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Martín Pendás Á, Francisco E. The role of references and the elusive nature of the chemical bond. Nat Commun 2022; 13:3327. [PMID: 35680893 PMCID: PMC9184482 DOI: 10.1038/s41467-022-31036-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Chemical bonding theory is of utmost importance to chemistry, and a standard paradigm in which quantum mechanical interference drives the kinetic energy lowering of two approaching fragments has emerged. Here we report that both internal and external reference biases remain in this model, leaving plenty of unexplored territory. We show how the former biases affect the notion of wavefunction interference, which is purportedly recognized as the most basic bonding mechanism. The latter influence how bonding models are chosen. We demonstrate that the use of real space analyses are as reference-less as possible, advocating for their use. Delocalisation emerges as the reference-less equivalent to interference and the ultimate root of bonding. Atoms (or fragments) in molecules should be understood as a statistical mixture of components differing in electron number, spin, etc. The theory of chemical bonding relies on arbitrary references. Here the authors report a fundamental study on the chemical bond showing that considering the binding fragments as objects in real space enables to eliminate inherent biases.
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Affiliation(s)
- Ángel Martín Pendás
- 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
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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.
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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;
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Pendás ÁM, Francisco E. Chemical Bonding from the Statistics of the Electron Distribution. Chemphyschem 2019; 20:2722-2741. [DOI: 10.1002/cphc.201900641] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de QuímicaUniversidad de Oviedo 33006- Oviedo Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Facultad de QuímicaUniversidad de Oviedo 33006- Oviedo Spain
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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.
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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.
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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.
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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
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Holguín-Gallego FJ, Chávez-Calvillo R, García-Revilla M, Francisco E, Pendás ÁM, Rocha-Rinza T. Electron correlation in the interacting quantum atoms partition via coupled-cluster lagrangian densities. J Comput Chem 2016; 37:1753-65. [DOI: 10.1002/jcc.24372] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Fernando José Holguín-Gallego
- Institute of Chemistry; National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria; Delegación Coyoacán C.P. 04510 Mexico City Mexico
| | - Rodrigo Chávez-Calvillo
- School of Chemistry; National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria; Delegación Coyoacán C.P. 04510 Mexico City Mexico
| | - Marco García-Revilla
- Department of Chemistry; Division of Natural and Exact Sciences; University of Guanajuato; C.P. 36050, Guanajuato Guanajuato Mexico
| | - Evelio Francisco
- Department of Physical and Analytical Chemistry; University of Oviedo; Julián Clavería 8 Oviedo Spain
| | - Ángel Martín Pendás
- Department of Physical and Analytical Chemistry; University of Oviedo; Julián Clavería 8 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
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Francisco E, Martín Pendás A. Towards an energy partition into real space resonance structures: 1- and 2-particle density matrix decomposition. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1121296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- E. Francisco
- Departamento de Química Física y Analítica. Facultad de Química. Universidad de Oviedo. Oviedo. Spain
| | - A. Martín Pendás
- Departamento de Química Física y Analítica. Facultad de Química. Universidad de Oviedo. Oviedo. Spain
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Chávez-Calvillo R, García-Revilla M, Francisco E, Martín Pendás Á, Rocha-Rinza T. Dynamical correlation within the Interacting Quantum Atoms method through coupled cluster theory. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Guevara-Vela JM, Chávez-Calvillo R, García-Revilla M, Hernández-Trujillo J, Christiansen O, Francisco E, Martín Pendás Á, Rocha-Rinza T. Hydrogen-Bond Cooperative Effects in Small Cyclic Water Clusters as Revealed by the Interacting Quantum Atoms Approach. Chemistry 2013; 19:14304-15. [DOI: 10.1002/chem.201300656] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/11/2013] [Indexed: 11/08/2022]
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Angeli C, Cimiraglia R, Malrieu JP. Non-orthogonal and orthogonal valence bond wavefunctions in the hydrogen molecule: the diabatic view. Mol Phys 2013. [DOI: 10.1080/00268976.2013.771803] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Celestino Angeli
- a Dipartimento di Scienze Chimiche e Farmaceutiche , Università di Ferrara , Ferrara , Italy
| | - Renzo Cimiraglia
- a Dipartimento di Scienze Chimiche e Farmaceutiche , Università di Ferrara , Ferrara , Italy
| | - Jean-Paul Malrieu
- b Laboratoire de Chimie et Physique Quantiques , Université Paul Sabatier , Toulouse , France
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García-Revilla M, Popelier PLA, Francisco E, Martín Pendás Á. Nature of Chemical Interactions from the Profiles of Electron Delocalization Indices. J Chem Theory Comput 2011; 7:1704-11. [PMID: 26596434 DOI: 10.1021/ct2001842] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We analyze the behavior of the profiles of delocalization indices (DIs) between relevant pairs of atoms along reaction coordinates for a set of model chemical processes. A relationship between the topology of the DI and the nature of the underlying chemical change is reported. As shown, exponential shapes correspond to the traditional category of repulsive/nonbonded interactions, while sigmoidal profiles signal the formation/breaking of chemical links.
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Affiliation(s)
- Marco García-Revilla
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo , E-33006-Oviedo, Spain
| | - Paul L A Popelier
- Manchester Interdisciplinary Biocentre (MIB) , 131 Princess Street, Manchester M1 7DN, United Kingdom and School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo , E-33006-Oviedo, Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo , E-33006-Oviedo, Spain
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Generalized electron number distribution functions: real space versus orbital space descriptions. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0809-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Francisco E, Martín Pendás A, Blanco MA. A connection between domain-averaged Fermi hole orbitals and electron number distribution functions in real space. J Chem Phys 2009; 131:124125. [DOI: 10.1063/1.3239467] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Pendás AM, Blanco MA, Francisco E. Steric repulsions, rotation barriers, and stereoelectronic effects: A real space perspective. J Comput Chem 2009; 30:98-109. [DOI: 10.1002/jcc.21034] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Evidence that the bond paths of the quantum theory of atoms-in-molecules (QTAIM) signal preferred quantum-mechanical exchange channels is presented. We show how bond paths between an atom A and the atoms B in its environment appear to be determined by competition among the A-B exchange-correlation energies that always contribute to stabilize the A-B interactions. These pairwise additive stabilizations depend neither on the attractive or repulsive nature of the classical electrostatic interaction between the atoms' charge densities, nor on the change in the self energies of the atoms involved. These other terms may well cause an overall molecular-energy increase in spite of a possibly large A-B exchange-correlation stabilization. After our proposal, bond paths, both at and out of equilibrium geometries, are endowed with a specific energetic meaning that should contribute to reconcile the orthodox QTAIM interpretation with other widely accepted views, and to settle recent controversies questioning the meaning of hydrogen-hydrogen bonding and the nature of the so-called "steric interactions", the role of bond paths in endohedral complexes, and the generality of the results provided by the QTAIM. Implications for the nature of more general closed-shell interactions are also briefly discussed.
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Affiliation(s)
- A Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain.
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Martín Pendás A, Francisco E, Blanco MA. Spin resolved electron number distribution functions: How spins couple in real space. J Chem Phys 2007; 127:144103. [DOI: 10.1063/1.2784392] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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