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, Journal Year: 2023, Volume and Issue: 63(14), P. 4312 - 4327

Published: July 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.

Language: Английский

Intermolecular Covalent Interactions: Nature and Directionality DOI Creative Commons
Lucas de Azevedo Santos, Teodorico C. Ramalho, Trevor A. Hamlin

et al.

Chemistry - A European Journal, Journal Year: 2022, Volume and Issue: 29(14)

Published: Dec. 7, 2022

Quantum chemical methods were employed to analyze the nature and origin of directionality pnictogen (PnB), chalcogen (ChB), halogen bonds (XB) in archetypal Fm Z⋅⋅⋅F- complexes (Z=Pn, Ch, X), using relativistic density functional theory (DFT) at ZORA-M06/QZ4P. Quantitative Kohn-Sham MO energy decomposition analyses (EDA) show that all these intermolecular interactions have common covalence, is, HOMO-LUMO interactions, provide a crucial contribution bond energy, besides electrostatic attraction. Strikingly, are directional (i.e., F-Z⋅⋅⋅F- is approximately linear) despite, not because of, which, fact, favor bending. This constitutes breakdown σ-hole model. It was shown how model fails by neglecting both, essential physics behind interaction electron-rich interactions. Our findings general extend neutral, weaker ClI⋅⋅⋅NH3 , HClTe⋅⋅⋅NH3 H2 ClSb⋅⋅⋅NH3 complexes.

Language: Английский

Citations

29
Factors contributing to halogen bond strength and stretch or contraction of internal covalent bond DOI
Mariusz Michalczyk, Beata Kizior, Wiktor Zierkiewicz

et al.

Physical Chemistry Chemical Physics, Journal Year: 2023, Volume and Issue: 25(4), P. 2907 - 2915

Published: Jan. 1, 2023

The halogen bond formed by a series of Lewis acids TF3X (T = C, Si, Ge, Sn, Pb; X Cl, Br, I) with NH3 is studied quantum chemical calculations. interaction energy closely mimicked the depth σ-hole on atom as well full electrostatic energy. There first trend which hole deepened if T to attached becomes more electron-withdrawing: C > Si Ge Sn Pb. On other hand, larger polarizable atoms are better able transmit electron-withdrawing power F substituents. combination these two opposing factors leaves PbF3X forming strongest XBs, followed CF3X, SiF3X engaging in weakest bonds. charge transfer from lone pair into σ*(TX) antibonding orbital tends elongate covalent TX bond, and this force largest for heavier atoms. contraction deepens at atom, would enhance both component This bond-shortening effect greatest lighter forces T-X contracting Cl but lengthening I.

Language: Английский

Citations

11
On the strength of hydrogen bonding within water clusters on the coordination limit DOI

Víctor Manuel Castor‐Villegas,

José Manuel Guevara‐Vela, Wilmer E. Vallejo Narváez

et al.

Journal of Computational Chemistry, Journal Year: 2020, Volume and Issue: 41(26), P. 2266 - 2277

Published: Aug. 6, 2020

Hydrogen bonds (HB) are arguably the most important noncovalent interactions in chemistry. We study herein how differences connectivity alter strength of HBs within water clusters different sizes. used for this purpose interacting quantum atoms energy partition, which allows quantification HB formation energies a molecular cluster. could expand our previously reported hierarchy these systems (Phys. Chem. Phys., 2016, 18, 19557) to include tetracoordinated monomers. Surprisingly, between molecules not strongest despite widespread occurrence motifs (e.g., ice Ih ). The H2 O involve tricoordinated Nonetheless, tetracoordination is preferred large because (a) it reduces anticooperativity associated with double donors and acceptors (b) results larger number favorable system. Finally, we also discuss importance exchange-correlation discriminate among examined types clusters, use above-mentioned scale quickly assess relative stability isomers given cluster, (c) findings research can be exploited indagate about polymorphs crystallography. Overall, expect that investigation will provide valuable insights into subtle interplay tri- as well ensuing interaction clusters.

Language: Английский

Citations

26
Challenging the electrostatic σ‐hole picture of halogen bonding using minimal models and the interacting quantum atoms approach DOI
Fernando Jiménez‐Grávalos, Miguel Gallegos, Ángel Martín Pendás

et al.

Journal of Computational Chemistry, Journal Year: 2021, Volume and Issue: 42(10), P. 676 - 687

Published: Feb. 10, 2021

Abstract Among the different noncovalent interactions, halogen bonds have captured wide attention in last years. Their stability has been rationalized electrostatic terms by appealing to σ ‐hole concept, a charge‐depleted region that is able interact favorably with electron rich moieties. This interpretation questioned, and this work set of anionic model systems are used shed some light on issue. We use interacting quantum atoms method, which provides an orbital invariant energy decomposition pure well isolated, we complement our insights analysis potentials (ESPs) as traditional descriptors charge accumulation like Laplacian density. The total interaction between species surprisingly destabilizing many examined, demonstrating although ‐holes might be qualitatively helpful, much care taken ascribing these electrostatics. It clearly shown delocalization essential understand complexes. evolution atomic charges aggregates forms reveals transfer picture central, bearing acts mere spectator. These may then not far from engaging classical 3c‐4e interaction. Since presence characterized ESP mapped suitable molecular envelope isosurface does guarantee attractive encourage employ wider perspective takes into account full distribution.

Language: Английский

Citations

23
Decorated crown ethers as selective ion traps: Solvent’s role in crown’s preference towards a specific ion DOI

Marijana Hercigonja,

Branislav Milovanović, Mihajlo Etinski

et al.

Journal of Molecular Liquids, Journal Year: 2023, Volume and Issue: 381, P. 121791 - 121791

Published: April 6, 2023

Language: Английский

Citations

9
Electrophilicity Indices and Halogen Bonds: Some New Alternatives to the Molecular Electrostatic Potential DOI
Guillaume Hoffmann, Vincent Tognetti, Laurent Joubert

et al.

The Journal of Physical Chemistry A, Journal Year: 2020, Volume and Issue: 124(10), P. 2090 - 2101

Published: March 2, 2020

We assess the ability of various atomic and molecular electrophilicity descriptors to predict strength halogen bonds. To this aim, several physicochemical quantities rooted within framework conceptual density functional theory were derived using second third order Taylor expansions electronic energy, their correlation binding energies compared with those obtained for more usual descriptors. This benchmark was performed a large representative database noncovalent complexes involving fluorine, chlorine, bromine atoms, showed that some these new quantities, in particular cubic index, exhibited transferability broadness application than did common such as electrostatic potential.

Language: Английский

Citations

20
Capture of CO2 by Melamine Derivatives: A DFT Study Combining the Relative Energy Gradient Method with an Interaction Energy Partitioning Scheme DOI Creative Commons
Maxime Ferrer, Ibón Alkorta, José Elguero

et al.

The Journal of Physical Chemistry A, Journal Year: 2024, Volume and Issue: 128(7), P. 1288 - 1296

Published: Feb. 13, 2024

A theoretical study of the interaction between melamine and CO2 was carried out using density functional theory (DFT) with B3LYP-D3(BJ)/aug-cc-pVTZ level theory. The presence anions interacting transforms weakly bonded tetrel complexes into adducts. Thus, acts as an FLP (frustrated Lewis pair) acid groups (NHs hydrogen bond donors) a base group (N triazine ring). application relative energy gradient formalism (REG) along reaction coordinate has demonstrated that ability melamine-anion systems to capture is linked its capacity polarize molecule. These results have been confirmed by placing melamine:CO2 complex in uniform electric field different strengths.

Language: Английский

Citations

2
Cooperativity and Anticooperativity in Ion‐Water Interactions: Implications for the Aqueous Solvation of Ions DOI
Arturo Sauza‐de la Vega, Tomás Rocha‐Rinza, José Manuel Guevara‐Vela

et al.

ChemPhysChem, Journal Year: 2021, Volume and Issue: 22(12), P. 1269 - 1285

Published: Feb. 26, 2021

Non-additive effects in hydrogen bonds (HB) take place as a consequence of electronic charge transfers. Therefore, it is natural to expect cooperativity and anticooperativity ion-water interactions. Nevertheless, investigations on this matter are scarce. This paper addresses the interactions (i) cations Li+ , Na+ K+ Be2+ Mg2+ Ca2+ together with (ii) anions F- Cl- Br- NO3- SO42- water clusters (H2 O)n n=1-8, these ions HBs within complete molecular adducts. We used quantum chemical topology tools, specifically theory atoms molecules interacting energy partition investigate non-additive among studied herein. Our results show decrease interaction between first neighbouring an increment coordination number. also found strong cooperative interplay ion-dipole systems. Such affects considerably their second solvation shells aqueous environments. Overall, we believe article provides valuable information about how contacts interact each other they relate interactions, such HBs, framework media.

Language: Английский

Citations

15
An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study of the Halogen Bond with Explicit Analysis of Electron Correlation DOI Creative Commons
Ibón Alkorta, Arnaldo F. Silva, Paul L. A. Popelier

et al.

Molecules, Journal Year: 2020, Volume and Issue: 25(11), P. 2674 - 2674

Published: June 9, 2020

Energy profiles of seven halogen-bonded complexes were analysed with the topological energy partitioning called Interacting Quantum Atoms (IQA) at MP4(SDQ)/6–31 + G(2d,2p) level theory. Explicit interatomic electron correlation energies are included in analysis. Four combine X2 (X = Cl or F) HCN NH3, while remaining three ClF HCN, NH3 N2. Each complex was systematically deformed by translating constituent molecules along its central axis linking X and N, reoptimising geometry. The Relative Gradient (REG) method (Theor. Chem. Acc. 2017, 136, 86) then computes which IQA most correlate total during process formation further compression beyond respective equilibrium geometries. It turns out that covalent (i.e., exchange) halogen bond, X…N, itself drives formation. When compressed from their to shorter X…N distance intra-atomic N is charge. REG analysis restricted between again formation, best described destabilisation through-space “outer” halogen.

Language: Английский

Citations

16
New insights in chemical reactivity from quantum chemical topology DOI
Johanna Klein, Paul Fleurat‐Lessard, Julien Pilmé

et al.

Journal of Computational Chemistry, Journal Year: 2021, Volume and Issue: 42(12), P. 840 - 854

Published: March 3, 2021

Abstract Based on the quantum chemical topology of modified electron localization function ELF x , an efficient and robust mechanistic methodology designed to identify favorable reaction pathway between two reactants is proposed. We first recall reshape how supermolecular interaction energy can be evaluated from only three distinct terms, namely intermolecular coulomb energy, exchange‐correlation intramolecular energies reactants. Thereafter, we show that reactivity driven by first‐order variation in defined terms response changes number electrons. Illustrative examples with formation dative bond B‐N involved BH 3 NH molecule typical hydrogen canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking E dual onto DFT surface calculated both An automated reaction‐path algorithm aimed determine most relative orientations when molecules each other also outlined.

Language: Английский

Citations

12