PS/
Articles/
2510001703
  • Open Access
  • Article

Ab initio Quantum-Chemical Calculations and Spectroscopic Studies of the Intramolecular π-Type Hydrogen Bonding in Small Cyclic Molecules

  • Esther J. Ocola 1, 2,   
  • Jaan Laane 1, 2, *

Received: 17 Sep 2025 | Revised: 11 Oct 2025 | Accepted: 14 Oct 2025 | Published: 20 Oct 2025

Abstract

Ab initio single-point energy computations at the CCSD(T)/aug-cc-pVTZ level have been carried out on nine molecules possessing intramolecular π-type hydrogen bonding. These computations were done using the calculated geometrical structures from CCSD/cc-pVTZ optimizations. The outcome has been analyzed together with previous spectroscopic and theoretical work.  Results are presented for 3-cyclopenten-1-ol, 2-indanol, 2-cylopenten-1-ol, 2-cyclohexen-1-ol, 3-cyclohexen-1-ol, and 2-cyclopropen-1-ol with O–H∙∙∙π(C=C) bonding. Results for 3-cyclopenten-1-amine and 2-cyclopropen1-amine with N–H∙∙∙π(C=C) bonding and for 2-cyclopropen-1-thiol with S–H∙∙∙π(C=C) bonding are also discussed. For each molecule, the conformer with a weak intramolecular π-type hydrogen bond was found to be the global minimum, with the exception of 2-cyclopropen-1-thiol. In this case, the S– H∙∙∙π bonded conformer is higher in energy, indicating a weaker interaction. The hydrogen bonded conformers for the cyclic alcohols typically have conformational energies about 250 to 350 cm−1 lower than the other conformers. For the amines the lowering is about half of that. The infrared and Raman spectra for several molecules in the O-H stretching region show hydrogen bonded conformers to be at the lowest frequencies. The calculated potential energy surfaces for six of the molecules are also presented.

Graphical Abstract

Image Viewer
Open in new tab
Download Image

References 

  • 1.
    Jeffrey, G.A.; Saenger, W. Hydrogen Bonding in Biological Structures, 2nd ed.; Springer: Berlin/Heidelberg, Germany, 1991.
  • 2.
    Jeffrey, G.A. An Introduction to Hydrogen Bonding; Oxford University Press: New York, NY, USA, 1997.
  • 3.
    Kojić-Prodić, B.K.; Molčanov, K. The Nature of Hydrogen Bond: New Insights into Old Theories. Acta Chim. Slov. 2008, 55, 692–708.
  • 4.
    Zhyganiuk, I.V.; Malomuzh, M.P. Physical Nature of Hydrogen Bond. Ukr. J. Phys. 2015, 60, 960–974.
  • 5.
    Grabowski, S.J. (Ed.) Hydrogen Bonding—New Insights, 1st ed.; Springer: Dordrecht, The Netherlands, 2006.
  • 6.
    Desiraju, G.R.; Steiner, T. The Weak Hydrogen Bond in Structural Chemistry and Biology, 1st ed.; Oxford University Press: New York, NY, USA, 1998; Reprinted 2001.
  • 7.
    Gilli, G.; Gilli, P. The Nature of the Hydrogen Bond–Outline of a Comprehensive Hydrogen Bond Theory, 1st ed.; Oxford University Press: New York, NY, USA, 2009.
  • 8.
    Steiner, T.; Koellner, G. Hydrogen Bonds with π-Acceptors in Proteins: Frequencies and Role in Stabilizing Local 3D Structures. J. Mol. Biol. 2001, 305, 535–557.
  • 9.
    Meyer, E.A.; Castellano, R.K.; Diederich, F. Interactions with Aromatic Rings in Chemical and Biological Recognition. Angew. Chem. Int. Ed. Engl. 2003, 42, 1210–1250.
  • 10.
    Liaquat, H.; Imran, M.; Saddique, Z.; et al. Exploring the Versatility of Hydrogen-Bonded Organic Frameworks: Advances in Design, Stability, and Multifunctional Applications. J. Mol. Struct. 2025, 1321, 140221.
  • 11.
    Elewa, A.M. Hydrogen-Bonded Organic Frameworks (HOFs) from Design to Environmental Application. J. Ind. Eng. Chem. 2025, 145, 169–190.
  • 12.
    Takasashi, O.; Kohno, Y.; Nishio, M. Relevance of Weak Hydrogen Bonds in the Conformation of Organic Compounds and Bioconjugates: Evidence from Recent Experimental Data and High-Level ab Initio MO Calculations. Chem. Rev. 2010, 110, 6049–6076.
  • 13.
    Salonen, L.M.; Ellermann, M.; Diederich, F. Aromatic Rings in Chemical and Biological Recognition: Energetics and Structures. Angew. Chem. Int. Ed. Engl. 2011, 50, 4808–4842.
  • 14.
    Arkas, M.; Kitsou, O.; Gkouma, A.; et al. The Role of Hydrogen Bonds in the Mesomorphic Behaviour of Supramolecular Assemblies Organized in Dendritic Architectures. Liq. Crys. Rev. 2019, 7, 60–105.
  • 15.
    Bu, R.; Xiong, Y.; Wei, X.; et al. Hydrogen Bonding in CHON-Containing Energetic Crystals: A Review. Cryst. Growth Des. 2019, 19, 5981−5997.
  • 16.
    Juhaś, M.; Zitko, J. Molecular Interactions of Pyrazine-Based Compounds to Proteins. J. Med. Chem. 2020, 63, 8901−8916.
  • 17.
    Liu, A.; Zhou, Y.; Yuan, L. Hydrogen-Bonded Aromatic Amide Macrocycles: Synthesis, Properties and Functions. Org. Biomol. Chem. 2022, 20, 9023–9051.
  • 18.
    Samuel, H.S.; Nweke-Maraizu, U.; Etim, E.E. Understanding Intermolecular and Intramolecular Hydrogen Bonds: Spectroscopic and Computational Approaches. J. Chem. Rev. 2023, 5, 439–465.
  • 19.
    Haque, A.; Alenezi, K.M.; Khan, M.S.; et al. Non-Covalent Interactions (NCIs) In π-Conjugated Functional Materials: Advances and Perspectives. Chem. Soc. Rev. 2023, 52, 454–472.
  • 20.
    Lin, L.; Jones, T.W.; Yang, T.C.J.; et al. Hydrogen Bonding in Perovskite Solar Cells. Matter 2024, 7, 38–58.
  • 21.
    Grabowski, S.J. Hydrogen Bond Types Which do not fit Accepted Definitions. Chem. Commun. 2024, 60, 6239–6255.
  • 22.
    Rao, C.N.R.; Murthy, A.S.N. Spectroscopic Studies of Hydrogen Bonding. In Developments in Applied Spectroscopy; Grove, E.L., Perkins, A.J., Eds.; Springer: Boston, MA, USA, 1970; Volume 7b, pp. 54–88.
  • 23.
    Møllendal, H. Recent Gas·Phase Studies of Intramolecular Hydrogen Bonding. In Structures and Conformations of Non-Rigid Molecules, NATO ASI Series, Series C: Mathematical and Physical Science; Laane, J., Dakkouri, M., van der Veken, B., et al., Eds.; Springer Science + Business Media, B.V.: Dordrecht, The Netherlands, 1993; Volume 410, pp. 277–301.
  • 24.
    Kovács, A.; Szabó, A.; Hargittai, I. Structural Characteristics of Intramolecular Hydrogen Bonding in Benzene Derivatives. Acc. Chem. Res. 2002, 35, 887–894.
  • 25.
    Lyssenko, K.A.; Antipin, M.Y. The Nature and Energy Characteristics of Intramolecular Hydrogen Bonds in crystals. Russ. Chem. Bull. 2006, 55, 1–15.
  • 26.
    Sobczyk, L.; Chudoba, D.; Tolstoy, P.M.; et al. Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding. Molecules 2016, 21, 1657.
  • 27.
    Hansen, P.E.; Spanget-Larsen, J. NMR and IR Investigations of Strong Intramolecular Hydrogen Bonds. Molecules 2017, 22, 552.
  • 28.
    Caron, G.; Vallaro, M.; Ermondi, G. High Throughput Methods to Measure the Propensity of Compounds to form Intramolecular Hydrogen Bonding. Med. Chem. Commun. 2017, 8, 1143–1151.
  • 29.
    Jezierska, A.; Tolstoy, P.M.; Panek, J.J.; et al. Intramolecular Hydrogen Bonds in Selected Aromatic Compounds: Recent Developments. Catalysts 2019, 9, 909.
  • 30.
    Caron, G.; Kihlberg, J.; Ermondi, G. Intramolecular Hydrogen Bonding: An Opportunity for Improved Design in Medicinal Chemistry. Med. Res. Rev. 2019, 39, 1707–1729.
  • 31.
    Deshmukh, M.M.; Gadre, S.R. Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy. Molecules 2021, 26, 2928.
  • 32.
    Hansen, P.E. A Spectroscopic Overview of Intramolecular Hydrogen Bonds of NH…O, S, N Type. Molecules 2021, 26, 2409.
  • 33.
    Hakobyan, R.M.; Shahkhatuni, A.G.; Polynski, M.V.; et al. The Role of the Nitro Group on the Formation of Intramolecular Hydrogen Bond in the Methyl Esters of 1-Vinyl-nitro-pyrazolecarboxylic Acids. J. Mol. Struct. 2025, 1322, 140350.
  • 34.
    Rouquet, E.; Dupont, J.; Vincent, J.; et al. The Role of Intramolecular Hydrogen Bonding in Photoelectron Circular Dichroism: The Diastereoisomers of 1-Amino-2-Indanol. Phys. Chem. Chem. Phys. 2025, 27, 2739–2748.
  • 35.
    Baker, A.W.; Shulgin, A.T. Intramolecular Hydrogen Bonds to π-Electrons and Other Weakly Basic Group. J. Am. Chem. Soc. 1958, 80, 5358–5363.
  • 36.
    Morokuma, K.; Wipff, G. Theoretical Evidence for Intramolecular Hydrogen Bonding in 7-Norbornenol. Chem. Phys. Lett. 1980, 74, 400–403.
  • 37.
    Smith, Z.; Carballo, N.; Wilson, E.B.; et al. Conformations, Possible Hydrogen Bonding, and Microwave Spectrum of 3-Buten-2-ol. J. Am. Chem. Soc. 1985, 107, 1951–1957.
  • 38.
    Bakke, J.M.; Schie, A.M.; Skjetne, T. Conformation of Allylic Alcohols and Intramolecular Hydrogen Bonding. Acta Chem. Scand. B 1986, 40, 703–710.
  • 39.
    Marstokk, K.-M.; Møllendal, H. Microwave Spectrum, Conformation and Intramolecular Hydrogen Bonding of 1,4-Pentadien-3-ol. Acta Chem. Scand. 1990, 44, 18–22.
  • 40.
    Marstokk, K.-M.; Møllendal, H.; Samdal, S. Microwave Spectrum, Conformation and Intramolecular Hydrogen Bonding of 1-Mercapto-2-propanol. Acta Chem. Scand. 1990, 44, 339–345.
  • 41.
    Melandri, S.; Favero, P.G.; Caminati, W. Detection of the syn Conformer of Ally1 Alcohol by Free Jet Microwave Spectroscopy. Chem. Phys. Lett. 1994, 223, 541–545.
  • 42.
    Bräse, S.; Klæboe, P.; Marstokk, K.-M.; et al. Conformational Properties of 2-Cyclopropylideneethanol as Studied by Microwave, Infrared and Raman Spectroscopy and by Ab Initio Computations. Acta Chem. Scand. 1998, 52, 1122–1136.
  • 43.
    Leonov, A.; Marstokk, K.-M.; de Meijere, A.; et al. Microwave Spectrum, Conformational Equilibrium, Intramolecular Hydrogen Bonding, Tunneling and Quantum Chemical Calculations for 1-Ethenylcyclopropan-1-ol. J. Phys. Chem. A 2000, 104, 4421–4428.
  • 44.
    Rademacher, P.; Khelashvili, L.; Kowski, K. Spectroscopic and Theoretical Studies on Intramolecular OH–π Hydrogen Bonding in 4-Substituted 2-Allylphenols. Org. Biomol. Chem. 2005, 3, 2620–2625.
  • 45.
    Isozaki, T.; Tsutsumi, Y.; Suzuki, T.; et al. Direct Evidence for Weak Intramolecular O–Hˑˑˑπ Hydrogen Bonding in 1-Hydroxytetralin. Chem. Phys. Lett. 2010, 495, 175–178.
  • 46.
    Miller, B.J.; Lane, J.R.; Kjaergaard, H.G. Intramolecular OH⋯π Interactions in Alkenols and Alkynols. Phys. Chem. Chem. Phys. 2011, 13, 14183–14193.
  • 47.
    Mackeprang, K.; Schrøder, S.D.; Kjaergaard, H.G. Weak Intramolecular OHˑˑˑπ Hydrogen Bonding in Methallyl- and Allyl-Carbinol. Chem. Phys. Lett. 2013, 582, 31–37.
  • 48.
    Das, P.; Das, P.K.; Arunan, E. Conformational Stability and Intramolecular Hydrogen Bonding in 1,2-Ethanediol and 1,4-Butanediol. J. Phys. Chem. A 2015, 119, 3710−3720.
  • 49.
    Al-Saadi, A.A.; Ocola, E.J.; Laane, J. Intramolecular π-Type Hydrogen Bonding and Conformations of 3-Cyclopenten-1-ol. 1. Theoretical Calculations. J. Phys. Chem. A 2010, 114, 7453–7456.
  • 50.
    Ocola, E.J.; Al-Saadi, A.A.; Mlynek, C.; et al. Intramolecular π-Type Hydrogen Bonding and Conformations of 3-Cyclopenten-1-ol. 2. Infrared and Raman Spectral Studies at High Temperatures. J. Phys. Chem. A 2010, 114, 7457–7461.
  • 51.
    Ocola, E.J. Vibrational and Theoretical Investigations of Molecular Conformations and Intramolecular π-Type Hydrogen Bonding. Ph. D. Thesis, Texas A & M University, College Station, TX, USA, 2011.
  • 52.
    Al-Saadi, A.A.; Wagner, M.; Laane, J. Spectroscopic and Computational Studies of the Intramolecular Hydrogen Bonding of 2-Indanol. J. Phys. Chem. A 2006, 110, 12292–12297.
  • 53.
    Ocola, E.J.; Laane, J. Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 2-Cyclopenten-1-ol. Molecules 2021, 26, 1106.
  • 54.
    Ocola, E.J.; Laane, J. Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 2-Cyclohexen-1-ol. J. Phys Chem. A 2016, 120, 74–80.
  • 55.
    Ocola, E.J.; Laane, J. Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 3-Cyclohexen-1-ol. J. Mol. Spectrosc. 2022, 387, 111663.
  • 56.
    Laane, J.; Ocola, E.J.; Chun, H.J. Vibrational Potential Energy Surfaces in Ground and Excited Electronic States. In Frontiers and Advances in Molecular Spectroscopy, 1st ed.; Laane, J., Ed.; Elsevier Publishing: Amsterdam, The Netherlands, 2017; Chapter 4, pp. 101–142.
  • 57.
    Ocola, E.J.; Laane, J. Theoretical Investigation of Intramolecular π-Type Hydrogen Bonding and Internal Rotation of 2-Cyclopropen-1-ol, 2-Cyclopropen-1-thiol and 2-Cyclopropen-1-amine. Mol. Phys. 2018, 17, 1404–1412.
  • 58.
    Varfolomeeva, V.V.; Terentev, A.V. Weak Intramolecular and Intermolecular Hydrogen Bonding of Benzyl Alcohol, 2-Phenylethanol and 2-Phenylethylamine in the Adsorption on Graphitized Thermal Carbon Black. Phys. Chem. Chem. Phys., 2015, 17, 24282–24293.
  • 59.
    Ocola, E.J.; Laane, J. Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 3-Cyclopentene-1-amine. J. Phys. Chem. A 2020, 124, 5907–5916.
  • 60.
    Marstokk, K.-M.; Møllendal, H. Microwave Spectrum, Conformation and Internal Hydrogen Bonding in N-Methylallylamine. Acta Chem. Scand. A 1986, 40, 615–621.
  • 61.
    Marstokk, K.-M.; Møllendal, H. Microwave Spectra and Weak Intramolecular Hydrogen Bonding in 3-Butene-1-Thiol And N-Methylallylamine. In Structure and Dynamics of Weakly Bound Molecular Complexes, NATO ASI Series, Series C: Mathematical and Physical Science; Weber, A., Ed.; Springer Science + Business Media, B.V.: Dordrecht, The Netherlands, 1993; Volume 212, pp. 57–68.
  • 62.
    Marstokk, K.-M.; Møllendal, H. Microwave Spectrum, Conformational Equilibria and Intramolecular Hydrogen Bonding of 1-Amino-3-butene. Acta Chem. Scand. A 1988, 42, 374–390.
  • 63.
    Marstokk, K.-M.; de Meijere, A.; Møllendal, H.; et al. Microwave Spectrum, Conformation, Dipole Moment and Quantum Chemical Calculations of 1-Amino-1-ethenylcyclopropane. J. Phys. Chem. A 2000, 104, 2897–2901.
  • 64.
    Sastry, K.V.L.N.; Dass, S.C.; Brooks, W.V.F.; et al. Microwave Spectrum, Dipole Moment, and Molecular Structure of Allyl Mercaptan. J. Mol. Spect. 1969, 31, 54–65.
  • 65.
    Marstokk, K.-M.; Møllendal, H. Microwave Spectrum, Conformational Equilibria, Intramolecular Hydrogen Bonding and Centrifugal Distortion of 3-Butene-1-thiol. Acta Chem. Scand. 1986, 40, 402–411.
  • 66.
    Laane, J. One-dimensional potential energy functions in vibrational spectroscopy. Q. Rev. Chem. Soc. 1971, 25, 533–552.
  • 67.
    Laane, J. Determination of Vibrational Potential Energy Surfaces from Raman and Infrared Spectra. Pure Appl. Chem. 1987, 59, 1307–1326.
  • 68.
    Laane, J. Vibrational Potential Energy Surfaces of Non-Rigid Molecules in Ground and Excited Electronic States. In Structures and Conformations of Non-Rigid Molecules, NATO ASI Series, Series C: Mathematical and Physical Science; Laane, J., Dakkouri, M., van der Veken, B., et al., Eds.; Springer Science + Business Media B.V.: Dordrecht, The Netherlands, 1993; Volume 410, 65-98.
  • 69.
    Laane, J. Vibrational Potential Energy Surfaces and Conformations of Molecules in Ground and Excited Electronic States. Annu. Rev. Phys. Chem. 1994, 45, 179–211.
  • 70.
    Laane, J. Spectroscopic Determination of Ground and Excited State Vibrational Potential Energy Surfaces. Int. Rev. Phys. Chem. 1999, 18, 301–341.
  • 71.
    Laane, J. Vibrational Potential Energy Surfaces of Non-Rigid Molecules in Exited Electronic States. In Structure and Dynamics of Electronic Excited States; Laane, J., Takahashi, H., Bandrauk, A., Eds.; Springer: Berlin, Germany, 1999; pp. 3–35.
  • 72.
    Laane, J. Experimental Determination of Vibrational Potential Energy Surfaces and Molecular Structures in Electronic Excited States. J. Chem. Phys. A 2000, 104, 7715–7733.
  • 73.
    Laane, J. Vibrational Potential Energy Surfaces in Electronic Excited States. In Frontiers of Molecular Spectroscopy, 1st ed.; Laane, J., Ed.; Elsevier Inc.: Amsterdam, The Netherlands, 2009; pp. 63–132.
  • 74.
    Ocola, E.J.; Laane, J. Beyond the Harmonic Oscillator; Highlights of Selected Studies of Vibrational Potential Energy Functions. Molecules 2025, 30, 1492.
  • 75.
    Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; et al. Gaussian 16 (Revision B.01); Gaussian Inc.: Wallingford, CT, USA, 2016.
  • 76.
    Dennington, R.D., II; Keith, T.A.; Millam, J.M. GaussView (6.1.1), Graphical Interface; Semichem Inc.: Shawnee, KS, USA, 2000–2019.
  • 77.
    Maple (2015, 2019.2); Maplesoft, a Division of Waterloo Maple Inc.: Waterloo, ON, Canada, 2015.
  • 78.
    Haller, K.; Chiang, W.-Y.; del Rosario, A.; et al. High-Temperature Vapor-Phase Raman Spectra and Assignment of the Low-Frequency Modes of trans-Stilbene and 4-Methoxy-trans-Stilbene. J. Mol. Struct. 1996, 379, 19−23.
  • 79.
    Laane, J.; Haller, K.; Sakurai, S.; et al. Raman Spectroscopy of Vapors at Elevated Temperatures. J. Mol. Struct. 2003, 650, 57−68.
Share this article:
Download PDF
Supplementary Materials
Issue
Volume 1, Issue 1
How to Cite
Ocola, E. J.; Laane, J. Ab initio Quantum-Chemical Calculations and Spectroscopic Studies of the Intramolecular π-Type Hydrogen Bonding in Small Cyclic Molecules. Photochemistry and Spectroscopy 2025, 1 (1), 2.
RIS
BibTex
Copyright & License
article copyright Image
Copyright (c) 2025 by the authors.