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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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2
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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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3
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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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4
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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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5
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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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6
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Batista-Romero FA, Pajón-Suárez P, Bernal-Uruchurtu MI, Hernández-Lamoneda R. Performance of local correlation methods for halogen bonding: The case of Br2-(H2O)n,n = 4,5 clusters and Br2@5(12)6(2) clathrate cage. J Chem Phys 2015; 143:094305. [PMID: 26342368 DOI: 10.1063/1.4929908] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The performance of local correlation methods is examined for the interactions present in clusters of bromine with water where the combined effect of hydrogen bonding (HB), halogen bonding (XB), and hydrogen-halogen (HX) interactions lead to many interesting properties. Local methods reproduce all the subtleties involved such as many-body effects and dispersion contributions provided that specific methodological steps are followed. Additionally, they predict optimized geometries that are nearly free of basis set superposition error that lead to improved estimates of spectroscopic properties. Taking advantage of the local correlation energy partitioning scheme, we compare the different interaction environments present in small clusters and those inside the 5(12)6(2) clathrate cage. This analysis allows a clear identification of the reasons supporting the use of local methods for large systems where non-covalent interactions play a key role.
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Affiliation(s)
- Fidel A Batista-Romero
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
| | - Pedro Pajón-Suárez
- Instituto Superior de Tecnologías y Ciencias Aplicadas (InSTEC), Habana 6163, Cuba
| | - Margarita I Bernal-Uruchurtu
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
| | - Ramón Hernández-Lamoneda
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
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7
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Dureckova H, Woo TK, Alavi S, Ripmeester JA. Molecular dynamics simulation of halogen bonding in Cl2, BrCl, and mixed Cl2/Br2 clathrate hydrates. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0593] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Clathrate hydrate phases of dihalogen molecules have properties that differ from those of other guest molecules of similar size. The water oxygen–chlorine distances in the structure I (sI) Cl2 hydrate are smaller than the sum of the van der Waals radii of oxygen and chlorine. Bromine hydrate forms a unique clathrate hydrate structure that is not seen in other guest substances. In mixed Cl2/Br2 structure I hydrate, the water oxygen–bromine distances are also smaller than the sum of the oxygen and bromine van der Waals radii. We previously studied the structure of three dihalogen clathrate hydrates using single crystal X-ray diffraction and described these structural features in terms of halogen bonding between the dihalogen and water molecules. In this work, we perform molecular dynamics simulations of cubic sI Cl2, mixed Cl2/Br2, and BrCl clathrate hydrate phases. We perform quantum chemical computations on the dihalogen molecules to determine the nature of σ-hole near the halogen atoms. We fit the electrostatic potential of the molecules to point charge models including dummy atoms that represent σ-holes adjacent to the halogen molecules. Molecular dynamics simulations are used to determine the lattice constants, radial distribution functions, and guest dynamics in these phases. We determine the effect of guest size and difference in halogen bonding on the properties of the clathrate hydrate phase. Simulations for the Cl2, BrCl, and mixed Cl2/Br2 hydrates are performed with small cages of the sI clathrate hydrate phases completely full or filled with experimental occupancies with Cl2 guests.
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Affiliation(s)
- Hana Dureckova
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tom K. Woo
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Saman Alavi
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - John A. Ripmeester
- National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
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Roncero O, Aguado A, Batista-Romero FA, Bernal-Uruchurtu MI, Hernández-Lamoneda R. Density-Difference-Driven Optimized Embedding Potential Method To Study the Spectroscopy of Br2 in Water Clusters. J Chem Theory Comput 2015; 11:1155-64. [DOI: 10.1021/ct501140p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Octavio Roncero
- Instituto de Física Fundamental (IFF-CSIC), C.S.I.C., Serrano 123, 28006 Madrid, Madrid, Spain
| | - Alfredo Aguado
- Departamento
de Química Física Aplicada (UAM), Unidad Asociada a
IFF-CSIC, Facultad de Ciencias Módulo 14, Universidad Autónoma de Madrid, 28049 Madrid, Madrid, Spain
| | - Fidel A. Batista-Romero
- Centro
de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México 62209
| | | | - Ramón Hernández-Lamoneda
- Centro
de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México 62209
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