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Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions

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A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: closed (30 September 2020) | Viewed by 50771

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Dr. Ilya G. Shenderovich

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Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
Interests: noncovalent interactions; H-bond; soft matter; surface; porous materials; NMR
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“Great things are done by a series of small things brought together.”
Vincent Van Gogh

Dear Colleagues,

Noncovalent interactions are the bridge between the ideal gas abstraction and the real world. For a long time, they were covered by two terms: van der Waals interactions and hydrogen bonding. Both experimental and quantum chemical studies have contributed to the understanding of the nature of these interactions. In the last decade, great progress has been made in identifying, quantifying, and visualizing noncovalent interactions. New types of interactions have been classified; their energetic and spatial properties have been tabulated.

In the past, most studies were limited to the analysis of the single strongest interaction in a molecular system under consideration, which was held responsible for the most important structural properties of the system. Despite this limitation, such an approach often results in satisfactory approximations of experimental data. However, it requires knowledge of the structure of the molecular system and the absence of other competing interactions. The current challenge is to go beyond this limitation.

This Special Issue will collect ideas on how to study the interplay of noncovalent interactions in complex molecular systems including the effects of cooperation and anti- cooperation, solvation, reaction field, steric hindrance, intermolecular dynamics and other weak but numerous impacts on molecular conformation, chemical reactivity, and condensed matter structure. Publications about experimental manifestations of these effects or their theoretical analysis are cordially invited.

The following three leading contributions initiate this flow of ideas:

Gerd Buntkowsky (Technische Universität Darmstadt, Garmany): “Noncovalent Interactions in Prison".
Slawomir Grabowski (UPV/EHU and DIPC - Donostia International Physics Center, Spain): “Noncovalent Interactions as Preliminary Stages of Chemical Reactions”.
Janez Mavri (National Institute of Chemistry, Slovenia), Mojca Kržan (University of Ljubljana, Slovenia), Robert Vianello (Ruđer Bošković Institute, Croatia) contribute a paper about the multiscale simulation of monoaminergic system in conjunction with an experiment.

Dr. Ilya Shenderovich
Guest Editor

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Keywords

Noncovalent
Interactions H-bond
Halogen bonds
Molecular recognition
IR and Raman spectroscopy
NMR
X-ray diffraction

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Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II) in Molecules (9 articles)

Published Papers (12 papers)

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Editorial

Jump to: Research, Review

4 pages, 180 KiB

Open AccessEditorial

Editorial to the Special Issue “Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions”

by Ilya G. Shenderovich

Molecules 2021, 26(1), 158; https://doi.org/10.3390/molecules26010158 - 31 Dec 2020

Cited by 1 | Viewed by 2009

Abstract

Noncovalent interactions allow our world to exist [...] Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

Research

Jump to: Editorial, Review

17 pages, 3297 KiB

Open AccessArticle

The Effect of Deuteration on the H₂ Receptor Histamine Binding Profile: A Computational Insight into Modified Hydrogen Bonding Interactions

by Lucija Hok, Janez Mavri and Robert Vianello

Molecules 2020, 25(24), 6017; https://doi.org/10.3390/molecules25246017 - 18 Dec 2020

Cited by 17 | Viewed by 4134

Abstract

We used a range of computational techniques to reveal an increased histamine affinity for its H₂ receptor upon deuteration, which was interpreted through altered hydrogen bonding interactions within the receptor and the aqueous environment preceding the binding. Molecular docking identified the area between third and fifth transmembrane α-helices as the likely binding pocket for several histamine poses, with the most favorable binding energy of −7.4 kcal mol⁻¹ closely matching the experimental value of −5.9 kcal mol⁻¹. The subsequent molecular dynamics simulation and MM-GBSA analysis recognized Asp98 as the most dominant residue, accounting for 40% of the total binding energy, established through a persistent hydrogen bonding with the histamine −NH₃⁺ group, the latter further held in place through the N–H∙∙∙O hydrogen bonding with Tyr250. Unlike earlier literature proposals, the important role of Thr190 is not evident in hydrogen bonds through its −OH group, but rather in the C–H∙∙∙π contacts with the imidazole ring, while its former moiety is constantly engaged in the hydrogen bonding with Asp186. Lastly, quantum-chemical calculations within the receptor cluster model and utilizing the empirical quantization of the ionizable X–H bonds (X = N, O, S), supported the deuteration-induced affinity increase, with the calculated difference in the binding free energy of −0.85 kcal mol⁻¹, being in excellent agreement with an experimental value of −0.75 kcal mol⁻¹, thus confirming the relevance of hydrogen bonding for the H₂ receptor activation. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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14 pages, 383 KiB

Open AccessArticle

Pinacolone-Alcohol Gas-Phase Solvation Balances as Experimental Dispersion Benchmarks

by Charlotte Zimmermann, Taija L. Fischer and Martin A. Suhm

Molecules 2020, 25(21), 5095; https://doi.org/10.3390/molecules25215095 - 3 Nov 2020

Cited by 8 | Viewed by 2716

Abstract

The influence of distant London dispersion forces on the docking preference of alcohols of different size between the two lone electron pairs of the carbonyl group in pinacolone was explored by infrared spectroscopy of the OH stretching fundamental in supersonic jet expansions of 1:1 solvate complexes. Experimentally, no pronounced tendency of the alcohol to switch from the methyl to the bulkier tert-butyl side with increasing size was found. In all cases, methyl docking dominates by at least a factor of two, whereas DFT-optimized structures suggest a very close balance for the larger alcohols, once corrected by CCSD(T) relative electronic energies. Together with inconsistencies when switching from a C4 to a C5 alcohol, this points at deficiencies of the investigated B3LYP and in particular TPSS functionals even after dispersion correction, which cannot be blamed on zero point energy effects. The search for density functionals which describe the harmonic frequency shift, the structural change and the energy difference between the docking isomers of larger alcohols to unsymmetric ketones in a satisfactory way is open. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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14 pages, 7128 KiB

Open AccessArticle

Halogenated Diazabutadiene Dyes: Synthesis, Structures, Supramolecular Features, and Theoretical Studies

by Valentine G. Nenajdenko, Namiq G. Shikhaliyev, Abel M. Maharramov, Khanim N. Bagirova, Gulnar T. Suleymanova, Alexander S. Novikov, Victor N. Khrustalev and Alexander G. Tskhovrebov

Molecules 2020, 25(21), 5013; https://doi.org/10.3390/molecules25215013 - 29 Oct 2020

Cited by 34 | Viewed by 2900

Abstract

Novel halogenated aromatic dichlorodiazadienes were prepared via copper-mediated oxidative coupling between the corresponding hydrazones and CCl₄. These rare azo-dyes were characterized using ¹H and ¹³C NMR techniques and X-ray diffraction analysis for five halogenated dichlorodiazadienes. Multiple non-covalent halogen···halogen interactions were detected in the solid state and studied by DFT calculations and topological analysis of the electron density distribution within the framework of Bader’s theory (QTAIM method). Theoretical studies demonstrated that non-covalent halogen···halogen interactions play crucial role in self-assembly of highly polarizable dichlorodiazadienes. Thus, halogen bonding can dictate a packing preference in the solid state for this class of dichloro-substituted heterodienes, which could be a convenient tool for a fine tuning of the properties of this novel class of dyes. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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22 pages, 4513 KiB

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Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates

by Kinga Jóźwiak, Aneta Jezierska, Jarosław J. Panek, Eugene A. Goremychkin, Peter M. Tolstoy, Ilya G. Shenderovich and Aleksander Filarowski

Molecules 2020, 25(20), 4720; https://doi.org/10.3390/molecules25204720 - 14 Oct 2020

Cited by 15 | Viewed by 6783

Abstract

Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases. A combination of the Infrared, Raman, Nuclear Magnetic Resonance, and Incoherent Inelastic Neutron Scattering spectroscopies and the Car–Parrinello Molecular Dynamics and Density Functional Theory calculations was used. This integrated approach made it possible to assess the balance of repulsive and attractive intramolecular interactions between adjacent carboxyl groups as well as to study the dependence of this balance on steric confinement and the effect of this balance on intermolecular interactions of the carboxyl groups. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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20 pages, 4356 KiB

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Mutual Relations between Substituent Effect, Hydrogen Bonding, and Aromaticity in Adenine-Uracil and Adenine-Adenine Base Pairs

by Paweł A. Wieczorkiewicz, Halina Szatylowicz and Tadeusz M. Krygowski

Molecules 2020, 25(16), 3688; https://doi.org/10.3390/molecules25163688 - 13 Aug 2020

Cited by 7 | Viewed by 3840

Abstract

The electronic structure of substituted molecules is governed, to a significant extent, by the substituent effect (SE). In this paper, SEs in selected nucleic acid base pairs (Watson-Crick, Hoogsteen, adenine-adenine) are analyzed, with special emphasis on their influence on intramolecular interactions, aromaticity, and base pair hydrogen bonding. Quantum chemistry methods—DFT calculations, the natural bond orbital (NBO) approach, the Harmonic Oscillator Model of Aromaticity (HOMA) index, the charge of the substituent active region (cSAR) model, and the quantum theory of atoms in molecules (QTAIM)—are used to compare SEs acting on adenine moiety and H-bonds from various substitution positions. Comparisons of classical SEs in adenine with those observed in para- and meta-substituted benzenes allow for the better interpretation of the obtained results. Hydrogen bond stability and its other characteristics (e.g., covalency) can be significantly changed as a result of the SE, and its consequences are dependent on the substitution position. These changes allow us to investigate specific relations between H-bond parameters, leading to conclusions concerning the nature of hydrogen bonding in adenine dimers—e.g., H-bonds formed by five-membered ring nitrogen acceptor atoms have an inferior, less pronounced covalent nature as compared to those formed by six-membered ring nitrogen. The energies of individual H-bonds (obtained by the NBO method) are analyzed and compared to those predicted by the Espinosa-Molins-Lecomte (EML) model. Moreover, both SE and H-bonds can significantly affect the aromaticity of adenine rings; long-distance SEs on π-electron delocalization are also documented. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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19 pages, 2153 KiB

Open AccessArticle

Combined X-ray Crystallographic, IR/Raman Spectroscopic, and Periodic DFT Investigations of New Multicomponent Crystalline Forms of Anthelmintic Drugs: A Case Study of Carbendazim Maleate

by Alexander P. Voronin, Artem O. Surov, Andrei V. Churakov, Olga D. Parashchuk, Alexey A. Rykounov and Mikhail V. Vener

Molecules 2020, 25(10), 2386; https://doi.org/10.3390/molecules25102386 - 21 May 2020

Cited by 26 | Viewed by 4512

Abstract

Synthesis of multicomponent solid forms is an important method of modifying and fine-tuning the most critical physicochemical properties of drug compounds. The design of new multicomponent pharmaceutical materials requires reliable information about the supramolecular arrangement of molecules and detailed description of the intermolecular interactions in the crystal structure. It implies the use of a combination of different experimental and theoretical investigation methods. Organic salts present new challenges for those who develop theoretical approaches describing the structure, spectral properties, and lattice energy E_latt. These crystals consist of closed-shell organic ions interacting through relatively strong hydrogen bonds, which leads to E_latt > 200 kJ/mol. Some technical problems that a user of periodic (solid-state) density functional theory (DFT) programs encounters when calculating the properties of these crystals still remain unsolved, for example, the influence of cell parameter optimization on the E_latt value, wave numbers, relative intensity of Raman-active vibrations in the low-frequency region, etc. In this work, various properties of a new two-component carbendazim maleate crystal were experimentally investigated, and the applicability of different DFT functionals and empirical Grimme corrections to the description of the obtained structural and spectroscopic properties was tested. Based on this, practical recommendations were developed for further theoretical studies of multicomponent organic pharmaceutical crystals. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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9 pages, 2592 KiB

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Catalytic Effect of Hydrogen Bond on Oxhydryl Dehydrogenation in Methanol Steam Reforming on Ni(111)

by Changming Ke and Zijing Lin

Molecules 2020, 25(7), 1531; https://doi.org/10.3390/molecules25071531 - 27 Mar 2020

Cited by 4 | Viewed by 2915

Abstract

Dehydrogenation of H₃COH and H₂O are key steps of methanol steam reforming on transition metal surfaces. Oxhydryl dehydrogenation reactions of H_xCOH (x = 0–3) and OH on Ni (111) were investigated by DFT calculations with the OptB88-vdW functional. The transition states were searched by the climbing image nudged elastic band method and the dimer method. The activation energies for the dehydrogenation of individual H_xCOH* are 68 to 91 kJ/mol, and reduced to 12–17 kJ/mol by neighboring OH*. Bader charge analysis showed the catalysis role of OH* can be attributed to the effect of hydrogen bond (H-bond) in maintaining the charge of oxhydryl H in the reaction path. The mechanism of H-bond catalysis was further demonstrated by the study of OH* and N* assisted dehydrogenation of OH*. Due to the universality of H-bond, the H-bond catalysis shown here, is of broad implication for studies of reaction kinetics. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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17 pages, 11412 KiB

Open AccessArticle

Phosphine Oxides as Spectroscopic Halogen Bond Descriptors: IR and NMR Correlations with Interatomic Distances and Complexation Energy

by Alexei S. Ostras’, Daniil M. Ivanov, Alexander S. Novikov and Peter M. Tolstoy

Molecules 2020, 25(6), 1406; https://doi.org/10.3390/molecules25061406 - 19 Mar 2020

Cited by 22 | Viewed by 4328

Abstract

An extensive series of 128 halogen-bonded complexes formed by trimethylphosphine oxide and various F-, Cl-, Br-, I- and At-containing molecules, ranging in energy from 0 to 124 kJ/mol, is studied by DFT calculations in vacuum. The results reveal correlations between R–X⋅⋅⋅O=PMe₃ halogen bond energy ΔE, X⋅⋅⋅O distance r, halogen’s σ-hole size, QTAIM parameters at halogen bond critical point and changes of spectroscopic parameters of phosphine oxide upon complexation, such as ³¹P NMR chemical shift, ΔδP, and P=O stretching frequency, Δν. Some of the correlations are halogen-specific, i.e., different for F, Cl, Br, I and At, such as ΔE(r), while others are general, i.e., fulfilled for the whole set of complexes at once, such as ΔE(ΔδP). The proposed correlations could be used to estimate the halogen bond properties in disordered media (liquids, solutions, polymers, glasses) from the corresponding NMR and IR spectra. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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16 pages, 3940 KiB

Open AccessFeature PaperArticle

Adduct under Field—A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding

by Ilya G. Shenderovich and Gleb S. Denisov

Molecules 2020, 25(3), 436; https://doi.org/10.3390/molecules25030436 - 21 Jan 2020

Cited by 20 | Viewed by 6124

Abstract

The location of a mobile proton in acid-base complexes in aprotic solvents can be predicted using a simplified Adduct under Field (AuF) approach, where solute–solvent effects on the geometry of hydrogen bond are simulated using a fictitious external electric field. The parameters of the field have been estimated using experimental data on acid-base complexes in CDF₃/CDClF₂. With some limitations, they can be applied to the chemically similar CHCl₃ and CH₂Cl₂. The obtained data indicate that the solute–solvent effects are critically important regardless of the type of complexes. The temperature dependences of the strength and fluctuation rate of the field explain the behavior of experimentally measured parameters. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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Review

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18 pages, 5749 KiB

Open AccessFeature PaperReview

Hydrogen Bond and Other Lewis Acid–Lewis Base Interactions as Preliminary Stages of Chemical Reactions

by Sławomir J. Grabowski

Molecules 2020, 25(20), 4668; https://doi.org/10.3390/molecules25204668 - 13 Oct 2020

Cited by 25 | Viewed by 4755

Abstract

Various Lewis acid–Lewis base interactions are discussed as initiating chemical reactions and processes. For example, the hydrogen bond is often a preliminary stage of the proton transfer process or the tetrel and pnicogen bonds lead sometimes to the S_N2 reactions. There are numerous characteristics of interactions being first stages of reactions; one can observe a meaningful electron charge transfer from the Lewis base unit to the Lewis acid; such interactions possess at least partly covalent character, one can mention other features. The results of different methods and approaches that are applied in numerous studies to describe the character of interactions are presented here. These are, for example, the results of the Quantum Theory of Atoms in Molecules, of the decomposition of the energy of interaction or of the structure-correlation method. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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31 pages, 9109 KiB

Open AccessReview

Small Molecules, Non-Covalent Interactions, and Confinement

by Gerd Buntkowsky and Michael Vogel

Molecules 2020, 25(14), 3311; https://doi.org/10.3390/molecules25143311 - 21 Jul 2020

Cited by 32 | Viewed by 4435

Abstract

This review gives an overview of current trends in the investigation of small guest molecules, confined in neat and functionalized mesoporous silica materials by a combination of solid-state NMR and relaxometry with other physico-chemical techniques. The reported guest molecules are water, small alcohols, and carbonic acids, small aromatic and heteroaromatic molecules, ionic liquids, and surfactants. They are taken as characteristic role-models, which are representatives for the typical classes of organic molecules. It is shown that this combination delivers unique insights into the structure, arrangement, dynamics, guest-host interactions, and the binding sites in these confined systems, and is probably the most powerful analytical technique to probe these systems. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions)

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