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GraphEGFR: Multi-task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-07 Bundit Boonyarit, Nattawin Yamprasert, Pawit Kaewnuratchadasorn, Jiramet Kinchakawat, Chanatkran Prommin, Thanyada Rungrotmongkol, Sarana Nutanong
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Front Cover J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-07 Rian Koots, Yu Wang, Marjan Mirahmadi, Jesús Pérez‐Ríos
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Range‐separated density functional theory using multiresolution analysis and quantum computing J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-06 Nicolas Poirier, Jakob S. Kottmann, Alán Aspuru‐Guzik, Luc Mongeau, Alireza Najafi‐Yazdi
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MzDOCK: A free ready‐to‐use GUI‐based pipeline for molecular docking simulations J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-04 Muzammil Kabier, Nicola Gambacorta, Daniela Trisciuzzi, Sunil Kumar, Orazio Nicolotti, Bijo Mathew
Molecular docking is by far the most preferred approach in structure‐based drug design for its effectiveness to predict the scoring and posing of a given bioactive small molecule into the binding site of its pharmacological target. Herein, we present MzDOCK, a new GUI‐based pipeline for Windows operating system, designed with the intent of making molecular docking easier to use and higher reproducible
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Interpretation of molecular electron transport in ab initio many‐electron framework incorporating zero‐point nuclear motion effects J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-04 Dávid P. Jelenfi, Attila Tajti, Péter G. Szalay
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An efficient method by combining different basis sets and SAPT levels J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-04 Zhihao Deng, Chang Liu, Zhongwei Li, Yingsheng Zhang
In symmetry‐adapted perturbation theory (SAPT), accurate calculations on non‐covalent interaction (NCI) for large complexes with more than 50 atoms are time‐consuming using large basis sets. More efficient ones with smaller basis sets usually result in poor prediction in terms of dispersion and overall energies. In this study, we propose two composite methods with baseline calculated at SAPT2/aug‐cc‐pVDZ
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The Nobel history of computational chemistry. A personal perspective J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-03 Russell J. Boyd
1 INTRODUCTION This article presents a personal view of selected Nobel Prizes in Chemistry. It is neither a comprehensive account of the science for which the Prizes were awarded, nor does it offer complete biographies of a remarkable group of scientists. It attempts to show the links between the prizes and chronicles the author's contacts with leading scientists over a span of almost six decades.
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Extended N‐centered ensemble density functional theory of double electronic excitations J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-03 Filip Cernatic, Emmanuel Fromager
A recent work (arXiv:2401.04685) has merged N‐centered ensembles of neutral and charged electronic ground states with ensembles of neutral ground and excited states, thus providing a general and in‐principle exact (so‐called extended N‐centered) ensemble density functional theory of neutral and charged electronic excitations. This formalism made it possible to revisit the concept of density‐functional
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Deep reinforcement learning in chemistry: A review J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-03 Bhuvanesh Sridharan, Animesh Sinha, Jai Bardhan, Rohit Modee, Masahiro Ehara, U. Deva Priyakumar
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Systematic improvement of empirical energy functions in the era of machine learning J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-02 Mike Devereux, Eric D. Boittier, Markus Meuwly
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Expanding chalcogen bonds in thiophenes to interactions with halogens J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-02 Bruna R. Ferreira, Francisco A. Martins, Matheus P. Freitas
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Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-30 Yuya Nakajima, Takuto Ohmura, Junji Seino
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Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-29 Ruiqin Xu, Zhongming Jiang, Qin Yang, Julien Bloino, Malgorzata Biczysko
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Machine learning for accuracy in density functional approximations J. Comput. Chem. (IF 3.0) Pub Date : 2024-04-26 Johannes Voss
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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
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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
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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
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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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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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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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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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Hydrolysis mechanism of the cyclohexaborate anion: Unraveling the intricacies J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-12 Lifan Jia, Yunxia Wang, Lulu Song, Ruirui Liu, Longgang Li, Jisheng Li, Yongquan Zhou, Jianmin Pan, Fayan Zhu
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RISMiCal: A software package to perform fast RISM/3D-RISM calculations J. Comput. Chem. (IF 3.0) Pub Date : 2024-03-12 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 : 2024-03-12 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 : 2024-03-08 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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