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Special Issue "Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions"

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

Deadline for manuscript submissions: 30 September 2020.

Special Issue Editor

Dr. Ilya G. Shenderovich
Website
Guest Editor
Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg, Germany
Interests: noncovalent interactions; H-bond; soft matter; surface; porous materials; NMR

Special Issue Information

“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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

 

Planned Papers
Title: Noncovalent Interactions in Prison

Author: Gerd Buntkowsky

Affiliation: Technische Universität Darmstadt, Garmany

 

Title: Noncovalent Interactions as Preliminary Stages of Chemical Reactions

Author: Slawomir Grabowski

Affiliation: UPV/EHU and DIPC - Donostia International Physics Center, Spain

 

Title: The multiscale simulation of monoaminergic system in conjunction with an experiment

Author: Janez Mavri (a), Mojca Kržan (b), Robert Vianello (c) 

Affiliation:

(a) National Institute of Chemistry, Slovenia

(b) University of Ljubljana, Slovenia

(c) Ruđer Bošković Institute, Croatia

 

Title: Interplay between substituent effect, hydrogen bonding and aromaticity in adenine-uracil and adenine-adenine base pairs

Author: Paweł A. Wieczorkiewicz (a), Halina Szatylowicz (a)*, Tadeusz M. Krygowski (b)

Affiliation: 

(a) Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
(b) Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland

 

Published Papers (4 papers)

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Research

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
Molecules 2020, 25(10), 2386; https://doi.org/10.3390/molecules25102386 - 21 May 2020
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 [...] Read more.
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 Elatt. These crystals consist of closed-shell organic ions interacting through relatively strong hydrogen bonds, which leads to Elatt > 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 Elatt 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
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Open AccessArticle
Catalytic Effect of Hydrogen Bond on Oxhydryl Dehydrogenation in Methanol Steam Reforming on Ni(111)
Molecules 2020, 25(7), 1531; https://doi.org/10.3390/molecules25071531 - 27 Mar 2020
Abstract
Dehydrogenation of H3COH and H2O are key steps of methanol steam reforming on transition metal surfaces. Oxhydryl dehydrogenation reactions of HxCOH (x = 0–3) and OH on Ni (111) were investigated by DFT calculations with the [...] Read more.
Dehydrogenation of H3COH and H2O are key steps of methanol steam reforming on transition metal surfaces. Oxhydryl dehydrogenation reactions of HxCOH (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 HxCOH* 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
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Open AccessArticle
Phosphine Oxides as Spectroscopic Halogen Bond Descriptors: IR and NMR Correlations with Interatomic Distances and Complexation Energy
Molecules 2020, 25(6), 1406; https://doi.org/10.3390/molecules25061406 - 19 Mar 2020
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 [...] Read more.
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 ΔEδP). 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
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Open AccessFeature PaperArticle
Adduct under Field—A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding
Molecules 2020, 25(3), 436; https://doi.org/10.3390/molecules25030436 - 21 Jan 2020
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 [...] Read more.
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
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