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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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3
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Guevara-Vela JM, Ochoa-Resendiz D, Costales A, Hernández-Lamoneda R, Martín Pendás Á. Halogen Bonds in Clathrate Cages: A Real Space Perspective. Chemphyschem 2018; 19:2512-2517. [DOI: 10.1002/cphc.201800474] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Indexed: 11/08/2022]
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
| | - Aurora Costales
- Departament of Analytical and Physical Chemistry; University of Oviedo; E-33006 Oviedo Spain
| | - Ramón Hernández-Lamoneda
- Centro de Investigaciones Químicas; Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca; 62209 Morelos México
| | - Ángel Martín Pendás
- Departament of Analytical and Physical Chemistry; University of Oviedo; E-33006 Oviedo Spain
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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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5
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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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Samanta AK, Wang Y, Mancini JS, Bowman JM, Reisler H. Energetics and Predissociation Dynamics of Small Water, HCl, and Mixed HCl–Water Clusters. Chem Rev 2016; 116:4913-36. [DOI: 10.1021/acs.chemrev.5b00506] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amit K. Samanta
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Yimin Wang
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - John S. Mancini
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M. Bowman
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Hanna Reisler
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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11
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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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12
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Hormain L, Monnerville M, Toubin C, Duflot D, Pouilly B, Briquez S, Bernal-Uruchurtu MI, Hernández-Lamoneda R. Ground state analytical ab initio intermolecular potential for the Cl 2-water system. J Chem Phys 2015; 142:144310. [DOI: 10.1063/1.4917028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bernal-Uruchurtu MI, Janda KC, Hernández-Lamoneda R. Motion of Br2 molecules in clathrate cages. A computational study of the dynamic effects on its spectroscopic behavior. J Phys Chem A 2015; 119:452-9. [PMID: 25531916 DOI: 10.1021/jp5082092] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work looks into the spectroscopic behavior of bromine molecules trapped in clathrate cages combining different methodologies. We developed a semiempirical quantum mechanical model to incorporate through molecular dynamics trajectories, the effect movement of bromine molecules in clathrate cages has on its absorption spectra. A simple electrostatic model simulating the cage environment around bromine predicts a blue shift in the spectra, in good agreement with the experimental evidence.
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Affiliation(s)
- M I Bernal-Uruchurtu
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos Av. Universidad 1001, Cuernavaca 62209, Morelos, México
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14
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Samanta AK, Ch’ng LC, Reisler H. Imaging bond breaking and vibrational energy transfer in small water containing clusters. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Branigan ET, Halberstadt N, Apkarian VA. Solvation dynamics through Raman spectroscopy: hydration of Br2 and Br3(-), and solvation of Br2 in liquid bromine. J Chem Phys 2011; 134:174503. [PMID: 21548695 DOI: 10.1063/1.3583477] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Raman spectroscopy of bromine in the liquid phase and in water illustrates uncommon principles and yields insights regarding hydration. In liquid Br(2), resonant excitation over the B((3)Π(0u)(+)) ← X((1)Σ(g)(+)) valence transition at 532 nm produces a weak resonant Raman (RR) progression accompanied by a five-fold stronger non-resonant (NR) scattering. The latter is assigned to pre-resonance with the C-state, which in turn must be strongly mixed with inter-molecular charge transfer states. Despite the electronic resonance, RR of Br(2) in water is quenched. At 532 nm, the homogeneously broadened fundamental is observed, as in the NR case at 785 nm. The implications of the quenching of RR scattering are analyzed in a simple, semi-quantitative model, to conclude that the inertial evolution of the Raman packet in aqueous Br(2) occurs along multiple equivalent water-Br(2) coordinates. In distinct contrast with hydrophilic hydration in small clusters and hydrophobic hydration in clathrates, it is concluded that the hydration shell of bromine in water consists of dynamically equivalent fluxional water molecules. At 405 nm, the RR progression of Br(3)(-) is observed, accompanied by difference transitions between the breathing of the hydration shell and the symmetric stretch of the ion. The RR scattering process in this case can be regarded as the coherent photo-induced electron transfer to the solvent and its radiative back-transfer.
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Affiliation(s)
- Edward T Branigan
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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Franklin-Mergarejo R, Rubayo-Soneira J, Halberstadt N, Ayed T, Bernal-Uruchurtu MI, Hernández-Lamoneda R, Janda KC. Large Shift and Small Broadening of Br2 Valence Band upon Dimer Formation with H2O: An Ab Initio Study. J Phys Chem A 2011; 115:5983-91. [DOI: 10.1021/jp110389z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ricardo Franklin-Mergarejo
- Instituto Superior de Tecnologías y Ciencias Aplicadas, Ave. Salvador Allende y Luaces, Quinta de los Molinos, Plaza, Habana 10600, Aptdo. Postal 6163, Ciudad Habana, Cuba
- Université de Toulouse, UPS, Laboratoire Collisions Agrégats Réactivité, IRSAMC, F-31062 Toulouse, France
- CNRS, UMR 5589, F-31062 Toulouse, France
| | - Jesus Rubayo-Soneira
- Instituto Superior de Tecnologías y Ciencias Aplicadas, Ave. Salvador Allende y Luaces, Quinta de los Molinos, Plaza, Habana 10600, Aptdo. Postal 6163, 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
| | - Tahra Ayed
- Centro de Investigaciones Químicas, UAEM, Cuernavaca, Mor. 62209, México
| | | | | | - Kenneth C. Janda
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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Franklin-Mergarejo R, Rubayo-Soneira J, Halberstadt N, Ayed T, Bernal Uruchurtu MI, Hernández-Lamoneda R, Janda KC. An ab initio calculation of the valence excitation spectrum of H2O...Cl2: comparison to condensed phase spectra. J Phys Chem A 2009; 113:7563-9. [PMID: 19419140 DOI: 10.1021/jp901488x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Valence electronic excitation spectra are calculated for the H(2)O...Cl(2) dimer using state-of-the art ab initio potentials for both the ground and the valence excited states, a basis set calculation of the ground state nuclear wave function, and a wave packet analysis to simulate the dynamics on the excited state surface. The peak of the H(2)O...Cl(2) dimer spectrum is blue-shifted by 1250 cm(-1) from that of the free Cl(2) molecule. This is less than the value previously estimated from vertical excitation energies but still significantly more than the blue shift in aqueous solution and clathrate-hydrate solid. Seventy percent of the blue shift is attributed to ground state stabilization, the rest to excited state repulsion. Spin-orbit effects are found to be small for this dimer. Homogeneous broadening is found to be slightly smaller for the dimer than for the free Cl(2). The reflection principle and spectator model approximations were tested and found to be quite satisfactory. This is promising for an eventual simulation of the condensed phase spectra.
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Affiliation(s)
- Ricardo Franklin-Mergarejo
- Instituto Superior de Tecnologías y Ciencias Aplicadas, Ave. Salvador Allende y Luaces, Quinta de los Molinos, Plaza, Habana 10600, Aptdo. Postal 6163, Ciudad Habana, Cuba
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Bernal-Uruchurtu MI, Hernández-Lamoneda R, Janda KC. On the Unusual Properties of Halogen Bonds: A Detailed ab Initio Study of X2−(H2O)1−5 clusters (X = Cl and Br). J Phys Chem A 2009; 113:5496-505. [DOI: 10.1021/jp900490p] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ramón Hernández-Lamoneda
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, 62209, México
| | - Kenneth C. Janda
- Department of Chemistry, University of California, Irvine, California 92697
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Bernal-Uruchurtu§ MI, Kerenskaya G, Janda KC. Structure, spectroscopy and dynamics of halogen molecules interacting with water. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350903017302] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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