International Journal of Molecular Sciences

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14 pages, 2153 KiB

Open AccessArticle

Insights into the Effect of Charges on Hydrogen Bonds

by Andrea Chimarro-Contreras, Yomaira Lopez-Revelo, Jorge Cardenas-Gamboa and Thibault Terencio

Int. J. Mol. Sci. 2024, 25(3), 1613; https://doi.org/10.3390/ijms25031613 - 28 Jan 2024

Viewed by 1029

Abstract

Previous computational and experimental studies showed that charges located at the surroundings of hydrogen bonds can exert two opposite effects on them: rupture or strengthening of the hydrogen bond. This work aims to generalize the effect of charges in different hydrogen-bonded systems and [...] Read more.

Previous computational and experimental studies showed that charges located at the surroundings of hydrogen bonds can exert two opposite effects on them: rupture or strengthening of the hydrogen bond. This work aims to generalize the effect of charges in different hydrogen-bonded systems and to propose a coherent explanation of this effect. For these purposes, 19 systems with intra- and intermolecular hydrogen bonds were studied computationally with DFT. The FT-IR spectra of the systems were simulated, and two energy components of the hydrogen bond were studied separately to determine their variation upon the presence of a charge: charge transfer and molecular overlap. It was determined that either the breaking or strengthening of the hydrogen bond can be favored one over the other, for instance, depending on the heteroatom involved in the hydrogen bond. In addition, it is showed that the strengthening of the hydrogen bond by the presence of a charge is directly related to the decrease in charge transfer between the monomers, which is explained by an increase in molecular overlapping, suggesting a more covalent character of the interaction. The understanding of how hydrogen bonds are affected by charges is important, as it is a key towards a strategy to manipulate hydrogen bonds at convenience. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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18 pages, 5410 KiB

Open AccessArticle

The Role H-Bonding and Supramolecular Structures in Homogeneous and Enzymatic Catalysis

by Ludmila I. Matienko, Elena M. Mil, Anastasia A. Albantova and Alexander N. Goloshchapov

Int. J. Mol. Sci. 2023, 24(23), 16874; https://doi.org/10.3390/ijms242316874 - 28 Nov 2023

Viewed by 1099

Abstract

The article analyzes the role of hydrogen bonds and supramolecular structures in enzyme catalysis and model systems. Hydrogen bonds play a crucial role in many enzymatic reactions. However, scientists have only recently attempted to harness the power of hydrogen bonds in homogeneous catalytic [...] Read more.

The article analyzes the role of hydrogen bonds and supramolecular structures in enzyme catalysis and model systems. Hydrogen bonds play a crucial role in many enzymatic reactions. However, scientists have only recently attempted to harness the power of hydrogen bonds in homogeneous catalytic systems. One of the newest directions is associated with attempts to control the properties of catalysts by influencing the “second coordination sphere” of metal complexes. The role H-bonding, and the building of stable supramolecular nanostructures due to intermolecular H-bonds, based on catalytic active heteroligand iron (Fe) or nickel (Ni) complexes formed during hydrocarbon oxidations were assessed via the AFM (Atomic-force microscopy) method, which was proposed and applied by authors of this manuscript. Th is article also discusses the roles of hydrogen bonds and supramolecular structures in oxidation reactions catalyzed by heteroligand Ni and Fe complexes, which are not only effective homogeneous catalysts but also structural and functional models of Oxygenases. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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20 pages, 9729 KiB

Open AccessArticle

Insight into Unusual Supramolecular Self-Assemblies of Terthiophenes Directed by Weak Hydrogen Bonding

by Shiv Kumar, Kristof Van Hecke and Franck Meyer

Int. J. Mol. Sci. 2023, 24(13), 11127; https://doi.org/10.3390/ijms241311127 - 5 Jul 2023

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Abstract

A supramolecular self-assembly of semiconducting polymers and small molecules plays an important role in charge transportation, performance, and lifetime of an optoelectronic device. Tremendous efforts have been put into the strategies to self-organize these materials. In this regard, here, we present the self-organization [...] Read more.

A supramolecular self-assembly of semiconducting polymers and small molecules plays an important role in charge transportation, performance, and lifetime of an optoelectronic device. Tremendous efforts have been put into the strategies to self-organize these materials. In this regard, here, we present the self-organization of terthiophene and its methyl alcohol derivative with 4,4′-bipyridine (44BiPy). An unexpected 2D layered organization of 5,5″-dimethyl-2,2′:5′,2″-terthiophene (DM3T) and 44BiPy was obtained and analyzed. Single-crystal X-ray diffraction analysis revealed that DM3T and 44BiPy consist of stacked, almost independent, infinite 2D layers while held together by weak hydrogen bonds. In addition to this peculiar supramolecular arrangement of these compounds, the investigation of their photophysical properties showed strong fluorescence quenching of DM3T by 44BiPy in the solid state, suggesting an efficient charge transfer. On the other hand, the methyl alcohol derivative of terthiophene, DM3TMeOH, organized in a closed cyclic motif with 44BiPy via hydrogen bonds. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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25 pages, 3853 KiB

Open AccessArticle

Unravelling the Mechanism and Governing Factors in Lewis Acid and Non-Covalent Diels–Alder Catalysis: Different Perspectives

by Lise Vermeersch, Frank De Proft, Vicky Faulkner and Freija De Vleeschouwer

Int. J. Mol. Sci. 2023, 24(5), 4938; https://doi.org/10.3390/ijms24054938 - 3 Mar 2023

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Abstract

In the current literature, many non-covalent interaction (NCI) donors have been proposed that can potentially catalyze Diels-Alder (DA) reactions. In this study, a detailed analysis of the governing factors in Lewis acid and non-covalent catalysis of three types of DA reactions was carried [...] Read more.

In the current literature, many non-covalent interaction (NCI) donors have been proposed that can potentially catalyze Diels-Alder (DA) reactions. In this study, a detailed analysis of the governing factors in Lewis acid and non-covalent catalysis of three types of DA reactions was carried out, for which we selected a set of hydrogen-, halogen-, chalcogen-, and pnictogen-bond donors. We found that the more stable the NCI donor–dienophile complex, the larger the reduction in DA activation energy. We also showed that for active catalysts, a significant part of the stabilization was caused by orbital interactions, though electrostatic interactions dominated. Traditionally, DA catalysis was attributed to improved orbital interactions between the diene and dienophile. Recently, Vermeeren and co-workers applied the activation strain model (ASM) of reactivity, combined with the Ziegler-Rauk-type energy decomposition analysis (EDA), to catalyzed DA reactions in which energy contributions for the uncatalyzed and catalyzed reaction were compared at a consistent geometry. They concluded that reduced Pauli repulsion energy, and not enhanced orbital interaction energy, was responsible for the catalysis. However, when the degree of asynchronicity of the reaction is altered to a large extent, as is the case for our studied hetero-DA reactions, the ASM should be employed with caution. We therefore proposed an alternative and complementary approach, in which EDA values for the catalyzed transition-state geometry, with the catalyst present or deleted, can be compared one to one, directly measuring the effect of the catalyst on the physical factors governing the DA catalysis. We discovered that enhanced orbital interactions are often the main driver for catalysis and that Pauli repulsion plays a varying role. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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7 pages, 962 KiB

Open AccessCommunication

UV Laser-Induced Phototransformations of Matrix-Isolated 5-Chloro-3-nitro-2-hydroxyacetophenone

by Magdalena Pagacz-Kostrzewa, Karolina Mucha, Maria Wierzejewska and Aleksander Filarowski

Int. J. Mol. Sci. 2023, 24(2), 1546; https://doi.org/10.3390/ijms24021546 - 12 Jan 2023

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Abstract

Conformational changes of 5-chloro-3-nitro-2-hydroxyacetophenone were studied by experimental and theoretical methods. Phototransformations of the compound were induced in low-temperature argon matrices by using UV radiation, which was followed by FT-IR measurements. Two types of changes within the molecule were detected: rotations of the [...] Read more.

Conformational changes of 5-chloro-3-nitro-2-hydroxyacetophenone were studied by experimental and theoretical methods. Phototransformations of the compound were induced in low-temperature argon matrices by using UV radiation, which was followed by FT-IR measurements. Two types of changes within the molecule were detected: rotations of the hydroxyl and acetyl groups. A new conformer without an intramolecular hydrogen bond was generated upon irradiation with λ = 330 nm, whereas the reverse reaction was observed at 415 nm. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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15 pages, 6548 KiB

Open AccessArticle

Molecular Pincers Using a Combination of N-H and C-H Donors for Anion Binding

by Jaehyeon Kim, Seung Hyeon Kim, Nam Jung Heo, Benjamin P. Hay and Sung Kuk Kim

Int. J. Mol. Sci. 2023, 24(1), 163; https://doi.org/10.3390/ijms24010163 - 22 Dec 2022

Cited by 1 | Viewed by 1593

Abstract

A naphthalene imide (1) and a naphthalene (2) bearing two pyrrole units have been synthesized, respectively, as anion receptors. It was revealed by ¹H NMR spectral studies carried out in CD₃CN that receptors 1 and 2 [...] Read more.

A naphthalene imide (1) and a naphthalene (2) bearing two pyrrole units have been synthesized, respectively, as anion receptors. It was revealed by ¹H NMR spectral studies carried out in CD₃CN that receptors 1 and 2 bind various anions via hydrogen bonds using both C-H and N-H donors. Compared with receptor 2, receptor 1 shows higher affinity for the test anions because of the enhanced acidity of its pyrrole NH and naphthalene CH hydrogens by the electron-withdrawing imide substituent. Molecular mechanics computations demonstrate that the receptors contact the halide anions via only one of the two respective available N-H and C-H donors whereas they use all four donors for binding of the oxyanions such as dihydrogen phosphate and hydrogen pyrophosphate. Receptor 1, a push-pull conjugated system, displays a strong fluorescence centered at 625 nm, while receptor 2 exhibits an emission with a maximum peak at 408 nm. In contrast, upon exposure of receptors 1 and 2 to the anions in question, their fluorescence was noticeably quenched particularly with relatively basic anions including F⁻, H₂PO₄⁻, HP₂O₇³⁻, and HCO₃⁻. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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12 pages, 1368 KiB

Open AccessArticle

Detecting the Hydrogen Bond Cooperativity in a Protein β-Sheet by H/D Exchange

by Jingwen Li, Jingfei Chen, Yefei Wang and Lishan Yao

Int. J. Mol. Sci. 2022, 23(23), 14821; https://doi.org/10.3390/ijms232314821 - 26 Nov 2022

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Abstract

The hydrogen bond (H-bond) cooperativity in the β-sheet of GB3 is investigated by a NMR hydrogen/deuterium (H/D) exchange method. It is shown that the weakening of one backbone N–H…O=C H-bond between two β-strands, β1 and β2, due to the exchange of NH to [...] Read more.

The hydrogen bond (H-bond) cooperativity in the β-sheet of GB3 is investigated by a NMR hydrogen/deuterium (H/D) exchange method. It is shown that the weakening of one backbone N–H…O=C H-bond between two β-strands, β1 and β2, due to the exchange of NH to ND of the H-bond donor in β1, perturbs the chemical shift of ¹³C_α, ¹³C_β, ¹H_α, ¹H_N, and ¹⁵N of the H-bond acceptor and its following residue in β2. Quantum mechanical calculations suggest that the -H-bond chemical shift isotope effect is caused by the structural reorganization in response to the H-bond weakening. This structural reorganization perturbs four neighboring H-bonds, with three being weaker and one being stronger, indicating that three H-bonds are cooperative and one is anticooperative with the perturbed H-bond. The sign of the cooperativity depends on the relative position of the H-bonds. This H-bond cooperativity, which contributes to β-sheet stability overall, can be important for conformational coupling across the β-sheet. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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19 pages, 1950 KiB

Open AccessArticle

Comprehensive Empirical Model of Substitution—Influence on Hydrogen Bonding in Aromatic Schiff Bases

by Katarzyna M. Krupka, Michał Pocheć, Jarosław J. Panek and Aneta Jezierska

Int. J. Mol. Sci. 2022, 23(20), 12439; https://doi.org/10.3390/ijms232012439 - 18 Oct 2022

Cited by 3 | Viewed by 1664

Abstract

In this work, over 500 structures of tri-ring aromatic Schiff bases with different substitution patterns were investigated to develop a unified description of the substituent effect on the intramolecular hydrogen bridge. Both proximal and distal effects were examined using Density Functional Theory (DFT) [...] Read more.

In this work, over 500 structures of tri-ring aromatic Schiff bases with different substitution patterns were investigated to develop a unified description of the substituent effect on the intramolecular hydrogen bridge. Both proximal and distal effects were examined using Density Functional Theory (DFT) in the gas phase and with solvent reaction field (Polarizable Continuum Model (PCM) and water as the solvent). In order to investigate and characterize the non-covalent interactions, a topological analysis was performed using the Quantum Theory of Atoms In Molecules (QTAIM) theory and Non-Covalent Interactions (NCI) index. The obtained results were summarized as the generalized, empirical model of the composite substituent effect, assessed using an additional group of simple ring-based Schiff bases. The composite substituent effect has been divided into separate increments describing the different interactions of the hydrogen bridge and the substituent: the classical substituent effect, involving resonance and induction mediated through the ring, steric increment based on substituent proximity to the bridge elements, and distal increment, derived from substitution on the distal ring. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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31 pages, 6090 KiB

Open AccessArticle

Hydrogen Bonding Drives Helical Chirality via 10-Membered Rings in Dipeptide Conjugates of Ferrocene-1,1′-Diamine

by Monika Kovačević, Dora Markulin, Matea Zelenika, Marko Marjanović, Marija Lovrić, Denis Polančec, Marina Ivančić, Jasna Mrvčić, Krešimir Molčanov, Valentina Milašinović, Sunčica Roca, Ivan Kodrin and Lidija Barišić

Int. J. Mol. Sci. 2022, 23(20), 12233; https://doi.org/10.3390/ijms232012233 - 13 Oct 2022

Cited by 4 | Viewed by 2016

Abstract

Considering the enormous importance of protein turns as participants in various biological events, such as protein–protein interactions, great efforts have been made to develop their conformationally and proteolytically stable mimetics. Ferrocene-1,1′-diamine was previously shown to nucleate the stable turn structures in peptides prepared [...] Read more.

Considering the enormous importance of protein turns as participants in various biological events, such as protein–protein interactions, great efforts have been made to develop their conformationally and proteolytically stable mimetics. Ferrocene-1,1′-diamine was previously shown to nucleate the stable turn structures in peptides prepared by conjugation with Ala (III) and Ala–Pro (VI). Here, we prepared the homochiral conjugates of ferrocene-1,1′-diamine with l-/d-Phe (32/35), l-/d-Val (33/36), and l-/d-Leu (34/37) to investigate (1) whether the organometallic template induces the turn structure upon conjugation with amino acids, and (2) whether the bulky or branched side chains of Phe, Val, and Leu affect hydrogen bonding. Detailed spectroscopic (IR, NMR, CD), X-ray, and DFT studies revealed the presence of two simultaneous 10-membered interstrand hydrogen bonds, i.e., two simultaneous β-turns in goal compounds. A preliminary biological evaluation of d-Leu conjugate 37 showed its modest potential to induce cell cycle arrest in the G0/G1 phase in the HeLa cell line but these results need further investigation. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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Review

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23 pages, 7328 KiB

Open AccessReview

C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids

by Zygmunt Stanislaw Derewenda

Int. J. Mol. Sci. 2023, 24(17), 13165; https://doi.org/10.3390/ijms241713165 - 24 Aug 2023

Cited by 6 | Viewed by 2033

Abstract

Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it [...] Read more.

Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids. Full article

(This article belongs to the Special Issue Recent Advances in Hydrogen Bonding)

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