1
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Mailhiot S, Peuravaara P, Egleston BD, Kearsey RJ, Mareš J, Komulainen S, Selent A, Kantola AM, Cooper AI, Vaara J, Greenaway RL, Lantto P, Telkki VV. Gas Uptake and Thermodynamics in Porous Liquids Elucidated by 129Xe NMR. J Phys Chem Lett 2024; 15:5323-5330. [PMID: 38724016 PMCID: PMC11129303 DOI: 10.1021/acs.jpclett.4c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 05/24/2024]
Abstract
We exploited 129Xe NMR to investigate xenon gas uptake and dynamics in a porous liquid formed by dissolving porous organic cages in a cavity-excluded solvent. Quantitative 129Xe NMR shows that when the amount of xenon added to the sample is lower than the amount of cages present (subsaturation), the porous liquid absorbs almost all xenon atoms from the gas phase, with 30% of the cages occupied with a Xe atom. A simple two-site exchange model enables an estimate of the chemical shift of 129Xe in the cages, which is in good agreement with the value provided by first-principles modeling. T2 relaxation times allow the determination of the exchange rate of Xe between the solvent and cage sites as well as the activation energies of the exchange. The 129Xe NMR analysis also enables determination of the free energy of confinement, and it shows that Xe binding is predominantly enthalpy-driven.
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Affiliation(s)
- Sarah
E. Mailhiot
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Petri Peuravaara
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Benjamin D. Egleston
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Rachel J. Kearsey
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Crown Street, Liverpool L69 7ZD, U.K.
| | - Jiří Mareš
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Sanna Komulainen
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Anne Selent
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Anu M. Kantola
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Andrew I. Cooper
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Crown Street, Liverpool L69 7ZD, U.K.
| | - Juha Vaara
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Rebecca L. Greenaway
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Perttu Lantto
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Ville-Veikko Telkki
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
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2
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Pollet R, Dognon JP, Berthault P. Isomer-Dependent Escape Rate of Xenon from a Water-Soluble Cryptophane Cage Studied by Ab Initio Molecular Dynamics. Chemphyschem 2024; 25:e202300509. [PMID: 37905939 DOI: 10.1002/cphc.202300509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
The escape of xenon from the anti and syn diastereomers of hexacarboxylic-cryptophane-222 in water has been studied by ab initio molecular dynamics simulations. The structures of both complexes, when the xenon atom is trapped inside their cages, have been compared and show no major differences. The free-energy profiles corresponding to the escape reaction have been calculated with the Blue Moon ensemble method using the distance between Xe and the center of mass of the cage as the reaction coordinate. The resulting free-energy barriers are very different; the escape rate is much faster in the case of the syn diastereomer, in agreement with experimental data obtained in hyperpolarized 129 Xe NMR. Our simulations reveal the mechanistic details for each diastereomer and provide an explanation for the different in-out xenon rates based on the solvation structure around the cages.
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Affiliation(s)
- R Pollet
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191, Gif-sur-Yvette, France
| | - J-P Dognon
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191, Gif-sur-Yvette, France
| | - P Berthault
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191, Gif-sur-Yvette, France
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3
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Saielli G. Computational NMR spectroscopy of 205 Tl. J Comput Chem 2023; 44:2016-2029. [PMID: 37367222 DOI: 10.1002/jcc.27176] [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: 04/07/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023]
Abstract
We have investigated the NMR chemical shift of 205 Tl in several thallium compounds, ranging from small covalent Tl(I) and Tl(III) molecules to supramolecular complexes with large organic ligands and some thallium halides. NMR calculations were run at the ZORA relativistic level, with and without spin-orbit coupling using few selected GGA and hybrid functionals, namely BP86, PBE, B3LYP, and PBE0. We also tested solvent effects both at the optimization level and at the NMR calculation step. At the ZORA-SO-PBE0 (COSMO) level of theory we find a very good performance of the computational protocol that allows to discard or retain possible structures/conformations based on the agreement between the calculated chemical shift and the experimental value.
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Affiliation(s)
- Giacomo Saielli
- CNR Institute on Membrane Technology, Unit of Padova, Padova, Italy
- Department of Chemical Sciences, University of Padova, Padova, Italy
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4
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Hilla P, Vaara J. NMR chemical shift of confined 129Xe: coordination number, paramagnetic channels and molecular dynamics in a cryptophane-A biosensor. Phys Chem Chem Phys 2023; 25:22719-22733. [PMID: 37606522 DOI: 10.1039/d3cp02695g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Advances in hyperpolarisation and indirect detection have enabled the development of xenon nuclear magnetic resonance (NMR) biosensors (XBSs) for molecule-selective sensing in down to picomolar concentration. Cryptophanes (Crs) are popular cages for hosting the Xe "spy". Understanding the microscopic host-guest chemistry has remained a challenge in the XBS field. While early NMR computations of XBSs did not consider the important effects of host dynamics and explicit solvent, here we model the motionally averaged, relativistic NMR chemical shift (CS) of free Xe, Xe in a prototypic CrA cage and Xe in a water-soluble CrA derivative, each in an explicit H2O solvent, over system configurations generated at three different levels of molecular dynamics (MD) simulations. We confirm the "contact-type" character of the Xe CS, arising from the increased availability of paramagnetic channels, magnetic couplings between occupied and virtual orbitals through the short-ranged orbital hyperfine operator, when neighbouring atoms are in contact with Xe. Remarkably, the Xe CS in the present, highly dynamic and conformationally flexible situations is found to depend linearly on the coordination number of the Xe atom. We interpret the high- and low-CS situations in terms of the magnetic absorption spectrum and choose our preference among the used MD methods based on comparison with the experimental CS. We check the role of spin-orbit coupling by comparing with fully relativistic CS calculations. The study outlines the computational workflow required to realistically model the CS of Xe confined in dynamic cavity structures under experimental conditions, and contributes to microscopic understanding of XBSs.
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Affiliation(s)
- Perttu Hilla
- NMR Research Unit, P.O. Box 3000, FI-90014 University of Oulu, Finland.
| | - Juha Vaara
- NMR Research Unit, P.O. Box 3000, FI-90014 University of Oulu, Finland.
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5
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Jayapaul J, Komulainen S, Zhivonitko VV, Mareš J, Giri C, Rissanen K, Lantto P, Telkki VV, Schröder L. Hyper-CEST NMR of metal organic polyhedral cages reveals hidden diastereomers with diverse guest exchange kinetics. Nat Commun 2022; 13:1708. [PMID: 35361759 PMCID: PMC8971460 DOI: 10.1038/s41467-022-29249-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 03/03/2022] [Indexed: 01/04/2023] Open
Abstract
Guest capture and release are important properties of self-assembling nanostructures. Over time, a significant fraction of guests might engage in short-lived states with different symmetry and stereoselectivity and transit frequently between multiple environments, thereby escaping common spectroscopy techniques. Here, we investigate the cavity of an iron-based metal organic polyhedron (Fe-MOP) using spin-hyperpolarized 129Xe Chemical Exchange Saturation Transfer (hyper-CEST) NMR. We report strong signals unknown from previous studies that persist under different perturbations. On-the-fly delivery of hyperpolarized gas yields CEST signatures that reflect different Xe exchange kinetics from multiple environments. Dilute pools with ~ 104-fold lower spin numbers than reported for directly detected hyperpolarized nuclei are readily detected due to efficient guest turnover. The system is further probed by instantaneous and medium timescale perturbations. Computational modeling indicates that these signals originate likely from Xe bound to three Fe-MOP diastereomers (T, C3, S4). The symmetry thus induces steric effects with aperture size changes that tunes selective spin manipulation as it is employed in CEST MRI agents and, potentially, impacts other processes occurring on the millisecond time scale.
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Affiliation(s)
- Jabadurai Jayapaul
- Molecular Imaging, Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125, Berlin, Germany.,Division of Translational Molecular Imaging, Deutsches Krebsforschungszentrum (DKFZ), 69120, Heidelberg, Germany
| | | | | | - Jiří Mareš
- NMR Research Unit, University of Oulu, 90014, Oulu, Finland.,Research Unit of Medical Imaging, Physics and Technology (MIPT), University of Oulu, 90014, Oulu, Finland
| | - Chandan Giri
- University of Jyvaskyla, Department of Chemistry, 40014, Jyväskylä, Finland
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, 40014, Jyväskylä, Finland
| | - Perttu Lantto
- NMR Research Unit, University of Oulu, 90014, Oulu, Finland.
| | | | - Leif Schröder
- Molecular Imaging, Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125, Berlin, Germany. .,Division of Translational Molecular Imaging, Deutsches Krebsforschungszentrum (DKFZ), 69120, Heidelberg, Germany.
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6
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Jaworski A, Hedin N. Local energy decomposition analysis and molecular properties of encapsulated methane in fullerene (CH 4@C 60). Phys Chem Chem Phys 2021; 23:21554-21567. [PMID: 34550137 DOI: 10.1039/d1cp02333k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methane has been successfully encapsulated within cages of C60 fullerene, which is an appropriate model system to study confinement effects. Its chemistry and physics are also relevant for theoretical model descriptions. Here we provide insights into intermolecular interactions and predicted spectroscopic responses of the CH4@C60 complex and compared them with results from other methods and with data from the literature. Local energy decomposition analysis (LED) within the domain-based local pair natural orbital coupled cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) framework was used, and an efficient protocol for studies of endohedral complexes of fullerenes is proposed. This approach allowed us to assess energies in relation to electronic and geometric preparation, electrostatics, exchange, and London dispersion for the CH4@C60 endohedral complex. The calculated stabilization energy of CH4 inside the C60 fullerene was -13.5 kcal mol-1 and its magnitude was significantly larger than the latent heat of evaporation of CH4. Evaluation of vibrational frequencies and polarizabilities of the CH4@C60 complex revealed that the infrared (IR) and Raman bands of the endohedral CH4 were essentially "silent" due to the dielectric screening effect of C60, which acted as a molecular Faraday cage. Absorption spectra in the UV-vis domain and ionization potentials of C60 and CH4@C60 were predicted. They were almost identical. The calculated 1H/13C NMR shifts and spin-spin coupling constants were in very good agreement with experimental data. In addition, reference DLPNO-CCSD(T) interaction energies for complexes with noble gases (Ng@C60; Ng = He, Ne, Ar, Kr) were calculated. The values were compared with those derived from supramolecular MP2/SCS-MP2 calculations and estimates with London-type formulas by Pyykkö and coworkers [Phys. Chem. Chem. Phys., 2010, 12, 6187-6203], and with values derived from DFT-based symmetry-adapted perturbation theory (DFT-SAPT) by Hesselmann & Korona [Phys. Chem. Chem. Phys., 2011, 13, 732-743]. Selected points at the potential energy surface of the endohedral He2@C60 trimer were considered. In contrast to previous theoretical attempts with the DFT/MP2/SCS-MP2/DFT-SAPT methods, our calculations at the DLPNO-CCSD(T) level of theory predicted the He2@C60 trimer to be thermodynamically stable, which is in agreement with experimental observations.
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Affiliation(s)
- Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Niklas Hedin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
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7
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Krivdin LB. Computational NMR of heavy nuclei involving 109Ag, 113Cd, 119Sn, 125Te, 195Pt, 199Hg, 205Tl, and 207Pb. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4976] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Bacanu GR, Rantaharju J, Hoffman G, Walkey MC, Bloodworth S, Concistrè M, Whitby RJ, Levitt MH. An Internuclear J-Coupling of 3He Induced by Molecular Confinement. J Am Chem Soc 2020; 142:16926-16929. [PMID: 32945165 DOI: 10.1021/jacs.0c08586] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The solution-state 13C NMR spectrum of the endofullerene 3He@C60 displays a doublet structure due to a J-coupling of magnitude 77.5 ± 0.2 mHz at 340 K between the 3He nucleus and a 13C nucleus of the enclosing carbon surface. The J-coupling increases in magnitude with increasing temperature. Quantum chemistry calculations successfully predict the approximate magnitude of the coupling. This observation shows that the mutual proximity of molecular or atomic species is sufficient to induce a finite scalar nuclear spin-spin coupling, providing that translational motion is restricted by confinement. The phenomenon may have applications to the study of surface interactions and to mechanically bound species.
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Affiliation(s)
| | - Jyrki Rantaharju
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Gabriela Hoffman
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Mark C Walkey
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Sally Bloodworth
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Maria Concistrè
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Richard J Whitby
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Malcolm H Levitt
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
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9
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Chemical shift extremum of 129Xe(aq) reveals details of hydrophobic solvation. Sci Rep 2018; 8:7023. [PMID: 29728689 PMCID: PMC5935698 DOI: 10.1038/s41598-018-25418-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/20/2018] [Indexed: 11/08/2022] Open
Abstract
The 129Xe chemical shift in an aqueous solution exhibits a non-monotonic temperature dependence, featuring a maximum at 311 K. This is in contrast to most liquids, where the monotonic decrease of the shift follows that of liquid density. In particular, the shift maximum in water occurs at a higher temperature than that of the maximum density. We replicate this behaviour qualitatively via a molecular dynamics simulation and computing the 129Xe chemical shift for snapshots of the simulation trajectory. We also construct a semianalytical model, in which the Xe atom occupies a cavity constituted by a spherical water shell, consisting of an even distribution of solvent molecules. The temperature dependence of the shift is seen to result from a product of the decreasing local water density and an increasing term corresponding to the energetics of the Xe-H2O collisions. The latter moves the chemical shift maximum up in temperature, as compared to the density maximum. In water, the computed temperature of the shift maximum is found to be sensitive to both the details of the binary chemical shift function and the coordination number. This work suggests that, material parameters allowing, the maximum should be exhibited by other liquids, too.
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10
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Komulainen S, Roukala J, Zhivonitko VV, Javed MA, Chen L, Holden D, Hasell T, Cooper A, Lantto P, Telkki VV. Inside information on xenon adsorption in porous organic cages by NMR. Chem Sci 2017; 8:5721-5727. [PMID: 28989612 PMCID: PMC5621166 DOI: 10.1039/c7sc01990d] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/14/2017] [Indexed: 11/21/2022] Open
Abstract
A solid porous molecular crystal formed from an organic cage, CC3, has unprecedented performance for the separation of rare gases. Here, xenon was used as an internal reporter providing extraordinarily versatile information about the gas adsorption phenomena in the cage and window cavities of the material. 129Xe NMR measurements combined with state-of-the-art quantum chemical calculations allowed the determination of the occupancies of the cavities, binding constants, thermodynamic parameters as well as the exchange rates of Xe between the cavities. Chemical exchange saturation transfer (CEST) experiments revealed a minor window cavity site with a significantly lower exchange rate than other sites. Diffusion measurements showed significantly reduced mobility of xenon with loading. 129Xe spectra also revealed that the cage cavity sites are preferred at lower loading levels, due to more favourable binding, whereas window sites come to dominate closer to saturation because of their greater prevalence.
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Affiliation(s)
- Sanna Komulainen
- NMR Research Unit , University of Oulu , P.O.Box 3000 , 90014 Oulu , Finland .
| | - Juho Roukala
- NMR Research Unit , University of Oulu , P.O.Box 3000 , 90014 Oulu , Finland .
| | - Vladimir V Zhivonitko
- Laboratory of Magnetic Resonance Microimaging , International Tomography Center SB RAS , Department of Natural Sciences , Novosibirsk State University , Instututskaya St. 3A, Pirogova St. 2 , 630090 Novosibirsk , Russia
| | | | - Linjiang Chen
- Department of Chemistry , Centre for Materials Discovery , University of Liverpool , Crown Street , Liverpool L69 7ZD , UK
| | - Daniel Holden
- Department of Chemistry , Centre for Materials Discovery , University of Liverpool , Crown Street , Liverpool L69 7ZD , UK
| | - Tom Hasell
- Department of Chemistry , Centre for Materials Discovery , University of Liverpool , Crown Street , Liverpool L69 7ZD , UK
| | - Andrew Cooper
- Department of Chemistry , Centre for Materials Discovery , University of Liverpool , Crown Street , Liverpool L69 7ZD , UK
| | - Perttu Lantto
- NMR Research Unit , University of Oulu , P.O.Box 3000 , 90014 Oulu , Finland .
| | - Ville-Veikko Telkki
- NMR Research Unit , University of Oulu , P.O.Box 3000 , 90014 Oulu , Finland .
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11
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Kaminský J, Vícha J, Bouř P, Straka M. Properties of the Only Thorium Fullerene, Th@C84, Uncovered. J Phys Chem A 2017; 121:3128-3135. [DOI: 10.1021/acs.jpca.7b00346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo náměstí
2, 166 10 Prague, Czech Republic
| | - Jan Vícha
- Center
of Polymer Systems, University Institute, Tomáš Bat’a University in Zlín, Třída T. Bati, 5678, CZ-76001, Zlín, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo náměstí
2, 166 10 Prague, Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo náměstí
2, 166 10 Prague, Czech Republic
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12
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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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13
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Roukala J, Orr ST, Hanna JV, Vaara J, Ivanov AV, Antzutkin ON, Lantto P. Experimental and First-Principles NMR Analysis of Pt(II) Complexes With O,O′-Dialkyldithiophosphate Ligands. J Phys Chem A 2016; 120:8326-8338. [PMID: 27687143 DOI: 10.1021/acs.jpca.6b09586] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juho Roukala
- NMR
Research Unit, University of Oulu, P.O. Box 3000, FI-90400 Oulu, Finland
| | - Simon T. Orr
- Department
of Physics, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - John V. Hanna
- Department
of Physics, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Juha Vaara
- NMR
Research Unit, University of Oulu, P.O. Box 3000, FI-90400 Oulu, Finland
| | - Alexander V. Ivanov
- Institute
of Geology and Nature Management, Far Eastern Branch of the Russian Academy of Sciences, Ryolochny Lane 1, Blagoveshchensk 675000, Amur Region, Russia
| | - Oleg N. Antzutkin
- Department
of Physics, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
- Chemistry
of Interfaces, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | - Perttu Lantto
- NMR
Research Unit, University of Oulu, P.O. Box 3000, FI-90400 Oulu, Finland
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14
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Dračínský M, Bouř P, Hodgkinson P. Temperature Dependence of NMR Parameters Calculated from Path Integral Molecular Dynamics Simulations. J Chem Theory Comput 2016; 12:968-73. [PMID: 26857802 DOI: 10.1021/acs.jctc.5b01131] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influence of temperature on NMR chemical shifts and quadrupolar couplings in model molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory (DFT) calculations of shielding and electric field gradient (EFG) tensors. An approach based on convoluting calculated shielding or EFG tensor components with probability distributions of selected bond distances and valence angles obtained from DFT-PIMD simulations at several temperatures is used to calculate the temperature effects. The probability distributions obtained from the quantum PIMD simulations, which includes nuclear quantum effects, are significantly broader and less temperature dependent than those obtained with conventional DFT molecular dynamics or with 1D scans through the potential energy surface. Predicted NMR observables for the model systems were in excellent agreement with experimental data.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry , Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry , Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Paul Hodgkinson
- Department of Chemistry, Durham University , South Road, DH1 3LE Durham, United Kingdom
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15
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On novel magnetic probe for fullerene characterization: Theoretical studies on NMR parameters of free and confined in fullerenes HD and H 2 molecules. J Mol Graph Model 2015; 62:26-37. [DOI: 10.1016/j.jmgm.2015.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/05/2015] [Accepted: 08/24/2015] [Indexed: 11/22/2022]
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16
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Roukala J, Zhu J, Giri C, Rissanen K, Lantto P, Telkki VV. Encapsulation of xenon by a self-assembled Fe4L6 metallosupramolecular cage. J Am Chem Soc 2015; 137:2464-7. [PMID: 25671394 DOI: 10.1021/ja5130176] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report (129)Xe NMR experiments showing that a Fe4L6 metallosupramolecular cage can encapsulate xenon in water with a binding constant of 16 M(-1). The observations pave the way for exploiting metallosupramolecular cages as economical means to extract rare gases as well as (129)Xe NMR-based bio-, pH, and temperature sensors. Xe in the Fe4L6 cage has an unusual chemical shift downfield from free Xe in water. The exchange rate between the encapsulated and free Xe was determined to be about 10 Hz, potentially allowing signal amplification via chemical exchange saturation transfer. Computational treatment showed that dynamical effects of Xe motion as well as relativistic effects have significant contributions to the chemical shift of Xe in the cage and enabled the replication of the observed linear temperature dependence of the shift.
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Affiliation(s)
- Juho Roukala
- NMR Research Group, Centre for Molecular Materials, University of Oulu , 90014 Oulu, Finland
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Radula-Janik K, Kupka T. 3He NMR studies on helium-pyrrole, helium-indole, and helium-carbazole systems: a new tool for following chemistry of heterocyclic compounds. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:103-109. [PMID: 25228253 DOI: 10.1002/mrc.4141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 08/04/2014] [Accepted: 08/08/2014] [Indexed: 06/03/2023]
Abstract
The (3)He nuclear magnetic shieldings were calculated for free helium atom and He-pyrrole, He-indole, and He-carbazole complexes. Several levels of theory, including Hartree-Fock (HF), Second-order Møller-Plesset Perturbation Theory (MP2), and Density Functional Theory (DFT) (VSXC, M062X, APFD, BHandHLYP, and mPW1PW91), combined with polarization-consistent pcS-2 and aug-pcS-2 basis sets were employed. Gauge-including atomic orbital (GIAO) calculated (3)He nuclear magnetic shieldings reproduced accurately previously reported theoretical values for helium gas. (3)He nuclear magnetic shieldings and energy changes as result of single helium atom approaching to the five-membered ring of pyrrole, indole, and carbazole were tested. It was observed that (3)He NMR parameters of single helium atom, calculated at various levels of theory (HF, MP2, and DFT) are sensitive to the presence of heteroatomic rings. The helium atom was insensitive to the studied molecules at distances above 5 Å. Our results, obtained with BHandHLYP method, predicted fairly accurately the He-pyrrole plane separation of 3.15 Å (close to 3.24 Å, calculated by MP2) and yielded a sizable (3)He NMR chemical shift (about -1.5 ppm). The changes of calculated nucleus-independent chemical shifts (NICS) with the distance above the rings showed a very similar pattern to helium-3 NMR chemical shift. The ring currents above the five-membered rings were seen by helium magnetic probe to about 5 Å above the ring planes verified by the calculated NICS index.
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Karjalainen J, Vaara J, Straka M, Lantto P. Xenon NMR of liquid crystals confined to cylindrical nanocavities: a simulation study. Phys Chem Chem Phys 2015; 17:7158-71. [DOI: 10.1039/c4cp04868g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coarse-grained simulations show that the 129Xe NMR shielding reflects the smooth changes of orientational order in liquid crystals confined to nanocavities.
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Affiliation(s)
| | - Juha Vaara
- NMR Research Group
- University of Oulu
- Oulu
- Finland
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague
- Czech Republic
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19
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Sure R, Tonner R, Schwerdtfeger P. A systematic study of rare gas atoms encapsulated in small fullerenes using dispersion corrected density functional theory. J Comput Chem 2014; 36:88-96. [DOI: 10.1002/jcc.23787] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/23/2014] [Accepted: 10/27/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Rebecca Sure
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, 0745 Auckland, New Zealand; Mulliken Center for Theoretical Chemistry, University of Bonn; Beringstr. 4 53115 Bonn Germany
| | - Ralf Tonner
- Fachbereich Chemie and Material Sciences Center, Philipps-Universität Marburg; 35032 Marburg Germany
| | - Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, 0745 Auckland, New Zealand; Fachbereich Chemie, Philipps-Universität Marburg; 35032 Marburg Germany
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20
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Schwerdtfeger P, Wirz LN, Avery J. The topology of fullerenes. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014; 5:96-145. [PMID: 25678935 PMCID: PMC4313690 DOI: 10.1002/wcms.1207] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fullerenes are carbon molecules that form polyhedral cages. Their bond structures are exactly the planar cubic graphs that have only pentagon and hexagon faces. Strikingly, a number of chemical properties of a fullerene can be derived from its graph structure. A rich mathematics of cubic planar graphs and fullerene graphs has grown since they were studied by Goldberg, Coxeter, and others in the early 20th century, and many mathematical properties of fullerenes have found simple and beautiful solutions. Yet many interesting chemical and mathematical problems in the field remain open. In this paper, we present a general overview of recent topological and graph theoretical developments in fullerene research over the past two decades, describing both solved and open problems. WIREs Comput Mol Sci 2015, 5:96-145. doi: 10.1002/wcms.1207 Conflict of interest: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland Auckland, New Zealand ; Fachbereich Chemie, Philipps-Universität Marburg Marburg, Germany
| | - Lukas N Wirz
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland Auckland, New Zealand
| | - James Avery
- Niels Bohr Institute, University of Copenhagen Copenhagen, Denmark
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21
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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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22
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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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23
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Nieradka M, Kupka T. Sensitivity of Noble Gas NMR Parameters to the Heterocyclic Ring Proximity. Density Functional Theory Studies of Ne–Furan and Ar–Furan Complexes. Chem Heterocycl Compd (N Y) 2014. [DOI: 10.1007/s10593-014-1492-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Sensitivity of 3He NMR Parameters to the Proximity of Heterocyclic Rings. The Helium–Furan Dimer. Chem Heterocycl Compd (N Y) 2014. [DOI: 10.1007/s10593-014-1490-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Garcia-Borràs M, Osuna S, Luis JM, Swart M, Solà M. The role of aromaticity in determining the molecular structure and reactivity of (endohedral metallo)fullerenes. Chem Soc Rev 2014; 43:5089-105. [DOI: 10.1039/c4cs00040d] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The molecular structure and chemical reactivity of endohedral metallofullerenes can be greatly predicted and rationalized by their local and global aromaticity.
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Affiliation(s)
- Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- 17071 Girona, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- 17071 Girona, Spain
| | - Josep M. Luis
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- 17071 Girona, Spain
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- 17071 Girona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)
- 08010 Barcelona, Spain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- 17071 Girona, Spain
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26
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Kupka T, Stachów M, Nieradka M, Radula-Janik K, Stobiński L, Kaminský J. From small to medium and beyond: a pragmatic approach in predicting properties of Ne containing structures. Mol Phys 2013. [DOI: 10.1080/00268976.2013.848301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Kupka T, Nieradka M, Kaminský J, Stobiński L. Modeling 21Ne NMR parameters for carbon nanosystems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:676-681. [PMID: 23970499 DOI: 10.1002/mrc.3999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 06/18/2013] [Accepted: 07/18/2013] [Indexed: 06/02/2023]
Abstract
The potential of nuclear magnetic resonance (NMR) technique in probing the structure of porous systems including carbon nanostructures filled with inert gases is analysed theoretically using accurate calculations of neon ((21) Ne) nuclear magnetic shieldings. The CBS estimates of (21) Ne NMR parameters were performed for single atom, its dimer and neon interacting with acetylene, ethylene and 1,3-cyclopentadiene. Several levels of theory including restricted Hartree-Fock (RHF), Møller-Plesset perturbation theory to the second order (MP2), density functional theory (DFT) with van Voorhis and Scuseria's t-dependent gradient-corrected correlation functional (VSXC), coupled cluster with single and doubles excitations (CCSD), with single, doubles and triples included in a perturbative way (CCSD(T)) and single, doubles and tripes excitations (CCSDT) combined with polarization-consistent aug-pcS-n series of basis sets were employed. The impact of neon confinement inside selected fullerene cages used as an NMR probe was studied at the RHF/pcS-2 level of theory. A sensitivity of neon probe to the proximity of multiple CC bonds in C2 H2 , C2 H4 , C5 H6 and inside C28 , C30 , C32 , C34 and C60 fullerenes was predicted from (21) Ne NMR parameters' changes. Copyright © 2013 John Wiley & Sons, Ltd.
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Affiliation(s)
- Teobald Kupka
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 45-052, Opole, Poland
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28
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Rastrelli F, Frezzato D, Lawler RG, Li Y, Turro NJ, Bagno A. Predicting the paramagnet-enhanced NMR relaxation of H₂ encapsulated in endofullerene nitroxides by density-functional theory calculations. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20110634. [PMID: 23918714 DOI: 10.1098/rsta.2011.0634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We have investigated the structure and nuclear magnetic resonance (NMR) spectroscopic properties of some dihydrogen endofullerene nitroxides by means of density-functional theory (DFT) calculations. Quantum versus classical roto-translational dynamics of H₂ have been characterized and compared. Geometrical parameters and hyperfine couplings calculated by DFT have been input to the Solomon-Bloembergen equations to predict the enhancement of the NMR longitudinal relaxation of H₂ due to coupling with the unpaired electron. Estimating the rotational correlation time via computed molecular volumes leads to a fair agreement with experiment for the simplest derivative; the estimate is considerably improved by recourse to the calculation of the diffusion tensor. For the other more flexible congeners, the agreement is less good, which may be due to an insufficient sampling of the conformational space. In all cases, relaxation by Fermi contact and Curie mechanisms is predicted to be negligible.
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Affiliation(s)
- Federico Rastrelli
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo, 35131 Padova, Italy
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29
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Kupka T, Stachów M, Stobiński L, Kaminský J. 3He NMR: from free gas to its encapsulation in fullerene. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:463-468. [PMID: 23737362 DOI: 10.1002/mrc.3972] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/16/2013] [Accepted: 05/01/2013] [Indexed: 06/02/2023]
Abstract
The (3)He nuclear magnetic shieldings were calculated for single helium atom, its dimer, simple models of fullerene cages (He@Cn), and single wall carbon nanotubes. The performances of several levels of theory (HF, MP2, DFT-VSXC, CCSD, CCSD(T), and CCSDT) were tested. Two sets of polarization-consistent basis sets were used (pcS-n and aug-pcS-n), and an estimate of (3)He nuclear magnetic shieldings in the complete basis set limit using a two-parameter fit was established. Theoretical (3)He results reproduced accurately previously reported theoretical values for helium gas, dimer, and helium probe inside several fullerene cages. Excellent agreement with experimental values was achieved. (3)He nuclear magnetic shieldings of single helium atom approaching various points of benzene ring were tested, and an impact of (3)He confinement within fullerene cages of different size on the (3)He chemical shift was determined.
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Affiliation(s)
- Teobald Kupka
- Faculty of Chemistry, University of Opole, 48, Oleska Street, 45-052, Opole, Poland
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30
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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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31
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Vaara J, Hanni M, Jokisaari J. Nuclear spin-spin coupling in a van der Waals-bonded system: Xenon dimer. J Chem Phys 2013; 138:104313. [DOI: 10.1063/1.4793745] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Kaminský J, Buděšínský M, Taubert S, Bouř P, Straka M. Fullerene C70 characterization by 13C NMR and the importance of the solvent and dynamics in spectral simulations. Phys Chem Chem Phys 2013; 15:9223-30. [DOI: 10.1039/c3cp50657f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Lantto P, Kangasvieri S, Vaara J. Electron correlation and relativistic effects in the secondary NMR isotope shifts of CSe2. Phys Chem Chem Phys 2013; 15:17468-78. [DOI: 10.1039/c3cp51904j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Lantto P, Kangasvieri S, Vaara J. Rovibrational effects on NMR shieldings in a heavy-element system: XeF2. J Chem Phys 2012; 137:214309. [DOI: 10.1063/1.4768471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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35
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Gąszowski D, Ilczyszyn M. Does hydrogen bonding to xenon affect its 129Xe NMR chemical shift? Computational study on selected Brønsted acid–xenon complexes. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.04.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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Bagno A, Saielli G. Understanding the Extraordinary Deshielding of129Xe in a Permetallated Cryptophane by Relativistic DFT. Chemistry 2012; 18:7341-5. [DOI: 10.1002/chem.201103979] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 03/06/2012] [Indexed: 11/05/2022]
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37
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Dračínský M, Bouř P. Vibrational averaging of the chemical shift in crystalline α-glycine. J Comput Chem 2012; 33:1080-9. [PMID: 22410968 DOI: 10.1002/jcc.22940] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/04/2012] [Accepted: 01/04/2012] [Indexed: 11/06/2022]
Abstract
Averaging of the chemical shift over the molecular motion improves the simulated data and provides additional information about the temperature dependence and system dynamics. However, crystal modeling is difficult due to the limited precision of the plane-wave density functional theory (DFT) methods and approximate vibrational schemes. On the glycine example, we investigate how the averaging can be achieved within the periodic boundary conditions at the DFT level. The nuclear motion is modeled with the vibrational configuration interaction, with other simplified quantum anharmonic schemes, and the classical Born-Oppenheimer molecular dynamics (BOMD). The results confirm a large vibrational contribution to the isotropic shielding values. Both the first and second derivatives of the shielding were found important for the quantum averaging. The first derivatives influence the shielding mostly due to the anharmonic character of the CH and NH stretching modes, whereas second derivatives produce most vibrational corrections associated with the lower-frequency vibrational modes. Temperature excitations of the lowest-frequency vibrational states and the expansion of the crystal cell both determine the temperature dependence of nuclear magnetic resonance parameters. The vibrational quantum approach as well as classical BOMD schemes provided temperature dependencies of the chemical shifts that are consistent with the previous experimental data.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague 166 10, Czech Republic.
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38
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Lantto P, Standara S, Riedel S, Vaara J, Straka M. Exploring new 129Xe chemical shift ranges in HXeY compounds: hydrogen more relativistic than xenon. Phys Chem Chem Phys 2012; 14:10944-52. [DOI: 10.1039/c2cp41240c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Dabbagh HA, Zamani M, Farrokhpour H. DFT investigation of endohedral boron oxide nanocapsules: Encapsulation of He, Ne, Ar, H, N, and Cl atoms. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.11.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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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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41
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Osuna S, Swart M, Solà M. The reactivity of endohedral fullerenes. What can be learnt from computational studies? Phys Chem Chem Phys 2011; 13:3585-603. [DOI: 10.1039/c0cp01594f] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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Roukala J, Maldonado AF, Vaara J, Aucar GA, Lantto P. Relativistic effects on group-12 metal nuclear shieldings. Phys Chem Chem Phys 2011; 13:21016-25. [DOI: 10.1039/c1cp22043h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Assignment of the He@C84 isomers in experimental NMR spectra using density functional calculations. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.09.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Wang C, Straka M, Pyykkö P. Formulations of the closed-shell interactions in endohedral systems. Phys Chem Chem Phys 2010; 12:6187-203. [DOI: 10.1039/b922808j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Kantola AM, Lantto P, Vaara J, Jokisaari J. Carbon and proton shielding tensors in methyl halides. Phys Chem Chem Phys 2010; 12:2679-92. [DOI: 10.1039/b923506j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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Dumez JN, Pickard CJ. Calculation of NMR chemical shifts in organic solids: accounting for motional effects. J Chem Phys 2009; 130:104701. [PMID: 19292543 DOI: 10.1063/1.3081630] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
NMR chemical shifts were calculated from first principles for well defined crystalline organic solids. These density functional theory calculations were carried out within the plane-wave pseudopotential framework, in which truly extended systems are implicitly considered. The influence of motional effects was assessed by averaging over vibrational modes or over snapshots taken from ab initio molecular dynamics simulations. It is observed that the zero-point correction to chemical shifts can be significant, and that thermal effects are particularly noticeable for shielding anisotropies and for a temperature-dependent chemical shift. This study provides insight into the development of highly accurate first principles calculations of chemical shifts in solids, highlighting the role of motional effects on well defined systems.
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Affiliation(s)
- Jean-Nicolas Dumez
- School of Physics and Astronomy, University of St-Andrews, St Andrews KY16 9SS, United Kingdom.
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47
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Hanni M, Lantto P, Vaara J. Pairwise additivity in the nuclear magnetic resonance interactions of atomic xenon. Phys Chem Chem Phys 2009; 11:2485-96. [PMID: 19325983 DOI: 10.1039/b821907a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.
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Affiliation(s)
- Matti Hanni
- NMR Research Group, Department of Physical Sciences, University of Oulu, P.O. Box 3000, FIN-90014, University of Oulu, Finland.
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Huber G, Beguin L, Desvaux H, Brotin T, Fogarty HA, Dutasta JP, Berthault P. Cryptophane-Xenon Complexes in Organic Solvents Observed through NMR Spectroscopy. J Phys Chem A 2008; 112:11363-72. [PMID: 18925727 DOI: 10.1021/jp807425t] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gaspard Huber
- CEA, IRAMIS, Service de Chimie Moléculaire, Laboratoire Structure et Dynamique par Résonance Magnétique, URA CEA/CNRS 331, 91191Gif-sur-Yvette, France, and CNRS, École Normale Supérieure de Lyon, Laboratoire de Chimie, 46 Allée d’Italie, F-69364 Lyon, France
| | - Lætitia Beguin
- CEA, IRAMIS, Service de Chimie Moléculaire, Laboratoire Structure et Dynamique par Résonance Magnétique, URA CEA/CNRS 331, 91191Gif-sur-Yvette, France, and CNRS, École Normale Supérieure de Lyon, Laboratoire de Chimie, 46 Allée d’Italie, F-69364 Lyon, France
| | - Hervé Desvaux
- CEA, IRAMIS, Service de Chimie Moléculaire, Laboratoire Structure et Dynamique par Résonance Magnétique, URA CEA/CNRS 331, 91191Gif-sur-Yvette, France, and CNRS, École Normale Supérieure de Lyon, Laboratoire de Chimie, 46 Allée d’Italie, F-69364 Lyon, France
| | - Thierry Brotin
- CEA, IRAMIS, Service de Chimie Moléculaire, Laboratoire Structure et Dynamique par Résonance Magnétique, URA CEA/CNRS 331, 91191Gif-sur-Yvette, France, and CNRS, École Normale Supérieure de Lyon, Laboratoire de Chimie, 46 Allée d’Italie, F-69364 Lyon, France
| | - Heather A. Fogarty
- CEA, IRAMIS, Service de Chimie Moléculaire, Laboratoire Structure et Dynamique par Résonance Magnétique, URA CEA/CNRS 331, 91191Gif-sur-Yvette, France, and CNRS, École Normale Supérieure de Lyon, Laboratoire de Chimie, 46 Allée d’Italie, F-69364 Lyon, France
| | - Jean-Pierre Dutasta
- CEA, IRAMIS, Service de Chimie Moléculaire, Laboratoire Structure et Dynamique par Résonance Magnétique, URA CEA/CNRS 331, 91191Gif-sur-Yvette, France, and CNRS, École Normale Supérieure de Lyon, Laboratoire de Chimie, 46 Allée d’Italie, F-69364 Lyon, France
| | - Patrick Berthault
- CEA, IRAMIS, Service de Chimie Moléculaire, Laboratoire Structure et Dynamique par Résonance Magnétique, URA CEA/CNRS 331, 91191Gif-sur-Yvette, France, and CNRS, École Normale Supérieure de Lyon, Laboratoire de Chimie, 46 Allée d’Italie, F-69364 Lyon, France
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