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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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Ochoa-Resendiz D, Gamboa-Suárez A, Hernández-Lamoneda R. Halogen bonding and rotational disorder in chlorine clathrate hydrate cages. J Chem Phys 2022; 156:124302. [DOI: 10.1063/5.0082604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a detailed theoretical characterization of the structure and interactions in dichlorine clathrate hydrate cages. In the case of the dodecahedral cage there is clear evidence of the presence of halogen bonding whereas in the tetrakaidecahedral the expected signatures are there but in a weaker form. Comparison is made with the available structural data from X-ray experiments, where the rotational motion of the dichlorine has been taken into account through Monte Carlo simulations illustrating delocalization effects associated with sampling multiple minima, specifically for the larger cage. Finally, the intermolecular potentials have been calculated with local correlation methods and energy decomposition analysis has been applied to shed light on the nature of the interactions.
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Li D, Xia T, Feng W, Cheng L. Revisiting the covalent nature of halogen bonding: a polarized three-center four-electron bond. RSC Adv 2021; 11:32852-32860. [PMID: 35493597 PMCID: PMC9042191 DOI: 10.1039/d1ra05695f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
As an important intermolecular interaction, halogen bonding has been studied extensively, but its nature still suffers from controversy without one uniform essence. Electrostatics, charge transfer, polarization and dispersion are emphasized, but the covalent nature is usually overlooked except for the strong halogen bonding species I3−, which is widely accepted as a result of a three-center four-electron (3c-4e) interaction. In our study, the potential energy surface of I3− has been evaluated to explore the dissociation from I3− to I2⋯I−. We found that different from an equivalent 3c-4e bond in I3−, I2⋯I− can be rationalized by a polarized one. In addition, when the orbitals are polarized, it is exactly what traditional charge transfer or the popular σ-hole picture describes. I3− can be described by the Lewis theory model with the middle I+ cation serving as the Lewis acid and two terminal I− anions acting as Lewis base. Therefore, we further extended this model to a series of I-containing species with chemical composition of L–I+–L, F−–I+–L and H3P–I+–L (L = OH−, F−, Cl−, Br−, I−, PH3, NH3, H2S, HI, H2O, HBr and HCl) to explore the nature of halogen bonding. When the forces of two bases around I+ are the same, it corresponds to an equivalent 3c-4e bond, such as I3−. Otherwise, it is a polarized multicenter bond, such as I2⋯I−. This work gives a new insight into the nature of halogen bonding compounds: besides the well-known I3−, the nature of the other species is also a multicenter bond, existing as equivalent and polarized 3c-4e bonds, respectively. The halogen bond could be described with a polarized 3c-4e bond.![]()
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Affiliation(s)
- Dan Li
- Department of Chemistry, Anhui University Hefei 230601 PR China
| | - Tao Xia
- Department of Chemistry, Anhui University Hefei 230601 PR China
| | - Wanwan Feng
- Department of Chemistry, Anhui University Hefei 230601 PR China
| | - Longjiu Cheng
- Department of Chemistry, Anhui University Hefei 230601 PR China .,Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University), Ministry of Education Hefei 230601 PR China
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Sauza-de la Vega A, Rocha-Rinza T, Guevara-Vela JM. Cooperativity and Anticooperativity in Ion-Water Interactions: Implications for the Aqueous Solvation of Ions. Chemphyschem 2021; 22:1269-1285. [PMID: 33635563 DOI: 10.1002/cphc.202000981] [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: 12/02/2020] [Revised: 02/24/2021] [Indexed: 01/03/2023]
Abstract
Non-additive effects in hydrogen bonds (HB) take place as a consequence of electronic charge transfers. Therefore, it is natural to expect cooperativity and anticooperativity in ion-water interactions. Nevertheless, investigations on this matter are scarce. This paper addresses the interactions of (i) the cations Li+ , Na+ , K+ , Be2+ , Mg2+ , and Ca2+ together with (ii) the anions F- , Cl- , Br- , NO3 - and SO4 2- with water clusters (H2 O)n , n=1-8, and the effects of these ions on the HBs within the complete molecular adducts. We used quantum chemical topology tools, specifically the quantum theory of atoms in molecules and the interacting quantum atoms energy partition to investigate non-additive effects among the interactions studied herein. Our results show a decrease on the interaction energy between ions and the first neighbouring water molecules with an increment of the coordination number. We also found strong cooperative effects in the interplay between HBs and ion-dipole interactions within the studied systems. Such cooperativity affects considerably the interactions among ions with their first and second solvation shells in aqueous environments. Overall, we believe this article provides valuable information about how ion-dipole contacts interact with each other and how they relate to other interactions, such as HBs, in the framework of non-additive effects in aqueous media.
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Affiliation(s)
- Arturo Sauza-de la Vega
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., 04510, CDMX, México
| | - Tomás Rocha-Rinza
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., 04510, CDMX, México
| | - José Manuel Guevara-Vela
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., 04510, CDMX, México
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5
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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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Jiménez‐Grávalos F, Gallegos M, Martín Pendás Á, Novikov AS. Challenging the electrostatic
σ
‐hole picture of halogen bonding using minimal models and the interacting quantum atoms approach. J Comput Chem 2021; 42:676-687. [DOI: 10.1002/jcc.26488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/10/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022]
Affiliation(s)
| | - Miguel Gallegos
- Department of Analytical and Physical Chemistry University of Oviedo Oviedo Spain
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry University of Oviedo Oviedo Spain
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8
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9
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Morera-Boado C, Gamboa-Suárez A, Bernal-Uruchurtu MI, Hernandez-Lamoneda R. Density Functional Study on the Fundamental and Valence Excited States of Dibromine in T, P, and H Clathrate Cages. J Phys Chem A 2020; 124:7692-7709. [DOI: 10.1021/acs.jpca.0c05360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cercis Morera-Boado
- CONACYT-Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca 62209, Morelos, México
| | - Antonio Gamboa-Suárez
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca 62209, Morelos, México
| | - Margarita I. Bernal-Uruchurtu
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca 62209, Morelos, México
| | - Ramón Hernandez-Lamoneda
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca 62209, Morelos, México
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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: 51] [Impact Index Per Article: 12.8] [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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11
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Castor-Villegas VM, Guevara-Vela JM, Vallejo Narváez WE, Martín Pendás Á, Rocha-Rinza T, Fernández-Alarcón A. On the strength of hydrogen bonding within water clusters on the coordination limit. J Comput Chem 2020; 41:2266-2277. [PMID: 32761858 DOI: 10.1002/jcc.26391] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 12/20/2022]
Abstract
Hydrogen bonds (HB) are arguably the most important noncovalent interactions in chemistry. We study herein how differences in connectivity alter the strength of HBs within water clusters of different sizes. We used for this purpose the interacting quantum atoms energy partition, which allows for the quantification of HB formation energies within a molecular cluster. We could expand our previously reported hierarchy of HB strength in these systems (Phys. Chem. Chem. Phys., 2016, 18, 19557) to include tetracoordinated monomers. Surprisingly, the HBs between tetracoordinated water molecules are not the strongest HBs despite the widespread occurrence of these motifs (e.g., in ice Ih ). The strongest HBs within H2 O clusters involve tricoordinated monomers. Nonetheless, HB tetracoordination is preferred in large water clusters because (a) it reduces HB anticooperativity associated with double HB donors and acceptors and (b) it results in a larger number of favorable interactions in the system. Finally, we also discuss (a) the importance of exchange-correlation to discriminate among the different examined types of HBs within H2 O clusters, (b) the use of the above-mentioned scale to quickly assess the relative stability of different isomers of a given water cluster, and (c) how the findings of this research can be exploited to indagate about the formation of polymorphs in crystallography. Overall, we expect that this investigation will provide valuable insights into the subtle interplay of tri- and tetracoordination in HB donors and acceptors as well as the ensuing interaction energies within H2 O clusters.
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Affiliation(s)
- Víctor Manuel Castor-Villegas
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico
| | - José Manuel Guevara-Vela
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico
| | - Wilmer E Vallejo Narváez
- Institute of Materials Research, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry, University of Oviedo, Oviedo, Spain
| | - Tomás Rocha-Rinza
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico
| | - Alberto Fernández-Alarcón
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico.,Universidad Iberoamericana, Prolongacion Paseo de Reforma 880, Mexico City, Mexico
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12
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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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13
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Structures and energetics of clusters surrounding diatomic anions stabilized by hydrogen, halogen, and other noncovalent bonds. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Li S, Xu T, van Mourik T, Früchtl H, Kirk SR, Jenkins S. Halogen and Hydrogen Bonding in Halogenabenzene/NH 3 Complexes Compared Using Next-Generation QTAIM. Molecules 2019; 24:E2875. [PMID: 31398800 PMCID: PMC6720212 DOI: 10.3390/molecules24162875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 11/17/2022] Open
Abstract
Next-generation quantum theory of atoms in molecules (QTAIM) was used to investigate the competition between hydrogen bonding and halogen bonding for the recently proposed (Y = Br, I, At)/halogenabenzene/NH3 complex. Differences between using the SR-ZORA Hamiltonian and effective core potentials (ECPs) to account for relativistic effects with increased atomic mass demonstrated that next-generation QTAIM is a much more responsive tool than conventional QTAIM. Subtle details of the competition between halogen bonding and hydrogen bonding were observed, indicating a mixed chemical character shown in the 3-D paths constructed from the bond-path framework set B. In addition, the use of SR-ZORA reduced or entirely removed spurious features of B on the site of the halogen atoms.
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Affiliation(s)
- Shuman Li
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource; National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal, Changsha 410081, Hunan, China
| | - Tianlv Xu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource; National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal, Changsha 410081, Hunan, China
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland, UK.
| | - Herbert Früchtl
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland, UK
| | - Steven R Kirk
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource; National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal, Changsha 410081, Hunan, China.
| | - Samantha Jenkins
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource; National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal, Changsha 410081, Hunan, China.
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Scheiner S, Michalczyk M, Zierkiewicz W. Structures of clusters surrounding ions stabilized by hydrogen, halogen, chalcogen, and pnicogen bonds. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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16
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Thakur S, Drew MGB, Franconetti A, Frontera A, Chattopadhyay S. Analysis of energies of halogen and hydrogen bonding interactions in the solid state structures of vanadyl Schiff base complexes. RSC Adv 2019; 9:4789-4796. [PMID: 35514651 PMCID: PMC9060597 DOI: 10.1039/c8ra09947b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/21/2019] [Indexed: 01/04/2023] Open
Abstract
Four vanadyl Schiff base complexes have been prepared and characterized. Energies of supramolecular interactions in complexes 1, 2 and 3 were estimated using DFT calculations, and further corroborated with NCI plot index computational tool.
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Affiliation(s)
- Snehasish Thakur
- Department of Chemistry
- Inorganic Section
- Jadavpur University
- Kolkata 700 032
- India
| | | | | | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma
- Spain
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Abstract
Halogens in a M–X bond are inhibited from forming a halogen bond but can do so in certain circumstances, with or without a σ-hole.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry
- Utah State University
- Logan
- USA
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