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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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Tama Saragi R, Li W, Juanes M, Enríquez L, Pinacho R, Rubio JE, Lesarri A. Rotational Spectroscopy and Conformational Flexibility of 2-Phenylethanethiol: The Dominant S-H⋅⋅⋅π Intramolecular Hydrogen Bond. Chemphyschem 2024; 25:e202300799. [PMID: 38282167 DOI: 10.1002/cphc.202300799] [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: 10/27/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
We present a rotational-computational investigation of the aromatic mercaptan 2-phenylethanethiol, addressing its potential energy surface, conformational equilibrium, internal dynamics and intramolecular interactions. The experiment used broadband chirped-pulse Fourier transform microwave spectroscopy in a supersonic jet expansion, recording the rotational spectrum in the 2-8 GHz frequency region. Two different conformers were detected in the spectrum. The most intense transitions correspond to a skew (gauche-gauche) conformation, identified as the global minimum. The spectra of ten different isotopologues were assigned for this species, leading to accurate effective and substitution structures. The weaker spectrum presents small tunnelling doublings caused by the torsional motion of the thiol group, which are only compatible with an antiperiplanar skeleton and a gauche thiol. The larger stability of the global minimum is attributed to an intramolecular S-H⋅⋅⋅π weak hydrogen bond. A comparison of the intramolecular interactions in the title molecule and 2-phenylethanol, similarly stabilized by a O-H⋅⋅⋅π hydrogen bond, shows the different strength of these interactions. Density functional (B3LYP-D3, B2PLYP-D3) and ab initio (MP2) calculations were conducted for the molecule.
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Affiliation(s)
- Rizalina Tama Saragi
- Departamento de Química Física y Química Inorgánica -, I.U. CINQUIMA, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén 7, 47011, Valladolid, Spain
- Present address: Institut für Ionenphysik und Angewandte Chemie, Universität Innsbruck, Technikerstr. 25/4. OG, 6020, Innsbruck, Austria
| | - Wenqin Li
- Departamento de Química Física y Química Inorgánica -, I.U. CINQUIMA, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén 7, 47011, Valladolid, Spain
| | - Marcos Juanes
- Departamento de Química Física y Química Inorgánica -, I.U. CINQUIMA, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén 7, 47011, Valladolid, Spain
| | - Lourdes Enríquez
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 11, 47011, Valladolid, Spain
| | - Ruth Pinacho
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 11, 47011, Valladolid, Spain
| | - José Emiliano Rubio
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 11, 47011, Valladolid, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica -, I.U. CINQUIMA, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén 7, 47011, Valladolid, Spain
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Pinjari A, Saraf D, Sengupta D. Molecular mechanisms underlying nanowire formation in pristine phthalocyanine. Phys Chem Chem Phys 2023; 25:30259-30268. [PMID: 37927067 DOI: 10.1039/d3cp03512c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Understanding the molecular processes of nanowire self-assembly is crucial for designing and controlling nanoscale structures that could lead to breakthroughs in functional materials. In this work, we focus on pristine phthalocyanines as a representative example of mesogenic supramolecular assemblies and have analyzed the formation of nanowires using classical molecular dynamics simulations. In the simulations, the molecules spontaneously form multi-columnar structures resembling supramolecular polymers that subsequently grow into more ordered aggregates. These self-assemblies are concentration dependent, leading to the formation of multi-columnar, dynamic aggregates at higher concentrations and nanowires at lower concentrations. The multi-columnar assemblies on a whole are more disordered than the nanowires, but have locally ordered domains of parallel facing molecules that can fluctuate while maintaining their overall shape. The nanowire formation at lower concentrations involves the initial interaction and clustering of randomly oriented phthalocyanine molecules, followed by the merging of small clusters into elongated segments and the eventual formation of a stable nanowire. We observe three main conformers in these self-assemblies, the parallel, T-shaped and edge-to-edge stacking of the phthalocyanine dimers. We calculate the underlying free energy landscape and show that the parallel conformers form the most stable configuration which is followed by the T-shaped and edge-to-edge dimer configurations. The findings provide insights into the mechanisms and pathways of nanowire formation and a step towards the understanding of self-assembly processes in supramolecular mesogens.
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Affiliation(s)
- Aadil Pinjari
- CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411 008, India.
| | - Deepashri Saraf
- CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411 008, India.
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411 008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
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Carter-Fenk K, Liu M, Pujal L, Loipersberger M, Tsanai M, Vernon RM, Forman-Kay JD, Head-Gordon M, Heidar-Zadeh F, Head-Gordon T. The Energetic Origins of Pi-Pi Contacts in Proteins. J Am Chem Soc 2023; 145. [PMID: 37917924 PMCID: PMC10655088 DOI: 10.1021/jacs.3c09198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein's stability and structure. Pi-pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi-pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi-pi contact motifs. We find that neutral pi-pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter-Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi-pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi-pi contacts in polar media and like typical ion-pi interactions in nonpolar environments. Like-charged pairs such as arginine-arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi-pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.
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Affiliation(s)
- Kevin Carter-Fenk
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Meili Liu
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Leila Pujal
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Matthias Loipersberger
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Maria Tsanai
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Robert M. Vernon
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Julie D. Forman-Kay
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Martin Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Farnaz Heidar-Zadeh
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
- Center
for Molecular Modeling (CMM), Ghent University, 9052 Zwijnaarde, Belgium
| | - Teresa Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
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Ma J, Insausti A, Hazrah AS, Xu Y. Deciphering the non-covalent interactions in the furan⋯hexane complex using rotational spectroscopy and theoretical analyses. J Chem Phys 2023; 159:134302. [PMID: 37782256 DOI: 10.1063/5.0166935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023] Open
Abstract
The rotational spectrum of a binary complex formed between furan and n-hexane was investigated using a chirped pulse Fourier transform microwave spectrometer in the range of 2-6 GHz. While furan has only one conformer, n-hexane exists in multiple conformations. The conformational landscape of the binary complex was systematically explored by using a semiempirical conformational search tool, namely CREST. The CREST conformational candidates were subjected to further geometry optimization and harmonic frequency calculations at the B3LYP-D3BJ/def2-TZVP level of theory, resulting in 34 minima within an energy window of 5 kJ mol-1. The three most stable furan⋯hexane minima all contain the most stable n-hexane conformer subunit and are separated by relatively low conformational conversion barriers. Additional calculations were carried out to support the conclusive identification of the global minimum structure responsible for the set of assigned rotational transitions. These include calculations at the B3LYP-D3BJ level with the aug-cc-pVTZ and 6-311++G(d,p) basis sets and the MP2/def2-TZVP level, as well as the single point energy calculations at the CCSD(T)-F12/cc-pVDZ level. Further non-covalent interaction and principal interacting orbital analyses show that the synergy of the πfuran → σ*hexane and σhexane → π*furan interactions plays an important role in stabilizing the observed furan-hexane conformer.
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Affiliation(s)
- Jiarui Ma
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Aran Insausti
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, Spain
| | - Arsh S Hazrah
- 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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