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Intramolecular Hydrogen Bonding 2021

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: 26 April 2024 | Viewed by 35583

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Dr. Mirosław Jabłoński

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Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
Interests: charge-inverted hydrogen bonds; inter- and intramolecular interactions; methods of estimating the interaction energy of intramolecular interactions; steric effects; substituent effects; QTAIM; computational chemistry
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Dear Colleagues,

The main place in the world of interactions is occupied by intermolecular hydrogen bonds. This is perfectly understandable because, having a moderate strength, they act as a glue that binds molecules into dimers or larger molecular aggregates, while allowing dynamic modifications, i.e., breaking and possibly creating other bonds. It seems that intramolecular hydrogen bonds are described somewhat less frequently. The reason may be a problem with the direct detection of intramolecular hydrogen bonding, which forces the use of some indirect methods, either experimental or theoretical, which in turn requires finding a reliable reference system. Often, finding such a reference system is not a trivial matter, even in planar molecules.

This Special Issue is mainly devoted to direct and indirect, both experimental and theoretical, methods of detecting intramolecular hydrogen bonding in various molecules, from simple, just a dozen atomic ones, to complex ones of biochemical importance. The articles are expected to describe the importance of the presence of intramolecular hydrogen bonding, e.g., on the preference and stabilization of a specific conformer, the effect on the global or local geometry of a molecule, its physicochemical properties, and biological functionality. Review papers on various aspects of intramolecular hydrogen bonding are particularly encouraged.

You may choose our Joint Special Issue in Chemistry.

Dr. Mirosław Jabłoński
Guest Editor

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Keywords

competition of interactions
conformer
evidence of stabilizing role
hydrogen bond strength
interaction energy
methods for determining the hydrogen bond strength
proton transfer
reference system
resonance-assisted hydrogen bond (RAHB)
role of intramolecular hydrogen bond
rotation barriers
stabilization

Related Special Issues

Intramolecular Hydrogen Bonding 2021 in Chemistry
Hydrogen Bonds in Molecules (26 articles)

Published Papers (13 papers)

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Editorial

Jump to: Research, Review

3 pages, 183 KiB

Open AccessEditorial

Intramolecular Hydrogen Bonding 2021

by Mirosław Jabłoński

Molecules 2021, 26(20), 6319; https://doi.org/10.3390/molecules26206319 - 19 Oct 2021

Cited by 4 | Viewed by 2043

Abstract

Undoubtedly, hydrogen bonds occupy a leading place in the rich world of intermolecular interactions [...] Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

Research

Jump to: Editorial, Review

25 pages, 8159 KiB

Open AccessFeature PaperArticle

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

by Karol Kułacz, Michał Pocheć, Aneta Jezierska and Jarosław J. Panek

Molecules 2021, 26(18), 5642; https://doi.org/10.3390/molecules26185642 - 17 Sep 2021

Cited by 6 | Viewed by 2147

Abstract

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller–Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP,

ω

B97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers’ stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm

^{- 1}

–1700 cm

^{- 1}

and 2300 cm

^{- 1}

–3400 cm

^{- 1}

in the gas phase and 600 cm

^{- 1}

–1800 cm

^{- 1}

and 2200 cm

^{- 1}

–3400 cm

^{- 1}

in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm

^{- 1}

–1700 cm

^{- 1}

and 2300 cm

^{- 1}

–3300 cm

^{- 1}

for the gas phase and one broad absorption region in the solid state between 700 cm

^{- 1}

and 3100 cm

^{- 1}

. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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13 pages, 2749 KiB

Open AccessFeature PaperArticle

Spectroscopic Identification of Hydrogen Bond Vibrations and Quasi-Isostructural Polymorphism in N-Salicylideneaniline

by Łukasz Hetmańczyk, Eugene A. Goremychkin, Janusz Waliszewski, Mikhail V. Vener, Paweł Lipkowski, Peter M. Tolstoy and Aleksander Filarowski

Molecules 2021, 26(16), 5043; https://doi.org/10.3390/molecules26165043 - 20 Aug 2021

Cited by 8 | Viewed by 2354

Abstract

The ortho-hydroxy aryl Schiff base 2-[(E)-(phenylimino)methyl]phenol and its deutero-derivative have been studied by the inelastic incoherent neutron scattering (IINS), infrared (IR) and Raman experimental methods, as well as by Density Functional Theory (DFT) and Density-Functional Perturbation Theory (DFPT) simulations. The assignments of vibrational modes within the 3500–50 cm⁻¹ spectral region made it possible to state that the strong hydrogen bond in the studied compound can be classified as the so-called quasi-aromatic bond. The isotopic substitution supplemented by the results of DFT calculations allowed us to identify vibrational bands associated with all five major hydrogen bond vibrations. Quasi-isostructural polymorphism of 2-[(E)-(phenylimino)methyl]phenol (SA) and 2-[(E)-(phenyl-D₅-imino)methyl]phenol (SA-C₆D₅) has been studied by powder X-ray diffraction in the 20–320 K temperature range. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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11 pages, 414 KiB

Open AccessArticle

On the Relationship between Hydrogen Bond Strength and the Formation Energy in Resonance-Assisted Hydrogen Bonds

by José Manuel Guevara-Vela, Miguel Gallegos, Mónica A. Valentín-Rodríguez, Aurora Costales, Tomás Rocha-Rinza and Ángel Martín Pendás

Molecules 2021, 26(14), 4196; https://doi.org/10.3390/molecules26144196 - 10 Jul 2021

Cited by 17 | Viewed by 2371

Abstract

Resonance-assisted hydrogen bonds (RAHB) are intramolecular contacts that are characterised by being particularly energetic. This fact is often attributed to the delocalisation of

π

electrons in the system. In the present article, we assess this thesis via the examination of the effect of [...] Read more.

Resonance-assisted hydrogen bonds (RAHB) are intramolecular contacts that are characterised by being particularly energetic. This fact is often attributed to the delocalisation of

π

electrons in the system. In the present article, we assess this thesis via the examination of the effect of electron-withdrawing and electron-donating groups, namely −F, −Cl, −Br, −CF₃, −N(CH₃)₂, −OCH₃, −NHCOCH₃ on the strength of the RAHB in malondialdehyde by using the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms (IQA) analyses. We show that the influence of the investigated substituents on the strength of the investigated RAHBs depends largely on its position within the

π

skeleton. We also examine the relationship between the formation energy of the RAHB and the hydrogen bond interaction energy as defined by the IQA method of wave function analysis. We demonstrate that these substituents can have different effects on the formation and interaction energies, casting doubts regarding the use of different parameters as indicators of the RAHB formation energies. Finally, we also demonstrate how the energy density can offer an estimation of the IQA interaction energy, and therefore of the HB strength, at a reduced computational cost for these important interactions. We expected that the results reported herein will provide a valuable understanding in the assessment of the energetics of RAHB and other intramolecular interactions. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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15 pages, 3287 KiB

Open AccessFeature PaperArticle

Perturbating Intramolecular Hydrogen Bonds through Substituent Effects or Non-Covalent Interactions

by Al Mokhtar Lamsabhi, Otilia Mó and Manuel Yáñez

Molecules 2021, 26(12), 3556; https://doi.org/10.3390/molecules26123556 - 10 Jun 2021

Cited by 7 | Viewed by 2186

Abstract

An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH₂(CH₂)_nCH₂NH₂ (n = 0–5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH₂(CH₂)_nCH₂NH₂ (n = 0–3) interact with BeF₂. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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19 pages, 5385 KiB

Open AccessArticle

A Family of Ethyl N-Salicylideneglycinate Dyes Stabilized by Intramolecular Hydrogen Bonding: Photophysical Properties and Computational Study

by Larisa E. Alkhimova, Maria G. Babashkina and Damir A. Safin

Molecules 2021, 26(11), 3112; https://doi.org/10.3390/molecules26113112 - 23 May 2021

Cited by 4 | Viewed by 2108

Abstract

In this work we report solvatochromic and luminescent properties of ethyl N-salicylideneglycinate (1), ethyl N-(5-methoxysalicylidene)glycinate (2), ethyl N-(5-bromosalicylidene)glycinate (3), and ethyl N-(5-nitrosalicylidene)glycinate (4) dyes. 1–4 correspond to a class of N-salicylidene aniline derivatives, whose photophysical properties are dictated by the intramolecular proton transfer between the OH-function and the imine N-atom, affording tautomerization between the enol-imine and keto-enamine forms. Photophysical properties of 1–4 were studied in different pure non-polar and (a)protic polar solvents as well as upon gradual addition of NEt₃, NaOH, and CH₃SO₃H. The DFT calculations were performed to verify the structures of 1–4 as well as their electronic and optical properties. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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11 pages, 2437 KiB

Open AccessArticle

Polymorphism and Conformational Equilibrium of Nitro-Acetophenone in Solid State and under Matrix Conditions

by Łukasz Hetmańczyk, Przemysław Szklarz, Agnieszka Kwocz, Maria Wierzejewska, Magdalena Pagacz-Kostrzewa, Mikhail Ya. Melnikov, Peter M. Tolstoy and Aleksander Filarowski

Molecules 2021, 26(11), 3109; https://doi.org/10.3390/molecules26113109 - 22 May 2021

Cited by 6 | Viewed by 2374

Abstract

Conformational and polymorphic states in the nitro-derivative of o-hydroxy acetophenone have been studied by experimental and theoretical methods. The potential energy curves for the rotation of the nitro group and isomerization of the hydroxyl group have been calculated by density functional theory (DFT) to estimate the barriers of the conformational changes. Two polymorphic forms of the studied compound were obtained by the slow and fast evaporation of polar and non-polar solutions, respectively. Both of the polymorphs were investigated by Infrared-Red (IR) and Raman spectroscopy, Incoherent Inelastic Neutron Scattering (IINS), X-ray diffraction, nuclear quadrupole resonance spectroscopy (NQR), differential scanning calorimetry (DSC) and density functional theory (DFT) methods. In one of the polymorphs, the existence of a phase transition was shown. The position of the nitro group and its impact on the crystal cell of the studied compound were analyzed. The conformational equilibrium determined by the reorientation of the hydroxyl group was observed under argon matrix isolation. An analysis of vibrational spectra was achieved for the interpretation of conformational equilibrium. The infrared spectra were measured in a wide temperature range to reveal the spectral bands that were the most sensitive to the phase transition and conformational equilibrium. The results showed the interrelations between intramolecular processes and macroscopic phenomena in the studied compound. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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12 pages, 2067 KiB

Open AccessFeature PaperArticle

Perturbing the O–H^…O Hydrogen Bond in 1-oxo-3-hydroxy-2-propene

by Ibon Alkorta, José Elguero and Janet E. Del Bene

Molecules 2021, 26(11), 3086; https://doi.org/10.3390/molecules26113086 - 21 May 2021

Cited by 2 | Viewed by 1746

Abstract

Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to identify and characterize equilibrium structures and transition structures on the 1-oxo-3-hydroxy-2-propene: Lewis acid potential energy surfaces, with the acids LiH, LiF, BeH₂, and BeF₂. Two equilibrium structures, one with the acid interacting with the C=O group and the other with the interaction occurring at the O–H group, exist on all surfaces. These structures are separated by transition structures that present the barriers to the interconversion of the two equilibrium structures. The structures with the acid interacting at the C=O group have the greater binding energies. Since the barriers to convert the structures with interaction occurring at the O–H group are small, only the isomers with interaction occurring at the C=O group could be experimentally observed, even at low temperatures. Charge-transfer energies were computed for equilibrium structures, and EOM-CCSD spin–spin coupling constants ^2hJ(O–O), ^1hJ(H–O), and ¹J(O–H) were computed for equilibrium and transition structures. These coupling constants exhibit a second-order dependence on the corresponding distances, with very high correlation coefficients. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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19 pages, 3843 KiB

Open AccessArticle

Focal Point Evaluation of Energies for Tautomers and Isomers for 3-hydroxy-2-butenamide: Evaluation of Competing Internal Hydrogen Bonds of Types -OH…O=, -OH…N, -NH…O=, and CH…X (X=O and N)

by Zikri Altun, Erdi Ata Bleda and Carl Trindle

Molecules 2021, 26(9), 2623; https://doi.org/10.3390/molecules26092623 - 30 Apr 2021

Cited by 4 | Viewed by 2279

Abstract

The title compound is a small molecule with many structural variations; it can illustrate a variety of internal hydrogen bonds, among other noncovalent interactions. Here we examine structures displaying hydrogen bonding between carbonyl oxygen and hydroxyl H; between carbonyl oxygen and amino H; hydroxyl H and amino N; hydroxyl O and amino H. We also consider H-bonding in its tautomer 2-oxopropanamide. By extrapolation algorithms applied to Hartree-Fock and correlation energies as estimated in HF, MP2, and CCSD calculations using the cc-pVNZ correlation-consistent basis sets (N = 2, 3, and 4) we obtain reliable relative energies of the isomeric forms. Assuming that such energy differences may be attributed to the presence of the various types of hydrogen bonding, we attempt to infer relative strengths of types of H-bonding. The Atoms in Molecules theory of Bader and the Local Vibrational Modes analysis of Cremer and Kraka are applied to this task. Hydrogen bonds are ranked by relative strength as measured by local stretching force constants, with the stronger =O…HO- > NH…O= > -OH…N well separated from a cluster > NH…O= ≈ >NH…OH ≈ CH…O= of comparable and intermediate strength. Weaker but still significant interactions are of type CH…N which is stronger than CH…OH. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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Review

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16 pages, 926 KiB

Open AccessFeature PaperReview

Modern Theoretical Approaches to Modeling the Excited-State Intramolecular Proton Transfer: An Overview

by Joanna Jankowska and Andrzej L. Sobolewski

Molecules 2021, 26(17), 5140; https://doi.org/10.3390/molecules26175140 - 25 Aug 2021

Cited by 28 | Viewed by 3774

Abstract

The excited-state intramolecular proton transfer (ESIPT) phenomenon is nowadays widely acknowledged to play a crucial role in many photobiological and photochemical processes. It is an extremely fast transformation, often taking place at sub-100 fs timescales. While its experimental characterization can be highly challenging, a rich manifold of theoretical approaches at different levels is nowadays available to support and guide experimental investigations. In this perspective, we summarize the state-of-the-art quantum-chemical methods, as well as molecular- and quantum-dynamics tools successfully applied in ESIPT process studies, focusing on a critical comparison of their specific properties. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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21 pages, 3212 KiB

Open AccessReview

Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy

by Milind M. Deshmukh and Shridhar R. Gadre

Molecules 2021, 26(10), 2928; https://doi.org/10.3390/molecules26102928 - 14 May 2021

Cited by 29 | Viewed by 2982

Abstract

Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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22 pages, 5329 KiB

Open AccessFeature PaperReview

A Spectroscopic Overview of Intramolecular Hydrogen Bonds of NH…O,S,N Type

by Poul Erik Hansen

Molecules 2021, 26(9), 2409; https://doi.org/10.3390/molecules26092409 - 21 Apr 2021

Cited by 15 | Viewed by 3423

Abstract

Intramolecular NH…O,S,N interactions in non-tautomeric systems are reviewed in a broad range of compounds covering a variety of NH donors and hydrogen bond acceptors. ¹H chemical shifts of NH donors are good tools to study intramolecular hydrogen bonding. However in some cases they have to be corrected for ring current effects. Deuterium isotope effects on ¹³C and ¹⁵N chemical shifts and primary isotope effects are usually used to judge the strength of hydrogen bonds. Primary isotope effects are investigated in a new range of magnitudes. Isotope ratios of NH stretching frequencies, νNH/ND, are revisited. Hydrogen bond energies are reviewed and two-bond deuterium isotope effects on ¹³C chemical shifts are investigated as a possible means of estimating hydrogen bond energies. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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37 pages, 2395 KiB

Open AccessReview

A Critical Overview of Current Theoretical Methods of Estimating the Energy of Intramolecular Interactions

by Mirosław Jabłoński

Molecules 2020, 25(23), 5512; https://doi.org/10.3390/molecules25235512 - 25 Nov 2020

Cited by 48 | Viewed by 3096

Abstract

This article is probably the first such comprehensive review of theoretical methods for estimating the energy of intramolecular hydrogen bonds or other interactions that are frequently the subject of scientific research. Rather than on a plethora of numerical data, the main focus is on discussing the theoretical rationale of each method. Additionally, attention is paid to the fact that it is very often possible to use several variants of a particular method. Both of the methods themselves and their variants often give wide ranges of the obtained estimates. Attention is drawn to the fact that the applicability of a particular method may be significantly limited by various factors that disturb the reliability of the estimation, such as considerable structural changes or new important interactions in the reference system. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding 2021)

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