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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Balodis M, Cordova M, Hofstetter A, Day GM, Emsley L. De Novo Crystal Structure Determination from Machine Learned Chemical Shifts. J Am Chem Soc 2022; 144:7215-7223. [PMID: 35416661 PMCID: PMC9052749 DOI: 10.1021/jacs.1c13733] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Determination of the three-dimensional atomic-level structure of powdered solids is one of the key goals in current chemistry. Solid-state NMR chemical shifts can be used to solve this problem, but they are limited by the high computational cost associated with crystal structure prediction methods and density functional theory chemical shift calculations. Here, we successfully determine the crystal structures of ampicillin, piroxicam, cocaine, and two polymorphs of the drug molecule AZD8329 using on-the-fly generated machine-learned isotropic chemical shifts to directly guide a Monte Carlo-based structure determination process starting from a random gas-phase conformation.
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Affiliation(s)
- Martins Balodis
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Manuel Cordova
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Graeme M Day
- School of Chemistry, University of Southampton, Highfield SO17 1BJ, Southampton, United Kingdom
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
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3
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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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4
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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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5
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Emwas AH, Szczepski K, Poulson BG, Chandra K, McKay RT, Dhahri M, Alahmari F, Jaremko L, Lachowicz JI, Jaremko M. NMR as a "Gold Standard" Method in Drug Design and Discovery. Molecules 2020; 25:E4597. [PMID: 33050240 PMCID: PMC7594251 DOI: 10.3390/molecules25204597] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Kacper Szczepski
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Benjamin Gabriel Poulson
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Kousik Chandra
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada;
| | - Manel Dhahri
- Biology Department, Faculty of Science, Taibah University, Yanbu El-Bahr 46423, Saudi Arabia;
| | - Fatimah Alahmari
- Nanomedicine Department, Institute for Research and Medical, Consultations (IRMC), Imam Abdulrahman Bin Faisal University (IAU), Dammam 31441, Saudi Arabia;
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, Università di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
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6
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Ilczyszyn MM, Ilczyszyn M, Selent M. Structure and stability of p-cresol – xenon clathrate: Raman spectroscopy study. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Engel EA, Anelli A, Hofstetter A, Paruzzo F, Emsley L, Ceriotti M. A Bayesian approach to NMR crystal structure determination. Phys Chem Chem Phys 2019; 21:23385-23400. [PMID: 31631196 DOI: 10.1039/c9cp04489b] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is particularly well suited to determine the structure of molecules and materials in powdered form. Structure determination usually proceeds by finding the best match between experimentally observed NMR chemical shifts and those of candidate structures. Chemical shifts for the candidate configurations have traditionally been computed by electronic-structure methods, and more recently predicted by machine learning. However, the reliability of the determination depends on the errors in the predicted shifts. Here we propose a Bayesian framework for determining the confidence in the identification of the experimental crystal structure, based on knowledge of the typical errors in the electronic structure methods. We demonstrate the approach on the determination of the structures of six organic molecular crystals. We critically assess the reliability of the structure determinations, facilitated by the introduction of a visualization of the similarity between candidate configurations in terms of their chemical shifts and their structures. We also show that the commonly used values for the errors in calculated 13C shifts are underestimated, and that more accurate, self-consistently determined uncertainties make it possible to use 13C shifts to improve the accuracy of structure determinations. Finally, we extend the recently-developed ShiftML model to render it more efficient, accurate, and, most importantly, to evaluate the uncertainties in its predictions. By quantifying the confidence in structure determinations based on ShiftML predictions we further substantiate that it provides a valid replacement for first-principles calculations in NMR crystallography.
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Affiliation(s)
- Edgar A Engel
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
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8
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Hofstetter A, Balodis M, Paruzzo FM, Widdifield CM, Stevanato G, Pinon AC, Bygrave PJ, Day GM, Emsley L. Rapid Structure Determination of Molecular Solids Using Chemical Shifts Directed by Unambiguous Prior Constraints. J Am Chem Soc 2019; 141:16624-16634. [PMID: 31117663 PMCID: PMC7540916 DOI: 10.1021/jacs.9b03908] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
NMR-based crystallography approaches involving the combination of crystal structure prediction methods, ab initio calculated chemical shifts and solid-state NMR experiments are powerful methods for crystal structure determination of microcrystalline powders. However, currently structural information obtained from solid-state NMR is usually included only after a set of candidate crystal structures has already been independently generated, starting from a set of single-molecule conformations. Here, we show with the case of ampicillin that this can lead to failure of structure determination. We propose a crystal structure determination method that includes experimental constraints during conformer selection. In order to overcome the problem that experimental measurements on the crystalline samples are not obviously translatable to restrict the single-molecule conformational space, we propose constraints based on the analysis of absent cross-peaks in solid-state NMR correlation experiments. We show that these absences provide unambiguous structural constraints on both the crystal structure and the gas-phase conformations, and therefore can be used for unambiguous selection. The approach is parametrized on the crystal structure determination of flutamide, flufenamic acid, and cocaine, where we reduce the computational cost by around 50%. Most importantly, the method is then shown to correctly determine the crystal structure of ampicillin, which would have failed using current methods because it adopts a high-energy conformer in its crystal structure. The average positional RMSE on the NMR powder structure is ⟨rav⟩ = 0.176 Å, which corresponds to an average equivalent displacement parameter Ueq = 0.0103 Å2.
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Affiliation(s)
- Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Martins Balodis
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Cory M Widdifield
- Department of Chemistry, Mathematics and Science Center , Oakland University , 146 Library Drive , Rochester , Michigan 48309-4479 , United States
| | - Gabriele Stevanato
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Arthur C Pinon
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Peter J Bygrave
- School of Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , United Kingdom
| | - Graeme M Day
- School of Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , United Kingdom
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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9
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Nyman J, Yu L, Reutzel-Edens SM. Accuracy and reproducibility in crystal structure prediction: the curious case of ROY. CrystEngComm 2019. [DOI: 10.1039/c8ce01902a] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Because of excessive electron delocalization, the polymorphs of ROY constitute a surprisingly challenging system for crystal structure prediction.
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Affiliation(s)
- Jonas Nyman
- School of Pharmacy
- University of Wisconsin – Madison
- Madison
- USA
- Small Molecule Design & Development
| | - Lian Yu
- School of Pharmacy
- University of Wisconsin – Madison
- Madison
- USA
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10
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Paruzzo FM, Hofstetter A, Musil F, De S, Ceriotti M, Emsley L. Chemical shifts in molecular solids by machine learning. Nat Commun 2018; 9:4501. [PMID: 30374021 PMCID: PMC6206069 DOI: 10.1038/s41467-018-06972-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/26/2018] [Indexed: 02/02/2023] Open
Abstract
Due to their strong dependence on local atonic environments, NMR chemical shifts are among the most powerful tools for strucutre elucidation of powdered solids or amorphous materials. Unfortunately, using them for structure determination depends on the ability to calculate them, which comes at the cost of high accuracy first-principles calculations. Machine learning has recently emerged as a way to overcome the need for quantum chemical calculations, but for chemical shifts in solids it is hindered by the chemical and combinatorial space spanned by molecular solids, the strong dependency of chemical shifts on their environment, and the lack of an experimental database of shifts. We propose a machine learning method based on local environments to accurately predict chemical shifts of molecular solids and their polymorphs to within DFT accuracy. We also demonstrate that the trained model is able to determine, based on the match between experimentally measured and ML-predicted shifts, the structures of cocaine and the drug 4-[4-(2-adamantylcarbamoyl)-5-tert-butylpyrazol-1-yl]benzoic acid. Solid-state nuclear magnetic resonance combined with quantum chemical shift predictions is limited by high computational cost. Here, the authors use machine learning based on local atomic environments to predict experimental chemical shifts in molecular solids with accuracy similar to density functional theory.
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Affiliation(s)
- Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Félix Musil
- Institut des Sciences et Génie Matériaux, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Sandip De
- Institut des Sciences et Génie Matériaux, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Michele Ceriotti
- Institut des Sciences et Génie Matériaux, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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11
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Kemnitzer TW, Tschense CBL, Wittmann T, Rössler EA, Senker J. Exploring Local Disorder within CAU-1 Frameworks Using Hyperpolarized 129Xe NMR Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:12538-12548. [PMID: 30247917 DOI: 10.1021/acs.langmuir.8b02592] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The sorption properties of metal-organic frameworks (MOFs) can be influenced by introducing covalently attached functional side chains, which make this subclass of porous materials promising for applications as diverse as gas storage and separation, catalysis, and drug delivery. The incorporation of side groups usually comes along with disorder, as the synthesis procedures rarely allow for one specific position among a larger group of equivalent sites to be selected. For a series of isoreticular CAU-1 frameworks, chosen as model compounds, one out of four positions at every linker is modified with equal probability. Here, we investigate the influence of this disorder on Ar sorption and 129Xe nuclear magnetic resonance spectroscopy using hyperpolarized 129Xe gas. Models used for predicting the pore dimensions as well as their distributions were derived from the unfunctionalized framework by replacing one proton at every linker with either an amino, an acetamide, or a methyl urea functionality. The resulting structures were optimized using density functional theory (DFT) calculations. Results from void analyses and Monte Carlo force field simulations suggest that for available Ar nonlocal DFT (NLDFT) kernels, neither the pore dimensions nor the distributions induced by the side-chain disorder are well-reproduced. By contrast, we found the 129Xe chemical shift analysis for the shift observed at high temperature to be well-suited to develop a detailed fingerprint of the porosity and side-chain disorder within the isoreticular CAU-1 series. After calibrating the 129Xe limiting shift of the amino-functionalized framework with DFT calculations, the downfield shifts for the other two derivatives are an excellent measure for the reduction of the accessible pore space and reveal a strong preference for the side chains toward the octahedral voids for both cases. We expect that the strategy presented here can be commonly applied to disorder phenomena within MOFs in the future.
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12
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Braun DE, Raabe K, Schneeberger A, Kahlenberg V, Griesser UJ. New Insights into Solid Form Stability and Hydrate Formation: o-Phenanthroline HCl and Neocuproine HCl. Molecules 2017; 22:molecules22122238. [PMID: 29244765 PMCID: PMC6149885 DOI: 10.3390/molecules22122238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 11/27/2022] Open
Abstract
The moisture- and temperature dependent stabilities and interrelation pathways of the practically relevant solid forms of o-phenanthroline HCl (1) and neocuproine HCl (2) were investigated using thermal analytical techniques (HSM, DSC and TGA) and gravimetric moisture sorption/desorption studies. The experimental stability data were correlated with the structural changes observed upon dehydration and the pairwise interaction and lattice energies calculated. For 1 the monohydrate was identified as the only stable form under conditions of RH typically found during production and storage, but at RH values >80% deliquescence occurs. The second compound, 2, forms an anhydrate and two different hydrates, mono- (2-Hy1) and trihydrate (2-Hy3). The 2-Hy1 structure was solved from SCXRD data and the anhydrate structure derived from a combination of PXRD and CSP. Depending on the environmental conditions (moisture) either 2-Hy1 or 2-Hy3 is the most sable solid form of 2 at RT. The monohydrates 1-Hy1 and 2-Hy1 show a high enthalpic stabilization (≥20 kJ mol−1) relative to the anhydrates. The anhydrates are unstable at ambient conditions and readily transform to the monohydrates even in the presence of traces of moisture. This study demonstrates how the right combination of experiment and theory can unravel the properties and interconversion pathways of solid forms.
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Affiliation(s)
- Doris E Braun
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria.
| | - Katharina Raabe
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria.
| | - Anna Schneeberger
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria.
| | - Volker Kahlenberg
- Institute of Mineralogy and Petrography, University of Innsbruck, Innrain 52, 6020 Innsbruck, Austria.
| | - Ulrich J Griesser
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria.
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13
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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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14
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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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15
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Evans JD, Jelfs KE, Day GM, Doonan CJ. Application of computational methods to the design and characterisation of porous molecular materials. Chem Soc Rev 2017; 46:3286-3301. [DOI: 10.1039/c7cs00084g] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Composed from discrete units, porous molecular materials (PMMs) possess properties not observed for conventional, extended solids. Molecular simulations provide crucial understanding for the design and characterisation of these unique materials.
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Affiliation(s)
- Jack D. Evans
- Chimie ParisTech
- PSL Research University
- CNRS
- Institut de Recherche de Chimie Paris
- 75005 Paris
| | - Kim E. Jelfs
- Department of Chemistry
- Imperial College London
- South Kensington
- London
- UK
| | - Graeme M. Day
- Computational Systems Chemistry
- School of Chemistry
- University of Southampton
- Highfield
- Southampton
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