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Morera-Boado C, Bernal-Uruchurtu MI. Interaction energy of Cl 2 and Br 2 with H 2 O: Exchange, dispersion and density the crucial ingredients. J Comput Chem 2023; 44:1073-1087. [PMID: 36578228 DOI: 10.1002/jcc.27066] [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: 03/23/2022] [Revised: 11/10/2022] [Accepted: 12/18/2022] [Indexed: 12/30/2022]
Abstract
Modern Density Functional Theory models are now suitable for many molecular and condensed phase studies. The study of noncovalent interactions, a well-known drawback, is no longer an insurmountable obstacle through design and empirical corrections. However, using empirical corrections as in the DFT-D methods might not be an all-in-one solution. This work uses a simple system, X2 -H2 O with X = Cl or Br, with two different interactions, halogen-bonded (XB) and hydrogen-halogen (HX), to investigate the capability of current density functional approximations (DFA) in predicting interaction energies with eight different exchange-correlation functionals. SAPT(DFT) provides, for all the studied cases, better predictions than the widely used supermolecular approach. In addition, the components of the interaction energy suggest where some of the shortcomings originate in each DFA. The analysis of the functionals used confirms that PBE0 and ω-B97X-D have a physically correct behavior. Using SAPT(DFT) and PBE0, and ω-B97X-D, we obtained the interaction energy of Cl2 and Br2 inside different clathrate cages and satisfactorily compared with wavefunction results; hence, the lower and upper limits of this value are defined: Cl2 @512 , -5.3 ± 0.3 kcal/mol; Cl2 @512 62 , -5.5 ± 0.1 kcal/mol; Br2 @512 62 , -7.6 ± 1.0 kcal/mol; Br2 @512 63 , -10.6 ± 1.0 kcal/mol; Br2 @512 64 , -10.9 ± 0.8 kcal/mol.
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Affiliation(s)
- Cercis Morera-Boado
- CONACYT - Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.,Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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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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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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Clathrate III (Bromine Hydrate): Structural Relationship with Clathrate I. Chemphyschem 2020; 21:1587-1596. [DOI: 10.1002/cphc.202000195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/20/2020] [Indexed: 11/07/2022]
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Batista-Romero FA, Pajón-Suárez P, Roncero O, Hernández-Lamoneda R. Nature of the guest-host interactions for dibromine in the T, P, and H clathrate cages. J Chem Phys 2017; 147:154301. [DOI: 10.1063/1.4993465] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Batista-Romero FA, Gamboa-Suárez A, Hernández-Lamoneda R, Janda KC. Nature of the valence excited states of bromine in the T and P clathrate cages. J Chem Phys 2017; 146:144311. [DOI: 10.1063/1.4979909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Fidel A. Batista-Romero
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Ave. Universidad 1001, Cuernavaca 62209 Morelos, Mexico
| | - Antonio Gamboa-Suárez
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Ave. Universidad 1001, Cuernavaca 62209 Morelos, Mexico
| | - Ramón Hernández-Lamoneda
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Ave. Universidad 1001, Cuernavaca 62209 Morelos, Mexico
| | - Kenneth C. Janda
- Department of Chemistry, University of California, Irvine, California 92697, USA
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Alcaraz-Torres A, Gamboa-Suárez A, Bernal-Uruchurtu MI. Is Br2 hydration hydrophobic? J Chem Phys 2017; 146:084501. [DOI: 10.1063/1.4975688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Alcaraz-Torres
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca, Morelos 62209,
México
| | - A. Gamboa-Suárez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca, Morelos 62209,
México
| | - M. I. Bernal-Uruchurtu
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca, Morelos 62209,
México
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Dureckova H, Woo TK, Udachin KA, Ripmeester JA, Alavi S. The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates. Faraday Discuss 2017; 203:61-77. [DOI: 10.1039/c7fd00064b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Clathrate hydrate phases of Cl2 and Br2 guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen–halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen–halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme–substrate compounds. The nature of the halogen–water interactions for the Cl2 and Br2 molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl2 and Br2 guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.
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Affiliation(s)
| | - Tom K. Woo
- Department of Chemistry
- University of Ottawa
- Ottawa
- Canada
| | | | - John A. Ripmeester
- National Research Council Canada
- Ottawa
- Canada
- Department of Chemical and Biological Engineering
- University of British Columbia
| | - Saman Alavi
- Department of Chemistry
- University of Ottawa
- Ottawa
- Canada
- National Research Council Canada
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Ochoa-Resendiz D, Batista-Romero FA, Hernández-Lamoneda R. Communication: Evidence of halogen bonds in clathrate cages. J Chem Phys 2016; 145:161104. [DOI: 10.1063/1.4966644] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- David Ochoa-Resendiz
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Morelos, México
- Instituto Tecnológico de Zacatepec, Calz. Tecnológico 27 Zacatepec 62780, Morelos, México
| | - Fidel A. Batista-Romero
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Morelos, México
- Instituto Superior de Tecnologías y Ciencias Aplicadas, Av. Salvador Allende y Luaces, La Habana 10600, Cuba
| | - Ramón Hernández-Lamoneda
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Morelos, México
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Franklin-Mergarejo R, Rubayo-Soneira J, Halberstadt N, Janda KC, Apkarian VA. A theoretical simulation of the resonant Raman spectroscopy of the H2O⋯Cl2 and H2O⋯Br2 halogen-bonded complexes. J Chem Phys 2016; 144:054307. [DOI: 10.1063/1.4940778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ricardo Franklin-Mergarejo
- Université de Toulouse, UPS, Laboratoire Collisions Agrégats Réactivité, IRSAMC, F-31062 Toulouse, France
- CNRS, UMR 5589, F-31062 Toulouse, France
- InSTEC, Quinta de los Molinos, Ave. Salvador Allende y Luaces, Plaza, Ciudad Habana, Cuba
| | - Jesús Rubayo-Soneira
- InSTEC, Quinta de los Molinos, Ave. Salvador Allende y Luaces, Plaza, Ciudad Habana, Cuba
| | - Nadine Halberstadt
- Université de Toulouse, UPS, Laboratoire Collisions Agrégats Réactivité, IRSAMC, F-31062 Toulouse, France
- CNRS, UMR 5589, F-31062 Toulouse, France
| | - Kenneth C. Janda
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
| | - V. Ara Apkarian
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
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Dureckova H, Woo TK, Alavi S. Molecular simulations and density functional theory calculations of bromine in clathrate hydrate phases. J Chem Phys 2016; 144:044501. [PMID: 26827220 DOI: 10.1063/1.4940321] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bromine forms a tetragonal clathrate hydrate structure (TS-I) very rarely observed in clathrate hydrates of other guest substances. The detailed structure, energetics, and dynamics of Br2 and Cl2 in TS-I and cubic structure I (CS-I) clathrate hydrates are studied in this work using molecular dynamics and quantum chemical calculations. X-ray diffraction studies show that the halogen-water-oxygen distances in the cages of these structures are shorter than the sum of the van der Waals radii of halogen and oxygen atoms. This suggests that the stabilizing effects of halogen bonding or other non-covalent interactions (NCIs) may contribute to the formation of the unique tetragonal bromine hydrate structure. We performed molecular dynamics simulations of Br2 and Cl2 clathrate hydrates using our previously developed five-site charge models for the dihalogen molecules [Dureckova et al. Can. J. Chem. 93, 864 (2015)] which reproduce the computed electrostatic potentials of the dihalogens and account for the electropositive σ-hole of the halogen bond donor (the dihalogen). Analysis of the radial distribution functions, enthalpies of encapsulation, velocity and orientation autocorrelation functions, and polar angle distributions are carried out for Br2 and Cl2 guests in various cages to contrast the properties of these guests in the TS-I and CS-I phases. Quantum chemical partial geometry optimizations of Br2 and Cl2 guests in the hydrate cages using the M06-2X functional give short halogen-water distances compatible with values observed in X-ray diffraction experiments. NCI plots of guest-cage structures are generated to qualitatively show the relative strength of the non-bonding interactions between dihalogens and water molecules. The differences between behaviors of Br2 and Cl2 guests in the hydrate cages may explain why bromine forms the unique TS-I phase.
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Affiliation(s)
- Hana Dureckova
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 5N6, Canada
| | - Tom K Woo
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 5N6, Canada
| | - Saman Alavi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 5N6, Canada
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