molecular Ion Pairs.
Volume 46, Number 6, 2025
Research Article
- Rui-Ying Liu, Qun-Yan Wu, Cong-Zhi Wang, Jian-Hui Lan, Cheng-Peng Li, Wei-Qun Shi:
Theoretical Insights Into Structures and U-C Bonding in the Uranium Benzyl Derivatives. - Awatef Hattab, Alhadji Malloum, Zoubeida Dhaouadi, Nino Russo:
Structures and Solvation Energies Effects Versus Temperature. An MP2 Investigations in the Framework of Cluster Model.
Short Communication
- Huicong Liang, Aowei Xie, Ning Hou, Fengjiao Wei, Ting Gao, Jiajie Li, Xinru Gao, Chuanqin Shi, Gaokeng Xiao, Ximing Xu:
Increase Docking Score Screening Power by Simple Fusion With CNNscore.
Research Article
- Oceane Mangel, Helene Jamet:
CH Bond Activation Mechanism by a High-Valent Dinuclear Copper Complex: Unraveling the Effect of a Base by a Theoretical Study. - Xu Lu, Wei Hong, Tingyu Liu, Huifang Li, Jianghai Wang:
Mechanistic Study of LIDT Reduction in KH2PO4 With Yi Predicted by Density Functional Theory. - Gerald Geudtner, Andreas M. Köster:
First Principles Global Optimization Method From Parallel Tempering Molecular Dynamics. - Adelaide Jesus, J. R. Lucena Jr., G. P. Rodrigues, G. Ogruc Ildiz, Silmar Andrade do Monte, E. Ventura, R. Fausto:
Infrared Spectrum and UV-Triggered Transformations of Matrix-Isolated Meta-Fluorothiophenol Supported by Ground and Excited State Theoretical Calculations.
Software note
- Rami M. Abdallah:
Extending Chemoinformatics Techniques With JMolecular Energy: A Robust CDK-Based Force Field Library.
Research Article
- Yongquan Jiang, Xin Xie, Yan Yang, Yuerui Liu, Kuanping Gong, Tianrui Li:
Dual-Branch Graph Neural Network for Predicting Molecular Odors and Discovering the Relationship Between Functional Groups and Odors.
Volume 46, Number 7, March 2025
Software note
- Andreas Vitalis, David Parker, Fabian Radler, Pablo A. Vargas-Rosales, Yang Zhang, Jean-Rémy Marchand, Amedeo Caflisch:
Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening.
Research Article
- Kangkan Sarmah, Ankur K. Guha:
Reversible Hydrogen Storage by Planar Hypercoordinate Hydrogen Clusters. - Vinay P. Majety, Armin Scrinzi:
Single- and Three-Photon Ionization of N 2 $$ {N}_2 $$ in Presence of Fano Resonances. - Mirza Wasif Baig, Marek Pederzoli, Mojmír Kývala, Jirí Pittner:
Quantum Chemical and Trajectory Surface Hopping Molecular Dynamics Study of Iodine-Based BODIPY Photosensitizer. - Amirhossein Bakhtiiari, Ruibin Liang:
Unraveling Solvent and Substituent Effects in the Photodynamics of Light-Dependent Microtubule Inhibitors for Cancer Phototherapy. - Ramakrishnan Thushara, Cherumuttathu H. Suresh:
Ladderenes as Covalently Condensed Acetylene: A DFT Investigation of Gold(I)-Catalyzed Mechanism, Substituent Effects and Energy Storage Potential. - Hongsong Feng, Jeffrey Y. Zhao, Guo-Wei Wei:
Multiscale Differential Geometry Learning for Protein Flexibility Analysis. - Shobhna, Ayishwarya Dutta, Hemant K. Kashyap:
Mechanistic Insight on Ethanol Driven Swelling and Disruption of Cholesterol Containing Biomimetic Vesicles From Coarse-Grained Molecular Dynamics.
Volume 46, Number 8, March 2025
Research Article
- Raza Ullah Khan, Ralf Tonner-Zech:
Optimizing Computational Parameters for Nuclear Electronic Orbital Density Functional Theory: A Benchmark Study on Proton Affinities. - Rodolpho L. R. Alves, Ezequiel Fragoso Vieira Leitão, E. Ventura, Silmar Andrade do Monte:
A Genuine Hydrocarbon Ion Pair More Stable Than Its Covalent Counterpart. A Computational Study. - Minghong Jiang, Zhanfeng Wang, Yicheng Chen, Wenhao Zhang, Zhenyu Zhu, Wenjie Yan, Jianming Wu, Xin Xu:
X2-PEC: A Neural Network Model Based on Atomic Pair Energy Corrections. - K. G. Kalamatianos, Olga N. Flenga:
Prediction of Activation Energies of Organic Molecules With at Most Seven Non-Hydrogen Atoms Using Quantum-Chemically Assisted ML. - Yusuke Nanba, Michihisa Koyama:
Physical Significance of Descriptors to Predict the Band Center of High-Entropy Nanoalloys. - Per E. M. Siegbahn:
The Mechanism of Nitrite Reductase.
Editorial
- Adélia J. A. Aquino, Mario Barbatti, Péter G. Szalay, Gernot Frenking:
Foreword to the Special Issue for Hans Lischka.
Research Article
- Rodrigo Mancini Santos, Teodorico C. Ramalho:
Molecular Dynamics-Assisted Interaction Between HABT and PI3K Enzyme: Exploring Metastable States for Promising Cancer Diagnosis Applications. - Felix Plasser:
On the Meaning of De-Excitations in Time-Dependent Density Functional Theory Computations. - Ján Simunek, Jozef Noga:
Is It Worth Running the Hartree-Fock Calculations With Localized Molecular Orbitals Within the Framework of Variational Coupled Cluster Singles Theory? - L. Biancorosso, Emanuele Coccia:
Study of the Photoinduced Charge Injection in the Reaction Intermediate of the Dehydrogenation of Formic Acid on Palladium. - Gideon Odonkor, Samuel O. Odoh:
Impact of Structure on Excitation Energies and S1-T1 Energy Gaps of Asymmetrical Systems of Interest for Inverted Singlet-Triplet Gaps.
Editorial
- Gernot Frenking:
Editorial Note.
Research Article
- Volker Staemmler, Robert Franke:
On the Origin of the Rotational Barrier in Ethane. - W. H. Eugen Schwarz, Gernot Frenking, Sudip Pan:
Clarification of Some Bonding Concepts: Virial Theorem, Electron Pair Repulsion, and Rotational Barriers.
Volume 46, Number 9, April 2025
Research Article
- Lawen Mohammed Rasul, Morteza Rouhani, Zohreh Mirjafary:
Computational Probing of Schleyer's Hyperconjugative Aromaticity in a Novel Designed Anion Acceptor.
Software note
- Mehmet Bozuyla, Alpaslan Bayrakdar, Yusuf Sert, Hasan Huseyin Kart, Sevgi Ozdemir Kart, Prasath Manivannan, Mehmet Hakki Alma:
CCPE: A Tool to Quickly Extract, Format, and Present the Outputs From Gaussian and VEDA Computational Chemistry Programs.
Volume 46, Number 10, April 2025
Research Article
- Ulviyya Askerova, Yusif Abdullayev, Namiq Shikhaliyev, Avtandil Talybov, Jochen Autschbach:
Can Water Trigger Room-Temperature Formation of Benzofuran-2(3H)-one Scaffolds From Vinyldiazene Derivatives? Computational Insights Into an Unusual Cyclization. - Anna M. Weidlich, Andreas Dreuw:
The Relation Between the Excited Electronic States of Acene Radical Cations and Neutrals - A Computational Analysis. - Lina Dong, Pengfei Li, Binju Wang:
Enhancing MM/P(G)BSA Methods: Integration of Formulaic Entropy for Improved Binding Free Energy Calculations. - Agnieszka Kacka-Zych, Abdellah Zeroual, Asad Syed, Ali H. Bahkali:
Docking Survey, ADME, Toxicological Insights, and Mechanistic Exploration of the Diels-Alder Reaction Between Hexachlorocyclopentadiene and Dichloroethylene. - Xihan Li, Kuanping Gong, Yongquan Jiang, Yan Yang, Tianrui Li:
MolRWKV: Conditional Molecular Generation Model Using Local Enhancement and Graph Enhancement. - Tatsuhiro Nakanishi, Takuro Tsutsumi, Yuriko Ono, Kazuki Sada, Tetsuya Taketsugu:
Unraveling Reaction Path Bifurcation: Insights Into Electron Movement via Natural Reaction Orbitals.
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