1
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Meyer KAE, Garand E. The impact of solvation on the structure and electric field strength in Li +GlyGly complexes. Phys Chem Chem Phys 2024; 26:12406-12421. [PMID: 38623633 DOI: 10.1039/d3cp06264c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
To scrutinise the impact of electric fields on the structure and vibrations of biomolecules in the presence of water, we study the sequential solvation of lithium diglycine up to three water molecules with cryogenic infrared action spectroscopy. Conformer-specific IR-IR spectroscopy and H2O/D2O isotopic substitution experiments provide most of the information required to decipher the structure of the observed conformers. Additional confirmation is provided by scaled harmonic vibrational frequency calculations using MP2 and DFT. The first water molecule is shown to bind to the Li+ ion, which weakens the electric field experienced by the peptide and as a consequence, also the strength of an internal NH⋯NH2 hydrogen bond in the diglycine backbone. The strength of this hydrogen bond decreases approximately linearly with the number of water molecules as a result of the decreasing electric field strength and coincides with an increase in the number of conformers observed in our spectra. The addition of two water molecules is already sufficient to change the preferred conformation of the peptide backbone, allowing for Li+ coordination to the lone pair of the terminal amine group.
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Affiliation(s)
- Katharina A E Meyer
- University of Wisconsin-Madison, Department of Chemistry, 1101 University Ave, Madison, WI 53706, USA.
| | - Etienne Garand
- University of Wisconsin-Madison, Department of Chemistry, 1101 University Ave, Madison, WI 53706, USA.
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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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Perera AS, Carlson CD, Cheramy J, Xu Y. Infrared and vibrational circular dichroism spectra of methyl β-D-glucopyranose in water: The application of the quantum cluster growth and clusters-in-a-liquid solvation models. Chirality 2023; 35:718-731. [PMID: 37162747 DOI: 10.1002/chir.23576] [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: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
The infrared (IR) and vibrational circular dichroism (VCD) spectra of methyl β-D-glucopyranose in water were measured. Both implicit and explicit solvation models were utilized to explain the observed spectra. The vast body of existing experimental and theoretical data suggested that about eight explicit water molecules are needed to account for the solvent effects, supported by the current Quantum Cluster Growth (QCG) analysis. Extensive manual and systematic conformational searches of the molecular target and its water clusters were carried out by using a recently developed conformational searching tool, conformer-rotamer ensemble sampling tool (CREST), and the microsolvation model in the associated QCG code. The Boltzmann averaged IR and VCD spectra of the methyl β-D-glucopyranose-(water)n (n = 8) conformers in the PCM of water provide better agreement with the experimental ones than those with n = 0, 1, and 2. The explicit solvation with eight water molecules was shown to greatly modify the conformational preference of methyl β-D-glucopyranose from its monomeric form. Further analyses show that the result is consistent with the existence of long-lived methyl β-D-glucopyranose monohydrates with the additional explicit water effects being accounted for with the quantum mechanical treatment of the other seven close-by water molecules in the PCM of water.
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Affiliation(s)
| | - Colton D Carlson
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Joseph Cheramy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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4
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Perez Mellor AF, Brazard J, Kozub S, Bürgi T, Szweda R, Adachi TBM. Unveiling the Configurational Landscape of Carbamate: Paving the Way for Designing Functional Sequence-Defined Polymers. J Phys Chem A 2023; 127:7309-7322. [PMID: 37624607 PMCID: PMC10493977 DOI: 10.1021/acs.jpca.3c02442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/11/2023] [Indexed: 08/26/2023]
Abstract
Carbamate is an emerging class of a polymer backbone for constructing sequence-defined, abiotic polymers. It is expected that new functional materials can be de novo designed by controlling the primary polycarbamate sequence. While amino acids have been actively studied as building blocks for protein folding and peptide self-assembly, carbamates have not been widely investigated from this perspective. Here, we combined infrared (IR), vibrational circular dichroism (VCD), and nuclear magnetic resonance (NMR) spectroscopy with density functional theory (DFT) calculations to understand the conformation of carbamate monomer units in a nonpolar, aprotic environment (chloroform). Compared with amino acid building blocks, carbamates are more rigid, presumably due to the extended delocalization of π-electrons on the backbones. Cis configurations of the amide bond can be energetically stable in carbamates, whereas peptides often assume trans configurations at low energies. This study lays an essential foundation for future developments of carbamate-based sequence-defined polymer material design.
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Affiliation(s)
- Ariel F. Perez Mellor
- Department
of Physical Chemistry, Sciences II, University
of Geneva, 30, Quai Ernest Ansermet, Geneva 1211, Switzerland
| | - Johanna Brazard
- Department
of Physical Chemistry, Sciences II, University
of Geneva, 30, Quai Ernest Ansermet, Geneva 1211, Switzerland
| | - Sara Kozub
- Łukasiewicz
Research Network − PORT Polish Center for Technology Development, Stabłowicka 147, Wrocław 54-066, Poland
| | - Thomas Bürgi
- Department
of Physical Chemistry, Sciences II, University
of Geneva, 30, Quai Ernest Ansermet, Geneva 1211, Switzerland
| | - Roza Szweda
- Łukasiewicz
Research Network − PORT Polish Center for Technology Development, Stabłowicka 147, Wrocław 54-066, Poland
| | - Takuji B. M. Adachi
- Department
of Physical Chemistry, Sciences II, University
of Geneva, 30, Quai Ernest Ansermet, Geneva 1211, Switzerland
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5
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Alshalalfeh M, Sun N, Moraes AH, Utani APA, Xu Y. Conformational Distributions of Phenyl β-D-Glucopyranoside and Gastrodin in Solution by Vibrational Optical Activity and Theoretical Calculations. Molecules 2023; 28:molecules28104013. [PMID: 37241754 DOI: 10.3390/molecules28104013] [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: 04/19/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The conformational landscapes of two highly flexible monosaccharide derivatives, namely phenyl β-D-glucopyranoside (ph-β-glu) and 4-(hydroxymethyl)phenyl β-D-glucopyranoside, also commonly known as gastrodin, were explored using a combined experimental and theoretical approach. For the infrared, Raman, and the associated vibrational optical activity (VOA), i.e., vibrational circular dichroism and Raman optical activity, experiments of these two compounds in DMSO and in water were carried out. Extensive and systematic conformational searches were performed using a recently developed conformational searching tool called CREST (conformer-rotamer ensemble sampling tool) in the two solvents. Fourteen and twenty-four low-energy conformers were identified at the DFT level for ph-β-glu and gastrodin, respectively. The spectral simulations of individual conformers were done at the B3LYP-D3BJ/def2-TZVPD level with the polarizable continuum model of the solvents. The VOA spectral features exhibit much higher specificity to conformational differences than their parent infrared and Raman. The excellent agreements achieved between the experimental and simulated VOA spectra allow for the extraction of experimental conformational distributions of these two carbohydrates in solution directly. The experimental percentage abundances based on the hydroxymethyl (at the pyranose ring) conformations G+, G-, and T for ph-β-glu were obtained to be 15%, 75%, and 10% in DMSO and 53%, 40%, and 7% in water, respectively, in comparison to the previously reported gas phase values of 68%, 25%, and 7%, highlighting the important role of solvents in conformational preferences. The corresponding experimental distributions for gastrodin are 56%, 22%, and 22% in DMSO and 70%, 21%, and 9% in water.
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Affiliation(s)
- Mutasem Alshalalfeh
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ningjie Sun
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- State Key Laboratory of Advanced Metallurgy, University of Science and Technology Beijing, Beijing 100083, China
| | | | | | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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6
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Yang Y, Krin A, Cai X, Poopari MR, Zhang Y, Cheeseman JR, Xu Y. Conformations of Steroid Hormones: Infrared and Vibrational Circular Dichroism Spectroscopy. Molecules 2023; 28:molecules28020771. [PMID: 36677830 PMCID: PMC9864676 DOI: 10.3390/molecules28020771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Steroid hormone molecules may exhibit very different functionalities based on the associated functional groups and their 3D arrangements in space, i.e., absolute configurations and conformations. Infrared (IR) and vibrational circular dichroism (VCD) spectra of four different steroid hormones, namely dehydroepiandrosterone (DHEA), 17α-methyltestosterone (MTTT), (16α,17)-epoxyprogesterone (Epoxy-P4), and dehydroepiandrosterone acetate (AcO-DHEA), were measured in deuterated dimethyl sulfoxide and some also in carbon tetrachloride. Extensive conformational searches were carried out using the recent developed conformer-rotamer ensemble sampling tool (CREST) which also accounts for solvent effects using an implicit solvation model. All the CREST conformational candidates were then reoptimized at the B3LYP-D3BJ/def2-TZVPD with the PCM of solvent. The good agreements between the experimental IR and VCD spectra and the theoretical simulations provide a conclusive information about their conformational distribution and absolute configurations. The experimental and theoretical IR and VCD spectra of AcO-DHEA in the carbonyl and alkene stretching region showed some discrepancies, and the possible causes related to solvent effects, large amplitude motions and levels of theory used in the modelling were explored in detail. As part of the investigation, additional calculations at the B3LYP-D3BJ/6-31++G (2d,p) and B3LYP-D3BJ/cc-pVTZ levels, as well as some 'mixed' calculations with the double-hybrid functional B2PLYP-D3 were also carried out. The results indicate that the double-hybrid functional is important for predicting the correct IR band pattern in the carbonyl and alkene stretching region.
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Affiliation(s)
- Yanqing Yang
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Anna Krin
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Centre for Science and Peace Research (ZNF), Universität Hamburg, Bogenallee 11, 20144 Hamburg, Germany
| | - Xiaoli Cai
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Key Laboratory for Green Chemical Process of Ministry of Education, Wuhan Institute of Technology, Wuhan 430073, China
| | | | - Yuefei Zhang
- Key Laboratory for Green Chemical Process of Ministry of Education, Wuhan Institute of Technology, Wuhan 430073, China
| | - James R. Cheeseman
- Gaussian Inc., 340 Quinnipiac St., Bldg., 40, Wallingford, CT 06492-4050, USA
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Correspondence: ; Tel.: +1-780-402-1244
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7
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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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8
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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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9
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Steber A, Li W, Pate BH, Lesarri A, Pérez C. The First Stages of Nanomicelle Formation Captured in the Sevoflurane Trimer. J Phys Chem Lett 2022; 13:3770-3775. [PMID: 35446045 PMCID: PMC9059180 DOI: 10.1021/acs.jpclett.2c00671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Self-aggregation of sevoflurane, an inhalable, fluorinated anesthetic, provides a challenge for current state-of-the-art high-resolution techniques due to its large mass and the variety of possible hydrogen bonds between monomers. Here we present the observation of sevoflurane trimer by chirped-pulse Fourier transform microwave spectroscopy, identified through the interplay of experimental and computational methods. The trimer (>600 Da), one of the largest molecular aggregates observed through rotational spectroscopy, does not resemble the binding (C-H···O) motif of the already characterized sevoflurane dimer, instead adapting a new binding configuration created predominantly from 17 CH···F hydrogen bonds that resembles a nanomicellar arrangement. The observation of such a heavy aggregate highlights the potential of rotational spectroscopy to study larger biochemical systems in the limit of spectroscopic congestion but also showcases the challenges ahead as the mass of the system increases.
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Affiliation(s)
- Amanda
L. Steber
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias-I.U. CINQUIMA, Universidad
de Valladolid, E-47011 Valladolid, Spain
| | - Wenqin Li
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias-I.U. CINQUIMA, Universidad
de Valladolid, E-47011 Valladolid, Spain
| | - Brooks H. Pate
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, United States
| | - Alberto Lesarri
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias-I.U. CINQUIMA, Universidad
de Valladolid, E-47011 Valladolid, Spain
| | - Cristóbal Pérez
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias-I.U. CINQUIMA, Universidad
de Valladolid, E-47011 Valladolid, Spain
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10
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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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11
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Yang Y, Cheramy J, Brehm M, Xu Y. Raman Optical Activity of N-Acetyl-L-Cysteine in water and in methanol: the "clusters-in-a-liquid" model and ab initio molecular dynamics simulations. Chemphyschem 2022; 23:e202200161. [PMID: 35353934 DOI: 10.1002/cphc.202200161] [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: 03/09/2022] [Revised: 03/29/2022] [Indexed: 11/06/2022]
Abstract
Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water and in methanol to evaluate the solvent effects. Two different solvation approaches, i.e. the DFT based clusters-in-a-liquid solvent model and the ab initio molecular dynamics (AIMD) simulations, were applied to simulate the Raman and ROA spectra. Systematic conformational searches were carried out using a recently developed conformational searching tool, CREST, with the inclusion of polarizable continuum model of water and of methanol. The CREST candidates of NALC and the NALC-solvent complexes were re-optimized and their Raman and ROA simulations were done at the B3LYP-D3BJ/def2-TZVP and the B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD simulations , which includes some anharmonic effects and all intermolecular interactions in solution, were performed. By empirically weighting the computed Raman and ROA spectra of each conformer, good agreements with the experimental data were achieved with both approaches, while AIMD offered some improvements in the carbonyl and in the low wavenumber regions over the static DFT approach. The pros and cons of these two different approaches for accounting the solvent effects on Raman and ROA of this flexible chiral system will also be discussed.
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Affiliation(s)
| | | | - Martin Brehm
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg, Chemistry, GERMANY
| | - Yunjie Xu
- University of Alberta Faculty of Science, Chemistry Department, 11227 Saskatchewan Drive, T6G 2G2, Edmonton, CANADA
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12
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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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13
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Wang H, Heger M, Al-Jabiri MH, Xu Y. Vibrational Spectroscopy of Homo- and Heterochiral Amino Acid Dimers: Conformational Landscapes. Molecules 2021; 27:38. [PMID: 35011269 PMCID: PMC8746356 DOI: 10.3390/molecules27010038] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/15/2021] [Accepted: 12/19/2021] [Indexed: 12/19/2022] Open
Abstract
The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary structures were further grouped into five different types based on their intermolecular binding topologies and subunit configurations. For each dimer species, there are eight to fourteen final conformational geometries within a 10 kJ mol-1 window of the global minimum structure for each species. The comparison between the experimental IRMPD spectra and the simulated harmonic IR features allowed us to clearly identify the types of structures responsible for the observation. The monomeric subunits of the observed homo- and heterochiral dimers are compared to the corresponding protonated/neutral amino acid monomers observed experimentally in previous IRMDP/rotational spectroscopic studies. Possible chirality and kinetic influences on the experimental IRMPD spectra are discussed.
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Affiliation(s)
| | | | | | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, AB T6G 2G2, Canada; (H.W.); (M.H.); (M.H.A.-J.)
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14
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Wu B, Hazrah AS, Seifert NA, Oswald S, Jäger W, Xu Y. Higher-Energy Hexafluoroisopropanol···Water Isomer and Its Large Amplitude Motions: Rotational Spectra and DFT Calculations. J Phys Chem A 2021; 125:10401-10409. [PMID: 34846154 DOI: 10.1021/acs.jpca.1c09058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rotational spectra of the 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP)···water complex were measured using a chirped pulse Fourier-transform microwave spectrometer. The spectral analyses, aided by density functional theory calculations, reveal two HFIP···water isomers: one previously reported, trans HFIP (HFIPt)···water (Phys. Chem. Chem. Phys. 2015, 119, 5650-5657), and a new isomer, gauche HFIP (HFIPg)···water. To confirm the identity of the new isomer, rotational spectra of seven of its deuterated species were also measured and analyzed. Both the experimental and theoretical pieces of evidence indicate that the intermolecular interaction with water preferentially stabilizes the HFIPg monomer configuration over the global minimum configuration, HFIPt. The relative energy difference between these monomeric forms is 4.1 kJ mol-1 and decreases to 2.5 kJ mol-1 in the respective monohydrates at the B3LYP-D3(BJ)/def2-QZVP level of theory. Both rigid and relaxed potential energy surface scans were carried out to gain insights into the large-amplitude water motions in HFIPg···water. The nonobservation of a water tunneling splitting in HFIPt···water has been explained to be a result of a barrier-less (after zero-point-energy correction) pathway for the water motion, whereas in HFIPg···water, a relatively large water tunneling barrier was identified as the cause of barely resolved water tunneling splittings. Noncovalent interaction and quantum theory of atoms and molecule analyses were used to evaluate the changes in HFIPg···water when going from the minimum to the transition state in terms of attractive interactions such as the OH···H and OH···F contacts. The effect of fluorination is discussed by comparing the vastly different binding topologies of isopropanol···water and HFIP···water.
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Affiliation(s)
- Bowei Wu
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2R3, Canada
| | - Arsh S Hazrah
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2R3, Canada
| | - Nathan A Seifert
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2R3, Canada.,Department of Chemistry and Chemical & Biomedical Engineering, University of New Haven, 300 Boston Post Rd, West Haven, Connecticut 06516, United States
| | - Sönke Oswald
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2R3, Canada.,Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2R3, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2R3, Canada
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15
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Meng D, Hao C, Cai J, Ma W, Chen C, Xu C, Xu L, Kuang H. Tailored Chiral Copper Selenide Nanochannels for Ultrasensitive Enantioselective Recognition and Detection. Angew Chem Int Ed Engl 2021; 60:24997-25004. [PMID: 34463011 DOI: 10.1002/anie.202109920] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/21/2021] [Indexed: 11/07/2022]
Abstract
We constructed a tailorable membrane channel system consisting of penicillamine molecules intercalated in copper selenide nanoparticles (Cu2-x Se NPs), which exhibited circular dichroism (CD) bands in the near infrared region (CD, 800-1600 nm) with a maximum intensity of 164.5 mdeg at 1440 nm. The chiral ligand hybridized to the surface of achiral Cu2-x Se NPs by breaking the intrinsic symmetry of Cu2-x Se NPs and further large-scale assembly induced strong optical activity. The fabricated multilayer chiral membrane achieved an increased rectification ratio (RR) up to 114. The integration of penicillamine allowed for high enantioselective recognition against naproxen,which displayed high sensitivity with a limit of detection (LOD) as low as 0.027 nM.
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Affiliation(s)
- Dan Meng
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Changlong Hao
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Jiarong Cai
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Wei Ma
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Chen Chen
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Liguang Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Hua Kuang
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
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16
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Meng D, Hao C, Cai J, Ma W, Chen C, Xu C, Xu L, Kuang H. Tailored Chiral Copper Selenide Nanochannels for Ultrasensitive Enantioselective Recognition and Detection. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dan Meng
- State Key Lab of Food Science and Technology International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 P. R. China
| | - Changlong Hao
- State Key Lab of Food Science and Technology International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 P. R. China
| | - Jiarong Cai
- State Key Lab of Food Science and Technology International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 P. R. China
| | - Wei Ma
- State Key Lab of Food Science and Technology International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 P. R. China
| | - Chen Chen
- State Key Lab of Food Science and Technology International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 P. R. China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 P. R. China
| | - Liguang Xu
- State Key Lab of Food Science and Technology International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 P. R. China
| | - Hua Kuang
- State Key Lab of Food Science and Technology International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology Jiangnan University Wuxi Jiangsu 214122 P. R. China
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17
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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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18
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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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19
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Calabrese C, Temelso B, Usabiaga I, Seifert NA, Basterretxea FJ, Prampolini G, Shields GC, Pate BH, Evangelisti L, Cocinero EJ. The Role of Non-Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane. Angew Chem Int Ed Engl 2021; 60:16894-16899. [PMID: 34028158 PMCID: PMC8362204 DOI: 10.1002/anie.202103900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/27/2021] [Indexed: 01/30/2023]
Abstract
The role of non-covalent interactions (NCIs) has broadened with the inclusion of new types of interactions and a plethora of weak donor/acceptor partners. This work illustrates the potential of chirped-pulse Fourier transform microwave technique, which has revolutionized the field of rotational spectroscopy. In particular, it has been exploited to reveal the role of NCIs' in the molecular self-aggregation of difluoromethane where a pentamer, two hexamers and a heptamer were detected. The development of a new automated assignment program and a sophisticated computational screening protocol was essential for identifying the homoclusters in conditions of spectral congestion. The major role of dispersion forces leads to less directional interactions and more distorted structures than those found in polar clusters, although a detailed analysis demonstrates that the dominant interaction energy is the pairwise interaction. The tetramer cluster is identified as a structural unit in larger clusters, representing the maximum expression of bond between dimers.
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Affiliation(s)
- Camilla Calabrese
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
- Instituto Biofisika (UPV/EHU, CSIC)48940LeioaSpain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)48940LeioaSpain
| | - Berhane Temelso
- George Mason UniversityInformation Technology ServicesFairfaxVA22030USA
| | - Imanol Usabiaga
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
- Instituto Biofisika (UPV/EHU, CSIC)48940LeioaSpain
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bolognavia S. Alberto 16348100RavennaItaly
| | - Nathan A. Seifert
- Department of ChemistryUniversity of VirginiaMcCormick RoadCharlottesvilleVA22903USA
| | - Francisco J. Basterretxea
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)Area della Ricercavia G. Moruzzi 156124PisaItaly
| | | | - Brooks H. Pate
- Department of ChemistryUniversity of VirginiaMcCormick RoadCharlottesvilleVA22903USA
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bolognavia S. Alberto 16348100RavennaItaly
| | - Emilio J. Cocinero
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
- Instituto Biofisika (UPV/EHU, CSIC)48940LeioaSpain
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20
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Calabrese C, Temelso B, Usabiaga I, Seifert NA, Basterretxea FJ, Prampolini G, Shields GC, Pate BH, Evangelisti L, Cocinero EJ. The Role of Non‐Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Camilla Calabrese
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Instituto Biofisika (UPV/EHU, CSIC) 48940 Leioa Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) 48940 Leioa Spain
| | - Berhane Temelso
- George Mason University Information Technology Services Fairfax VA 22030 USA
| | - Imanol Usabiaga
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Instituto Biofisika (UPV/EHU, CSIC) 48940 Leioa Spain
- Dipartimento di Chimica “Giacomo Ciamician” Università degli Studi di Bologna via S. Alberto 163 48100 Ravenna Italy
| | - Nathan A. Seifert
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22903 USA
| | - Francisco J. Basterretxea
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR) Area della Ricerca via G. Moruzzi 1 56124 Pisa Italy
| | | | - Brooks H. Pate
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22903 USA
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician” Università degli Studi di Bologna via S. Alberto 163 48100 Ravenna Italy
| | - Emilio J. Cocinero
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Instituto Biofisika (UPV/EHU, CSIC) 48940 Leioa Spain
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21
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Wu B, Seifert NA, Oswald S, Jäger W, Xu Y. Rotational Spectrum and Molecular Structures of the Binary Aggregates of 1,1,1,3,3,3-Hexafluoro-2-propanol with Ne and Ar. J Phys Chem A 2021; 125:5355-5364. [PMID: 34115508 DOI: 10.1021/acs.jpca.1c03757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structures and binding topologies of two binary van der Waals complexes 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP)···Ne and ···Ar were investigated. The rotational spectra of these two complexes including several isotopic species containing 20Ne, 22Ne, 40Ar, 13C, and hydroxyl D were measured using a chirped pulse Fourier transform microwave spectrometer and a cavity-based Fourier transform microwave spectrometer. While HFIP was shown to exist in both the gauche and trans configurations based on previous reports, the rare gas atom is predicted to attach to HFIP in several different binding topologies, leading to a total of nine possible structural isomers for each complex. Only one isomer was detected for each species, and it corresponds to the most stable one predicted, based on the comparison of the experimental rotational constants and electric dipole moment components with the theoretical predictions and on the isotopic data. We applied quantum theory of atoms in molecules (QTAIM) and electrostatic potential calculations to examine the different rare gas binding sites and to explore the nature of the interactions in these two complexes and several previously reported alcohol···Ar complexes. The effects of fluorination are also discussed by comparison with the binary complexes of isopropanol···Ne and ···Ar.
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Affiliation(s)
- Bowei Wu
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
| | - Nathan A Seifert
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
| | - Sönke Oswald
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstraße 6, Göttingen 37077, Germany
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
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22
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Yang Y, Cheramy J, Xu Y. Matrix Isolation-Vibrational Circular Dichroism Spectroscopic Study of Conformations and Non-Covalent Interactions of Tetrahydro-2-Furoic Acid. Chemphyschem 2021; 22:1336-1343. [PMID: 33945674 DOI: 10.1002/cphc.202100256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/01/2021] [Indexed: 11/10/2022]
Abstract
The conformational landscape and aggregation behaviour of tetrahydro-2-furoic acid (THFA) were investigated by using matrix isolation-vibrational circular dichroism (MI-VCD). The well-resolved experimental MI-IR and MI-VCD features in an argon matrix at 10 K allow one to identify two dominant monomeric conformations as trans-THFA where the hydroxyl and carbonyl groups of COOH are at opposite sides, as well as one cis-conformer. At 24 K and 30 K deposition temperatures, the experimental IR and VCD spectral features reveal further growth of the binary THFA aggregates. Systematic conformational searches identified three vastly different binary binding topologies, resulting in a few hundred stable (THFA)2 conformers. Interestingly, the main binary structures observed correspond to an unusual type of structure which is made of two trans-THFA subunits, in contrast to the usual double H-bonded ring binary structures, identified in a previous solution study. The present work showcases the power of MI-VCD spectroscopy in revealing unusual structures formed in a cold rare gas matrix.
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Affiliation(s)
- Yanqing Yang
- Chemistry Department, University of Alberta Edmonton, Alberta, Canada, T6G 2G2
| | - Joseph Cheramy
- Chemistry Department, University of Alberta Edmonton, Alberta, Canada, T6G 2G2
| | - Yunjie Xu
- Chemistry Department, University of Alberta Edmonton, Alberta, Canada, T6G 2G2
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23
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Domingos SR, Pérez C, Kreienborg NM, Merten C, Schnell M. Dynamic chiral self-recognition in aromatic dimers of styrene oxide revealed by rotational spectroscopy. Commun Chem 2021; 4:32. [PMID: 36697526 PMCID: PMC9814401 DOI: 10.1038/s42004-021-00468-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/01/2021] [Indexed: 01/28/2023] Open
Abstract
Chiral molecular recognition is a pivotal phenomenon in biomolecular science, governed by subtle balances of intermolecular forces that are difficult to quantify. Non-covalent interactions involving aromatic moieties are particularly important in this realm, as recurring motifs in biomolecular aggregation. In this work, we use high-resolution broadband rotational spectroscopy to probe the dynamic conformational landscape enclosing the self-pairing topologies of styrene oxide, a chiral aromatic system. We reach a definite assignment of four homochiral and two heterochiral dimers using auxiliary quantum chemistry calculations as well as structure-solving methods based on experimental isotopic information. A complete picture of the dimer conformational space is obtained, and plausible routes for conformational relaxation are derived. Molecular structures are discussed in terms of conformational flexibility, the concerted effort of weak intermolecular interactions, and their role in the expression of the molecular fit.
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Affiliation(s)
- Sérgio R. Domingos
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, Hamburg, 22607 Germany ,grid.8051.c0000 0000 9511 4342Present Address: CFisUC, Department of Physics, University of Coimbra, Coimbra, 3004-516 Portugal
| | - Cristóbal Pérez
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, Hamburg, 22607 Germany
| | - Nora M. Kreienborg
- grid.5570.70000 0004 0490 981XRuhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, Bochum, 44801 Germany
| | - Christian Merten
- grid.5570.70000 0004 0490 981XRuhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, Bochum, 44801 Germany
| | - Melanie Schnell
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, Hamburg, 22607 Germany ,grid.9764.c0000 0001 2153 9986Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, Kiel, 24118 Germany
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24
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Xie F, Seifert NA, Hazrah AS, Jäger W, Xu Y. Conformational Landscape, Chirality Recognition and Chiral Analyses: Rotational Spectroscopy of Tetrahydro-2-Furoic Acid⋅⋅⋅Propylene Oxide Conformers. Chemphyschem 2021; 22:455-460. [PMID: 33453085 DOI: 10.1002/cphc.202000995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/31/2020] [Indexed: 11/05/2022]
Abstract
A chiral adduct formed between a chiral carboxylic acid, tetrahydro-2-furoic acid (THFA), and a chiral ester, propylene oxide (PO), was investigated using rotational spectroscopy and DFT calculations. Isolated THFA exists dominantly as three different conformers: I, II, and III in a jet, with I and II taking on the trans-COOH configuration and III having the cis-COOH configuration. We utilized CREST, a conformational ensemble space exploration tool, to identify the possible conformations of the binary adduct, THFA⋅⋅⋅PO. Subsequent DFT geometry optimizations predicted about two hundred homochiral and heterochiral binary structures with 28 low energy structures within an energy window of 15 kJ mol-1 . A rich broadband rotational spectrum was obtained with a mixture of trace amounts of THFA+PO in neon in a supersonic jet expansion. Six THFA⋅⋅⋅PO conformers were identified experimentally. Kinetically favored binary products which contain trans-COOH I dominate among the observed conformers, while thermodynamically more stable adducts were also detected. Detailed analyses of the structures of the observed conformers show interesting chirality-controlled structural preferences. Such non-covalently bound chiral contact pairs are the foundation of chiral-tag rotational spectroscopy, an exciting new analytical application of rotational spectroscopy for determination of enantiomeric excess. Enantiomeric excess analyses were performed and the results are discussed.
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Affiliation(s)
- Fan Xie
- Department of Chemistry, University of Alberta Edmonton, Alberta, T6G 2G2, Canada
| | - Nathan A Seifert
- Current address: Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Arsh S Hazrah
- 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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25
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Salthammer T, Monegel F, Schulz N, Uhde E, Grimme S, Seibert J, Hohm U, Palm W. Sensory Perception of Non-Deuterated and Deuterated Organic Compounds. Chemistry 2021; 27:1046-1056. [PMID: 33058253 PMCID: PMC7839723 DOI: 10.1002/chem.202003754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/10/2020] [Indexed: 11/24/2022]
Abstract
The chemical background of olfactory perception has been subject of intensive research, but no available model can fully explain the sense of smell. There are also inconsistent results on the role of the isotopology of molecules. In experiments with human subjects it was found that the isotope effect is weak with acetone and D6 -acetone. In contrast, clear differences were observed in the perception of octanoic acid and D15 -octanoic acid. Furthermore, a trained sniffer dog was initially able to distinguish between these isotopologues of octanoic acid. In chromatographic measurements, the respective deuterated molecule showed weaker interaction with a non-polar liquid phase. Quantum chemical calculations give evidence that deuterated octanoic acid binds more strongly to a model receptor than non-deuterated. In contrast, the binding of the non-deuterated molecule is stronger with acetone. The isotope effect is calculated in the framework of statistical mechanics. It results from a complicated interplay between various thermostatistical contributions to the non-covalent free binding energies and it turns out to be very molecule-specific. The vibrational terms including non-classical zero-point energies play about the same role as rotational/translational contributions and are larger than bond length effects for the differential isotope perception of odor for which general rules cannot be derived.
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Affiliation(s)
- Tunga Salthammer
- Department of Material Analysis and Indoor ChemistryFraunhofer WKI38108BraunschweigGermany
| | - Friederike Monegel
- Department of Material Analysis and Indoor ChemistryFraunhofer WKI38108BraunschweigGermany
| | - Nicole Schulz
- Department of Material Analysis and Indoor ChemistryFraunhofer WKI38108BraunschweigGermany
| | - Erik Uhde
- Department of Material Analysis and Indoor ChemistryFraunhofer WKI38108BraunschweigGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitute for Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Jakob Seibert
- Mulliken Center for Theoretical ChemistryInstitute for Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Uwe Hohm
- Institute of Physical and Theoretical ChemistryUniversity of Braunschweig—Institute of Technology38106BraunschweigGermany
| | - Wolf‐Ulrich Palm
- Institute of Sustainable and Environmental ChemistryLeuphana University Lüneburg21335LüneburgGermany
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26
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Lu T, Xie F, Seifert NA, Jäger W, Xu Y. Conformational landscape and intricate conformational relaxation paths of 4,4,4-trifluoro-1-butanol: Rotational spectroscopy and quantum chemical calculations. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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27
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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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28
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Xie F, Seifert NA, Jäger W, Xu Y. Conformational Panorama and Chirality Controlled Structure–Energy Relationship in a Chiral Carboxylic Acid Dimer. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Fan Xie
- 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
- Chemical Sciences and Engineering Division Argonne National Laboratory Argonne IL 60439 USA
| | - 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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29
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Xie F, Seifert NA, Jäger W, Xu Y. Conformational Panorama and Chirality Controlled Structure–Energy Relationship in a Chiral Carboxylic Acid Dimer. Angew Chem Int Ed Engl 2020; 59:15703-15710. [DOI: 10.1002/anie.202005685] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/27/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Fan Xie
- 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
- Chemical Sciences and Engineering Division Argonne National Laboratory Argonne IL 60439 USA
| | - 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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30
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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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31
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Pérez C, Steber AL, Temelso B, Kisiel Z, Schnell M. Water Triggers Hydrogen-Bond-Network Reshaping in the Glycoaldehyde Dimer. Angew Chem Int Ed Engl 2020; 59:8401-8405. [PMID: 32096889 PMCID: PMC7318665 DOI: 10.1002/anie.201914888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/28/2020] [Indexed: 11/19/2022]
Abstract
Carbohydrates are ubiquitous biomolecules in nature. The vast majority of their biomolecular activity takes place in aqueous environments. Molecular reactivity and functionality are, therefore, often strongly influenced by not only interactions with equivalent counterparts, but also with the surrounding water molecules. Glycoaldehyde (Gly) represents a prototypical system to identify the relevant interactions and the balance that governs them. Here we present a broadband rotational‐spectroscopy study on the stepwise hydration of the Gly dimer with up to three water molecules. We reveal the preferred hydrogen‐bond networks formed when water molecules sequentially bond to the sugar dimer. We observe that the dimer structure and the hydrogen‐bond networks at play remarkably change upon the addition of just a single water molecule to the dimer. Further addition of water molecules does not significantly alter the observed hydrogen‐bond topologies.
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Affiliation(s)
- Cristóbal Pérez
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.,Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118, Kiel, Germany
| | - Amanda L Steber
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.,Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118, Kiel, Germany
| | - Berhane Temelso
- Division of Information Technology, College of Charleston, Charleston, SC, 29424, USA
| | - Zbigniew Kisiel
- Institute of Physics, Polish Academy of Sciences, 02-668, Warszawa, Poland
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.,Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118, Kiel, Germany
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32
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Pérez C, Steber AL, Temelso B, Kisiel Z, Schnell M. Water Triggers Hydrogen‐Bond‐Network Reshaping in the Glycoaldehyde Dimer. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Cristóbal Pérez
- Deutsches Elektronen-Synchrotron DESY Notkestraße 85 22607 Hamburg Germany
- Christian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Amanda L. Steber
- Deutsches Elektronen-Synchrotron DESY Notkestraße 85 22607 Hamburg Germany
- Christian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Berhane Temelso
- Division of Information Technology College of Charleston Charleston SC 29424 USA
| | - Zbigniew Kisiel
- Institute of Physics Polish Academy of Sciences 02-668 Warszawa Poland
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY Notkestraße 85 22607 Hamburg Germany
- Christian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
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33
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Pérez-Mellor A, Le Barbu-Debus K, Zehnacker A. Solid-state synthesis of cyclo LD-diphenylalanine: A chiral phase built from achiral subunits. Chirality 2020; 32:693-703. [PMID: 32078197 DOI: 10.1002/chir.23195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/21/2022]
Abstract
The solid-state structure of LL/DD or LD/DL diphenylalanine diluted in KBr pellets is studied by infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy. The structure depends on the absolute configuration of the residues. The natural LL diphenylalanine exists as a mixture of neutral and zwitterionic structures, depending on the humidity of the sample, while mostly the zwitterion is observed for LD diphenylalanine whatever the experimental conditions. The system undergoes spontaneous cyclization upon heating at 125°C, resulting to the formation of a diketopiperazine (DKP) dipeptide as the only product. The reaction is faster for LD than for LL diphenylalanine. As expected, LL and DD diphenylalanine react to form the LL and DD enantiomers of cyclo diphenylalanine. Interestingly, the DKP dipeptides formed from the LD or DL diphenylalanine show unexpected optical activity, with opposite VCD spectra for the products formed from the LD and DL reagents. This is explained in terms of chirality synchronization between the monomers within the crystal, which retain the symmetry of the reagent, resulting to the formation of a new chiral phase made from transiently chiral molecules.
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Affiliation(s)
- Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, University Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, University Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, University Paris-Sud, Université Paris-Saclay, Orsay, France
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34
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Fatima M, Maué D, Pérez C, Tikhonov DS, Bernhard D, Stamm A, Medcraft C, Gerhards M, Schnell M. Structures and internal dynamics of diphenylether and its aggregates with water. Phys Chem Chem Phys 2020; 22:27966-27978. [DOI: 10.1039/d0cp04104a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report on a detailed multi-spectroscopic analysis of the structures and internal dynamics of diphenylether and its aggregates with up to three water molecules by employing molecular beam experiments.
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Affiliation(s)
- M. Fatima
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - D. Maué
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - C. Pérez
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - D. S. Tikhonov
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - D. Bernhard
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - A. Stamm
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - C. Medcraft
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - M. Gerhards
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - M. Schnell
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
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35
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Juanes M, Saragi RT, Pinacho R, Rubio JE, Lesarri A. Sulfur hydrogen bonding and internal dynamics in the monohydrates of thenyl mercaptan and thenyl alcohol. Phys Chem Chem Phys 2020; 22:12412-12421. [DOI: 10.1039/d0cp01706j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Water forms weak H-bonds with thenyl compounds, simultaneously retaining internal mobility in the dimer.
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Affiliation(s)
- Marcos Juanes
- Departamento de Química Física y Química Inorgánica and I.U. CINQUIMA
- Facultad de Ciencias
- Universidad de Valladolid, Paseo de Belén, 7
- 47011 Valladolid
- Spain
| | - Rizalina Tama Saragi
- Departamento de Química Física y Química Inorgánica and I.U. CINQUIMA
- Facultad de Ciencias
- Universidad de Valladolid, Paseo de Belén, 7
- 47011 Valladolid
- Spain
| | - Ruth Pinacho
- Departamento de Electrónica
- Escuela de Ingeniería de Telecomunicaciones
- Universidad de Valladolid
- Paseo de Belén, 15
- 47011 Valladolid
| | - José E. Rubio
- Departamento de Electrónica
- Escuela de Ingeniería de Telecomunicaciones
- Universidad de Valladolid
- Paseo de Belén, 15
- 47011 Valladolid
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica and I.U. CINQUIMA
- Facultad de Ciencias
- Universidad de Valladolid, Paseo de Belén, 7
- 47011 Valladolid
- Spain
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36
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Oswald S, Suhm MA. Soft experimental constraints for soft interactions: a spectroscopic benchmark data set for weak and strong hydrogen bonds. Phys Chem Chem Phys 2019; 21:18799-18810. [PMID: 31453998 DOI: 10.1039/c9cp03651b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An experimental benchmark data base on rotational constants, vibrational properties and energy differences for weakly and more strongly hydrogen-bonded complexes and their constituents from the spectroscopic literature is assembled. It is characterized in detail and finally contracted to a more compact, discriminatory set (ENCH-51, for Experimental Non-Covalent Harmonic with 51 entries). The meeting points between theory and experiment consist of equilibrium rotational constants and harmonic frequencies and energies, which are back-corrected from experimental observables and are very easily accessible by quantum chemical calculations. The relative performance of B3LYP-D3, PBE0-D3 and M06-2X density functional theory predictions with a quadruple-zeta basis set is used to illustrate systematic errors, error compensation and selective performance for structural, vibrational and energetical observables. The current focus is on perspectives and different benchmarking methodologies, rather than on a specific theoretical method or a specific class of compounds. Extension of the data base in chemical, observable and quantum chemical method space is encouraged.
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Affiliation(s)
- Sönke Oswald
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany.
| | - Martin A Suhm
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany.
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37
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Calabrese C, Li W, Prampolini G, Evangelisti L, Uriarte I, Cacelli I, Melandri S, Cocinero EJ. A General Treatment to Study Molecular Complexes Stabilized by Hydrogen‐, Halogen‐, and Carbon‐Bond Networks: Experiment and Theory of (CH
2
F
2
)
n
⋅⋅⋅(H
2
O)
m. Angew Chem Int Ed Engl 2019; 58:8437-8442. [DOI: 10.1002/anie.201902753] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/05/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Camilla Calabrese
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Biofisika Institute, (CSIC, UPV/EHU) 48080 Bilbao Spain
| | - Weixing Li
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bologna via Selmi 2 I-40126 Bologna Italy
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)Area della Ricerca via G. Moruzzi 1 I-56124 Pisa Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bologna via Selmi 2 I-40126 Bologna Italy
- Department of ChemistryUniversity of Virginia McCormick Road VA 22903 Charlottesville USA
| | - Iciar Uriarte
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Biofisika Institute, (CSIC, UPV/EHU) 48080 Bilbao Spain
| | - Ivo Cacelli
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)Area della Ricerca via G. Moruzzi 1 I-56124 Pisa Italy
- Dipartimento di Chimica e Chimica IndustrialeUniversità di Pisa via Risorgimento 35 I-56126 Pisa Italy
| | - Sonia Melandri
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bologna via Selmi 2 I-40126 Bologna Italy
| | - Emilio J. Cocinero
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Biofisika Institute, (CSIC, UPV/EHU) 48080 Bilbao Spain
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38
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Calabrese C, Li W, Prampolini G, Evangelisti L, Uriarte I, Cacelli I, Melandri S, Cocinero EJ. A General Treatment to Study Molecular Complexes Stabilized by Hydrogen‐, Halogen‐, and Carbon‐Bond Networks: Experiment and Theory of (CH
2
F
2
)
n
⋅⋅⋅(H
2
O)
m
. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Camilla Calabrese
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Biofisika Institute, (CSIC, UPV/EHU) 48080 Bilbao Spain
| | - Weixing Li
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bologna via Selmi 2 I-40126 Bologna Italy
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)Area della Ricerca via G. Moruzzi 1 I-56124 Pisa Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bologna via Selmi 2 I-40126 Bologna Italy
- Department of ChemistryUniversity of Virginia McCormick Road VA 22903 Charlottesville USA
| | - Iciar Uriarte
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Biofisika Institute, (CSIC, UPV/EHU) 48080 Bilbao Spain
| | - Ivo Cacelli
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)Area della Ricerca via G. Moruzzi 1 I-56124 Pisa Italy
- Dipartimento di Chimica e Chimica IndustrialeUniversità di Pisa via Risorgimento 35 I-56126 Pisa Italy
| | - Sonia Melandri
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bologna via Selmi 2 I-40126 Bologna Italy
| | - Emilio J. Cocinero
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Biofisika Institute, (CSIC, UPV/EHU) 48080 Bilbao Spain
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39
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Xie F, Seifert NA, Heger M, Thomas J, Jäger W, Xu Y. The rich conformational landscape of perillyl alcohol revealed by broadband rotational spectroscopy and theoretical modelling. Phys Chem Chem Phys 2019; 21:15408-15416. [DOI: 10.1039/c9cp03028j] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We explore the conformational landscape of perillyl alcohol in order to properly account for the sources of the conformers observed.
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Affiliation(s)
- Fan Xie
- Chemistry Department
- The University of Alberta
- Edmonton
- Canada
| | | | - Matthias Heger
- Chemistry Department
- The University of Alberta
- Edmonton
- Canada
| | - 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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