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Structure, Energy and Dynamics of Molecular Interactions

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 5154

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Department of Chemistry and Center for Nanoscience and Nanotechnology, National Sun Yat-sen University, 70 Lien-Hai Road, Kaohsiung, Taiwan
Interests: physical chemistry of materials and biophysical chemistry; nuclear magnetic resonance spectroscopy and imaging; quantum mechanics and molecular dynamics simulation
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Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
Interests: study of molecules and their interactions by spectroscopic methods; unsaturated carbocations
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

From the development of a new material for mobile phone screens, photovoltaic plates or fuel cells to understanding of the etiology of a disease, the pharmacology of a drug, or the action mechanism of a drug delivery system, intermolecular interactions often play an essential role. Compared to intramolecular interactions, intermolecular interactions involve a higher level of complexity, and they generally are far less tractable and more challenging. In addition, intermolecular interactions bring more diverse and more complex dynamics. Consequently, their relationship with the property and function is much harder to pinpoint and often ambiguous. Both the experimental methodologies and theoretical arsenal need to be extended and upgraded. On the other hand, however, with a much larger parameter space, intermolecular interactions provide abundant and unique opportunities for scientists to explore, manipulate, optimize, and diversify their systems of interest. This Special Issue collects papers on the investigation of intermolecular interactions in various systems in chemistry, biology, materials science, and other fields, reporting new experimental and theoretical findings and advances in experimental techniques, theoretical methods, as well as numerical modeling. While this Special Issue emphasizes conclusive, clear-cut, original, and illuminating insights, it also welcomes provocative and intriguing new results. Articles of both experimental and theoretical research and critical reviews are to be considered.

Dr. Shangwu Ding
Prof. Dr. Evgenii Stoyanov
Guest Editors

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Published Papers (3 papers)

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Research

7 pages, 1354 KiB  
Communication
Spontaneous Transition of Alkyl Carbocations to Unsaturated Vinyl-Type Carbocations in Organic Solutions
by Evgenii S. Stoyanov and Irina V. Stoyanova
Int. J. Mol. Sci. 2023, 24(2), 1802; https://doi.org/10.3390/ijms24021802 - 16 Jan 2023
Cited by 2 | Viewed by 1322
Abstract
It was found that alkyl carbocations, when their salts are dissolved in common organochlorine solvents, decompose to unsaturated vinyl-type carbocations that are stabler in solutions. This is a convenient method for obtaining salts of vinyl cations and their solutions for further research. Full article
(This article belongs to the Special Issue Structure, Energy and Dynamics of Molecular Interactions)
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26 pages, 9979 KiB  
Article
Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry
by Barbora Stratilová, Eva Stratilová, Maria Hrmova and Stanislav Kozmon
Int. J. Mol. Sci. 2022, 23(19), 11838; https://doi.org/10.3390/ijms231911838 - 5 Oct 2022
Cited by 2 | Viewed by 1593
Abstract
Xyloglucan endotransglycosylases (XETs) play key roles in the remodelling and reconstruction of plant cell walls. These enzymes catalyse homo-transglycosylation reactions with xyloglucan-derived donor and acceptor substrates and hetero-transglycosylation reactions with a variety of structurally diverse polysaccharides. In this work, we describe the basis [...] Read more.
Xyloglucan endotransglycosylases (XETs) play key roles in the remodelling and reconstruction of plant cell walls. These enzymes catalyse homo-transglycosylation reactions with xyloglucan-derived donor and acceptor substrates and hetero-transglycosylation reactions with a variety of structurally diverse polysaccharides. In this work, we describe the basis of acceptor substrate binding specificity in non-specific Tropaeolum majus (TmXET6.3) and specific Populus tremula x tremuloides (PttXET16A) XETs, using molecular docking and molecular dynamics (MD) simulations combined with binding free energy calculations. The data indicate that the enzyme-donor (xyloglucan heptaoligosaccharide or XG-OS7)/acceptor complexes with the linear acceptors, where a backbone consisted of glucose (Glc) moieties linked via (1,4)- or (1,3)-β-glycosidic linkages, were bound stably in the active sites of TmXET6.3 and PttXET16A. Conversely, the acceptors with the (1,6)-β-linked Glc moieties were bound stably in TmXET6.3 but not in PttXET16A. When in the (1,4)-β-linked Glc containing acceptors, the saccharide moieties were replaced with mannose or xylose, they bound stably in TmXET6.3 but lacked stability in PttXET16A. MD simulations of the XET-donor/acceptor complexes with acceptors derived from (1,4;1,3)-β-glucans highlighted the importance of (1,3)-β-glycosidic linkages and side chain positions in the acceptor substrates. Our findings explain the differences in acceptor binding specificity between non-specific and specific XETs and associate theoretical to experimental data. Full article
(This article belongs to the Special Issue Structure, Energy and Dynamics of Molecular Interactions)
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21 pages, 7184 KiB  
Article
The Chloronium Cation [(C2H3)2Cl+] and Unsaturated C4-Carbocations with C=C and C≡C Bonds in Their Solid Salts and in Solutions: An H1/C13 NMR and Infrared Spectroscopic Study
by Evgenii S. Stoyanov and Irina V. Stoyanova
Int. J. Mol. Sci. 2022, 23(16), 9111; https://doi.org/10.3390/ijms23169111 - 14 Aug 2022
Cited by 3 | Viewed by 1673
Abstract
Solid salts of the divinyl chloronium (C2H3)2Cl+ cation (I) and unsaturated C4H6Cl+ and C4H7+ carbocations with the highly stable CHB11Hal11 anion [...] Read more.
Solid salts of the divinyl chloronium (C2H3)2Cl+ cation (I) and unsaturated C4H6Cl+ and C4H7+ carbocations with the highly stable CHB11Hal11 anion (Hal=F, Cl) were obtained for the first time. At 120 °C, the salt of the chloronium cation decomposes, yielding a salt of the C4H5+ cation. This thermally stable (up to 200 °C) carbocation is methyl propargyl, CH≡C-C+-H-CH3 (VI), which, according to quantum chemical calculations, should be energetically much less favorable than other isomers of the C4H7+ cations. Cation VI readily attaches HCl to the formal triple C≡C bond to form the CHCl=CH-C+H-CH3 cation (VII). In infrared spectra of cations I, VI, and VII, frequencies of C=C and C≡C stretches are significantly lower than those predicted by calculations (by 400–500 cm−1). Infrared and 1H/13C magic-angle spinning NMR spectra of solid salts of cations I and VI and high-resolution 1H/13C NMR spectra of VII in solution in SO2ClF were interpreted. On the basis of the spectroscopic data, the charge and electron density distribution in the cations are discussed. Full article
(This article belongs to the Special Issue Structure, Energy and Dynamics of Molecular Interactions)
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