1
|
Gimferrer M, Salvador P. Exact decompositions of the total KS-DFT exchange-correlation energy into one- and two-center terms. J Chem Phys 2023; 158:234105. [PMID: 37326158 DOI: 10.1063/5.0142778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
In the so-called Interacting Quantum Atoms (IQA) approach, the molecular energy is numerically decomposed as a sum of atomic and diatomic contributions. While proper formulations have been put forward for both Hartree-Fock and post-Hartree-Fock wavefunctions, this is not the case for the Kohn-Sham density functional theory (KS-DFT). In this work, we critically analyze the performance of two fully additive approaches for the IQA decomposition of the KS-DFT energy, namely, the one from Francisco et al., which uses atomic scaling factors, and that from Salvador and Mayer based upon the bond order density (SM-IQA). Atomic and diatomic exchange-correlation (xc) energy components are obtained for a molecular test set comprising different bond types and multiplicities and along the reaction coordinate of a Diels-Alder reaction. Both methodologies behave similarly for all systems considered. In general, the SM-IQA diatomic xc components are less negative than the Hartree-Fock ones, which is in good agreement with the known effect of electron correlation upon (most) covalent bonds. In addition, a new general scheme to minimize the numerical error of the sum of two-electron energy contributions (i.e., Coulomb and exact exchange) in the framework of overlapping atoms is described in detail.
Collapse
Affiliation(s)
- Martí Gimferrer
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Pedro Salvador
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| |
Collapse
|
2
|
Non-covalent interactions from a Quantum Chemical Topology perspective. J Mol Model 2022; 28:276. [PMID: 36006513 PMCID: PMC9411098 DOI: 10.1007/s00894-022-05188-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/07/2022] [Indexed: 11/12/2022]
Abstract
About half a century after its little-known beginnings, the quantum topological approach called QTAIM has grown into a widespread, but still not mainstream, methodology of interpretational quantum chemistry. Although often confused in textbooks with yet another population analysis, be it perhaps an elegant but somewhat esoteric one, QTAIM has been enriched with about a dozen other research areas sharing its main mathematical language, such as Interacting Quantum Atoms (IQA) or Electron Localisation Function (ELF), to form an overarching approach called Quantum Chemical Topology (QCT). Instead of reviewing the latter’s role in understanding non-covalent interactions, we propose a number of ideas emerging from the full consequences of the space-filling nature of topological atoms, and discuss how they (will) impact on interatomic interactions, including non-covalent ones. The architecture of a force field called FFLUX, which is based on these ideas, is outlined. A new method called Relative Energy Gradient (REG) is put forward, which is able, by computation, to detect which fragments of a given molecular assembly govern the energetic behaviour of this whole assembly. This method can offer insight into the typical balance of competing atomic energies both in covalent and non-covalent case studies. A brief discussion on so-called bond critical points is given, highlighting concerns about their meaning, mainly in the arena of non-covalent interactions.
Collapse
|
3
|
Barrales-Martínez C, Gutiérrez-Oliva S, Toro-Labbé A, Pendás ÁM. Interacting Quantum Atoms Analysis of the Reaction Force: A Tool to Analyze Driving and Retarding Forces in Chemical Reactions. Chemphyschem 2021; 22:1976-1988. [PMID: 34293240 DOI: 10.1002/cphc.202100428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/21/2021] [Indexed: 12/22/2022]
Abstract
The analysis of the reaction force and its topology has provided a wide range of fruitful concepts in the theory of chemical reactivity over the years, allowing to identify chemically relevant regions along a reaction profile. The reaction force (RF), a projection of the Hellmann-Feynman forces acting on the nuclei of a molecular system onto a suitable reaction coordinate, is partitioned using the interacting quantum atoms approach (IQA). The exact IQA molecular energy decomposition is now shown to open a unique window to identify and quantify the chemical entities that drive or retard a chemical reaction. The RF/IQA coupling offers an extraordinarily detailed view of the type and number of elementary processes that take reactants into products, as tested on two sets of simple reactions.
Collapse
Affiliation(s)
- César Barrales-Martínez
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Departamento de Química-Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Departamento de Química-Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain
| |
Collapse
|
4
|
Gallegos M, Costales A, Pendás ÁM. Energetic Descriptors of Steric Hindrance in Real Space: An Improved IQA Picture*. Chemphyschem 2021; 22:775-787. [PMID: 33497008 DOI: 10.1002/cphc.202000975] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/05/2021] [Indexed: 11/11/2022]
Abstract
Steric hindrance (SH) plays a central role in the modern chemical narrative, lying at the core of chemical intuition. As it however happens with many successful chemical concepts, SH lacks an underlying physically sound root, and multiple mutually inconsistent approximations have been devised to relate this fuzzy concept to computationally derivable descriptors. We here argue that being SH related to spatial as well as energetic features of interacting systems, SH can be properly handled if we chose a real space energetic stance like the Interacting Quantum Atoms (IQA) approach. Drawing on previous work by Popelier and coworkers (ChemistryOpen 8, 560, 2019) we build an energetic estimator of SH, referred to as EST . We show that the rise in the self-energy of a fragment that accompanies steric congestion is a faithful proxy for the chemist's SH concept if we remove the effect of charge transfer. This can be done rigorously, and the EST here defined provides correct sterics even for hydrogen atoms, where the plain use of deformation energies leads to non-chemical results. The applicability of EST is validated in several chemical scenarios, going from atomic compressions to archetypal SN2 reactions. EST is shown to be a robust steric hindrance descriptor.
Collapse
Affiliation(s)
- Miguel Gallegos
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006, Oviedo, Spain
| | - Aurora Costales
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006, Oviedo, Spain
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006, Oviedo, Spain
| |
Collapse
|
5
|
Sudarvizhi V, Balakrishnan T, Percino MJ, Stoeckli-Evans H, Thamotharan S. Evaluation of charge assisted hydrogen bonds in L-(S)-lysinium L-(S)-mandelate dihydrate and L-(S)-alanine L-(S)-mandelic acid complexes: Inputs from Hirshfeld surface, PIXEL energy and QTAIM analysis. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
6
|
An energy decomposition analysis approach to the rotational barriers of amides and thioamides. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
7
|
Guevara-Vela JM, Francisco E, Rocha-Rinza T, Martín Pendás Á. Interacting Quantum Atoms-A Review. Molecules 2020; 25:E4028. [PMID: 32899346 PMCID: PMC7504790 DOI: 10.3390/molecules25174028] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
The aim of this review is threefold. On the one hand, we intend it to serve as a gentle introduction to the Interacting Quantum Atoms (IQA) methodology for those unfamiliar with it. Second, we expect it to act as an up-to-date reference of recent developments related to IQA. Finally, we want it to highlight a non-exhaustive, yet representative set of showcase examples about how to use IQA to shed light in different chemical problems. To accomplish this, we start by providing a brief context to justify the development of IQA as a real space alternative to other existent energy partition schemes of the non-relativistic energy of molecules. We then introduce a self-contained algebraic derivation of the methodological IQA ecosystem as well as an overview of how these formulations vary with the level of theory employed to obtain the molecular wavefunction upon which the IQA procedure relies. Finally, we review the several applications of IQA as examined by different research groups worldwide to investigate a wide variety of chemical problems.
Collapse
Affiliation(s)
- José Manuel Guevara-Vela
- Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., Mexico City 04510, Mexico; (J.M.G.-V.); (T.R.-R.)
| | - Evelio Francisco
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006 Oviedo, Spain;
| | - Tomás Rocha-Rinza
- Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., Mexico City 04510, Mexico; (J.M.G.-V.); (T.R.-R.)
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006 Oviedo, Spain;
| |
Collapse
|
8
|
Cukrowski I, de Lange JH, van Niekerk DME, Bates TG. Molecular Orbitals Support Energy-Stabilizing "Bonding" Nature of Bader's Bond Paths. J Phys Chem A 2020; 124:5523-5533. [PMID: 32520541 DOI: 10.1021/acs.jpca.0c02234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Our MO-based findings proved a bonding nature of each density bridge (DB, or a bond path with an associated critical point, CP) on a Bader molecular graph. A DB pinpoints universal physical and net energy-lowering processes that might, but do not have to, lead to a chemical bond formation. Physical processes leading to electron density (ED) concentration in internuclear regions of three distinctively different homopolar H,H atom-pairs as well as classical C-C and C-H covalent bonds were found to be exactly the same. Notably, properties of individual MOs are internuclear-region specific as they (i) concentrate, deplete, or do not contribute to ED at a CP and (ii) delocalize electron-pairs through either in- (positive) or out-of-phase (negative) interference. Importantly, dominance of a net ED concentration and positive e--pairs delocalization made by a number of σ-bonding MOs is a common feature at a CP. This feature was found for the covalently bonded atoms as well as homopolar H,H atom-pairs investigated. The latter refer to a DB-free H,H atom-pair of the bay in the twisted biphenyl (Bph) and DB-linked H,H atom-pairs (i) in cubic Li4H4, where each H atom is involved in three highly repulsive interactions (over +80 kcal/mol), and (ii) in a weak attractive interaction when sterically clashing in the planar Bph.
Collapse
Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Jurgens H de Lange
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Daniël M E van Niekerk
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Thomas G Bates
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| |
Collapse
|
9
|
Casals‐Sainz JL, Guevara‐Vela JM, Francisco E, Rocha‐Rinza T, Martín Pendás Á. Efficient implementation of the interacting quantum atoms energy partition of the second‐order Møller–Plesset energy. J Comput Chem 2020; 41:1234-1241. [DOI: 10.1002/jcc.26169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 12/19/2022]
Affiliation(s)
| | - José Manuel Guevara‐Vela
- Institute of Chemistry, National Autonomous University of Mexico, Circuito ExteriorCiudad Universitaria Mexico City Mexico
| | - Evelio Francisco
- Department of Analytical and Physical ChemistryUniversity of Oviedo Oviedo Spain
| | - Tomás Rocha‐Rinza
- Institute of Chemistry, National Autonomous University of Mexico, Circuito ExteriorCiudad Universitaria Mexico City Mexico
| | - Ángel Martín Pendás
- Department of Analytical and Physical ChemistryUniversity of Oviedo Oviedo Spain
| |
Collapse
|
10
|
Casals‐Sainz JL, Francisco E, Martín Pendás Á. The Activation Strain Model in the Light of Real Space Energy Partitions. Z Anorg Allg Chem 2020. [DOI: 10.1002/zaac.202000038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- José Luis Casals‐Sainz
- Departamento de Química Física y Analítica Facultad de Química Universidad de Oviedo 33006 Oviedo Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica Facultad de Química Universidad de Oviedo 33006 Oviedo Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica Facultad de Química Universidad de Oviedo 33006 Oviedo Spain
| |
Collapse
|
11
|
Berryman VEJ, Shephard JJ, Ochiai T, Price AN, Arnold PL, Parsons S, Kaltsoyannis N. Quantum chemical topology and natural bond orbital analysis of M–O covalency in M(OC6H5)4 (M = Ti, Zr, Hf, Ce, Th, Pa, U, Np). Phys Chem Chem Phys 2020; 22:16804-16812. [DOI: 10.1039/d0cp02947e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
VXC(M,O): the exchange–correlation metric quantifies covalency between M and O atomic basins in M(OC6H5)4 (M = Ti, Zr, Hf, Ce, Th, Pa, U, Np).
Collapse
Affiliation(s)
| | - Jacob J. Shephard
- EaStCHEM School of Chemistry and The Centre for Science at Extreme Conditions
- The University of Edinburgh
- Edinburgh
- UK
| | - Tatsumi Ochiai
- EaStCHEM School of Chemistry
- The University of Edinburgh
- Edinburgh
- UK
- Department of Chemistry
| | - Amy N. Price
- EaStCHEM School of Chemistry
- The University of Edinburgh
- Edinburgh
- UK
| | - Polly L. Arnold
- EaStCHEM School of Chemistry
- The University of Edinburgh
- Edinburgh
- UK
- Department of Chemistry
| | - Simon Parsons
- EaStCHEM School of Chemistry and The Centre for Science at Extreme Conditions
- The University of Edinburgh
- Edinburgh
- UK
| | - Nikolas Kaltsoyannis
- Department of Chemistry
- School of Natural Sciences
- The University of Manchester
- Manchester
- UK
| |
Collapse
|
12
|
Andrés J, Ayers PW, Boto RA, Carbó-Dorca R, Chermette H, Cioslowski J, Contreras-García J, Cooper DL, Frenking G, Gatti C, Heidar-Zadeh F, Joubert L, Martín Pendás Á, Matito E, Mayer I, Misquitta AJ, Mo Y, Pilmé J, Popelier PLA, Rahm M, Ramos-Cordoba E, Salvador P, Schwarz WHE, Shahbazian S, Silvi B, Solà M, Szalewicz K, Tognetti V, Weinhold F, Zins ÉL. Nine questions on energy decomposition analysis. J Comput Chem 2019; 40:2248-2283. [PMID: 31251411 DOI: 10.1002/jcc.26003] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 01/05/2023]
Abstract
The paper collects the answers of the authors to the following questions: Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the "natural selection" process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross-validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the "standard model" of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another? © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Juan Andrés
- Departament de Ciències Experimentals Universitat Jaume I, 12080, Castelló, Spain
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, L8S 4M1, Hamilton, Ontario, Canada
| | | | - Ramon Carbó-Dorca
- Institut de Química Computational i Catàlisi, Universitat de Girona, C/M Aurelia Capmany 69, 17003, Girona, Spain
| | - Henry Chermette
- Université Lyon 1 et UMR CNRS 5280 Institut Sciences Analytiques, Université de Lyon, 69622, Paris, France
| | - Jerzy Cioslowski
- Institute of Physics, University of Szczecin, Wielkopolska, 15, 70-451, Szczecin, Poland
| | | | - David L Cooper
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, United Kingdom
| | - Gernot Frenking
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerweinstr. 4, 35032, Marburg, Germany
| | - Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, 20133, Milan, Italy and Istituto Lombardo Accademia di Scienze e Lettere, via Brera 28, 20121, Milan, Italy
| | - Farnaz Heidar-Zadeh
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg and Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Laurent Joubert
- COBRA UMR 6014 & FR 3038, INSA Rouen, CNRS, Université de Rouen Normandie, Mont-St-Aignan, France
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Eduard Matito
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080, Donostia, Euskadi, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Euskadi, Spain
| | - István Mayer
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - Alston J Misquitta
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Yirong Mo
- Chemistry Department, Western Michigan University, Kalamazoo, Michigan, 49008
| | - Julien Pilmé
- Sorbonne Université, CNRS, LCT, UMR 7616, 4 place Jussieu, 75005, Paris, France
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, United Kingdom.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Martin Rahm
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Eloy Ramos-Cordoba
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080, Donostia, Euskadi, Spain
| | - Pedro Salvador
- Institut de Química Computacional i Catàlisi, Universitat de Girona, C/M Aurelia Capmany 69, 17003, Girona, Spain
| | - W H Eugen Schwarz
- Theoretical Chemistry Center at Tsinghua University, Beijing, 100084, China.,Physical and Theoretical Chemistry Laboratory, Faculty of Science and Engineering, University of Siegen, Siegen, 57068, Germany
| | - Shant Shahbazian
- Department of Physics, Shahid Beheshti University, P.O. Box 19395-4716, G. C., Evin, 19839, Tehran, Iran
| | - Bernard Silvi
- Sorbonne Université, CNRS, LCT, UMR 7616, 4 place Jussieu, 75005, Paris, France
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi, Universitat de Girona, C/M Aurelia Capmany 69, 17003, Girona, Spain
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Vincent Tognetti
- COBRA UMR 6014 & FR 3038, INSA Rouen, CNRS, Université de Rouen Normandie, Mont-St-Aignan, France
| | - Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Émilie-Laure Zins
- Sorbonne Université, UPMC Univ. Paris 06, MONARIS, UMR 8233, Université Pierre et Marie Curie, 4 Place Jussieu, Case Courrier 49, 75252, Paris, France
| |
Collapse
|
13
|
Tetrel Interactions from an Interacting Quantum Atoms Perspective. Molecules 2019; 24:molecules24122204. [PMID: 31212835 PMCID: PMC6632095 DOI: 10.3390/molecules24122204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tetrel bonds, the purportedly non-covalent interaction between a molecule that contains an atom of group 14 and an anion or (more generally) an atom or molecule with lone electron pairs, are under intense scrutiny. In this work, we perform an interacting quantum atoms (IQA) analysis of several simple complexes formed between an electrophilic fragment (A) (CH3F, CH4, CO2, CS2, SiO2, SiH3F, SiH4, GeH3F, GeO2, and GeH4) and an electron-pair-rich system (B) (NCH, NCO-, OCN-, F-, Br-, CN-, CO, CS, Kr, NC-, NH3, OC, OH2, SH-, and N3-) at the aug-cc-pvtz coupled cluster singles and doubles (CCSD) level of calculation. The binding energy ( E bind AB ) is separated into intrafragment and inter-fragment components, and the latter in turn split into classical and covalent contributions. It is shown that the three terms are important in determining E bind AB , with absolute values that increase in passing from electrophilic fragments containing C, Ge, and Si. The degree of covalency between A and B is measured through the real space bond order known as the delocalization index ( δ AB ). Finally, a good linear correlation is found between δ AB and E xc AB , the exchange correlation (xc) or covalent contribution to E bind AB .
Collapse
|
14
|
Mitoraj MP, Babashkina MG, Robeyns K, Sagan F, Szczepanik DW, Seredina YV, Garcia Y, Safin DA. Chameleon-like Nature of Anagostic Interactions and Its Impact on Metalloaromaticity in Square-Planar Nickel Complexes. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mariusz P. Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
- Institute of Chemistry, University of Tyumen, Perekopskaya Street 15a, 625003 Tyumen, Russian Federation
| | - Koen Robeyns
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
| | - Filip Sagan
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Dariusz W. Szczepanik
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Yulia V. Seredina
- Institute of Chemistry, University of Tyumen, Perekopskaya Street 15a, 625003 Tyumen, Russian Federation
| | - Yann Garcia
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
| | - Damir A. Safin
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
- Institute of Chemistry, University of Tyumen, Perekopskaya Street 15a, 625003 Tyumen, Russian Federation
| |
Collapse
|
15
|
Díaz N, Jiménez-Grávalos F, Suárez D, Francisco E, Martín-Pendás Á. Fluorine conformational effects characterized by energy decomposition analysis. Phys Chem Chem Phys 2019; 21:25258-25275. [DOI: 10.1039/c9cp05009d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fluorine associated classical and quantum effects are quantified by the interacting quantum atoms method to identify the factors controlling the conformation in organofluorine molecules.
Collapse
Affiliation(s)
- Natalia Díaz
- Departamento de Química Física y Analítica
- Universidad de Oviedo
- 33006 Oviedo
- Spain
| | | | - Dimas Suárez
- Departamento de Química Física y Analítica
- Universidad de Oviedo
- 33006 Oviedo
- Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica
- Universidad de Oviedo
- 33006 Oviedo
- Spain
| | - Ángel Martín-Pendás
- Departamento de Química Física y Analítica
- Universidad de Oviedo
- 33006 Oviedo
- Spain
| |
Collapse
|
16
|
Popelier PLA, Maxwell PI, Thacker JCR, Alkorta I. A relative energy gradient (REG) study of the planar and perpendicular torsional energy barriers in biphenyl. Theor Chem Acc 2018; 138:12. [PMID: 30872951 PMCID: PMC6383956 DOI: 10.1007/s00214-018-2383-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022]
Abstract
Biphenyl is a prototype molecule, the study of which is important for a proper understanding of stereo-electronic effects. In the gas phase it has an equilibrium central torsion angle of ~ 45° and shows both a planar (0°) and a perpendicular (90°) torsional energy barrier. The latter is analysed for the first time. We use the newly proposed REG method, which is an exhaustive procedure that automatically ranks atomic energy contributions according to their importance in explaining the energy profile of a total system. Here, the REG method operates on energy contributions computed by the interacting quantum atoms method. This method is minimal in architecture and provides a crisp picture of well-defined and well-separated electrostatic, steric and exchange (covalent) energies at atomistic level. It is shown that the bond critical point occurring between the ortho-hydrogens in the planar geometry has been wrongly interpreted as a sign of repulsive interaction. A convenient metaphor of analysing football matches is introduced to clarify the role of a REG analysis.
Collapse
Affiliation(s)
- Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN UK
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Peter I. Maxwell
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN UK
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Joseph C. R. Thacker
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN UK
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| |
Collapse
|
17
|
Jara-Cortés J, Landeros-Rivera B, Hernández-Trujillo J. Unveiling the role of intra and interatomic interactions in the energetics of reaction schemes: a quantum chemical topology analysis. Phys Chem Chem Phys 2018; 20:27558-27570. [PMID: 30371704 DOI: 10.1039/c8cp03775b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work we present a detailed analysis of selected reaction schemes in terms of the atomic components of the electronic energy defined by the quantum theory of atoms in molecules and the interacting quantum atoms method. The aim is to provide an interpretation tool for the energy change involved in a chemical reaction by means of the atomic and interaction contributions to the energies of the molecules involved. Ring strain in cyclic alkanes, the resonance energy of aromatic and antiaromatic molecules, local aromaticity in polycyclic aromatic hydrocarbons, intermolecular bonding in hydrogen fluoride clusters, and hydration of d-block metal dications were selected for the study. It was found that in addition to the changes in the strong C-C interactions in the carbon skeleton of the organic molecular rings, other contributions not usually considered to be important such as those between C and H atoms (either bonded or not) need to be considered in order to account for the net energy changes. The analysis unveils the role of the ionic and covalent contributions to the hydrogen bonding in HF clusters and the energetic origin and extent of cooperative effects involved. Moreover, the "double-hump" behavior observed for the hydration energy trend of [M(H2O)6]2+ complexes is explained in terms of the deformation energy of the metal cation and the increasingly covalent metal-water interactions. In addition, proper comparisons with the description provided by other methodologies are briefly discussed. The topological approach proposed in this contribution proves to be useful for the description of energy changes of apposite reaction schemes in chemically meaningful terms.
Collapse
Affiliation(s)
- Jesús Jara-Cortés
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, México City, 04510, Mexico.
| | | | | |
Collapse
|
18
|
Thacker JCR, Vincent MA, Popelier PLA. Using the Relative Energy Gradient Method with Interacting Quantum Atoms to Determine the Reaction Mechanism and Catalytic Effects in the Peptide Hydrolysis in HIV-1 Protease. Chemistry 2018; 24:11200-11210. [PMID: 29802794 PMCID: PMC6099506 DOI: 10.1002/chem.201802035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 11/10/2022]
Abstract
The reaction mechanism in an active site is of the utmost importance when trying to understand the role that an enzyme plays in biological processes. In a recently published paper [Theor. Chem. Acc. 2017, 136, 86], we formalised the Relative Energy Gradient (REG) method for automating an Interacting Quantum Atoms (IQA) analysis. Here, the REG method is utilised to determine the mechanism of peptide hydrolysis in the aspartic active site of the enzyme HIV-1 Protease. Using the REG method along with the IQA approach we determine the mechanism of peptide hydrolysis without employing any arbitrary parameters and with remarkable ease (albeit at large computational cost: the system contains 133 atoms, which means that there are 17 689 individual IQA terms to be calculated). When REG and IQA work together it is possible to determine a reaction mechanism at atomistic resolution from data directly derived from quantum calculations, without arbitrary parameters. Moreover, the mechanism determined by this novel method gives concrete insight into how the active site residues catalyse peptide hydrolysis.
Collapse
Affiliation(s)
- Joseph C. R. Thacker
- Manchester Institute of Biotechnology (MIB)131 Princess StreetManchesterM1 7DNUK
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Mark A. Vincent
- Manchester Institute of Biotechnology (MIB)131 Princess StreetManchesterM1 7DNUK
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB)131 Princess StreetManchesterM1 7DNUK
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| |
Collapse
|
19
|
Menéndez-Crespo D, Costales A, Francisco E, Martín Pendás Á. Real-Space In Situ Bond Energies: Toward A Consistent Energetic Definition of Bond Strength. Chemistry 2018; 24:9101-9112. [DOI: 10.1002/chem.201800979] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Menéndez-Crespo
- Departamento de Química Física y Analítica; Facultad de Química; Universidad de Oviedo; 33006- Oviedo Spain
| | - Aurora Costales
- Departamento de Química Física y Analítica; Facultad de Química; Universidad de Oviedo; 33006- Oviedo Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica; Facultad de Química; Universidad de Oviedo; 33006- Oviedo Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica; Facultad de Química; Universidad de Oviedo; 33006- Oviedo Spain
| |
Collapse
|
20
|
Suárez D, Díaz N, Francisco E, Martín Pendás A. Application of the Interacting Quantum Atoms Approach to the S66 and Ionic-Hydrogen-Bond Datasets for Noncovalent Interactions. Chemphyschem 2018; 19:973-987. [DOI: 10.1002/cphc.201701021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/19/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Dimas Suárez
- Departamento de Química Física y Analítica; Universidad de Oviedo; Julián Clavería 8. 33006 Oviedo (Asturias) Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica; Universidad de Oviedo; Julián Clavería 8. 33006 Oviedo (Asturias) Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica; Universidad de Oviedo; Julián Clavería 8. 33006 Oviedo (Asturias) Spain
| | - Angel Martín Pendás
- Departamento de Química Física y Analítica; Universidad de Oviedo; Julián Clavería 8. 33006 Oviedo (Asturias) Spain
| |
Collapse
|
21
|
Munarriz J, Velez E, Casado MA, Polo V. Understanding the reaction mechanism of the oxidative addition of ammonia by (PXP)Ir(i) complexes: the role of the X group. Phys Chem Chem Phys 2018; 20:1105-1113. [PMID: 29238771 DOI: 10.1039/c7cp07453k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An analysis of the electronic rearrangements for the oxidative addition of ammonia to a set of five representative (PXP)Ir pincer complexes (X = B, CH, O, N, SiH) is performed. We aim to understand the factors controlling the activation and reaction energies of this process by combining different theoretical strategies based on DFT calculations. Interestingly, complexes featuring higher activation barriers yield more exothermic reactions. The analysis of the reaction path using the bonding evolution theory shows that the main chemical events, N-H bond cleavage and Ir-H bond formation, take place before the transition structure is reached. Metal oxidation implies an electron density transfer from non-shared Ir pairs to the Ir-N bond. This decrement in the atomic charge of the metal provokes different effects in the ionic contribution of the Ir-X bonding depending on the nature of the X atom as shown by the interacting quantum atoms methodology.
Collapse
Affiliation(s)
- J Munarriz
- Departamento de Química Física and Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | | | | | | |
Collapse
|
22
|
Pendás ÁM, Guevara-Vela JM, Crespo DM, Costales A, Francisco E. An unexpected bridge between chemical bonding indicators and electrical conductivity through the localization tensor. Phys Chem Chem Phys 2018; 19:1790-1797. [PMID: 28044163 DOI: 10.1039/c6cp07617c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While the modern theory of the insulating state shows that the conducting or insulating properties of a system can be extracted solely from the ground state properties via the so-called localization tensor (LT), no chemical reading of this important quantity has ever been offered. Here, a remarkable link between the LT and the bond orders as described by the delocalization indices (DIs) of chemical bonding theory is reported. This is achieved through a real space partition of the LT into intra- and interatomic contributions. We show that the convergence or divergence of the LT in the thermodynamic limit, which signals the insulating or conducting nature of an extended system, respectively, can be nailed down to DIs. This allows for the exploitation of traditional chemical intuition to identify essential and spectator atomic groups in determining electrical conductivity. The thermodynamic limit of the LT is controlled by the spatial decay rate of the interatomic DIs, exponential in insulators and power-law in conductors. Computational data of a few selected toy systems corroborate our results.
Collapse
Affiliation(s)
- Ángel Martín Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain.
| | | | | | - Aurora Costales
- Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain.
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain.
| |
Collapse
|
23
|
Thacker JCR, Popelier PLA. Fluorine Gauche Effect Explained by Electrostatic Polarization Instead of Hyperconjugation: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study. J Phys Chem A 2018; 122:1439-1450. [PMID: 29381361 DOI: 10.1021/acs.jpca.7b11881] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an interacting quantum atoms (IQA) study of the gauche effect by comparing 1,2-difluoroethane, 1,2-dichloroethane, and three conformers of 1,2,3,4,5,6-hexafluorocyclohexane. In the 1,2-difluoroethane, the gauche effect is observed in that the gauche conformation is more stable than the anti, whereas in 1,2-dichloroethane the opposite is true. The analysis performed here is exhaustive and unbiased thanks to using the recently introduced relative energy gradient (REG) method [ Thacker , J. C. R. ; Popelier , P. L. A. Theor. Chem. Acc . 2017 , 136 , 86 ], as implemented in the in-house program ANANKE. We challenge the common explanation that hyperconjugation is responsible for the gauche stability in 1,2-difluoroethane and instead present electrostatics as the cause of gauche stability. Our explanation of the gauche effect is also is seen in other molecules displaying local gauche conformations, such as the recently synthesized "all-cis" hexafluorocyclohexane and its conformers where all the fluorine atoms are in the equatorial positions. Using our extension of the traditional IQA methodology that allows for the partitioning of electrostatic terms into polarization and charge transfer, we propose that the cause of gauche stability is 1,3 C···F electrostatic polarization interactions. In other words, if a number of fluorine atoms are aligned, then the stability due to polarization of nearby carbon atoms is increased.
Collapse
Affiliation(s)
- Joseph C R Thacker
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester M1 7DN, Great Britain.,School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, Great Britain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester M1 7DN, Great Britain.,School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, Great Britain
| |
Collapse
|
24
|
Maxwell P, Pendás ÁM, Popelier PLA. Extension of the interacting quantum atoms (IQA) approach to B3LYP level density functional theory (DFT). Phys Chem Chem Phys 2018; 18:20986-1000. [PMID: 26804126 DOI: 10.1039/c5cp07021j] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
An interaction between two atoms, bonded or non-bonded, consists of interatomic contributions: electrostatic energy, exchange energy and electronic correlation energy. Together with the intra-atomic energy of an atom, these contributions are the basic components of the Interacting Quantum Atom (IQA) energy decomposition scheme. Here, we investigate IQA's proper use in conjunction with an explicit implementation of the B3LYP functional. The recovery of the total molecular energy from the IQA components is emphasised, for the first time. A systematic study of three model systems of biological relevance, N-methylacetamide (NMA), the doubly capped tripeptide GlyGlyGly and an alloxan dimer, shows the stabilization effect of B3LYP on most of the interatomic exchange energies (V) compared to their Hartree-Fock values. Diagrams of exchange energies versus interatomic distance show the clustering of interactions, one cluster for each 1,n (n = 1 to 6 where the atoms are separated by n - 1 bonds). The positioning of some V values outside their expected cluster marks interesting interactions.
Collapse
Affiliation(s)
- Peter Maxwell
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, UK. and School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Ángel Martín Pendás
- Departamento de Quimica Fisica y Analitica, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, UK. and School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| |
Collapse
|
25
|
Casals-Sainz JL, Jiménez-Grávalos F, Costales A, Francisco E, Pendás ÁM. Beryllium Bonding in the Light of Modern Quantum Chemical Topology Tools. J Phys Chem A 2018; 122:849-858. [DOI: 10.1021/acs.jpca.7b10714] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Aurora Costales
- Departamento de Química Física
y Analítica, Universidad de Oviedo, Oviedo 33006, Spain
| | - Evelio Francisco
- Departamento de Química Física
y Analítica, Universidad de Oviedo, Oviedo 33006, Spain
| | - Ángel Martín Pendás
- Departamento de Química Física
y Analítica, Universidad de Oviedo, Oviedo 33006, Spain
| |
Collapse
|
26
|
Casalz-Sainz JL, Guevara-Vela JM, Francisco E, Rocha-Rinza T, Martín Pendás Á. Where Does Electron Correlation Lie? Some Answers from a Real Space Partition. Chemphyschem 2017; 18:3553-3561. [DOI: 10.1002/cphc.201700940] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/04/2017] [Indexed: 11/09/2022]
Affiliation(s)
- José Luis Casalz-Sainz
- Departament of Analytical and Physical Chemistry; University of Oviedo; E-33006 Oviedo Spain
| | | | - Evelio Francisco
- Departament of Analytical and Physical Chemistry; University of Oviedo; E-33006 Oviedo Spain
| | - Tomás Rocha-Rinza
- Institute of Chemistry; National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P.; 04510 Mexico City Mexico
| | - Ángel Martín Pendás
- Departament of Analytical and Physical Chemistry; University of Oviedo; E-33006 Oviedo Spain
| |
Collapse
|
27
|
Zhao L, von Hopffgarten M, Andrada DM, Frenking G. Energy decomposition analysis. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1345] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lili Zhao
- Institute of Advanced Synthesis, School of Chemistry and Molecular EngineeringJiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University Nanjing China
| | | | | | - Gernot Frenking
- Institute of Advanced Synthesis, School of Chemistry and Molecular EngineeringJiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University Nanjing China
- Fachbereich ChemiePhilipps‐Universität Marburg Marburg Germany
- Donostia International Physics Center (DIPC) Donostia Spain
| |
Collapse
|
28
|
Maxwell PI, Popelier PLA. Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective. J Comput Chem 2017; 38:2459-2474. [PMID: 28841241 PMCID: PMC5659141 DOI: 10.1002/jcc.24904] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 01/06/2023]
Abstract
Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and atomic levels are observed across both (1) the three amino acids and (2) the φ/ψ scans in Ramachandran plots. At the molecular level, it is surprisingly electrostatic destabilization that causes the high-energy regions in the Ramachandran plot, not molecular steric hindrance (related to the intra-atomic energy). At the functional group and atomic levels, the importance of key peptide atoms (Oi-1 , Ci , Ni , Ni+1 ) and some sidechain hydrogen atoms (Hγ ) are identified as responsible for the destabilization seen in the energetically disfavored Ramachandran regions. Consistently, the Oi-1 atoms are particularly important for the explanation of dipeptide intrinsic behavior, where electrostatic and steric destabilization unusually complement one another. The findings suggest that, at least for these dipeptides, it is the peptide group atoms that dominate the intrinsic behavior, more so than the sidechain atoms. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Peter I. Maxwell
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain and School of Chemistry, University of Manchester, Oxford RoadManchesterGreat BritainM13 9PL
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain and School of Chemistry, University of Manchester, Oxford RoadManchesterGreat BritainM13 9PL
| |
Collapse
|
29
|
Jara-Cortés J, Hernández-Trujillo J. Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method. J Comput Chem 2017; 39:1103-1111. [PMID: 29076165 DOI: 10.1002/jcc.25089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 09/04/2017] [Accepted: 10/06/2017] [Indexed: 01/21/2023]
Abstract
A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clar's sextet rules devised for aromatic systems. In addition, the H⋯H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Jesús Jara-Cortés
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, México City, 04510, México
| | | |
Collapse
|
30
|
Jara-Cortés J, Guevara-Vela JM, Martín Pendás Á, Hernández-Trujillo J. Chemical bonding in excited states: Energy transfer and charge redistribution from a real space perspective. J Comput Chem 2017; 38:957-970. [PMID: 28266036 DOI: 10.1002/jcc.24769] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 11/11/2022]
Abstract
This work provides a novel interpretation of elementary processes of photophysical relevance from the standpoint of the electron density using simple model reactions. These include excited states of H2 taken as a prototype for a covalent bond, excimer formation of He2 to analyze non-covalent interactions, charge transfer by an avoided crossing of electronic states in LiF and conical interesections involved in the intramolecular scrambling in C2 H4 . The changes of the atomic and interaction energy components along the potential energy profiles are described by the interacting quantum atoms approach and the quantum theory of atoms in molecules. Additionally, the topological analysis of one- and two-electron density functions is used to explore basic reaction mechanisms involving excited and degenerate states in connection with the virial theorem. This real space approach allows to describe these processes in a unified way, showing its versatility and utility in the study of chemical systems in excited states. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Jesús Jara-Cortés
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, México City, 04510, México
| | - José Manuel Guevara-Vela
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain
| | | |
Collapse
|
31
|
Francisco E, Menéndez Crespo D, Costales A, Martín Pendás Á. A multipolar approach to the interatomic covalent interaction energy. J Comput Chem 2017; 38:816-829. [PMID: 28211059 DOI: 10.1002/jcc.24758] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 11/08/2022]
Abstract
Interatomic exchange-correlation energies correspond to the covalent energetic contributions to an interatomic interaction in real space theories of the chemical bond, but their widespread use is severely limited due to their computationally intensive character. In the same way as the multipolar (mp) expansion is customary used in biomolecular modeling to approximate the classical Coulomb interaction between two charge densities ρA(r) and ρB(r), we examine in this work the mp approach to approximate the interatomic exchange-correlation (xc) energies of the Interacting Quantum Atoms method. We show that the full xc mp series is quickly divergent for directly bonded atoms (1-2 pairs) albeit it works reasonably well most times for 1- n (n > 2) interactions. As with conventional perturbation theory, we show numerically that the xc series is asymptotically convergent and that, a truncated xc mp approximation retaining terms up to l1+l2=2 usually gives relatively accurate results, sometimes even for directly bonded atoms. Our findings are supported by extensive numerical analyses on a variety of systems that range from several standard hydrogen bonded dimers to typically covalent or aromatic molecules. The exact algebraic relationship between the monopole-monopole xc mp term and the inter-atomic bond order, as measured by the delocalization index of the quantum theory of atoms in molecules, is also established. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Evelio Francisco
- Departamento de Química Física y Analítica, Facultad de Química. Universidad de Oviedo, Oviedo, 33006, Spain
| | - Daniel Menéndez Crespo
- Departamento de Química Física y Analítica, Facultad de Química. Universidad de Oviedo, Oviedo, 33006, Spain
| | - Aurora Costales
- Departamento de Química Física y Analítica, Facultad de Química. Universidad de Oviedo, Oviedo, 33006, Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química. Universidad de Oviedo, Oviedo, 33006, Spain
| |
Collapse
|
32
|
Moreno-Alcántar G, Manuel Guevara-Vela J, Delgadillo-Ruíz R, Rocha-Rinza T, Martín Pendás Á, Flores-Álamo M, Torrens H. Structural effects of trifluoromethylation and fluorination in gold(i) BIPHEP fluorothiolates. NEW J CHEM 2017. [DOI: 10.1039/c7nj02202f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ligand effects on the non-covalent interactions of phosphine gold(i) fluorothiolates were analysed using the QTAIM and NCI.
Collapse
Affiliation(s)
- Guillermo Moreno-Alcántar
- School of Chemistry
- National Autonomous University of Mexico
- Circuito Escolar
- Ciudad Universitaria
- Delegación Coyoacán
| | | | - Rafael Delgadillo-Ruíz
- School of Chemistry
- National Autonomous University of Mexico
- Circuito Escolar
- Ciudad Universitaria
- Delegación Coyoacán
| | - Tomás Rocha-Rinza
- Institute of Chemistry
- National Autonomous University of Mexico
- Circuito Exterior
- Ciudad Universitaria
- Delegación Coyoacán
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry
- University of Oviedo
- E-33006
- Julían Clavería
- Oviedo
| | - Marcos Flores-Álamo
- School of Chemistry
- National Autonomous University of Mexico
- Circuito Escolar
- Ciudad Universitaria
- Delegación Coyoacán
| | - Hugo Torrens
- School of Chemistry
- National Autonomous University of Mexico
- Circuito Escolar
- Ciudad Universitaria
- Delegación Coyoacán
| |
Collapse
|
33
|
Barquera-Lozada JE. Torquoselectivity in Cyclobutene Ring Openings and the Interatomic Interactions That Control Them. J Phys Chem A 2016; 120:8450-8460. [PMID: 27723338 DOI: 10.1021/acs.jpca.6b08771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Torquoselectivity has explained diasteromeric preferences of a number electrocyclic ring openings. The quantum theory of atoms in molecules (QTAIM), the electron localizability indicator (ELI-D), and the interacting quantum atoms (IQA) energy partition method are used to evaluate qualitatively and quantitatively the atomic interactions behind the torquoselectivity of a series of 3-substituted cyclobutenes. ELI-D topology and IQA energies show that the interaction between the distal terminus carbon atom of cyclobutene (C4) with the substituent at C3 (R5) in the transition state governs torquoselectivities. In the case of 3-borylcyclobutene, this interaction is so strong that a protocovalent bond is actually formed between B5 and C4. The evaluation of the interatomic energies allowed us to identify an additional interaction that contribute to a minor extent to the stabilization of the TS. Despite the fact that C4,R5 interaction is the main cause of the torquoselectivity, a bonding path (BP) between these two atoms was not observed. However, the lack of a BP between C4 and R5 does not mean that the topology of the electron density was not affected by the interaction of these two atoms. Surprisingly, we found a strong correlation between the density at the bond critical point (BCP) and the BP shape of C3-C4 breaking bond with the observed activation energies and torquoselectivities.
Collapse
Affiliation(s)
- José Enrique Barquera-Lozada
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito exterior, Ciudad Universitaria Coyoacán, México, D.F., México 04510
| |
Collapse
|
34
|
Cukrowski I, Sagan F, Mitoraj MP. On the Stability of Cis- and Trans-2-Butene Isomers. An Insight Based on the FAMSEC, IQA, and ETS-NOCV Schemes. J Comput Chem 2016; 37:2783-2798. [PMID: 27730662 DOI: 10.1002/jcc.24504] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/08/2016] [Accepted: 09/10/2016] [Indexed: 01/19/2023]
Abstract
In the present account, the real space fragment attributed molecular system energy change (FAMSEC) approach, interacting quantum atoms energy decomposition scheme as well as molecular orbitals based the extended transition state scheme coupled with natural orbitals for chemical valence (ETS-NOCV) have been, for the first time, successfully used to delineate factors of importance for stability of the 2-butene conformers (cis-eq, cis-TS, trans-eq, trans-TS). Our results demonstrate that atoms of the controversial H-H contact in cis-eq (i) are involved in attractive interaction dominated by the exchange-correlation term, (ii) are weekly stabilized, (iii) show trends in several descriptors found in other typical H-bonds, and (iv) are part of most stabilized CH-HC fragment (loc-FAMSEC = -3.6 kcal/mol) with most favourably changed intrafragment interactions on trans-eq→cis-eq. Moreover, lower stability of cis-eq vs. trans-eq is linked with the entire HCCH (ethylenic) fragment which destabilized cis-eq (mol-FAMSEC, +3.9 kcal/mol) the most. Although the H-H contact can be linked with smaller, relative to trans-, rotational energy barrier in cis-2-butene, we have proven that to rationalize this phenomenon one must account for changes in interactions between various fragments that constitute the entire molecule. Importantly, we discovered a number of comparable trends in fundamental properties of equivalent molecular fragments on a methyl group rotation; for example, interaction between BP-free H-atoms in trans-eq (involving CH bonds of the methyl and ethylenic units) and BP-linked H-atoms in cis-eq. Clearly, rotational energy barrier cannot be entirely (i) rationalized by the properties of or (ii) attributed to the H-H contact in cis-eq. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Filip Sagan
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Mariusz Paweł Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| |
Collapse
|
35
|
Salter EA, Wierzbicki A. The response electron–electron repulsion energy and energy component analysis in CC/MBPT methods. Struct Chem 2016. [DOI: 10.1007/s11224-016-0775-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
36
|
Matczak P. Intramolecular C–H···H–C Contacts in Diheteroaryl Ketones and Thioketones: A Theoretical Analysis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20150229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Piotr Matczak
- Department of Theoretical and Structural Chemistry, Faculty of Chemistry, University of Łódź
| |
Collapse
|
37
|
On Quantum Chemical Topology. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2016. [DOI: 10.1007/978-3-319-29022-5_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
38
|
|
39
|
Fletcher TL, Davie SJ, Popelier PLA. Prediction of Intramolecular Polarization of Aromatic Amino Acids Using Kriging Machine Learning. J Chem Theory Comput 2015; 10:3708-19. [PMID: 26588516 DOI: 10.1021/ct500416k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Present computing power enables novel ways of modeling polarization. Here we show that the machine learning method kriging accurately captures the way the electron density of a topological atom responds to a change in the positions of the surrounding atoms. The success of this method is demonstrated on the four aromatic amino acids histidine, phenylalanine, tryptophan, and tyrosine. A new technique of varying training set sizes to vastly reduce training times while maintaining accuracy is described and applied to each amino acid. Each amino acid has its geometry distorted via normal modes of vibration over all local energy minima in the Ramachandran map. These geometries are then used to train the kriging models. Total electrostatic energies predicted by the kriging models for previously unseen geometries are compared to the true energies, yielding mean absolute errors of 2.9, 5.1, 4.2, and 2.8 kJ mol(-1) for histidine, phenylalanine, tryptophan, and tyrosine, respectively.
Collapse
Affiliation(s)
- Timothy L Fletcher
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester, M1 7DN, Great Britain.,School of Chemistry, University of Manchester , Oxford Road, Manchester, M13 9PL, Great Britain
| | - Stuart J Davie
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester, M1 7DN, Great Britain.,School of Chemistry, University of Manchester , Oxford Road, Manchester, M13 9PL, Great Britain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester, M1 7DN, Great Britain.,School of Chemistry, University of Manchester , Oxford Road, Manchester, M13 9PL, Great Britain
| |
Collapse
|
40
|
Stojanović M, Aleksić J, Baranac-Stojanović M. The effect of steric repulsion on the torsional potential of n-butane: a theoretical study. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
41
|
Bartashevich EV, Pendás ÁM, Tsirelson VG. An anatomy of intramolecular atomic interactions in halogen-substituted trinitromethanes. Phys Chem Chem Phys 2015; 16:16780-9. [PMID: 25001471 DOI: 10.1039/c4cp01257g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The intramolecular interactions in substituted trinitromethanes, XC(NO2)3 (X = F, Cl, I, H) are studied and clarified by using a combination of the Quantum Theory of Atoms in Molecules (QTAIM), the non-covalent interaction analysis and the Interacting Quantum Atoms (IQA) methods. The stretching vibration modes are formed by the concerted displacements of atoms involved in the covalent bonds showing the significant multiatomic influence in substituted trinitromethanes. In agreement with that, the arrangement of the local reduced density gradient minima indicates that the electron density favors the non-covalent intramolecular interactions X···O and N···O. However, the corresponding QTAIM bond paths are not formed; instead, contacts, which we call uncompleted links in this context, are accompanied by "quasi-bonding channels" corresponding to the λ2() ≤ 0 regions on the sign[λ2(r)]ρ(r) contour maps. The intramolecular IQA energy contributions signal the appreciable electron exchange between the pairs of atoms associated with potential atomic interactions or the bond-path-free non-covalent links. The IQA analysis shows that the electrostatic term destabilizes FC(NO2)3 and distinctly stabilizes IC(NO2)3, whereas it is close to neutral in ClC(NO2)3. The exchange energy between the X atom and the NO2 groups, in contrast, stabilizes all the molecules.
Collapse
Affiliation(s)
- Ekaterina V Bartashevich
- Department of Chemistry, South Ural State University (National Research University), 454080 Chelyabinsk, Russia.
| | | | | |
Collapse
|
42
|
Tiana D, Francisco E, Macchi P, Sironi A, Martín Pendás A. An Interacting Quantum Atoms Analysis of the Metal–Metal Bond in [M2(CO)8]n Systems. J Phys Chem A 2015; 119:2153-60. [DOI: 10.1021/acs.jpca.5b00070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Davide Tiana
- Department
of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, U.K
| | - E. Francisco
- Departamento
de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006- Oviedo, Spain
| | - P. Macchi
- Department
of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Angelo Sironi
- Department
of Chemistry, University of Milan, Via Golgi 19, 20133 Milan, Italy
| | - A. Martín Pendás
- Departamento
de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006- Oviedo, Spain
| |
Collapse
|
43
|
|
44
|
|
45
|
Ferro-Costas D, Mosquera RA. Excluding hyperconjugation from the Z conformational preference and investigating its origin: formic acid and beyond. Phys Chem Chem Phys 2015; 17:26946-54. [DOI: 10.1039/c5cp03805g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A scheme indicating that the preference for the Z conformer in proteins is chemically equivalent to that of amides. Other compounds, such as carboxylic acids, also exhibit the same conformational trend.
Collapse
Affiliation(s)
- David Ferro-Costas
- Departamento de Química Física
- Universidade de Vigo
- Facultade de Química
- 36310 Vigo
- Spain
| | - Ricardo A. Mosquera
- Departamento de Química Física
- Universidade de Vigo
- Facultade de Química
- 36310 Vigo
- Spain
| |
Collapse
|
46
|
Cortés-Guzmán F, Cuevas G, Martín Pendás Á, Hernández-Trujillo J. The rotational barrier of ethane and some of its hexasubstituted derivatives in terms of the forces acting on the electron distribution. Phys Chem Chem Phys 2015; 17:19021-9. [DOI: 10.1039/c5cp02774h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rotational barrier of ethane and some of its hexasubstituted derivatives is mainly a consequence of the decrease of the attractive forces acting on the electron density of the central C atoms.
Collapse
Affiliation(s)
- Fernando Cortés-Guzmán
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito Escolar
- Cd. Universitaria
- Mexico, D.F
| | - Gabriel Cuevas
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito Escolar
- Cd. Universitaria
- Mexico, D.F
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica
- Facultad de Química
- Universidad de Oviedo
- E-33006-Oviedo
- Spain
| | - Jesús Hernández-Trujillo
- Facultad de Química
- Universidad Nacional Autónoma de México
- Circuito Escolar
- Cd. Universitaria
- Mexico, D.F
| |
Collapse
|
47
|
Uzoh OG, Galek PTA, Price SL. Analysis of the conformational profiles of fenamates shows route towards novel, higher accuracy, force-fields for pharmaceuticals. Phys Chem Chem Phys 2015; 17:7936-48. [DOI: 10.1039/c4cp05525j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational barriers of the fenamates which lead to conformational polymorphism can be represented by a novel, physically motivated, model intramolecular potential suitable for extension to other pharmaceuticals.
Collapse
Affiliation(s)
- Ogaga G. Uzoh
- Department of Chemistry
- University College London
- London
- UK
| | | | - Sarah L. Price
- Department of Chemistry
- University College London
- London
- UK
| |
Collapse
|
48
|
Foroutan-Nejad C, Shahbazian S, Marek R. Toward a Consistent Interpretation of the QTAIM: Tortuous Link between Chemical Bonds, Interactions, and Bond/Line Paths. Chemistry 2014; 20:10140-52. [DOI: 10.1002/chem.201402177] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Indexed: 11/10/2022]
|
49
|
Parafiniuk M, Mitoraj MP. On the origin of internal rotation in ammonia borane. J Mol Model 2014; 20:2272. [PMID: 24863530 PMCID: PMC4072093 DOI: 10.1007/s00894-014-2272-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/24/2014] [Indexed: 01/18/2023]
Abstract
The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol−1), based on the charge transfer from the occupied σ (B–H) orbitals into the empty σ*(N–H), slightly favors the staggered conformation over the eclipsed one; however, the barrier to internal rotation in ammonia borane can be understood predominantly in a ‘classical’ way, as originating from the steric (Pauli) repulsion contributions (of the kinetic origin) that act solely between N–H and B–H bonds. Repulsion between the lone pair of ammonia and the adjacent B–H bonds was found to be dominant in absolute terms; however, it does not determine the rotational barrier. Similar conclusions on the role of CH↔HC repulsion appeared to be valid for isoelectronic ethane. Pauli (kinetic) repulsion acting between the N-H and B-H bonds of ammonia borane ![]()
Collapse
Affiliation(s)
- Monika Parafiniuk
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R.Ingardena 3, 30-060 Krakow, Poland
| | - Mariusz P. Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R.Ingardena 3, 30-060 Krakow, Poland
| |
Collapse
|
50
|
Ferro-Costas D, Pendás ÁM, González L, Mosquera RA. Beyond the molecular orbital conception of electronically excited states through the quantum theory of atoms in molecules. Phys Chem Chem Phys 2014; 16:9249-58. [DOI: 10.1039/c4cp00431k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Application of QTAIM electron density analysis and energy partitioning based on it provide quantitative support for qualitative predictions derived from the MO paradigm, as well as further descriptions for electron density rearrangements in electronically excited states.
Collapse
Affiliation(s)
- David Ferro-Costas
- Departamento de Química Física
- Universidade de Vigo
- Facultade de Química
- 36310 Vigo, Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica
- Facultad de Química
- Universidad de Oviedo
- 33006-Oviedo, Spain
| | - Leticia González
- Institute of Theoretical Chemistry
- University of Vienna
- 1090 Vienna, Austria
| | - Ricardo A. Mosquera
- Departamento de Química Física
- Universidade de Vigo
- Facultade de Química
- 36310 Vigo, Spain
| |
Collapse
|