Special Issue "Theoretical Investigation on Non-covalent Interactions"

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Crystal Engineering".

Deadline for manuscript submissions: 25 May 2023 | Viewed by 12929

Special Issue Editors

Dr. Alexander S. Novikov
E-Mail Website
Guest Editor
1. Institute of Chemistry, Saint Petersburg State University, Universitetsky pr., 26, 198504 Stary Petergof, Russia
2. Infochemistry Scientific Center, ITMO University, Lomonosova st., 9, 191002 Saint Petersburg, Russia
Interests: non-covalent interactions; computational chemistry; computer modelling; reaction mechanisms; data science; artificial intelligence
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Longjiu Cheng
E-Mail Website
Guest Editor
Computational chemistry, Anhui University, Hefei 230093, China
Interests: non-covalent Interaction; theoretical and computational chemistry

Special Issue Information

Dear Colleagues,

The problem of non-covalent interactions in crystals is one of the paradigms for computer modelling and theoretical studies in chemistry and related fields of knowledge (crystallography, biology, physics, mathematics, and computer science). Modern methods of data science, artificial intelligence, and quantum and computational chemistry are widely used for the investigation of nature and various properties of different non-covalent interactions (hydrogen, halogen, chalcogen, pnictogen, tetrel, and semi-coordination bonds; agosic and anagosic interactions; stacking, anion/cation–π interactions; metallophilic interactions, etc.).

Our Special Issue welcomes contributions from researchers focused on this subject to highlight and overview modern trends and attract the attention of the scientific community to the problem of theoretical investigation on non-covalent interactions.

All types of papers (reviews, full papers, communications, technical notes, highlights, etc.) are welcome for consideration.

Dr. Alexander S. Novikov
Prof. Dr. Longjiu Cheng
Guest Editors

Manuscript Submission Information

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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. Crystals is an international peer-reviewed open access monthly 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

  • non-covalent interactions
  • computer modeling
  • computational chemistry
  • data science
  • crystal engineering

Published Papers (9 papers)

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Editorial

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Editorial
Theoretical Investigation on Non-Covalent Interactions
Crystals 2022, 12(2), 167; https://doi.org/10.3390/cryst12020167 - 24 Jan 2022
Viewed by 1321
Abstract
This editorial is dedicated to announcing the Special Issue “Theoretical investigation on non-covalent interactions” of Crystals. The Special Issue covers the most recent progress in the rapidly growing fields of data science, artificial intelligence, and quantum and computational chemistry in topics relevant [...] Read more.
This editorial is dedicated to announcing the Special Issue “Theoretical investigation on non-covalent interactions” of Crystals. The Special Issue covers the most recent progress in the rapidly growing fields of data science, artificial intelligence, and quantum and computational chemistry in topics relevant to the problem of theoretical investigation on non-covalent interactions (including, but not limited to, hydrogen, halogen, chalcogen, pnictogen, tetrel, and semi-coordination bonds; agosic and anagosic interactions; stacking, anion-/cation–π interactions; metallophilic interactions, etc.). The main successes of my colleagues and I in the field of fundamental theoretical studies of non-covalent interactions in various chemical compounds over the past year are briefly highlighted. Full article
(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)

Research

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Article
Quantum Chemical Studies on the Adsorption of Hexachlorobenzene, Decachlorobiphenyl, Benzene, and Biphenyl by BN-Doped Graphene and C-Doped Hexagonal Boron Nitride Modified with β-Cyclodextrin
Crystals 2023, 13(2), 266; https://doi.org/10.3390/cryst13020266 - 03 Feb 2023
Viewed by 134
Abstract
In this study, the adsorption of aromatic organic pollutants such as hexachlorobenzene, decachlorobiphenyl, benzene, and biphenyl by 2D nanomaterials was investigated using quantum chemical methods. The calculation results include reaction enthalpies, non-covalent intermolecular and intramolecular interactions, optimized structures, hydrogen bonds, and molecular electrostatic [...] Read more.
In this study, the adsorption of aromatic organic pollutants such as hexachlorobenzene, decachlorobiphenyl, benzene, and biphenyl by 2D nanomaterials was investigated using quantum chemical methods. The calculation results include reaction enthalpies, non-covalent intermolecular and intramolecular interactions, optimized structures, hydrogen bonds, and molecular electrostatic potentials. Fukui’s FMO electrophile sensitivity is used to predict the most reactive positions on the chemical species for both nucleophilic and electrophilic roles. The results of hard–soft acid-base reactivity descriptors show that the electronic structures of BN-doped graphene and C-doped hexagonal boron nitride depend on the degree of doping and the modification of β-cyclodextrin. C doping helps to significantly improve the conductivity of h-BN, and β-cyclodextrin enhances the binding stability of aromatic organic pollutants. Hydrogen bonding between β-cyclodextrin and chlorine-substituted compounds can enhance non-covalent interactions. In particular, the high adsorption capacity and electron transfer capacity of decachlorobiphenyl laid the foundation for the development of new sensors. Full article
(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)
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Article
Computational Studies on the Interaction of Organophosphorus Pesticides with Acetylcholinesterase and Butyrylcholinesterase: Quantum Chemical Cluster Model and HSAB Approaches
Crystals 2023, 13(1), 153; https://doi.org/10.3390/cryst13010153 - 16 Jan 2023
Viewed by 402
Abstract
In the present study, the interaction between organophosphorus pesticides and cholinesterase enzymes was investigated by quantum chemical cluster model and hard-soft acid-base (HSAB) approaches. The computational results of the equilibrium structure and reaction enthalpy were used to decipher the mechanism of organophosphorus pesticides [...] Read more.
In the present study, the interaction between organophosphorus pesticides and cholinesterase enzymes was investigated by quantum chemical cluster model and hard-soft acid-base (HSAB) approaches. The computational results of the equilibrium structure and reaction enthalpy were used to decipher the mechanism of organophosphorus pesticides coumaphos, dicrotophos, phorate, and terbufos, which interacted with the molecular cluster models of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes. In addition, the HOMO-LUMO energy gap and the HSAB descriptors prove that AChE has outstanding electron acceptability, which is suitable as a biosensing material. In terms of the calculated electronic spectrum, because the energy level of the ground state and the excited state are changed after adding pesticides with enzymes, a significant red shift phenomenon will occur. Full article
(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)
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Article
Bifurcated Halogen Bond-Driven Supramolecular Double Helices from 1,2-Dihalotetrafluorobenzene and 2,2′-Bi(1,8-naphthyridine)
Crystals 2022, 12(7), 937; https://doi.org/10.3390/cryst12070937 - 02 Jul 2022
Cited by 1 | Viewed by 944
Abstract
The unique enantiomeric pairs of double helices have been found in the structure of the cocrystal between 1,2-diiodotetrafluorobenzene and 2,2′-bi(1,8-naphthyridine). The formation of the supramolecular double helices is driven by the strong bifurcated iodine bonds which can force the herringbone packing arrangement of [...] Read more.
The unique enantiomeric pairs of double helices have been found in the structure of the cocrystal between 1,2-diiodotetrafluorobenzene and 2,2′-bi(1,8-naphthyridine). The formation of the supramolecular double helices is driven by the strong bifurcated iodine bonds which can force the herringbone packing arrangement of the molecules 2,2′-bi(1,8-naphthyridine) into a face-to-face π···π stacking pattern. In contrast, the cocrystal between 1,2-dibromotetrafluorobenzene (or 1,2-dichlorotetrafluorobenzene) and 2,2′-bi(1,8-naphthyridine) was not obtained under the same conditions. The interaction energies of the bifurcated halogen bonds and π···π stacking interactions were computed with the reliable dispersion-corrected density functional theory. The computational results show that the bifurcated iodine bond is much stronger than the bifurcated bromine bond and bifurcated chlorine bond, and it is the much stronger bifurcated iodine bond that makes the cocrystal of 1,2-diiodotetrafluorobenzene and 2,2′-bi(1,8-naphthyridine) much easier to be synthesized. Full article
(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)
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Article
Hydrogen Bonds in Precursor Solution: The Origin of the Anomalous JV Curves in Perovskite Solar Cells
Crystals 2022, 12(5), 610; https://doi.org/10.3390/cryst12050610 - 26 Apr 2022
Cited by 1 | Viewed by 1022
Abstract
Perovskite Solar Cells are a promising solar energy harvesting technology due to their low cost and high-power conversion efficiency. A high-quality perovskite layer is fundamental for a highly efficient perovskite Solar Cell. Utilizing a gas quenching process (GQP) can eliminate the need for [...] Read more.
Perovskite Solar Cells are a promising solar energy harvesting technology due to their low cost and high-power conversion efficiency. A high-quality perovskite layer is fundamental for a highly efficient perovskite Solar Cell. Utilizing a gas quenching process (GQP) can eliminate the need for toxic, flammable, and expensive anti-solvents in the preparation of perovskite layers. It is a promising candidate technology for large scale preparation of perovskite layers, as it can be easily integrated in a production line by coupling up-scalable techniques. The GQP removes the need for polar solvents in the precursor solution layer by using nitrogen flow, rather than extracting them with non-polar solvents. The crystallization dynamics in this process can be significantly different. In this study, we found that the quality of perovskite crystal from GQP is much more sensitive to Lewis base molecules (LBMs) in the precursor solution than it is in anti-solvents technology. Thus, the processing parameters of the LBMs in anti-solvents technology cannot be directly transferred to the GQP. An XRD and 1H NMR study explains the origin of the S-shaped JV curves and how these LBMs hinder the reaction between PbI2 and monovelent cations. Full article
(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)
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Article
π-Hole Tetrel Bonds—Lewis Acid Properties of Metallylenes
Crystals 2022, 12(1), 112; https://doi.org/10.3390/cryst12010112 - 15 Jan 2022
Cited by 3 | Viewed by 710
Abstract
The MP2/aug-cc-pVTZ calculations were performed on the dihalometallylenes to indicate their Lewis acid and Lewis base sites. The results of the Cambridge Structural Database search show corresponding and related crystal structures where the tetrel center often possesses the configuration of a trigonal bipyramid [...] Read more.
The MP2/aug-cc-pVTZ calculations were performed on the dihalometallylenes to indicate their Lewis acid and Lewis base sites. The results of the Cambridge Structural Database search show corresponding and related crystal structures where the tetrel center often possesses the configuration of a trigonal bipyramid or octahedron. The calculations were also carried out on dimers of dichlorogermylene and dibromogermylene and on complexes of these germylenes with one and two 1,4-dioxide molecules. The Ge⋯Cl, Ge⋯Br, and Ge⋯O interactions are analyzed. The Ge⋯O interactions in the above mentioned germylene complexes may be classified as the π-hole tetrel bonds. The MP2 calculations are supported by the results of the Quantum Theory of Atoms in Molecules (QTAIM) and the Natural Bond Orbital (NBO) approaches. Full article
(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)
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Article
The Crystal Structure Elucidation of a Tetrapeptide Analog of Somatostatin DOTA-Phe-D-Trp-Lys-Thr-OMe
Crystals 2022, 12(1), 12; https://doi.org/10.3390/cryst12010012 - 22 Dec 2021
Viewed by 1880
Abstract
Herewith, we report for the first time the crystal structure of tetrapeptide FwKT (Phe-D-Trp-Lys-Thr), which is considered to represent an epitope for biomedically relevant hormone somatostatin. The target molecule was successfully crystalized, solved and refined as a conjugate of the tetrapeptide moiety bearing [...] Read more.
Herewith, we report for the first time the crystal structure of tetrapeptide FwKT (Phe-D-Trp-Lys-Thr), which is considered to represent an epitope for biomedically relevant hormone somatostatin. The target molecule was successfully crystalized, solved and refined as a conjugate of the tetrapeptide moiety bearing a protective group DOTA at the N-terminus and methylated at the O-terminus. The combination of a hormone active site and a powerful chelator make the substance a highly prospective targeted drug delivery system, especially for peptide receptor radionuclide therapy (PRRT) applications. Full article
(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)
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Article
Synthesis, Structure and Evaluation of the N-(2-Acetyl-4-(styryl)phenyl)-4-benzenesulfonamide Derivatives for Anticholinesterase and Antioxidant Activities
Crystals 2021, 11(4), 341; https://doi.org/10.3390/cryst11040341 - 28 Mar 2021
Cited by 3 | Viewed by 1275
Abstract
N-(2-Acetyl-4-bromophenyl)-4-methylbenzenesulfonamide (2) was transformed into 5-(4-methoxymethylstyryl)-2-(p-tolylsulfonamido)acetophenone (3a) and 5-(4- trifluoromethylstyryl)-2-(p-tolylsulfonamido)acetophenone (3b). Their structures were determined using a combination of NMR (1H & 13C) and mass spectroscopic as well as [...] Read more.
N-(2-Acetyl-4-bromophenyl)-4-methylbenzenesulfonamide (2) was transformed into 5-(4-methoxymethylstyryl)-2-(p-tolylsulfonamido)acetophenone (3a) and 5-(4- trifluoromethylstyryl)-2-(p-tolylsulfonamido)acetophenone (3b). Their structures were determined using a combination of NMR (1H & 13C) and mass spectroscopic as well as single crystal X-ray diffraction techniques. These compounds and the corresponding precursor, 2-amino-5-bromoacetophenone (1), were evaluated through enzymatic assays in vitro for inhibitory effect against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) activities as well as antioxidant effect through the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and nitric oxide (NO) free radical scavenging assays. Molecular docking was performed on 3a to determine plausible protein–ligand interactions on a molecular level. Their drug likeness properties (absorption, distribution, metabolism, and excretion) and ability to cross the blood–brain barrier (BBB) have also been predicted at theoretical level. Full article
(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)
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Review

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Review
Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins
Crystals 2021, 11(9), 1032; https://doi.org/10.3390/cryst11091032 - 27 Aug 2021
Cited by 14 | Viewed by 4534
Abstract
Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic [...] Read more.
Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners. Full article
(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)
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