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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.
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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
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2
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Zapata-Acevedo CA, Guevara-Vela JM, Popelier PLA, Rocha Rinza T. Binding Energy Partition of Promising IRAK-4 Inhibitor (Zimlovisertib) for the Treatment of COVID-19 Pneumonia. Chemphyschem 2022; 23:e202200455. [PMID: 36044560 PMCID: PMC9538207 DOI: 10.1002/cphc.202200455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/19/2022] [Indexed: 01/05/2023]
Abstract
The technique of Fragment-Based Drug Design (FBDD) considers the interactions of different moieties of molecules with biological targets for the rational construction of potential drugs. One basic assumption of FBDD is that the different functional groups of a ligand interact with a biological target in an approximately additive, that is, independent manner. We investigated the interactions of different fragments of ligands and Interleukin-1 Receptor-Associated Kinase 4 (IRAK-4) throughout the FBDD design of Zimlovisertib, a promising anti-inflammatory, currently in trials to be used for the treatment of COVID-19 pneumonia. We utilised state-of-the-art methods of wave function analyses mainly the Interacting Quantum Atoms (IQA) energy partition for this purpose. By means of IQA, we assessed the suitability of every change to the ligand in the five stages of FBDD which led to Zimlovisertib on a quantitative basis. We determined the energetics of the interaction of different functional groups in the ligands with the IRAK-4 protein target and thereby demonstrated the adequacy (or lack thereof) of the changes made across the design of this drug. This analysis permits to verify whether a given alteration of a prospective drug leads to the intended tuning of non-covalent interactions with its protein objective. Overall, we expect that the methods exploited in this paper will prove valuable in the understanding and control of chemical modifications across FBDD processes.
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Affiliation(s)
- César Arturo Zapata-Acevedo
- Tecnologico de Monterrey: Instituto Tecnologico y de Estudios Superiores de MonterreyChemistryAv. Carlos Lazo 100Santa Fe, La Loma01389Álvaro ObregónMEXICO
| | | | - Paul L. A. Popelier
- UoM: The University of ManchesterChemistryOxford RoadM13 9PLManchesterUNITED KINGDOM
| | - Tomás Rocha Rinza
- Institute Of Chemistry, National Autonomous University of MexicoDepartment of Physical ChemistryCircuito Exterior, Ciudad Universitaria04510Mexico CityMEXICO
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3
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Jara-Cortés J, Matta CF, Hernández-Trujillo J. A fast approximate extension of the interacting quantum atoms energy decomposition to excited states. J Comput Chem 2022; 43:1068-1078. [PMID: 35470908 DOI: 10.1002/jcc.26863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/11/2022]
Abstract
An approach is developed for the fast calculation of the interacting quantum atoms energy decomposition (IQA) from the information contained in the first order reduced density matrix only. The proposed methodology utilizes an approximate exchange-correlation density from Density Matrix Functional Theory without the need to evaluate the correlation-exchange contribution directly. Instead, weight factors are estimated to decompose the exact Vxc into atomic and pairwise contributions. In this way, the sum of the IQA contributions recovers the energy obtained from the electronic structure calculation. This method can, hence, be applied to obtain atomic contributions in excited states on the same footing as in their ground states using any method that delivers the reduced first-order density matrix. In this way, one can locate chromophores from first principles quantum chemical calculations. Test calculations on the ground and excited states of a set of small molecules indicate that the scaled atomic contributions reproduce vertical electronic transition energies calculated exactly. This approach may be useful to extend the applicability of the IQA approach in the study of large photochemical systems especially when the calculations of the second order reduced density matrices is prohibitive or not possible.
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Affiliation(s)
- Jesús Jara-Cortés
- Unidad Académica de Ciencias Básicas e Ingenierías, Universidad Autónoma de Nayarit, Tepic, Mexico
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada
| | - Jesús Hernández-Trujillo
- Departamento de Física y Química Teórica, Facultad de Química, UNAM. Circuito Escolar, Ciudad Universitaria, Mexico City, Mexico
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Jara-Cortés J, Leal-Sánchez E, Francisco E, Pérez-Pimienta JA, Martín Pendás Á, Hernández-Trujillo J. Implementation of the interacting quantum atom energy decomposition using the CASPT2 method. Phys Chem Chem Phys 2021; 23:27508-27519. [PMID: 34874377 DOI: 10.1039/d1cp02837e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present an implementation of the interacting quantum atom (IQA) energy decomposition scheme using the complete active space second-order perturbation theory (CASPT2). This combination yields a real-space interpretation tool with a proper account of the static and dynamic correlation that is particularly relevant for the description of processes in electronic excited states. The IQA/CASPT2 approach allows determination of the energy redistribution that takes place along a photophysical/photochemical deactivation path in terms of self- and interatomic contributions. The applicability of the method is illustrated by the description of representative processes spanning different bonding regimes: noble gas excimer and exciplex formation, the reaction of ozone with a chlorine atom, and the photodissociations of formaldehyde and cyclobutane. These examples show the versatility of using CASPT2 with the significant information provided by the IQA partition to describe chemical processes with a large multiconfigurational character.
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Affiliation(s)
- Jesús Jara-Cortés
- Unidad Académica de Ciencias Básicas e Ingenierías, Universidad Autónoma de Nayarit, Tepic 63155, Mexico.
| | - Edith Leal-Sánchez
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, México City 04510, Mexico
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Faculta de Química, Universidad de Oviedo, Oviedo 33006, Spain
| | - José A Pérez-Pimienta
- Unidad Académica de Ciencias Básicas e Ingenierías, Universidad Autónoma de Nayarit, Tepic 63155, Mexico.
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Faculta de Química, Universidad de Oviedo, Oviedo 33006, Spain
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Guerra C, Ayarde-Henríquez L, Duque-Noreña M, Cárdenas C, Pérez P, Chamorro E. On the nature of bonding in the photochemical addition of two ethylenes: C-C bond formation in the excited state? Phys Chem Chem Phys 2021; 23:20598-20606. [PMID: 34505860 DOI: 10.1039/d1cp03554a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, the 2s + 2s (face-to-face) prototypical example of a photochemical reaction has been re-examined to characterize the evolution of chemical bonding. The analysis of the electron localization function (as an indirect measure of the Pauli principle) along the minimum energy path provides strong evidence supporting that CC bond formation occurs not in the excited state but in the ground electronic state after crossing the rhombohedral S1/S0 conical intersection.
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Affiliation(s)
- Cristian Guerra
- Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Químicas, Avenida República 275, 8370146, Santiago, Chile.
| | - Leandro Ayarde-Henríquez
- Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Químicas, Avenida República 275, 8370146, Santiago, Chile.
| | - Mario Duque-Noreña
- Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Químicas, Avenida República 275, 8370146, Santiago, Chile.
| | - Carlos Cárdenas
- Universidad de Chile, Facultad de Ciencias, Departamento de Física, Avenida Las Palmeras 3425, Santiago, Chile. .,Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), 9170124 Santiago, Chile
| | - Patricia Pérez
- Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Químicas, Avenida República 275, 8370146, Santiago, Chile.
| | - Eduardo Chamorro
- Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Químicas, Avenida República 275, 8370146, Santiago, Chile.
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Fernández-Alarcón A, Guevara-Vela JM, Casals-Sainz JL, Francisco E, Costales A, Martín Pendás Á, Rocha-Rinza T. The nature of the intermolecular interaction in (H 2X) 2 (X = O, S, Se). Phys Chem Chem Phys 2021; 23:10097-10107. [PMID: 33876160 DOI: 10.1039/d1cp00047k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bonds (HBs) are crucial non-covalent interactions in chemistry. Recently, the occurrence of an HB in (H2S)2 has been reported (Arunan et al., Angew. Chem., Int. Ed., 2018, 57, 15199), challenging the textbook view of H2S dimers as mere van der Waals clusters. We herein try to shed light on the nature of the intermolecular interactions in the H2O, H2S, and H2Se dimers via correlated electronic structure calculations, Symmetry Adapted Perturbation Theory (SAPT) and Quantum Chemical Topology (QCT). Although (H2S)2 and (H2Se)2 meet some of the criteria for the occurrence of an HB, potential energy curves as well as SAPT and QCT analyses indicate that the nature of the interaction in (H2O)2 is substantially different (e.g. more anisotropic) from that in (H2S)2 and (H2Se)2. QCT reveals that the HB in (H2O)2 includes substantial covalent, dispersion and electrostatic contributions, while the last-mentioned component plays only a minor role in (H2S)2 and (H2Se)2. The major contributions to the interactions of the dimers of H2S and H2Se are covalency and dispersion as revealed by the exchange-correlation components of QCT energy partitions. The picture yielded by SAPT is somewhat different but compatible with that offered by QCT. Overall, our results indicate that neither (H2S)2 nor (H2Se)2 are hydrogen-bonded systems, showing how the nature of intermolecular contacts involving hydrogen atoms evolves in a group down the periodic table.
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Affiliation(s)
- Alberto Fernández-Alarcón
- Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, C.P. 04510, Mexico City, Mexico.
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Fernández-Alarcón A, Guevara-Vela JM, Casals-Sainz JL, Costales A, Francisco E, Martín Pendás Á, Rocha Rinza T. Photochemistry in Real Space: Batho- and Hypsochromism in the Water Dimer. Chemistry 2020; 26:17035-17045. [PMID: 32822523 DOI: 10.1002/chem.202002854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Indexed: 11/09/2022]
Abstract
The development of chemical intuition in photochemistry faces several difficulties that result from the inadequacy of the one-particle picture, the Born-Oppenheimer approximation, and other basic ideas used to build models. It is shown herein how real-space approaches can be efficiently used to gain valuable insights in photochemistry through a simple example of red and blue shift effects: the double hypso- and bathochromic shifts in the low-lying valence excited states of (H2 O)2 . It is demonstrated that 1) the use of these techniques allows the perturbative language used in the theory of intermolecular interactions, even in the strongly interacting short-range regime, to be maintained; 2) one and only one molecule is photoexcited in each of the addressed excited states and 3) the electrostatic interaction between the in-the-cluster molecular dipoles provides a fairly intuitive rationalisation of the observed batho- and hypsochromism. The methods exploited and illustrated herein are able to maintain the individuality and properties of the interacting entities in a molecular aggregate, and thereby they allow chemical intuition in general states, at any geometry and using a broad variety of electronic structure methods to be kept and built.
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Affiliation(s)
- Alberto Fernández-Alarcón
- Institute of Chemistry, National Autonomous University of Mexico, 04510, Mexico City, Mexico.,Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | | | - José Luis Casals-Sainz
- Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | - Aurora Costales
- Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | - Evelio Francisco
- Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | - Tomás Rocha Rinza
- Institute of Chemistry, National Autonomous University of Mexico, 04510, Mexico City, Mexico
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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: 55] [Impact Index Per Article: 13.8] [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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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
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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 .
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