How to Compute Atomistic Insight in DFT Clusters: The REG-IQA Approach DOI Creative Commons
Fabio Falcioni, Paul L. A. Popelier

Journal of Chemical Information and Modeling, Год журнала: 2023, Номер 63(14), С. 4312 - 4327

Опубликована: Июль 10, 2023

The relative energy gradient (REG) method is paired with the topological partitioning interacting quantum atoms (IQA), as REG-IQA, to provide detailed and unbiased knowledge on intra- interatomic interactions. REG operates a sequence of geometries representing dynamical change system. Its recent application peptide hydrolysis human immunodeficiency virus-1 (HIV-1) protease (PDB code: 4HVP) has demonstrated its full potential in recovering reaction mechanisms through-space electrostatic exchange–correlation effects, making it compelling tool for analyzing enzymatic reactions. In this study, computational efficiency REG-IQA 133-atom HIV-1 mechanical system analyzed every detail substantially improved by means three different approaches. first approach smaller integration grids IQA integrations reduces overhead about factor 3. second uses line-simplification Ramer–Douglas–Peucker (RDP) algorithm, which outputs minimal number necessary analysis predetermined root mean squared error (RMSE) tolerance. This cuts time whole 2 if an RMSE 0.5 kJ/mol considered. third consists “biased” or “unbiased” selection specific subset initial model wave-function, results more than 10-fold speed-up per geometry calculation, without deterioration outcome analysis. Finally, show capability these approaches, findings gathered from are also applied named haloalcohol dehalogenase (HheC). summary, study takes computationally feasible highly accurate level, viable multitude systems.

Язык: Английский

Hydrogen vs Halogen-Bonded R22(8) Rings in Organic Crystal Structures DOI Creative Commons
Catharine Esterhuysen

Crystal Growth & Design, Год журнала: 2023, Номер 24(2), С. 859 - 870

Опубликована: Дек. 26, 2023

Hydantoins and halohydantoins are five-membered heterocyclic rings where the N–X (X = H, Cl, Br, I) units exhibit similar geometries, such that they should form analogous hydrogen or halogen bond geometries. However, although an R22(8) hydrogen-bonded ring interacting through amide moieties is most common supramolecular synthon for hydantoins published in Cambridge Structural Database (CSD), only one halohydantoin crystal structure exhibits a halogen-bonded motif. Analysis of structures CSD density functional theory calculations show origin this difference not relative strengths vs bonding, as latter typically stronger, greater directionality but rather presence close, repulsive X···X contacts rings.

Язык: Английский

Процитировано

2
Fluorine as a Lewis acid: A symmetry‐adapted perturbation theory based on density functional theory and interacting quantum atoms study of noncovalent interactions in the NCF⋯NH3 complex DOI
Nasim Orangi, Kiamars Eskandari

Journal of Computational Chemistry, Год журнала: 2020, Номер 41(17), С. 1598 - 1605

Опубликована: Апрель 19, 2020

Abstract Different computational methods are used to investigate the nature of interaction in NCF⋯NH 3 model complex, which fluorine atom acts as a Lewis acid and forms noncovalent bond with ammonia (Lewis base). Symmetry‐adapted perturbation theory based on density functional (SAPT(DFT)) indicates that complex is mainly electrostatics. However, dispersion induction terms also play important roles. Although interactions typically classified halogen bonds, they somewhat different from well‐known bonds iodine, bromine, chlorine. The NCCl⋯NH NCBr⋯NH directional C  X N (X = Cl or Br) angle tends be linear. In contrast, not directional; energy shows no sensitivity angular ( F ) distortions, profile flat over wide range (from 180° about 140° ). for angles less than 130° , curve clear dependence between NCF NH becomes stronger decreases. It seems at tighter angles, tetrel‐bonded preferred. Moreover, interacting quantum atoms (IQA) analysis competition intra‐atomic interatomic determines geometry complex.

Язык: Английский

Процитировано

5
A relative energy gradient (REG) study of the nitrogen inversion in N-substituted aziridines DOI
Ibón Alkorta, José Elguero, Paul L. A. Popelier

и другие.

Chemical Physics Letters, Год журнала: 2020, Номер 758, С. 137927 - 137927

Опубликована: Авг. 26, 2020

Язык: Английский

Процитировано

5
Implementation of the interacting quantum atom energy decomposition using the CASPT2 method DOI
Jesús Jara‐Cortés, Edith Leal-Sánchez, E. Francisco

и другие.

Physical Chemistry Chemical Physics, Год журнала: 2021, Номер 23(48), С. 27508 - 27519

Опубликована: Янв. 1, 2021

We present an implementation of the interacting quantum atom (IQA) energy decomposition scheme using complete active space second-order perturbation theory (CASPT2). This combination yields a real-space interpretation tool with proper account static and dynamic correlation that is particularly relevant for description processes in electronic excited states. The IQA/CASPT2 approach allows determination redistribution takes place along photophysical/photochemical deactivation path terms self- interatomic contributions. applicability method illustrated by representative spanning different bonding regimes: noble gas excimer exciplex formation, reaction ozone chlorine atom, photodissociations formaldehyde cyclobutane. These examples show versatility CASPT2 significant information provided IQA partition to describe chemical large multiconfigurational character.

Язык: Английский

Процитировано

5
How to Compute Atomistic Insight in DFT Clusters: The REG-IQA Approach DOI Creative Commons
Fabio Falcioni, Paul L. A. Popelier

Journal of Chemical Information and Modeling, Год журнала: 2023, Номер 63(14), С. 4312 - 4327

Опубликована: Июль 10, 2023

The relative energy gradient (REG) method is paired with the topological partitioning interacting quantum atoms (IQA), as REG-IQA, to provide detailed and unbiased knowledge on intra- interatomic interactions. REG operates a sequence of geometries representing dynamical change system. Its recent application peptide hydrolysis human immunodeficiency virus-1 (HIV-1) protease (PDB code: 4HVP) has demonstrated its full potential in recovering reaction mechanisms through-space electrostatic exchange–correlation effects, making it compelling tool for analyzing enzymatic reactions. In this study, computational efficiency REG-IQA 133-atom HIV-1 mechanical system analyzed every detail substantially improved by means three different approaches. first approach smaller integration grids IQA integrations reduces overhead about factor 3. second uses line-simplification Ramer–Douglas–Peucker (RDP) algorithm, which outputs minimal number necessary analysis predetermined root mean squared error (RMSE) tolerance. This cuts time whole 2 if an RMSE 0.5 kJ/mol considered. third consists “biased” or “unbiased” selection specific subset initial model wave-function, results more than 10-fold speed-up per geometry calculation, without deterioration outcome analysis. Finally, show capability these approaches, findings gathered from are also applied named haloalcohol dehalogenase (HheC). summary, study takes computationally feasible highly accurate level, viable multitude systems.

Язык: Английский

Процитировано

1