1
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Dupont J, Hartwig B, Le Barbu-Debus K, Lepere V, Guillot R, Suhm MA, Zehnacker A. Homochiral vs. heterochiral preference in chiral self-recognition of cyclic diols. Phys Chem Chem Phys 2024; 26:10610-10621. [PMID: 38506638 DOI: 10.1039/d4cp00351a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The structure and clustering propensity of a chiral derivative of cis-1,2-cyclohexanediol, namely, 1-phenyl-cis-1,2-cyclohexanediol (cis-PCD), has been studied under supersonic expansion conditions by combining laser spectroscopy with quantum chemistry calculations. The presence of the phenyl substituent induces conformational locking relative to cis-1,2-cyclohexanediol (cis-CD), and only one conformer of the bare molecule is observed by both Raman and IR-UV double resonance spectroscopy. The homochiral preference inferred for the dimer formation at low enough temperature is in line with the formation of a conglomerate in the solid state. The change in clustering propensity in cis-PCD relative to trans-1,2-cyclohexanediol (trans-CD), which shows heterochiral preference, is explained by the presence of the phenyl substituent rather than the effect of cis-trans isomerism. Indeed the transiently chiral cis-CD also forms preferentially heterodimers, whose structure is very close to that of the corresponding trans-CD dimer.
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Affiliation(s)
- Jennifer Dupont
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, rue André Rivière, Université Paris-Saclay, F-91405 Orsay, France.
| | - Beppo Hartwig
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, rue André Rivière, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, rue André Rivière, Université Paris-Saclay, F-91405 Orsay, France.
| | - Regis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), 17 Av. des Sciences Université Paris-Saclay, F-91405 Orsay, France
| | - Martin A Suhm
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, rue André Rivière, Université Paris-Saclay, F-91405 Orsay, France.
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2
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Lu T, Xie F, Seifert NA, Hamidi Mejlej R, Jäger W, Xu Y. Binary conformers of a flexible, long-chain fluoroalcohol: dispersion controlled selectivity and relative abundances in a jet. Phys Chem Chem Phys 2024; 26:10538-10545. [PMID: 38505957 DOI: 10.1039/d4cp00401a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The complex conformational panorama of binary 4,4,4-trifluoro-1-butanol (TFB) aggregates was investigated using chirped-pulse Fourier transform microwave spectroscopy, aided by conformational searches using CREST (Conformer-Rotamer Ensemble Sampling Tool) and quantum chemistry calculations. From nearly 1500 initial dimer geometries, 16 most stable binary candidates were obtained within a relative energy window of ∼4 kJ mol-1. Rotational spectra of five binary conformers were experimentally observed in supersonic expansion and assigned. Interestingly, three out of the five observed binary conformers are composed solely of monomer conformers, which were not observed in their isolated gas phase forms in jet expansion. In addition, an observed dimer that is made exclusively of the most stable TFB monomer subunits does not correspond to the global minimum. The intricate kinetically and thermodynamically controlled dimer formation mechanisms are discussed, and a modified kinetic-thermodynamic model was developed, providing conformational abundances that are in good agreement with the experiment. Subsequent non-covalent interaction analyses reveal that the observed conformers are held together by one primary O-H⋯O hydrogen bond and secondary intermolecular C-H⋯O, C-H⋯F, and/or O-H⋯F interactions, as well as C-H⋯H-C London dispersion interactions between the methylene groups. Further symmetry-adapted perturbation theory analyses of the TFB dimer conformers and related alcohol dimers reveal a considerable rise in dispersion contributions with increasing n-alkyl carbon chain length and highlight the role of dispersion interactions in preferentially stabilizing the global minimum of the TFB dimer.
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Affiliation(s)
- Tao Lu
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada.
- Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Fan Xie
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada.
| | - Nathan A Seifert
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada.
- Chemistry and Chemical & Biomedical Engineering Department, University of New Haven, 300 Boston Post Rd, West Haven, CT 06516, USA
| | - Reihaneh Hamidi Mejlej
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada.
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada.
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada.
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3
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Wu B, Seifert NA, Oswald S, Jäger W, Xu Y. Rotational Spectroscopy of the 2,2,3,3,3-Pentafluoropropanol⋅⋅⋅Water Complex: Conformations and Large Amplitude Motions. Chemphyschem 2022; 23:e202200348. [PMID: 35759723 DOI: 10.1002/cphc.202200348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/24/2022] [Indexed: 11/08/2022]
Abstract
The 2,2,3,3,3-pentafluoropropanol (PFP) monomer can exist in five conformations defined by the CCCO and CCOH dihedral angles: four mirror-imaged pairs (G+g+/G-g-, G+g-/G-g+, G+t/G-t, Tg+/Tg-) and an achiral Tt form. We examined the conformational landscape of the PFP⋅⋅⋅water complex using chirped pulsed Fourier transform microwave spectroscopy and theoretical calculations. Rotational spectra of two PFP⋅⋅⋅water conformers, PFPG+g+⋅⋅⋅WH and PFPTg+⋅⋅⋅WH , and seven deuterated isotopologues of each, were assigned. Tunneling splittings were observed for both conformers and are attributed to the exchange of the bonded and non-bonded hydrogen atoms of water. On the other hand, the tunneling splitting associated with the OH flipping motion in PFPTg+/Tg- appears to be quenched upon hydrogen bonding with water. The large amplitude motions associated with the water subunits were examined in detail to explain the very different magnitudes of the experimental and theoretical permanent electric dipole moment components. The study highlights the challenge in correctly identifying the conformers observed when large amplitude motions are involved. Quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analyses, as well as electrostatic potential (ESP) calculations were carried out to explore the nature of the non-covalent interactions and to appreciate the effects of fluorination.
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Affiliation(s)
- Bowei Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Nathan A Seifert
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.,Chemistry and Chemical & Biomedical Engineering Department University of New Haven, 300 Boston Post Rd, West Haven, CT, 06516, USA
| | - Sönke Oswald
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.,Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstraße 6, 37077, Göttingen, Germany
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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4
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Yang Q, Carlson CD, Jäger W, Xu Y. Conformational Landscape of the Hydrogen-Bonded 1-Phenyl-2,2,2-Trilfuoroethanol···1,4-Dioxane Complex: Dispersion Interactions and Conformational Conversion. J Phys Chem A 2022; 126:2942-2949. [PMID: 35507825 DOI: 10.1021/acs.jpca.2c01667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A rotational spectrum of the hydrogen-bonded complex between 1-phenyl-2,2,2-trilfuoroethanol (PhTFE), a chiral fluoroalcohol, and 1,4-dioxane, a common solvent for organic reactions, was measured using a chirped pulse Fourier transform microwave spectrometer. Initial theoretical conformational searches were carried out using CREST, a recently developed conformational searching tool. Subsequent geometry optimization and harmonic frequency calculations at the B3LYP-D3(BJ)/def2-TZVP level of theory yielded nearly 30 binary conformers of which 13 are within an energy window of ∼5 kJ mol-1. Interestingly, while the O-H···O hydrogen bond dominates the attractive binary interactions, the complex conformational landscape is mainly controlled by subtle dispersion interactions between the phenyl and 1,4-dioxane rings. Two sets of rotational transitions were assigned in the experimental spectrum and attributed to the two most stable conformers of PhTFE···1,4-dioxane. The quantum theory of atoms in molecules (QTAIM), noncovalent interactions (NCI), and symmetry-adapted perturbation theory (SAPT) analyses were employed in order to appreciate how the phenyl ring and O-H functional groups influence the intermolecular interaction and conformational distribution of the binary complex. The main PhTFE conformation within the complex, identified experimentally, is different from that of the isolated PhTFE monomer reported previously.
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Affiliation(s)
- Qian Yang
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Colton D Carlson
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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5
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Juanes M, Saragi RT, Pérez C, Enríquez L, Jaraíz M, Lesarri A. Torsional chirality and molecular recognition: the homo and heterochiral dimers of thenyl and furfuryl alcohol. Phys Chem Chem Phys 2022; 24:8999-9006. [PMID: 35380144 DOI: 10.1039/d2cp00479h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Furfuryl alcohol and thenyl alcohol contain a labile torsional chiral center, producing transiently chiral enantiomers interconverting in the nanosecond time-scale. We explored chiral molecular recognition using the weakly-bound intermolecular dimers of both alcohols, freezing stereomutation. Supersonic jet broadband microwave spectroscopy revealed homo and heterochiral diastereoisomers for each alcohol dimer and the structural characteristics of the clusters. All dimers are primarily stabilized by a moderately intense O-H⋯O hydrogen bond, but differ in the secondary interactions, which introduce additional hydrogen bonds either to the ring oxygen in furfuryl alcohol or to the π ring system in thenyl alcohol. Density-functional calculations (B2PLYP-D3(BJ)/def2-TZVP) show no clear preferences for a particular stereochemistry in the dimers, with relative energies of the order 1-2 kJ mol-1. The study suggests opportunities for the investigation of chiral recognition in molecules with torsional barriers in between transient and permanent interconversion regimes.
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Affiliation(s)
- Marcos Juanes
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain.
| | - Rizalina Tama Saragi
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain.
| | - Cristóbal Pérez
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain.
| | - Lourdes Enríquez
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 15, 47011 Valladolid, Spain
| | - Martín Jaraíz
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 15, 47011 Valladolid, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain.
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6
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Wu B, Seifert NA, Insausti A, Ma J, Oswald S, Jaeger W, Xu Y. 2,2,3,3,3-pentafluoro-1-propanol and its dimer: structural diversity, conformational conversion, and tunnelling motion. Phys Chem Chem Phys 2022; 24:14975-14984. [DOI: 10.1039/d2cp01895k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rotational spectra of the 2,2,3,3,3-pentafluoro-1-propanol (PFP) were measured using cavity and chirped pulse Fourier transform microwave spectrometers. Of the nine possible PFP configurations which include four mirror-imaged pairs and an...
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7
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Medel R, Camiruaga A, Saragi RT, Pinacho P, Pérez C, Schnell M, Lesarri A, Suhm MA, Fernández JA. Rovibronic signatures of molecular aggregation in the gas phase: subtle homochirality trends in the dimer, trimer and tetramer of benzyl alcohol. Phys Chem Chem Phys 2021; 23:23610-23624. [PMID: 34661223 DOI: 10.1039/d1cp03508h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular aggregation is of paramount importance in many chemical processes, including those in living beings. Thus, characterization of the intermolecular interactions is an important step in its understanding. We describe here the aggregation of benzyl alcohol at the molecular level, a process governed by a delicate equilibrium between OH⋯O and OH⋯π hydrogen bonds and dispersive interactions. Using microwave, FTIR, Raman and mass-resolved double-resonance IR/UV spectroscopic techniques, we explored the cluster growth up to the tetramer and found a complex landscape, partly due to the appearance of multiple stereoisomers of very similar stability. Interestingly, a consistently homochiral synchronization of transiently chiral monomer conformers was observed during cluster growth to converge in the tetramer, where the fully homochiral species dominates the potential energy surface. The data on the aggregation of benzyl alcohol also constitute an excellent playground to fine-tune the parameters of the most advanced functionals.
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Affiliation(s)
- Robert Medel
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
| | - Ander Camiruaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 4894 Leioa, Spain.
| | - Rizalina Tama Saragi
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011 Valladolid, Spain
| | - Pablo Pinacho
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.,Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118 Kiel, Germany
| | - Cristóbal Pérez
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.,Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118 Kiel, Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.,Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118 Kiel, Germany
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011 Valladolid, Spain
| | - Martin A Suhm
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 4894 Leioa, Spain.
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8
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Molecular Recognition, Transient Chirality and Sulfur Hydrogen Bonding in the Benzyl Mercaptan Dimer. Symmetry (Basel) 2021. [DOI: 10.3390/sym13112022] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The homodimers of transiently chiral molecules offer physical insight into the process of molecular recognition, the preference for homo or heterochiral aggregation and the nature of the non-covalent interactions stabilizing the adducts. We report the observation of the benzyl mercaptan dimer in the isolation conditions of a supersonic jet expansion, using broadband (chirped-pulse) microwave spectroscopy. A single homochiral isomer was observed for the dimer, stabilized by a cooperative sequence of S-H···S and S-H···π hydrogen bonds. The structural data, stabilization energies and energy decomposition describe these non-covalent interactions as weak and dispersion-controlled. A comparison is also provided with the benzyl alcohol dimer.
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9
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Juanes M, Usabiaga I, León I, Evangelisti L, Fernández JA, Lesarri A. The Six Isomers of the Cyclohexanol Dimer: A Delicate Test for Dispersion Models. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marcos Juanes
- Departamento de Química Física y Química Inorgánica—I.U. CINQUIMA Universidad de Valladolid Paseo de Belén, 7 47011 Valladolid Spain
| | - Imanol Usabiaga
- Departamento de Química Física Universidad del País Vasco Ap. 644 48080 Bilbao Spain
- Instituto Biofisika (CSIC, UPV/EHU) 48940 Leioa Spain
| | - Iker León
- Departamento de Química Física y Química Inorgánica—I.U. CINQUIMA Universidad de Valladolid Paseo de Belén, 7 47011 Valladolid Spain
- Departamento de Química Física Universidad del País Vasco Ap. 644 48080 Bilbao Spain
| | - Luca Evangelisti
- Dipartimento di Chimica “G. Ciamician” Università di Bologna Via Selmi, 2 40126 Bologna Italy
| | - José A. Fernández
- Departamento de Química Física Universidad del País Vasco Ap. 644 48080 Bilbao Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica—I.U. CINQUIMA Universidad de Valladolid Paseo de Belén, 7 47011 Valladolid Spain
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10
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Juanes M, Usabiaga I, León I, Evangelisti L, Fernández JA, Lesarri A. The Six Isomers of the Cyclohexanol Dimer: A Delicate Test for Dispersion Models. Angew Chem Int Ed Engl 2020; 59:14081-14085. [DOI: 10.1002/anie.202005063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/11/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Marcos Juanes
- Departamento de Química Física y Química Inorgánica—I.U. CINQUIMA Universidad de Valladolid Paseo de Belén, 7 47011 Valladolid Spain
| | - Imanol Usabiaga
- Departamento de Química Física Universidad del País Vasco Ap. 644 48080 Bilbao Spain
- Instituto Biofisika (CSIC, UPV/EHU) 48940 Leioa Spain
| | - Iker León
- Departamento de Química Física y Química Inorgánica—I.U. CINQUIMA Universidad de Valladolid Paseo de Belén, 7 47011 Valladolid Spain
- Departamento de Química Física Universidad del País Vasco Ap. 644 48080 Bilbao Spain
| | - Luca Evangelisti
- Dipartimento di Chimica “G. Ciamician” Università di Bologna Via Selmi, 2 40126 Bologna Italy
| | - José A. Fernández
- Departamento de Química Física Universidad del País Vasco Ap. 644 48080 Bilbao Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica—I.U. CINQUIMA Universidad de Valladolid Paseo de Belén, 7 47011 Valladolid Spain
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11
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Juanes M, Saragi RT, Caminati W, Lesarri A. The Hydrogen Bond and Beyond: Perspectives for Rotational Investigations of Non‐Covalent Interactions. Chemistry 2019; 25:11402-11411. [DOI: 10.1002/chem.201901113] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/15/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Marcos Juanes
- Departamento de Química Física y Química Inorgánica—IU CINQUIMAFacultad de CienciasUniversidad de Valladolid 47011 Valladolid Spain
| | - Rizalina T. Saragi
- Departamento de Química Física y Química Inorgánica—IU CINQUIMAFacultad de CienciasUniversidad de Valladolid 47011 Valladolid Spain
| | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”Università di Bologna Via Selmi 2 40126 Bologna Italy
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica—IU CINQUIMAFacultad de CienciasUniversidad de Valladolid 47011 Valladolid Spain
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12
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Seifert NA, Thomas J, Jäger W, Xu Y. Rotational spectra and theoretical study of tetramers and trimers of 2-fluoroethanol: dramatic intermolecular compensation for intramolecular instability. Phys Chem Chem Phys 2018; 20:27630-27637. [DOI: 10.1039/c8cp05653f] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cooperativity and chirality dominate in stabilizing the 2-fluoroethanol tetramer, thanks to a fully bifurcated C–H⋯F H-bond network.
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Affiliation(s)
| | - Javix Thomas
- Chemistry Department, The University of Alberta
- Edmonton
- Canada
| | - Wolfgang Jäger
- Chemistry Department, The University of Alberta
- Edmonton
- Canada
| | - Yunjie Xu
- Chemistry Department, The University of Alberta
- Edmonton
- Canada
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13
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Spada L, Tasinato N, Bosi G, Vazart F, Barone V, Puzzarini C. On the competition between weak O-H···F and C-H···F hydrogen bonds, in cooperation with C-H···O contacts, in the difluoromethane - tert-butyl alcohol cluster. JOURNAL OF MOLECULAR SPECTROSCOPY 2017; 337:90-95. [PMID: 28919646 PMCID: PMC5597040 DOI: 10.1016/j.jms.2017.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The 1:1 complex of tert-butyl alcohol with difluoromethane has been characterized by means of a joint experimental-computational investigation. Its rotational spectrum has been recorded by using a pulsed-jet Fourier-Transform microwave spectrometer. The experimental work has been guided and supported by accurate quantum-chemical calculations. In particular, the computed potential energy landscape pointed out the formation of three stable isomers. However, the very low interconversion barriers explain why only one isomer, showing one O-H···F and two C-H···O weak hydrogen bonds, has been experimentally characterized. The effect of the H → tert-butyl- group substitution has been analyzed from the comparison to the difluoromethane-water adduct.
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Affiliation(s)
- Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)
| | - Giulio Bosi
- Dipartimento di Chimica ″G. Ciamician″ dell'Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Fanny Vazart
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)
| | - Cristina Puzzarini
- Dipartimento di Chimica ″G. Ciamician″ dell'Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
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14
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Huang W, Thomas J, Jäger W, Xu Y. Tunnelling and barrier-less motions in the 2-fluoroethanol–water complex: a rotational spectroscopic and ab initio study. Phys Chem Chem Phys 2017; 19:12221-12228. [DOI: 10.1039/c7cp01666b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Rotational spectrum of 2-fluoroethanol–water reveals interesting water and methyl internal rotation tunneling and barrier-less motions in the hydrogen-bonded complex.
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Affiliation(s)
- Wenyuan Huang
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | - Javix Thomas
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | - Wolfgang Jäger
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | - Yunjie Xu
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
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15
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Becucci M, Melandri S. High-Resolution Spectroscopic Studies of Complexes Formed by Medium-Size Organic Molecules. Chem Rev 2016; 116:5014-37. [DOI: 10.1021/acs.chemrev.5b00512] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maurizio Becucci
- Department
of Chemistry “Ugo Schiff” and European Laboratory for
Nonlinear Spectroscopy, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Sonia Melandri
- Department
of Chemistry “Giacomo Ciamician”, University of Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
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Thomas J, Liu X, Jäger W, Xu Y. Unusual H-Bond Topology and Bifurcated H-bonds in the 2-Fluoroethanol Trimer. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505934] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Thomas J, Liu X, Jäger W, Xu Y. Unusual H-Bond Topology and Bifurcated H-bonds in the 2-Fluoroethanol Trimer. Angew Chem Int Ed Engl 2015; 54:11711-5. [PMID: 26276699 DOI: 10.1002/anie.201505934] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Indexed: 11/06/2022]
Abstract
By using a combination of rotational spectroscopy and ab initio calculations, an unusual H-bond topology was revealed for the 2-fluoroethanol trimer. The trimer exhibits a strong heterochiral preference and adopts an open OH⋅⋅⋅OH H-bond topology while utilizing two types of bifurcated H-bonds involving organic fluorine. This is in stark contrast to the cyclic OH⋅⋅⋅OH H-bond topology adopted by trimers of water and other simple alcohols. The strengths of different H-bonds in the trimer were analyzed by using the quantum theory of atoms in molecules. The study showcases a remarkable example of a chirality-induced switch in H-bond topology in a simple transient chiral fluoroalcohol. It provides important insight into the H-bond topologies of small fluoroalcohol aggregates, which are proposed to play a key role in protein folding and in enantioselective reactions and separations where fluoroalcohols serve as a (co)solvent.
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Affiliation(s)
- Javix Thomas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Xunchen Liu
- School of Mechanical Engineering, Shanghai Jiao Tong University, No.800 Dong Chuan Road, Shanghai, 200240 (P.R. China)
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada).
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Seifert NA, Pérez C, Neill JL, Pate BH, Vallejo-López M, Lesarri A, Cocinero EJ, Castaño F. Chiral recognition and atropisomerism in the sevoflurane dimer. Phys Chem Chem Phys 2015; 17:18282-7. [DOI: 10.1039/c5cp01025j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transient chirality in the anesthetic sevoflurane results in two different homo- and heterochiral clusters on formation of the dimer, as observed by rotational spectroscopy.
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Affiliation(s)
| | - Cristóbal Pérez
- Department of Chemistry
- University of Virginia
- Charlottesville
- USA
| | - Justin L. Neill
- Department of Chemistry
- University of Virginia
- Charlottesville
- USA
| | - Brooks H. Pate
- Department of Chemistry
- University of Virginia
- Charlottesville
- USA
| | - Montserrat Vallejo-López
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV-EHU)
- 48080 Bilbao
- Spain
| | - Fernando Castaño
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV-EHU)
- 48080 Bilbao
- Spain
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Thomas J, Xu Y. Chirality Synchronization in Trifluoroethanol Dimer Revisited: The Missing Heterochiral Dimer. J Phys Chem Lett 2014; 5:1850-1855. [PMID: 26273864 DOI: 10.1021/jz500718f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chirality self-recognition in the dimer of transient chiral 2,2,2-trifluoroethanol (TFE) is studied using chirped pulse and cavity-based Fourier transform microwave spectroscopy with the aid of ab initio calculations. The broad-band and extreme high-resolution capabilities enable us to assign rotational spectra of the most stable homo- and heterochiral dimers and analyze their structural and dynamical properties in detail. A strong preference for the homochiral over the heterochiral diastereomers is observed. The current study unambiguously identifies the structure of the most stable homochiral dimer and supports the identification by the previous low-resolution infrared study. More importantly, it also indisputably detects the so far elusive, most stable heterochiral dimer.
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Affiliation(s)
- Javix Thomas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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Dalvit C, Vulpetti A. Fluorine-protein interactions and ¹⁹F NMR isotropic chemical shifts: An empirical correlation with implications for drug design. ChemMedChem 2011; 6:104-14. [PMID: 21117131 DOI: 10.1002/cmdc.201000412] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An empirical correlation between the fluorine isotropic chemical shifts, measured by ¹⁹F NMR spectroscopy, and the type of fluorine-protein interactions observed in crystal structures is presented. The CF, CF₂, and CF₃ groups present in fluorinated ligands found in the Protein Data Bank were classified according to their ¹⁹F NMR chemical shifts and their close intermolecular contacts with the protein atoms. Shielded fluorine atoms, i.e., those with increased electron density, are observed primarily in close contact to hydrogen bond donors within the protein structure, suggesting the possibility of intermolecular hydrogen bond formation. Deshielded fluorines are predominantly found in close contact with hydrophobic side chains and with the carbon of carbonyl groups of the protein backbone. Correlation between the ¹⁹F NMR chemical shift and hydrogen bond distance, both derived experimentally and computed through quantum chemical methods, is also presented. The proposed "rule of shielding" provides some insight into and guidelines for the judicious selection of appropriate fluorinated moieties to be inserted into a molecule for making the most favorable interactions with the receptor.
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Affiliation(s)
- Claudio Dalvit
- Italian Institute of Technology, Drug Discovery and Development Department, Genova, Italy.
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Thomas J, Sunahori FX, Borho N, Xu Y. Chirality Recognition in the Glycidol⋅⋅⋅Propylene Oxide Complex: A Rotational Spectroscopic Study. Chemistry 2011; 17:4582-7. [DOI: 10.1002/chem.201003536] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Javix Thomas
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada), Fax: (+1) 780‐492‐8231
| | - Fumie X. Sunahori
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada), Fax: (+1) 780‐492‐8231
| | - Nicole Borho
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada), Fax: (+1) 780‐492‐8231
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada), Fax: (+1) 780‐492‐8231
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Samsonov SA, Salwiczek M, Anders G, Koksch B, Pisabarro MT. Fluorine in protein environments: a QM and MD study. J Phys Chem B 2010; 113:16400-8. [PMID: 19947631 DOI: 10.1021/jp906402b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncanonical amino acids with newly designed side-chain functionalities represent powerful tools to improve structural, biological, and pharmacological properties of peptides and proteins. In this context, fluorinated amino acids have increasingly gained importance. Despite the current wide use of fluorination in protein engineering, the basic properties of fluorine in protein environments are still not completely understood. Our aim has been to characterize the physicochemical properties of fluorinated amino acids by using quantum mechanics (QM) and molecular dynamics (MD) approaches. We have analyzed geometry, charges, and hydrogen bonding abilities of several ethane fluorinated derivatives at different QM theory levels and have used them as simplified models for fluorinated amino acid side chains. We have parametrized four fluorinated L-amino acids for the AMBER ff94/99 force field: 4-monofluoroethylglycine (MfeGly), 4,4-difluoroethylglycine (DfeGly), 4,4,4-trifluoroethylglycine (TfeGly), and 4,4-difluoropropylglycine (DfpGly). We have characterized them in terms of molecular volumes, conformational preferences, and hydration properties. The obtained results illustrate that fluorine and hydrogen atoms of fluoromethyl groups could be potential acceptors or donors of weak hydrogen bonds in protein environments. Hydration of the studied fluorinated amino acids was found to be more favorable than for their nonfluorinated analogues, and hydrophobicity was observed to increase with the number of fluorine atoms, which is in accordance with the experimental retention times we obtain for these amino acids. This study broadens our understanding of the properties of fluorine within protein environments, which is important to exploit the full potential of fluorine's unique properties for applications in the field of protein engineering.
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Affiliation(s)
- Sergey A Samsonov
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany
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