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Selent M, Nyman J, Roukala J, Ilczyszyn M, Oilunkaniemi R, Bygrave PJ, Laitinen R, Jokisaari J, Day GM, Lantto P. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129 Xe NMR Spectroscopy. Chemistry 2017; 23:5258-5269. [PMID: 28111848 PMCID: PMC5763392 DOI: 10.1002/chem.201604797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 11/09/2022]
Abstract
An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by 129 Xe NMR spectroscopy. The high sensitivity of the 129 Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.
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Affiliation(s)
- Marcin Selent
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland.,Faculty of Chemistry, Wrocław University, Joliot Curie 14, 50-383, Wrocław, Poland
| | - Jonas Nyman
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Juho Roukala
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland
| | - Marek Ilczyszyn
- Faculty of Chemistry, Wrocław University, Joliot Curie 14, 50-383, Wrocław, Poland
| | - Raija Oilunkaniemi
- Laboratory of Inorganic Chemistry, University of Oulu, 90014, Oulu, Finland
| | - Peter J Bygrave
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Risto Laitinen
- Laboratory of Inorganic Chemistry, University of Oulu, 90014, Oulu, Finland
| | - Jukka Jokisaari
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland
| | - Graeme M Day
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Perttu Lantto
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland
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Siuda P, Sadlej J. Calculations of NMR properties for sI and sII clathrate hydrates of methane, ethane and propane. J Mol Model 2014; 20:2511. [PMID: 25408508 PMCID: PMC4236610 DOI: 10.1007/s00894-014-2511-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/20/2014] [Indexed: 11/04/2022]
Abstract
Calculations of NMR parameters (the absolute shielding constants and the spin-spin coupling constants) for 5(12), 5(12)6(2) and 5(12)6(4) cages enclathrating CH4, C2H6 and C3H8 molecules are presented. The DFT/B3LYP/HuzIII-su3 level of theory was employed. The (13)C shielding constants of guest molecules are close to available experimental data. In two cases (the ethane in 5(12) and the propane in 5(12)6(2) cages) the (13)C shielding constants are reported for the first time. Inversion of the methyl/methylene (13)C and (1)H shielding constants order is found for propane in the 5(12)6(2) cage. Topological criteria are used to interpret the changes of values of NMR parameters of water molecules and they establish a connection between single cages and bulk crystal.
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Affiliation(s)
- Paweł Siuda
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Joanna Sadlej
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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3
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Dubost E, Dognon JP, Rousseau B, Milanole G, Dugave C, Boulard Y, Léonce E, Boutin C, Berthault P. Understanding a Host-Guest Model System through129Xe NMR Spectroscopic Experiments and Theoretical Studies. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Dubost E, Dognon JP, Rousseau B, Milanole G, Dugave C, Boulard Y, Léonce E, Boutin C, Berthault P. Understanding a Host-Guest Model System through129Xe NMR Spectroscopic Experiments and Theoretical Studies. Angew Chem Int Ed Engl 2014; 53:9837-40. [DOI: 10.1002/anie.201405349] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Indexed: 11/06/2022]
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Shin K, Moudrakovski IL, Davari MD, Alavi S, Ratcliffe CI, Ripmeester JA. Crystal engineering the clathrate hydrate lattice with NH4F. CrystEngComm 2014. [DOI: 10.1039/c3ce41661e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Standara S, Kulhánek P, Marek R, Straka M. 129Xe NMR chemical shift in Xe@C60calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent. J Comput Chem 2013; 34:1890-8. [DOI: 10.1002/jcc.23334] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/17/2013] [Accepted: 04/19/2013] [Indexed: 11/11/2022]
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Castiglione F, Simonutti R, Mauri M, Mele A. Cage-Like Local Structure of Ionic Liquids Revealed by a (129)Xe Chemical Shift. J Phys Chem Lett 2013; 4:1608-1612. [PMID: 26282967 DOI: 10.1021/jz400617v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The chemical shift of xenon (at natural abundance) dissolved in a variety of 1-butyl-3-methylimidazolium-based ionic liquids (ILs) has been measured with (129)Xe NMR spectroscopy. The large chemical shift differences observed are mainly related to the type of anion; the strongest deshielding effect is observed ILs with I(-), Br(-), and Cl(-) anions, and the strongest shielding is found for the bis(trifluoromethanesulfonyl)imide ([Tf2N](-))-based IL. The measured (129)Xe chemical shift variations correlate well with the IL structure organization imposed by the anions and with the size of the empty voids due to charge alternation patterns. Descriptors taken from literature data on X-ray and neutron scattering, as well as single-crystal structures where available, support this interpretation. The proposed methodology adds a new investigating tool to the elucidation of the short-range order in ILs. The observed chemical shift trend provides information about how these solvents are organized.
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Affiliation(s)
- Franca Castiglione
- †Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza L. Da Vinci 32, 20133 Milano, Italy
| | - Roberto Simonutti
- ‡Dipartimento di Scienza dei Materiali, Università degli Studi di Milano Bicocca, Via Roberto Cozzi 53, 20125 Milano, Italy
| | - Michele Mauri
- ‡Dipartimento di Scienza dei Materiali, Università degli Studi di Milano Bicocca, Via Roberto Cozzi 53, 20125 Milano, Italy
| | - Andrea Mele
- †Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza L. Da Vinci 32, 20133 Milano, Italy
- §CNR - Istituto di Chimica del Riconoscimento Molecolare, Via L. Mancinelli 7, 20131 Milano, Italy
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Ilczyszyn M, Selent M, Ilczyszyn MM. Participation of Xenon Guest in Hydrogen Bond Network of β-Hydroquinone Crystal. J Phys Chem A 2012; 116:3206-14. [DOI: 10.1021/jp210670k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marek Ilczyszyn
- Faculty of Chemistry, Wrocław University, 50-383 Wrocław,
Joliot Curie 14, Poland
| | - Marcin Selent
- Faculty of Chemistry, Wrocław University, 50-383 Wrocław,
Joliot Curie 14, Poland
- Department of Physics, University of Oulu, 90014 Oulu, Finland
| | - Maria M. Ilczyszyn
- Faculty of Chemistry, Wrocław University, 50-383 Wrocław,
Joliot Curie 14, Poland
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Standara S, Kulhánek P, Marek R, Horníček J, Bouř P, Straka M. Simulations of 129Xe NMR chemical shift of atomic xenon dissolved in liquid benzene. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0930-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Kida M, Hori A, Sakagami H, Takeya S, Kamata Y, Takahashi N, Ebinuma T, Narita H. 13C Chemical Shifts of Propane Molecules Encaged in Structure II Clathrate Hydrate. J Phys Chem A 2011; 115:643-7. [DOI: 10.1021/jp106115d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Masato Kida
- Methane Hydrate Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-17 Tsukisamu Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Akira Hori
- Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | | | - Satoshi Takeya
- RIIF, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1, Higashi, Tsukuba, 305-8565, Japan
| | - Yasushi Kamata
- Methane Hydrate Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-17 Tsukisamu Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Nobuo Takahashi
- Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | - Takao Ebinuma
- Methane Hydrate Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-17 Tsukisamu Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Hideo Narita
- Methane Hydrate Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-17 Tsukisamu Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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Siuda P, Sadlej J. Nuclear Magnetic Resonance Parameters for Methane Molecule Trapped in Clathrate Hydrates. J Phys Chem A 2011; 115:612-9. [DOI: 10.1021/jp110587x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Paweł Siuda
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Joanna Sadlej
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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Alavi S, Dornan P, Woo TK. Determination of NMR lineshape anisotropy of guest molecules within inclusion complexes from molecular dynamics simulations. Chemphyschem 2008; 9:911-9. [PMID: 18386265 DOI: 10.1002/cphc.200700805] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Nonspherical cages in inclusion compounds can result in non-uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO(2) molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO(2) guests in terms of a polar angle theta and azimuth angle phi and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO(2) sI clathrate. The experimental (13)C NMR lineshapes of CO(2) guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the (13)C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required.
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Affiliation(s)
- Saman Alavi
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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14
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Casabianca LB, de Dios AC. Ab initiocalculations of NMR chemical shifts. J Chem Phys 2008; 128:052201. [DOI: 10.1063/1.2816784] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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15
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Wen Q, Jäger W. Rotational Spectra of the Xe−(H2O)2 van der Waals Trimer: Xenon as a Probe of Electronic Structure and Dynamics. J Phys Chem A 2007; 111:2093-7. [PMID: 17388264 DOI: 10.1021/jp0663863] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rotational spectra of three isotopomers of the Xe-(H2O)2 van der Waals trimer were recorded using a pulsed-nozzle, Fourier transform microwave spectrometer. Nine [nine, four] a-type and twelve [eleven, seven] b-type transitions were measured for the 132Xe-(H2O)2 [129Xe-(H2O)2, 131Xe-(H2O)2] isotopomer. The determined rotational and centrifugal distortion constants were used to extract information about the structure and vibrational motions of the complex. The nuclear quadrupole hyperfine structures due to the 131Xe (nuclear spin quantum number I=3/2) nucleus were also detected. The large value of the off-diagonal nuclear quadrupole coupling constant chiab in particular provides detailed insight into the electronic environment of the xenon atom and the orientations of the water molecules within the complex. An effective structure that best reproduces the experimental 131Xe nuclear quadrupole coupling constants is rationalized by ab initio calculations. An overall goal of this line of work is to determine how the successive solvation of a xenon atom with water molecules affects the xenon electron distribution and its intermolecular interactions. The results may provide molecular level interpretations of 129Xe NMR data from, for example, imaging experiments.
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Affiliation(s)
- Qing Wen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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16
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Sears DN, Jameson CJ. The Xe shielding surfaces for Xe interacting with linear molecules and spherical tops. J Chem Phys 2006; 121:2151-7. [PMID: 15260769 DOI: 10.1063/1.1758691] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 129Xe nuclear magnetic resonance spectrum of xenon in gas mixtures of Xe with other molecules provides a test of the ab initio surfaces for the intermolecular shielding of Xe in the presence of the other molecule. We examine the electron correlation contributions to the Xe-CO2, Xe-N2, Xe-CO, Xe-CH4, and Xe-CF4 shielding surfaces and test the calculations against the experimental temperature dependence of the density coefficients of the Xe chemical shift in the gas mixtures at infinite dilution in Xe. Comparisons with the gas phase data permit the refinement of site-site potential functions for Xe-N2, Xe-CO, and Xe-CF4 especially for atom-Xe distances in the range 3.5-6 A. With the atom-atom shielding surfaces and potential parameters obtained in the present work, construction of shielding surfaces and potentials for applications such as molecular dynamics averaging of Xe chemical shifts in liquid solvents containing CH3, CH2, CF3, and CF2 groups is possible.
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Affiliation(s)
- Devin N Sears
- Department of Chemistry, M/C-111, University of Illinois at Chicago, 60607-7061, USA
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Alavi S, Ripmeester JA, Klug DD. Stability of rare gas structure H clathrate hydrates. J Chem Phys 2006; 125:104501. [PMID: 16999535 DOI: 10.1063/1.2238864] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Molecular dynamics simulations are used to study the stability of structure H (sH) clathrate hydrates with the rare gases Ne, Ar, Kr, and Xe. Simulations on a 3 x 3 x 3 sH unit cell replica are performed at ambient pressure at 40 and 100 K temperatures. The small and medium (s+m) cages of the sH unit cell are assigned rare gas guest occupancies of 1 and for large (l) cages guest occupancies of 1-6 are considered. Radial distribution functions for guest pairs with occupancies in the l-l, l-(s+m), and (s+m)-(s+m) cages are presented. The unit cell volumes and configurational energies are studied as a function of large cage occupancy for the rare gases. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies at 100 K and 1 bar and 20 kbar pressures. These studies show that the most stable argon clathrate has five guests in the large cages. For krypton and xenon the most stable configurations have three and two guests in the large cages, respectively.
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Affiliation(s)
- Saman Alavi
- Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada.
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Sears DN, Wasylishen RE, Ueda T. Grand Canonical Monte Carlo Simulations of the 129Xe NMR Line Shapes of Xenon Adsorbed in (±)-[Co(en)3]Cl3. J Phys Chem B 2006; 110:11120-7. [PMID: 16771374 DOI: 10.1021/jp061655a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The 129Xe NMR line shapes of xenon adsorbed in the nanochannels of the (+/-)-[Co(en)3]Cl3 ionic crystal have been calculated by grand canonical Monte Carlo (GCMC) simulations. The results of our GCMC simulations illustrate their utility in predicting 129Xe NMR chemical shifts in systems containing a transition metal. In particular, the nanochannels of (+/-)-[Co(en)3]Cl3 provide a simple, yet interesting, model system that serves as a building block toward understanding xenon chemical shifts in more complex porous materials containing transition metals. Using only the Xe-C and Xe-H potentials and shielding response functions derived from the Xe@CH4 van der Waals complex to model the interior of the channel, the GCMC simulations correctly predict the 129Xe NMR line shapes observed experimentally (Ueda, T.; Eguchi, T.; Nakamura, N.; Wasylishen, R. E. J. Phys. Chem. B 2003, 107, 180-185). At low xenon loading, the simulated 129Xe NMR line shape is axially symmetric with chemical-shift tensor components delta(parallel) = 379 ppm and delta(perpendicular) = 274 ppm. Although the simulated isotropic chemical shift, delta(iso) = 309 ppm, is overestimated, the anisotropy of the chemical-shift tensor is correctly predicted. The simulations provide an explanation for the observed trend in the 129Xe NMR line shapes as a function of the overhead xenon pressure: delta(perpendicular) increased from 274 to 292 ppm, while delta(parallel) changed by only 3 ppm over the entire xenon loading range. The overestimation of the isotropic chemical shifts is explained based upon the results of quantum mechanical 129Xe shielding calculations of xenon interacting with an isolated (+/-)-[Co(en)3]Cl3 molecule. The xenon chemical shift is shown to be reduced by about 12% going from the Xe@[Co(en)3]Cl3 van der Waals complex to the Xe@C2H6 fragment.
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Affiliation(s)
- Devin N Sears
- Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB, Canada, T6G 2G2
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Soldatov DV, Moudrakovski IL, Grachev EV, Ripmeester JA. Micropores in Crystalline Dipeptides as Seen from the Crystal Structure, He Pycnometry, and 129Xe NMR Spectroscopy. J Am Chem Soc 2006; 128:6737-44. [PMID: 16704277 DOI: 10.1021/ja060474j] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eight crystalline dipeptides were studied: AV (Ala-Val), VA (Val-Ala), AI (Ala-Ile), VV (Val-Val), IA (Ile-Ala), IV (Ile-Val), VI (Val-Ile), and LS (Leu-Ser) (all LL isomers). The first seven form an isostructural series (space group P6(1)), whereas LS has a different structure (P6(5)). All structures display H-bonded tubular assemblies of the dipeptide molecules resulting in open ultramicropores in the form of isolated one-dimensional (1D) channels. The total porosity of the materials ranges from 4 to 12% (micropore volume from 0.04 to 0.12 cm(3)/g). Calculations based on the crystal structures, He pycnometry, and solid-state (129)Xe NMR methods were used to obtain a comprehensive description of the geometry and properties of the micropores. The following order was established for the channel diameter: AV > VA > AI > VV > IA > IV > VI, with >5 A for AV and <4 A for VI; LS is close to AI. The observed sorption behavior cannot be described adequately based on the crystal structure and can only be understood if one takes into account the dynamics of the host matrix. The pores are chiral, with the center of the channel describing a right-handed helix (left-handed for LS). The following order was established for the channel helicity: VA > IA > IV > AV approximately AI approximately VV > VI > LS, with a helix diameter of approximately 2 A for VA, IA, and IV and approximately 1 A or less for the remaining dipeptides. A comparison of the dipeptides studied with other supramolecular materials is given and the potential for applications is discussed.
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Affiliation(s)
- Dmitriy V Soldatov
- Nikolaev Institute of Inorganic Chemistry, Russian Academy of Sciences, Novosibirsk, Russia.
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Chihaia V, Adams S, Kuhs WF. Molecular dynamics simulations of properties of a (001) methane clathrate hydrate surface. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2005.05.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Alavi S, Ripmeester JA, Klug DD. NMR shielding constants for hydrogen guest molecules in structure II clathrates. J Chem Phys 2005; 123:051107. [PMID: 16108623 DOI: 10.1063/1.2000258] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Proton NMR shielding constants and chemical shifts for hydrogen guests in small and large cages of structure II clathrates are calculated using density-functional theory and the gauge-invariant atomic-orbital method. Shielding constants are calculated at the B3LYP level with the 6-311++G(d,p) basis set. The calculated chemical shifts are corrected with a linear regression to reproduce the experimental chemical shifts of a set of standard molecules. The calculated chemical shifts of single hydrogen molecules in the small and large structure II cages are 4.94 and 4.84 ppm, respectively, which show that within the error range of the method the H2 guest molecules in the small and large cages cannot be distinguished. Chemical shifts are also calculated for double occupancy of the hydrogen guests in small cages, and double, triple, and quadruple occupancy in large cages. Multiple occupancy changes the chemical shift of the hydrogen guests by approximately 0.2 ppm. The relative effects of other guest molecules and the cage on the chemical shift are studied for the cages with multiple occupancies.
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Affiliation(s)
- Saman Alavi
- Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada.
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Jameson CJ, Sears DN, Murad S. Molecular dynamics averaging of Xe chemical shifts in liquids. J Chem Phys 2004; 121:9581-92. [PMID: 15538880 DOI: 10.1063/1.1807817] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Xe nuclear magnetic resonance chemical shift differences that afford the discrimination between various biological environments are of current interest for biosensor applications and medical diagnostic purposes. In many such environments the Xe signal appears close to that in water. We calculate average Xe chemical shifts (relative to the free Xe atom) in solution in eleven liquids: water, isobutane, perfluoro-isobutane, n-butane, n-pentane, neopentane, perfluoroneopentane, n-hexane, n-octane, n-perfluorooctane, and perfluorooctyl bromide. The latter is a liquid used for intravenous Xe delivery. We calculate quantum mechanically the Xe shielding response in Xe-molecule van der Waals complexes, from which calculations we develop Xe (atomic site) interpolating functions that reproduce the ab initio Xe shielding response in the complex. By assuming additivity, these Xe-site shielding functions can be used to calculate the shielding for any configuration of such molecules around Xe. The averaging over configurations is done via molecular dynamics (MD). The simulations were carried out using a MD technique that one of us had developed previously for the simulation of Henry's constants of gases dissolved in liquids. It is based on separating a gaseous compartment in the MD system from the solvent using a semipermeable membrane that is permeable only to the gas molecules. We reproduce the experimental trends in the Xe chemical shifts in n-alkanes with increasing number of carbons and the large chemical shift difference between Xe in water and in perfluorooctyl bromide. We also reproduce the trend for a given solvent of decreasing Xe chemical shift with increasing temperature. We predict chemical shift differences between Xe in alkanes vs their perfluoro counterparts.
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Affiliation(s)
- Cynthia J Jameson
- Department of Chemistry, MC-111, University of Illinois at Chicago, Chicago, Illinois 60607-7061, USA
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Jameson CJ, Stueber D. The nuclear magnetic resonance line shapes of Xe in the cages of clathrate hydrates. J Chem Phys 2004; 120:10200-14. [PMID: 15268044 DOI: 10.1063/1.1718349] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We report, for the first time, a prediction of the line shapes that would be observed in the (129)Xe nuclear magnetic resonance (NMR) spectrum of xenon in the cages of clathrate hydrates. We use the dimer tensor model to represent pairwise contributions to the intermolecular magnetic shielding tensor for Xe at a specific location in a clathrate cage. The individual tensor components from quantum mechanical calculations in clathrate hydrate structure I are represented by contributions from parallel and perpendicular tensor components of Xe-O and Xe-H dimers. Subsequently these dimer tensor components are used to reconstruct the full magnetic shielding tensor for Xe at an arbitrary location in a clathrate cage. The reconstructed tensors are employed in canonical Monte Carlo simulations to find the Xe shielding tensor component along a particular magnetic field direction. The shielding tensor component weighted according to the probability of finding a crystal fragment oriented along this direction in a polycrystalline sample leads to a predicted line shape. Using the same set of Xe-O and Xe-H shielding functions and the same Xe-O and Xe-H potential functions we calculate the Xe NMR spectra of Xe atom in 12 distinct cage types in clathrate hydrates structures I, II, H, and bromine hydrate. Agreement with experimental spectra in terms of the number of unique tensor components and their relative magnitudes is excellent. Agreement with absolute magnitudes of chemical shifts relative to free Xe atom is very good. We predict the Xe line shapes in two cages in which Xe has not yet been observed.
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Affiliation(s)
- Cynthia J Jameson
- Department of Chemistry, M/C-111, University of Illinois at Chicago, Chicago, IL 60607-7061, USA
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