Literature DB >> 32470306

NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions.

Roberto Álvarez Boto, Francesca Peccati, Rubén Laplaza, Chaoyu Quan, Alessandra Carbone, Jean-Philip Piquemal, Yvon Maday, Julia Contreras-Garcia.   

Abstract

The NonCovalent Interaction index (NCI) enables to identify attractive and repulsive noncovalent interactions from promolecular densities in a fast manner. However, the approach remained up to now qualitative, only providing visual information. We present a new version of NCIPLOT, NCIPLOT4, which allows quantifying the properties of the NCI regions (volume, charge) in small and big systems in a fast manner. Examples are provided of how this new twist enables to characterize and retrieve local information in supramolecular chemistry and biosystems at the static and dynamic level.

Year:  2020        PMID： 32470306     DOI： 10.1021/acs.jctc.0c00063

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN： 1549-9618            Impact factor:   6.006


  15 in total

1.  Understanding the reaction mechanism of the CO2 and cyclohexene oxide copolymerization catalyzed by zinc(II) and magnesium(II) catalysts: a DFT approach.

Authors:  Lucas W de Lima; Sara Figueirêdo de Alcântara Morais; Ataualpa A C Braga
Journal:  J Mol Model       Date:  2022-09-14       Impact factor: 2.172

2.  Ammonia quantum tunneling in cold rare-gas He and Ar clusters and factorial design approach for methodology evaluation.

Authors:  Caio M Porto; Gabriel de A Barros; Lucas C Santana; Ana C Moralles; Nelson H Morgon
Journal:  J Mol Model       Date:  2022-09-05       Impact factor: 2.172

3.  Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase.

Authors:  Sehr Naseem-Khan; Madison B Berger; Emmett M Leddin; Yazdan Maghsoud; G Andrés Cisneros
Journal:  J Chem Inf Model       Date:  2022-04-18       Impact factor: 6.162

4.  Focal Point Evaluation of Energies for Tautomers and Isomers for 3-Hydroxy-2-Butenamide: Evaluation of Competing Internal Hydrogen Bonds of Types -OH…O=, -OH…N, -NH…O=, and CH…X (X=O and N).

Authors:  Zikri Altun; Erdi Ata Bleda; Carl Trindle
Journal:  Molecules       Date:  2021-04-30       Impact factor: 4.411

5.  Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population.

Authors:  Yudibeth Sixto-López; José Correa-Basurto; Martiniano Bello; Bruno Landeros-Rivera; Jose Antonio Garzón-Tiznado; Sarita Montaño
Journal:  Sci Rep       Date:  2021-02-25       Impact factor: 4.379

6.  An Androsterone-H2 @C60 hybrid: Synthesis, Properties and Molecular Docking Simulations with SARS-Cov-2.

Authors:  Margarita Suárez; Kamil Makowski; Reinier Lemos; Luis Almagro; Hortensia Rodríguez; María Ángeles Herranz; Dolores Molero; Orlando Ortiz; Enrique Maroto; Fernando Albericio; Yasujiro Murata; Nazario Martín
Journal:  Chempluschem       Date:  2021-02-04       Impact factor: 3.210

7.  A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers.

Authors:  Rafael E O Rocha; Elton J F Chaves; Pedro H C Fischer; Leon S C Costa; Igor Barden Grillo; Luiz E G da Cruz; Fabiana C Guedes; Carlos H da Silveira; Marcus T Scotti; Alex D Camargo; Karina S Machado; Adriano V Werhli; Rafaela S Ferreira; Gerd B Rocha; Leonardo H F de Lima
Journal:  J Biomol Struct Dyn       Date:  2021-05-10

8.  Atomistic fibrillar architectures of polar prion-inspired heptapeptides.

Authors:  Francesca Peccati; Marta Díaz-Caballero; Susanna Navarro; Luis Rodríguez-Santiago; Salvador Ventura; Mariona Sodupe
Journal:  Chem Sci       Date:  2020-11-02       Impact factor: 9.825

Review 9.  Computational Tools to Rationalize and Predict the Self-Assembly Behavior of Supramolecular Gels.

Authors:  Ruben Van Lommel; Wim M De Borggraeve; Frank De Proft; Mercedes Alonso
Journal:  Gels       Date:  2021-07-09

10.  Computational Investigation on the Origin of Atroposelectivity for the Cinchona Alkaloid Primary Amine-Catalyzed Vinylogous Desymmetrization of N-(2-t-Butylphenyl)maleimides.

Authors:  Nicolò Tampellini; Paolo Righi; Giorgio Bencivenni
Journal:  J Org Chem       Date:  2021-08-04       Impact factor: 4.354
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