1
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Torres-Hernández F, Pinillos P, Li W, Saragi RT, Camiruaga A, Juanes M, Usabiaga I, Lesarri A, Fernández JA. Competition between O-H and S-H Intermolecular Interactions in Conformationally Complex Systems: The 2-Phenylethanethiol and 2-Phenylethanol Dimers. J Phys Chem Lett 2024; 15:5674-5680. [PMID: 38767855 PMCID: PMC11145646 DOI: 10.1021/acs.jpclett.4c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
Noncovalent interactions involving sulfur centers play a relevant role in biological and chemical environments. Yet, detailed molecular descriptions are scarce and limited to very simple model systems. Here we explore the formation of the elusive S-H···S hydrogen bond and the competition between S-H···O and O-H···S interactions in pure and mixed dimers of the conformationally flexible molecules 2-phenylethanethiol (PET) and 2-phenylethanol (PEAL), using the isolated and size-controlled environment of a jet expansion. The structure of both PET-PET and PET-PEAL dimers was unraveled through a comprehensive methodology that combined rotationally resolved microwave spectroscopy, mass-resolved isomer-specific infrared laser spectroscopy, and quantum chemical calculations. This synergic experimental-computational approach offered unique insights into the potential energy surface, conformational equilibria, molecular structure, and intermolecular interactions of the dimers. The results show a preferential order for establishing hydrogen bonds following the sequence S-H···S < S-H···O ≲ O-H···S < O-H···O, despite the hydrogen bond only accounting for a fraction of the total interaction energy.
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Affiliation(s)
- Fernando Torres-Hernández
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Paul Pinillos
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Wenqin Li
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias - I.U. CINQUIMA, Universidad
de Valladolid, Paseo de Belén, 7, E-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, E-47011 Valladolid, Spain
| | - Ander Camiruaga
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Marcos Juanes
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias - I.U. CINQUIMA, Universidad
de Valladolid, Paseo de Belén, 7, E-47011 Valladolid, Spain
| | - Imanol Usabiaga
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Alberto Lesarri
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias - I.U. CINQUIMA, Universidad
de Valladolid, Paseo de Belén, 7, E-47011 Valladolid, Spain
| | - José A. Fernández
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
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2
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Silva WGDP, Poonia T, van Wijngaarden J. Exploring the conformational landscape, hydrogen bonding, and internal dynamics in the diallyl ether and diallyl sulfide monohydrates. J Chem Phys 2024; 160:044302. [PMID: 38258923 DOI: 10.1063/5.0180901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
The conformational spaces of the diallyl ether (DAE) and diallyl sulfide (DAS) monohydrates were explored using rotational spectroscopy from 6 to 19 GHz. Calculations at the B3LYP-D3(BJ)/aug-cc-pVTZ level suggested significant differences in their conformational behavior, with DAE-w exhibiting 22 unique conformers and DAS-w featuring three stable structures within 6 kJ mol-1. However, only transitions from the lowest energy conformer of each were experimentally observed. Spectral analysis confirmed that binding with water does not alter the conformational preference for the lowest energy structure of the monomers, but it does influence the relative stabilities of all other conformers, particularly in the case of DAE. Non-covalent interaction and quantum theory of atoms in molecules analyses showed that the observed conformer for each complex is stabilized by two intermolecular hydrogen bonds (HBs), where water primarily interacts with the central oxygen or sulfur atom of the diallyl compounds, along with secondary interactions involving the allyl groups. The nature of these interactions was further elucidated using symmetry-adapted perturbation theory, which suggests that the primary HB interaction with S in DAS is weaker and more dispersive in nature compared to the primary HB in DAE. This supports the experimental observation of a tunneling splitting exclusively in the rotational spectrum of DAS-w, as the weaker contact allows water to undergo internal motions within the complex, as shown based on calculated transition state structures for possible tunneling pathways.
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Affiliation(s)
- Weslley G D P Silva
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- I. Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, 50937 Köln, Germany
| | - Tamanna Poonia
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Jennifer van Wijngaarden
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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3
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Yang T, Xu Y, Wang Z, Feng C, Feng G. Noncovalent interactions of aromatic heterocycles: rotational spectroscopy and theoretical calculations of the thiazole-CF 4 and thiazole-SF 6 complexes. Phys Chem Chem Phys 2023; 25:25566-25572. [PMID: 37718685 DOI: 10.1039/d3cp02363j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The complexes of thiazole with CF4 and SF6 have been investigated by Fourier transform microwave spectroscopy and quantum chemical calculations. One rotational spectrum was observed for the thiazole-CF4 complex. Experiments and theoretical computations confirmed that the observed structure of thiazole-CF4 is primarily formed due to N⋯CCF4 interaction with the C atom of CF4 located in the plane of the thiazole ring. The rotational transitions of thiazole-CF4 exhibit A/E torsional splitting induced by the internal rotation of the -CF3 top. The potential barrier of the -CF3 internal rotation is 0.2411(1) kJ mol-1, consistent with the calculated value (∼0.3 kJ mol-1). For the thiazole-SF6 complex, one conformer with SF6 located above the thiazole ring is detected. The observed structure of thiazole-SF6 is mainly stabilized by van der Waals interactions. The energy decomposition analysis reveals that the electrostatics and dispersion are the dominant attractive contributions to the formation of thiazole-CF4 and thiazole-SF6 dimers, whereas the weight of the dispersion term becomes more significant in the thiazole-SF6 complex compared to that of the thiazole-CF4 complex.
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Affiliation(s)
- Tingting Yang
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Yugao Xu
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Zhen Wang
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Chunmei Feng
- Hongzhiwei Technology (Shanghai) Co. Ltd., Xinjinqiao Rd., 1599, Pudong, Shanghai, China
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
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4
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Tripathi MK, Ramanathan V. Nature and Strength of Sulfur-Centered Hydrogen Bond in Methanethiol Aqueous Solutions. J Phys Chem A 2023; 127:2265-2273. [PMID: 36867672 DOI: 10.1021/acs.jpca.2c08314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Methanethiol (M) and water (W) clusters like dimers (M1W1, M2, and W2), trimers (M1W2, M2W1, M3, and W3), and tetramers (M1W3, M2W2, M3W1, M4, and W4) were studied to assess the strength of sulfur-centered hydrogen bonding using different levels of theories, viz, HF, MP2, MP3, MP4, B3LYP, B3LYP-D3, CCSD, CCSD(T)-F12, and CCSD(T) along with aug-cc-pVNZ (where N = D, T, and Q) basis sets. Interaction energies were found to be in the range of -3.3 to -5.3 kcal/mol for the dimers, -8.0 to -16.7 kcal/mol for the trimers, and -13.5 to -29.5 kcal/mol for the tetramers at the B3LYP-D3/CBS limit level of theory. Normal modes of vibrations computed at the B3LYP/cc-pVDZ level of theory were seen to be in good agreement with the experimental values. Local energy decomposition calculations using the DLPNO-CCSD(T) level of theory indicated the domination of electrostatic interactions' contribution to the interaction energy in all cluster systems. Furthermore, atoms in molecules and natural bond orbital calculations both carried out at the B3LYP-D3/aug-cc-pVQZ level of theory aided in visualizing the hydrogen bonds besides proving a rationale for the strength of the hydrogen bonds and thereby the stability of these cluster systems.
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Affiliation(s)
| | - V Ramanathan
- Department of Chemistry, IIT(BHU) Varanasi, Varanasi, U.P. 221005 India
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Lu T, Zhang J, Xu Y, Wang Z, Feng G, Zeng Z. Hydrogen bond interactions between thioethers and amides: A joint rotational spectroscopic and theoretical study of the formamide⋯dimethyl sulfide adduct. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 288:122199. [PMID: 36473293 DOI: 10.1016/j.saa.2022.122199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/17/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
The rotational spectrum of the binary adduct of formamide (HCONH2) with dimethyl sulfide (DMS) has been investigated employing cavity-based Fourier transform microwave spectroscopy combined with theoretical computations. Experimentally, only one isomer of the adduct was unambiguously observed and assigned according to the theoretically predicted spectroscopic parameters, and its rotational spectrum displays the hyperfine splittings associated with the 14N nuclear quadrupole coupling effect. The observed isomer exhibits Cs symmetry, such that the ∠CSC angle of the DMS subunit is bisected by the ab-plane of the HCONH2 moiety. The two moieties in the detected isomer are connected via one primary NH···S and two secondary CH···O hydrogen bonds. Quantum theory of atoms in molecules (QTAIM), non-covalent interaction (NCI), natural bond orbital (NBO) and symmetry-adapted perturbation theory (SAPT) approaches were utilized for characterizing the intermolecular interactions occurring in the titled adduct. Additionally, the adduct of HCONH2 with dimethyl ether (DME) was also theoretically investigated to compare the difference in structure and energy characteristics between the NH···S and NH···O hydrogen bonds.
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Affiliation(s)
- Tao Lu
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China; School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China.
| | - Jiaqi Zhang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Yugao Xu
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Zhen Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Zhu Zeng
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China.
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6
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Juanes M, Saragi RT, Pérez C, Evangelisti L, Enríquez L, Jaraíz M, Lesarri A. Hydrogen Bonding in the Dimer and Monohydrate of 2-Adamantanol: A Test Case for Dispersion-Corrected Density Functional Methods. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082584. [PMID: 35458782 PMCID: PMC9030514 DOI: 10.3390/molecules27082584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/10/2022] [Accepted: 04/15/2022] [Indexed: 11/29/2022]
Abstract
Weakly-bound intermolecular clusters constitute reductionist physical models for non-covalent interactions. Here we report the observation of the monomer, the dimer and the monohydrate of 2-adamantanol, a secondary alcohol with a bulky ten-carbon aliphatic skeleton. The molecular species were generated in a supersonic jet expansion and characterized using broadband chirped-pulse microwave spectroscopy in the 2–8 GHz frequency region. Two different gauche-gauche O-H···O hydrogen-bonded isomers were observed for the dimer of 2-adamantanol, while a single isomer was observed for the monomer and the monohydrate. The experimental rotational parameters were compared with molecular orbital calculations using density functional theory (B3LYP-D3(BJ), B2PLYP-D3(BJ), CAM-B3LYP-D3(BJ), ωB97XD), additionally providing energetic and electron density characterization. The shallow potential energy surface makes the dimer an interesting case study to benchmark dispersion-corrected computational methods and conformational search procedures.
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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; (M.J.); (R.T.S.); (C.P.)
| | - 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; (M.J.); (R.T.S.); (C.P.)
| | - 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; (M.J.); (R.T.S.); (C.P.)
| | - Luca Evangelisti
- Dipartimento di Chimica ‘‘Giacomo Ciamician’’, Università di Bologna, Via Selmi, 2, 40126 Bologna, Italy;
| | - Lourdes Enríquez
- Departamento de Electrónica, Escuela Técnica Superior de Ingenieros de Telecomunicación, Universidad de Valladolid, Paseo de Belén, 15, 47011 Valladolid, Spain; (L.E.); (M.J.)
| | - Martín Jaraíz
- Departamento de Electrónica, Escuela Técnica Superior de Ingenieros de Telecomunicación, Universidad de Valladolid, Paseo de Belén, 15, 47011 Valladolid, Spain; (L.E.); (M.J.)
| | - 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; (M.J.); (R.T.S.); (C.P.)
- Correspondence: ; Tel.: +34-983-185895
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7
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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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8
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Pramanik M, Mathuri A, Mal P. t BuOLi-promoted terminal alkyne functionalizations by aliphatic thiols and alcohols. Org Biomol Chem 2022; 20:2671-2680. [PMID: 35293412 DOI: 10.1039/d2ob00079b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Selective radical addition to terminal alkynes is always a difficult task to achieve because it gives a mixture of stereo- and regioisomers. Herein we describe the selective addition of aliphatic thiols or alcohols to N-phenylpropiolamides (terminal alkynes) using lithium tert-butoxide (tBuOLi) in ethanol as a promoter. Mechanistically, it has been shown that the reaction proceeded through the generation of a thiyl radical intermediate, and the amide group in N-phenylpropiolamide could help in the activation of the alkyne, which led to thioacetalization via the formation of a (Z)-selective anti-Markovnikov vinyl sulfide. The (Z)-selectivity during the formation of vinyl sulfides was controlled by an intramolecular sulfur⋯oxygen interaction.
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Affiliation(s)
- Milan Pramanik
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
| | - Ashis Mathuri
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
| | - Prasenjit Mal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
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9
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Fargher HA, Sherbow TJ, Haley MM, Johnson DW, Pluth MD. C-H⋯S hydrogen bonding interactions. Chem Soc Rev 2022; 51:1454-1469. [PMID: 35103265 PMCID: PMC9088610 DOI: 10.1039/d1cs00838b] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The short C-H⋯S contacts found in available structural data for both small molecules and larger biomolecular systems suggest that such contacts are an often overlooked yet important stabilizing interaction. Moreover, many of these short C-H⋯S contacts meet the definition of a hydrogen bonding interaction. Using available structural data from the Cambridge Structural Database (CSD), as well as selected examples from the literature in which important C-H⋯S contacts may have been overlooked, we highlight the generality of C-H⋯S hydrogen bonding as an important stabilizing interaction. To uncover and establish the generality of these interactions, we compare C-H⋯S contacts with other traditional hydrogen bond donors and acceptors as well as investigate how coordination number and metal bonding affect the preferred geometry of interactions in the solid state. This work establishes that the C-H⋯S bond meets the definition of a hydrogen bond and serves as a guide to identify C-H⋯S hydrogen bonds in diverse systems.
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Affiliation(s)
- Hazel A. Fargher
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Tobias J. Sherbow
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Michael M. Haley
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Darren W. Johnson
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Michael D. Pluth
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403-1253, USA
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10
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Saragi RT, Juanes M, Abad JL, Pinacho R, Rubio JE, Lesarri A. Chirality-Puckering correlation and intermolecular interactions in Sphingosines: Rotational spectroscopy of jaspine B3 and its monohydrate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120531. [PMID: 34857464 DOI: 10.1016/j.saa.2021.120531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/09/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Chirality is determinant for sphingosine biofunctions and pharmacological activity, yet the reasons for the biological chiral selection are not well understood. Here, we characterized the intra- and intermolecular interactions at the headgroup of the cytotoxic anhydrophytosphingosine jaspine B, revealing chirality-dependent correlations between the puckering of the ring core and the formation of amino-alcohol hydrogen bond networks, both in the monomer and the monohydrate. Following the specific synthesis of a shortened 3-carbon side-chain molecule, denoted jaspine B3, six different isomers were observed in a jet expansion using broadband (chirped-pulsed) rotational spectroscopy. Additionally, a single isomer of the jaspine B3 monohydrate was observed, revealing the insertion of water in between the hydroxy and amino groups and the formation of a network of O-H···N-H···Oring hydrogen bonds. The specific jaspine B3 stereochemistry thus creates a double-faced molecule where the exposed lone-pair electrons may easily catalyze the formation of intermolecular aggregates and determine the sphingosine biological properties.
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Affiliation(s)
- Rizalina T Saragi
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, Valladolid 47011, Spain
| | - Marcos Juanes
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, Valladolid 47011, Spain
| | - José L Abad
- Research Unit on BioActive Molecules (RUBAM), Departament de Química Biològica, Institut de Química Avançada de Catalunya (IQAC-CSIC), Jordi Girona 18-26, Barcelona 08034, Spain
| | - Ruth Pinacho
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 11 Valladolid 47011, Spain
| | - José E Rubio
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 11 Valladolid 47011, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, Valladolid 47011, Spain
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11
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Paul A, Thomas R. Evidences for sulfur centered hydrogen bond with sulfur atoms as a donor in aromatic thiols and aliphatic thiols in aqueous solution. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118078] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Fischer TLL, Bödecker MADI, Zehnacker A, Mata RA, Suhm MA. Setting up the HyDRA blind challenge for the microhydration of organic molecules. Phys Chem Chem Phys 2022; 24:11442-11454. [DOI: 10.1039/d2cp01119k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates...
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13
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Chirality, structure and hydrogen bonding in dithiols: Rotational spectrum of the chiral and meso 2,3-butanedithiol. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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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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15
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Yamamoto E, Kawai Y, Takakura K, Kimura M, Murayama H, Matsueda H, Otsuki S, Sakata H, Tokunaga M. Convenient Unsymmetrical Disulfane Synthesis: Basic Zeolite‐Catalyzed Thiol‐Disulfane Exchange Reaction. ChemCatChem 2021. [DOI: 10.1002/cctc.202101092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Eiji Yamamoto
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Yasutaka Kawai
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Kei Takakura
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Moemi Kimura
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Haruno Murayama
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Hironobu Matsueda
- Fine Synthesis Technical Div. 1 DIC Corporation 18 Higashifukashiba Kamisu Ibaraki 314-0193 Japan
| | - Shujiro Otsuki
- Fine Synthesis Technical Div. 1 DIC Corporation 18 Higashifukashiba Kamisu Ibaraki 314-0193 Japan
| | - Hiroshi Sakata
- Fine Synthesis Technical Div. 1 DIC Corporation 18 Higashifukashiba Kamisu Ibaraki 314-0193 Japan
| | - Makoto Tokunaga
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
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16
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Silva WGDP, van Wijngaarden J. Hydrogen bonding networks and cooperativity effects in the aqueous solvation of trimethylene oxide and sulfide rings by microwave spectroscopy and computational chemistry. J Chem Phys 2021; 155:034305. [PMID: 34293887 DOI: 10.1063/5.0056833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The intermolecular interactions responsible for the microsolvation of the highly flexible trimethylene oxide (TMO) and trimethylene sulfide (TMS) rings with one and two water (w) molecules were investigated using rotational spectroscopy (8-22 GHz) and quantum chemical calculations. The observed patterns of transitions are consistent with the most stable geometries of the TMO-w, TMO-(w)2, and TMS-w complexes at the B2PLYP-D3(BJ)/aug-cc-pVTZ level and were confirmed using spectra of the 18O isotopologue. Due to its effectively planar backbone, TMO offers one unique binding site for solvation, while water can bind to the puckered TMS ring in either an axial or equatorial site of the heteroatom. In all clusters, the first water molecule binds in the σv symmetry plane of the ring monomer and serves as a hydrogen bond donor to the heteroatom. The second water molecule is predicted to form a cooperative hydrogen bonding network between the three moieties. Secondary C-H⋯O interactions are a key stabilizing influence in trimers and also drive the preferred binding site in the TMS clusters with the axial binding site preferred in TMS-w and the equatorial form calculated to be more stable in the dihydrate. Using an energy partition scheme from the symmetry-adapted perturbation theory for the O, S, and Se containing mono- and dihydrates, the intermolecular interactions are revealed to be mainly electrostatic, but the dispersive character of the contacts is enhanced with the increasing size of the ring's heteroatom due to the key role of longer-range secondary interactions.
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Affiliation(s)
- Weslley G D P Silva
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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17
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Pramanik M, Mathuri A, Mal P. Sulfuroxygen interaction-controlled ( Z)-selective anti-Markovnikov vinyl sulfides. Chem Commun (Camb) 2021; 57:5698-5701. [PMID: 33982682 DOI: 10.1039/d1cc01257f] [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
The sulfur oxygen (SO) interaction was used herein to obtain (Z)-selective anti-Markovnikov vinyl sulfides from the addition of thiyl radicals to terminal alkynes. DFT calculations predicted that SO interaction originated from the delocalization of the lone-pair of the carbonyl oxygen to the adjacent σ* orbital of the S atom of C-S.
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Affiliation(s)
- Milan Pramanik
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
| | - Ashis Mathuri
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
| | - Prasenjit Mal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
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18
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Saragi R, Juanes M, Pérez C, Pinacho P, Tikhonov DS, Caminati W, Schnell M, Lesarri A. Switching Hydrogen Bonding to π-Stacking: The Thiophenol Dimer and Trimer. J Phys Chem Lett 2021; 12:1367-1373. [PMID: 33507084 PMCID: PMC8812119 DOI: 10.1021/acs.jpclett.0c03797] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We used jet-cooled broadband rotational spectroscopy to explore the balance between π-stacking and hydrogen-bonding interactions in the self-aggregation of thiophenol. Two different isomers were detected for the thiophenol dimer, revealing dispersion-controlled π-stacked structures anchored by a long S-H···S sulfur hydrogen bond. The weak intermolecular forces allow for noticeable internal dynamics in the dimers, as tunneling splittings are observed for the global minimum. The large-amplitude motion is ascribed to a concerted inversion motion between the two rings, exchanging the roles of the proton donor and acceptor in the thiol groups. The determined torsional barrier of B2 = 250.3 cm-1 is consistent with theoretical predictions (290-502 cm-1) and the monomer barrier of 277.1(3) cm-1. For the thiophenol trimer, a symmetric top structure was assigned in the spectrum. The results highlight the relevance of substituent effects to modulate π-stacking geometries and the role of the sulfur-centered hydrogen bonds.
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Affiliation(s)
- Rizalina
Tama Saragi
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias-I.U. CINQUIMA, Universidad
de Valladolid, Paseo de Belén, 7, E-47011 Valladolid, Spain
| | - Marcos Juanes
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias-I.U. CINQUIMA, Universidad
de Valladolid, Paseo de Belén, 7, E-47011 Valladolid, Spain
| | - Cristóbal Pérez
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Str.
1, D-24118 Kiel, Germany
| | - Pablo Pinacho
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Str.
1, D-24118 Kiel, Germany
| | - Denis S. Tikhonov
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Str.
1, D-24118 Kiel, Germany
| | - Walther Caminati
- Dipartimento
di Chimica Giacomo Ciamician, Via Selmi, 2, I-40126 Bologna, Italy
| | - Melanie Schnell
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Str.
1, D-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, E-47011 Valladolid, Spain
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19
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Jennings JJ, Milic M, Targos K, Franz AK. NMR quantification of H-bond donating ability for bioactive functional groups and isosteres. Eur J Med Chem 2020; 207:112693. [PMID: 32862126 DOI: 10.1016/j.ejmech.2020.112693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/15/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022]
Abstract
The H-bond donating ability for 127 compounds including drug fragments and isosteres have been quantified using a simple and rapid method with 31P NMR spectroscopy. Functional groups important to medicinal chemistry were evaluated including carboxylic acids, alcohols, phenols, thioic acids and nitrogen group H-bond donors. 31P NMR shifts for binding to a phosphine oxide probe have a higher correlation with equilibrium constants for H-bonding (log KHA) than acidity (pKa), indicating that these binding experiments are representative of H-bonding ability and not proton transfer. Additionally, 31P NMR binding data for carboxylic acid isosteres correlates with physicochemical properties such as lipophilicity, membrane permeability and plasma protein binding. This method has been used to evaluate the H-bond donating ability of small molecule drug compounds such as NSAIDs and antimicrobials.
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Affiliation(s)
- Julia J Jennings
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, United States
| | - Mira Milic
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, United States
| | - Karina Targos
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, United States
| | - Annaliese K Franz
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, United States.
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