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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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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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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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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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Front Cover J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-12 Andreas J. Achazi, Xhesilda Fataj, Philip Rohland, Martin D. Hager, Ulrich S. Schubert, Doreen Mollenhauer
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Quantum mechanical study of transition metal hydrides: Comparison of determined molecular properties with experimental data J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-10 Adam Vavrečka, Kateřina Fatková, Jaroslav V. Burda
This study compares results of four relativistic pseudopotential basis sets, which differ mainly by their size: double‐zeta introduced by Hay and Wadt from Los Alamos National Laboratory (LANL2DZ), triple‐zeta based on Stuttgart energy‐consistent scalar‐relativistic pseudopotential (SDD3), its extension with 2fg polarization functions, and combination of Stuttgart pseudopotentials with quintuple‐zeta
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Expanding horizons in conceptual density functional theory: Novel ensembles and descriptors to decipher reactivity patterns J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-05 Guillaume Hoffmann, Frédéric Guégan, Vanessa Labet, Laurent Joubert, Henry Chermette, Christophe Morell, Vincent Tognetti
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Discovering trends in the Lewis acidity of beryllium and magnesium hydrides and fluorides with increasing clusters size J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-03 Otilia Mó, M. Merced Montero‐Campillo, Manuel Yáñez, Ibon Alkorta, José Elguero
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Investigating the interplay between charge transfer and CO2 insertion in the adsorption of a NiFe catalyst for CO2 electroreduction on a graphite support through DFT computational approaches J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-02 Subash Arjunan, Joshua M. Sims, Carole Duboc, Pascale Maldivi, Anne Milet
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Machine-learning descriptor search on the density of states profile of bimetallic alloy systems and comparison with the d-band center theory J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-29 Atsushi Ishikawa
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How do spin‐scaled double hybrids designed for excitation energies perform for noncovalent excited‐state interactions? An investigation on aromatic excimer models J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-30 Amy C. Hancock, Erica Giudici, Lars Goerigk
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Active‐learning for global optimization of Ni‐Ceria nanoparticles: The case of Ce4−xNixO8−x (x = 1, 2, 3) J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-29 Lizandra Barrios Herrera, Maicon Pierre Lourenço, Jiří Hostaš, Patrizia Calaminici, Andreas M. Köster, Alain Tchagang, Dennis R. Salahub
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Dichroism of plasmonic chiral nanoalloys by rational design J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-29 Pierpaolo D'Antoni, Daniele Toffoli, Giovanna Fronzoni, Mauro Stener, Luca Sementa, Alessandro Fortunelli
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Foreword to the special issue for Elfi Kraka J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-28 Adelia Aquino, Hans Lischka, Gernot Frenking
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Synergistic regulation of chloride anion recognition using a triple‐functional sites receptor with two different cationic effectors J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-28 Qingqing Yao, Kun Yuan, Mengyang Li, Yaoxiao Zhao, Yanzhi Liu, Xiang Zhao
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Investigating proton tunneling dynamics in the time‐dependent Schrödinger equation J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-25 Luca Nanni
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A theoretical investigation of benzothiadiazole derivatives for high efficiency OLEDs J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-23 Zhiye Zhu, Xiaoqing Wei, Wanzhen Liang
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Opto‐electronic and thermophysical characteristics of A2TlAgF6 (A = Rb, Cs) for green technology applications J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-22 Samah Al‐Qaisi, Nazia Iram, Saidi Samah, Afaf Khadr Alqorashi, A. I. Aljameel, Tahani A. Alrebdi, Zeesham Abbas, S. Bouzgarrou, Md. Ferdous Rahman, Ajay Singh Verma
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A new chapter in the never ending story of cycloadditions: The puzzling case of SO2 and acetylene J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-22 Zoi Salta, Oscar N. Ventura, Nadjib Rais, Nicola Tasinato, Vincenzo Barone
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Modeling solvent effects and convergence of 31P‐NMR shielding calculations with COBRAMM J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-22 Francesco Calcagno, Boris Maryasin, Marco Garavelli, Davide Avagliano, Ivan Rivalta
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Front Cover J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-21 Ronit Sarangi, Kaushik D. Nanda, Anna I. Krylov
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Synergy of machine learning and density functional theory calculations for predicting experimental Lewis base affinity and Lewis polybase binding atoms J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-19 Hieu Huynh, Khanh Le, Linh Vu, Trang Nguyen, Matthew Holcomb, Stefano Forli, Hung Phan
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Py3BR: A software for computing atomic three-body recombination rates J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-14 Rian Koots, Yu Wang, Marjan Mirahmadi, Jesús Pérez-Ríos
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Simulation study on functional group-modified Ni-MOF-74 for CH4/N2 adsorption separation J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-14 Yueyang Zhang, Gaofeng Hu, Xueting Gao, Zhuxia Zhang, Peng Cui
This study employs grand canonical Monte Carlo (GCMC) simulations to investigate the impact of functional group modifications (CH3, OH, NH2, and OLi) on the adsorption performance of CH4/N2 on Ni-MOF-74. The results revealed that functional group modifications significantly increased the adsorption capacity of Ni-MOF-74 for both CH4 and N2. The packed methyl groups in CH3-Ni-MOF-74 create an environment
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Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-16 Dmitri G. Fedorov
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Explainable artificial intelligence in the design of selective carbonic anhydrase I‐II inhibitors via molecular fingerprinting J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-16 Kevser Kübra Kırboğa, Mesut Işık
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Hydrolysis mechanism of the cyclohexaborate anion: Unraveling the intricacies J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-13 Lifan Jia, Yunxia Wang, Lulu Song, Ruirui Liu, Longgang Li, Jisheng Li, Yongquan Zhou, Jianmin Pan, Fayan Zhu
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β‐sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-13 Sian Xiao, Mayar Tarek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
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RISMiCal: A software package to perform fast RISM/3D‐RISM calculations J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-13 Yutaka Maruyama, Norio Yoshida
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Resolving coupled pH titrations using alchemical free energy calculations J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-13 Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys
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Predicting the propene stereoselectivity on transition metal catalysts: A daunting task for density functional theory J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-12 Olga D'Anania, Eugenio Romano, Vincenzo Barone, Giovanni Talarico
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β‐D‐Glucopyranose—silver+ (1:1) complex as a small gas molecule scavenger J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-09 Sukanta Mondal
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On the performance of composite schemes in determining equilibrium molecular structures J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-07 Nitai P. Sahoo, Peter R. Franke, John F. Stanton
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Study of absorption and emission spectra of substituted terthiophene compounds by methods of theoretical chemistry J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-04 Tomáš Kužela, Dmitrij Bondarev, Eva Kutálková, Zuzana Benková, Josef Hrnčiřík, Marek Ingr
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Thermal isomerization rates in retinal analogues using Ab‐Initio molecular dynamics J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-28 Simon Ghysbrecht, Bettina G. Keller
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Machine learning assisted analysis of equivalent circuit usage in electrochemical impedance spectroscopy applications J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-26 Carl Philipp Klemm, Till Frömling
Electrical equivalent circuits are a widely applied tool with which electrical processes can be rationalized. There is a wide‐ranging selection of fields from bioelectrochemistry to batteries to fuel cells making use of this tool. Enabling meta‐analysis on the similarities and differences in the used circuits will help to identify commonly used circuits and aid in evaluating the underlying physics
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Development of a bottom‐up coarse‐grained model for interactions of lipids with TiO2$$ {}_2 $$ nanoparticles J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-21 Mikhail Ivanov, Alexander P. Lyubartsev
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Potential energy surfaces and dynamic properties via ab initio composite and density functional approaches J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-20 Prajay Patel, Joseph Chung, Max Aksel Bowman, Inga Ulusoy, Angela K. Wilson
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An enantioselective study of β‐cyclodextrin and ionic liquid‐β‐cyclodextrin towards propranolol enantiomers by molecular dynamic simulations J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-19 Mohamad Adil Iman Ishak, Tan Tiek Aun, Nadiah Sidek, Sharifah Mohamad, Khairulazhar Jumbri, Ninie Suhana Abdul Manan
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Chalcogen atom effect on the intersystem crossing kinetic constant of oxygen- and sulfur disubstituted heteroporphyrins J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-16 Wichien Sang-aroon, Marta Erminia Alberto, Marirosa Toscano, Nino Russo
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Pnictogen bond-driven control of the molecular interaction between organophosphorus and acetylcholinesterase enzyme J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-16 Gustavo A. Andolpho, Teodorico C. Ramalho
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Reinforcement learning for in silico determination of adsorbate—substrate structures J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-15 Maicon Pierre Lourenço, Jiří Hostaš, Colin Bellinger, Alain Tchagang, Dennis R. Salahub
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Quantum cluster equilibrium theory applied to liquid ammonia J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-14 Josué Maya, Alhadji Malloum, Jean Jules Fifen, Zoubeida Dhaouadi, Henri Paul Ekobena Fouda, Jeanet Conradie
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“On-the-fly” Crystal: How to reliably and automatically characterize and construct potential energy surfaces J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-14 Mahdi Aarabi, Ankit Pandey, Bill Poirier
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On the antibacterial photodynamic inactivation mechanism of Emodin and Dermocybin natural photosensitizers: A theoretical investigation J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-13 Alessandra Gilda Ritacca, Mario Prejanò, Marta Erminia Alberto, Tiziana Marino, Marirosa Toscano, Nino Russo
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A density-fitting implementation of the density-based basis-set correction method J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-13 Andreas Heßelmann, Emmanuel Giner, Peter Reinhardt, Peter J. Knowles, Hans-Joachim Werner, Julien Toulouse
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FFLUX molecular simulations driven by atomic Gaussian process regression models J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-12 Yulian T. Manchev, Paul L. A. Popelier
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PyRETIS 3: Conquering rare and slow events without boundaries J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-12 Wouter Vervust, Daniel T. Zhang, An Ghysels, Sander Roet, Titus S. van Erp, Enrico Riccardi
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Front Cover J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-09 Satoi Wada, Takuro Tsutsumi, Kenichiro Saita, Tetsuya Taketsugu
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Theoretical prediction of closed-shell paramagnetism for scandium and yttrium hydride J. Comput. Chem. (IF 3.0) Pub Date : 2024-02-09 Laura Grazioli, Luca T. Schleicher, Stella Stopkowicz, Jürgen Gauss