Crystals

Editorial

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5 pages, 230 KiB

Open AccessEditorial

Recent Progress in Theoretical Studies and Computer Modeling of Non-Covalent Interactions

by Alexander S. Novikov

Crystals 2023, 13(2), 361; https://doi.org/10.3390/cryst13020361 - 20 Feb 2023

Cited by 2 | Viewed by 1185

Abstract

It is not at all surprising that the topic of non-covalent interactions, a key pillar of supramolecular chemistry, has seen interest grow enormously within the last decade [...] Full article

(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)

3 pages, 198 KiB

Open AccessEditorial

Theoretical Investigation on Non-Covalent Interactions

by Alexander S. Novikov

Crystals 2022, 12(2), 167; https://doi.org/10.3390/cryst12020167 - 24 Jan 2022

Cited by 1 | Viewed by 2224

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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52 pages, 27214 KiB

Open AccessArticle

Physical and Mathematical Models of Quantum Dielectric Relaxation in Electrical and Optoelectric Elements Based on Hydrogen-Bonded Crystals

by Valeriy Kalytka, Ali Mekhtiyev, Yelena Neshina, Aliya Alkina, Raushan Aimagambetova, Gabit Mukhambetov, Aleksandr Bashirov, Dmitriy Afanasyev, Arkadiy Bilichenko, Dinara Zhumagulova, Zukhra Ismailova and Yelena Senina

Crystals 2023, 13(9), 1353; https://doi.org/10.3390/cryst13091353 - 06 Sep 2023

Viewed by 735

Abstract

The quantum statistical properties of the proton subsystem in hydrogen-bonded crystals (HBC) are investigated. Based on the non-stationary Liouville operator equation (taking into account a number of assumptions established in the experiment), a quantum kinetic equation is constructed for the ensemble of non-interacting [...] Read more.

The quantum statistical properties of the proton subsystem in hydrogen-bonded crystals (HBC) are investigated. Based on the non-stationary Liouville operator equation (taking into account a number of assumptions established in the experiment), a quantum kinetic equation is constructed for the ensemble of non-interacting protons (an ideal proton gas) moving in the crystal potential image perturbed by the external electric field. The balanced density matrix for the unperturbed proton subsystem is constructed using the quantum canonical Gibbs distribution, and the non-balanced density matrix is calculated from the solutions of the nonlinear quantum kinetic equation by methods in linear approximation of perturbation theory for the blocking electrode model. Full quantum mechanical averaging of the polarization operator makes it possible to study the theoretical frequency-temperature spectra of the complex dielectric permittivity (CDP) calculated using quantum relaxation parameters that differ significantly from their semiclassical counterparts. A scheme is presented for an analytical study of the dielectric loss tangent in the region of quantum nonlinear relaxation in HBC. The results obtained in the given paper are of scientific interest in developing the theoretical foundations of proton conduction processes in energy-independent memory elements (with anomalously high residual polarization) based on thin films of ferroelectric materials in the ultralow temperature range (1–10 K). The theoretical results obtained have a direct application to the study of the tunneling mechanisms of spontaneous polarization in ferroelectric HBC with a rectangular hysteresis loop, in particular in crystals of potassium dideutrophosphate (KDP), widely used in nonlinear optics and laser technology. The quantum properties of proton relaxation in HBC can be applied in the future to the study of solid-state electrolytes with high proton conductivity for hydrogen energy, capacitor technology (superionics, varicodes), and elements of MIS and MSM structures in the development of resonant tunnel diodes for microelectronics and computer technology. Full article

(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)

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15 pages, 2207 KiB

Open AccessArticle

Assessing the Possibility and Properties of Types I and II Chalcogen Bonds

by Steve Scheiner

Crystals 2023, 13(5), 766; https://doi.org/10.3390/cryst13050766 - 04 May 2023

Cited by 2 | Viewed by 1234

Abstract

Type I and II halogen bonds are well-recognized motifs that commonly occur within crystals. Quantum calculations are applied to examine whether such geometries might occur in their closely related chalcogen bond cousins. Homodimers are constructed of the R1R2C=Y and R1R2Y monomers, wherein Y [...] Read more.

Type I and II halogen bonds are well-recognized motifs that commonly occur within crystals. Quantum calculations are applied to examine whether such geometries might occur in their closely related chalcogen bond cousins. Homodimers are constructed of the R1R2C=Y and R1R2Y monomers, wherein Y represents a chalcogen atom, S, Se, or Te; R1 and R2 refer to either H or F. A Type II (T2) geometry wherein the lone pair of one Y is closely aligned with a σ-hole of its partner represents a stable arrangement for all except YH2, although not all such structures are true minima. The symmetric T1 geometry in which each Y atom serves as both electron donor and acceptor in the chalcogen bond is slightly higher in energy for R1R2C=Y, but the reverse is true for R1R2Y. Due to their deeper σ-holes, the latter molecules engage in stronger chalcogen bonds than do the former, with the exception of H2Y, whose dimers are barely bound. The interaction energies rise as the Y atom grows larger: S < Se < Te. Full article

(This article belongs to the Special Issue Theoretical Investigation on Non-covalent Interactions)

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13 pages, 3494 KiB

Open AccessArticle

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

by Chien-Lin Lee, Tai-Chao Chang and Chia Ming Chang

Crystals 2023, 13(2), 266; https://doi.org/10.3390/cryst13020266 - 03 Feb 2023

Cited by 1 | Viewed by 1678

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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13 pages, 2793 KiB

Open AccessArticle

Computational Studies on the Interaction of Organophosphorus Pesticides with Acetylcholinesterase and Butyrylcholinesterase: Quantum Chemical Cluster Model and HSAB Approaches

by Shu-Chun Chi and Chia Ming Chang

Crystals 2023, 13(1), 153; https://doi.org/10.3390/cryst13010153 - 16 Jan 2023

Viewed by 1661

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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10 pages, 2180 KiB

Open AccessArticle

Bifurcated Halogen Bond-Driven Supramolecular Double Helices from 1,2-Dihalotetrafluorobenzene and 2,2′-Bi(1,8-naphthyridine)

by Ziyu Wang

Crystals 2022, 12(7), 937; https://doi.org/10.3390/cryst12070937 - 02 Jul 2022

Cited by 1 | Viewed by 1641

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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15 pages, 2669 KiB

Open AccessArticle

Hydrogen Bonds in Precursor Solution: The Origin of the Anomalous J–V Curves in Perovskite Solar Cells

by Lin Zhang, Lin Yao, Yanfang Chu, Lei Zhao, Hongmei Zhao, Yuchen Sun, Jing Li and Junjie He

Crystals 2022, 12(5), 610; https://doi.org/10.3390/cryst12050610 - 26 Apr 2022

Cited by 1 | Viewed by 1838

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 J–V 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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14 pages, 2879 KiB

Open AccessArticle

π-Hole Tetrel Bonds—Lewis Acid Properties of Metallylenes

by Sławomir J. Grabowski

Crystals 2022, 12(1), 112; https://doi.org/10.3390/cryst12010112 - 15 Jan 2022

Cited by 17 | Viewed by 1609

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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11 pages, 2726 KiB

Open AccessArticle

The Crystal Structure Elucidation of a Tetrapeptide Analog of Somatostatin DOTA-Phe-D-Trp-Lys-Thr-OMe

by Sabina Diusenova, Sergey Arkhipov, Dmitry Avdeev, Pavel Dorovatovskii, Derenik Khachatryan, Vladimir Lazarenko, Michael Medvedev, Alena Nikolaeva, Mikhail Ovchinnikov, Maria Sidorova and Yan Zubavichus

Crystals 2022, 12(1), 12; https://doi.org/10.3390/cryst12010012 - 22 Dec 2021

Cited by 1 | Viewed by 2978

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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19 pages, 3273 KiB

Open AccessArticle

Synthesis, Structure and Evaluation of the N-(2-Acetyl-4-(styryl)phenyl)-4-benzenesulfonamide Derivatives for Anticholinesterase and Antioxidant Activities

by Malose J. Mphahlele, Samantha Gildenhuys and Sizwe J. Zamisa

Crystals 2021, 11(4), 341; https://doi.org/10.3390/cryst11040341 - 28 Mar 2021

Cited by 4 | Viewed by 2133

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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13 pages, 1814 KiB

Open AccessReview

Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins

by Sonia Khemaissa, Sandrine Sagan and Astrid Walrant

Crystals 2021, 11(9), 1032; https://doi.org/10.3390/cryst11091032 - 27 Aug 2021

Cited by 38 | Viewed by 12050

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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