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Simple Substances of Non-metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 16137

Special Issue Editor

Prof. Dr. Oleg V. Mikhailov

E-Mail Website
Guest Editor
Department of Analytical Chemistry, National Research Technological University, K. Marx Street 68, 420015 Kazan, Russia
Interests: coordination chemistry; quantum chemistry; chemistry of macrocyclic compounds; nanosciences; scientometrics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Simple substances formed by p-elements–non-metals have attracted the attention of scientists from different areas even before the formation of chemistry as a science occurred. Despite the relative simplicity of their chemical composition, and sometimes molecular and crystal structures, they have a number of specific (sometimes unique) properties, owing to which they have found many applications in various branches of science and practice of anthropogenic activity. Suffice it to mention in this connection such allotropic modifications of carbon as graphite and diamond (already known in ancient times), carbyne, fullerenes, and nanotubes (which became known already at the turn of the 20th/21st centuries). Despite the incredibly significant achievements in this field of chemical science, there are still many questions, and first of all, the possibility of the existence of new, unknown to science, polynuclear simple substances formed by both carbon and atoms of other p-elements, primarily nitrogen, phosphorus, oxygen, and sulfur. In this context, it becomes important to predict both the possibility of their existence and the determination of the quantitative parameters of their molecular and/or crystal structures that determine their physicochemical properties. This problem, as is known, is currently being successfully solved owing to the availability of both modern quantum-chemical methods of calculation (and, first of all, the density functional theory (DFT) method), and computer technologies and corresponding experimental techniques. At the same time, theoretical works devoted to quantum-chemical calculations of the above simple substances both via the DFT method and more advanced methods are still relatively few in the literature.

This Special Issue aims to include mainly original full articles and short messages devoted to quantum-chemical calculations of the molecular structures of polynuclear simple substances formed by non-metals of p-elements (both neutral and polynuclear monoelement cations and anions). This mainly concerns polynuclear simple substances formed by carbon atoms, nitrogen, phosphorus, oxygen and sulfur; however, articles devoted to polynuclear simple substances and of other non-metallic elements (boron, silicon, arsenic, etc.) can also be submitted for publication in this Special Issue. We welcome articles in which, along with the required quantum-chemical calculations, experimental data will also be presented to evaluate the reliability of these calculations. Review articles may also be submitted for publication in this Special Issue (including author reviews, the emphasis of which is mainly on the work of their authors).

Prof. Dr. Oleg V. Mikhailov
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 submissions that pass pre-check are 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • simple substance
  • p-element
  • carbon
  • nitrogen
  • oxygen
  • phosphorus
  • sulfur
  • quantum-chemical modeling
  • DFT

Published Papers (8 papers)

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Editorial

Jump to: Research, Review

3 pages, 462 KiB  
Editorial
Preface from the Guest Editor of Special Issue “Simple Substances of Non-Metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry”
by Oleg V. Mikhailov
Int. J. Mol. Sci. 2021, 22(2), 815; https://doi.org/10.3390/ijms22020815 - 15 Jan 2021
Cited by 1 | Viewed by 1262
Abstract
According to the traditional definition of the concept of “simple substance” adopted in chemistry, it is as a chemical compound, the structural unit of which (molecule, ion, radical, the link of the polymer chain, the unit cell of the crystal lattice, etc [...] [...] Read more.
According to the traditional definition of the concept of “simple substance” adopted in chemistry, it is as a chemical compound, the structural unit of which (molecule, ion, radical, the link of the polymer chain, the unit cell of the crystal lattice, etc [...] Full article
(This article belongs to the Special Issue Simple Substances of Non-metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry)

Research

Jump to: Editorial, Review

15 pages, 11340 KiB  
Article
The Accuracy of Semi-Empirical Quantum Chemistry Methods on Soot Formation Simulation
by Yang Cong, Yu Zhai, Xin Chen and Hui Li
Int. J. Mol. Sci. 2022, 23(21), 13371; https://doi.org/10.3390/ijms232113371 - 02 Nov 2022
Cited by 1 | Viewed by 2693
Abstract
Soot molecules are hazardous compounds threatening human health. Computational chemistry provides efficient tools for studying them. However, accurate quantum chemistry calculation is costly for the simulation of large-size soot molecules and high-throughput calculations. Semi-empirical (SE) quantum chemistry methods are optional choices for balancing [...] Read more.
Soot molecules are hazardous compounds threatening human health. Computational chemistry provides efficient tools for studying them. However, accurate quantum chemistry calculation is costly for the simulation of large-size soot molecules and high-throughput calculations. Semi-empirical (SE) quantum chemistry methods are optional choices for balancing computational costs. In this work, we validated the performances of several widely used SE methods in the description of soot formation. Our benchmark study focuses on, but is not limited to, the validation of the performances of SE methods on reactive and non-reactive MD trajectory calculations. We also examined the accuracy of SE methods of predicting soot precursor structures and energy profiles along intrinsic reaction coordinate(s) (IRC). Finally, we discussed the spin density predicted by SE methods. The SE methods validated include AM1, PM6, PM7, GFN2-xTB, DFTB2, with or without spin-polarization, and DFTB3. We found that the shape of MD trajectory profiles, the relative energy, and molecular structures predicted by SE methods are qualitatively correct. We suggest that SE methods can be used in massive reaction soot formation event sampling and primary reaction mechanism generation. Yet, they cannot be used to provide quantitatively accurate data, such as thermodynamic and reaction kinetics ones. Full article
(This article belongs to the Special Issue Simple Substances of Non-metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry)
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21 pages, 7821 KiB  
Article
Virtual Vibrational Analytics of Reduced Graphene Oxide
by Elena F. Sheka and Nadezhda A. Popova
Int. J. Mol. Sci. 2022, 23(13), 6978; https://doi.org/10.3390/ijms23136978 - 23 Jun 2022
Cited by 6 | Viewed by 1308
Abstract
The digital twin concept lays the foundation of the virtual vibrational analytics suggested in the current paper. The latter presents extended virtual experiments aimed at determining the specific features of the optical spectra of the studied molecules that provide reliable express analysis of [...] Read more.
The digital twin concept lays the foundation of the virtual vibrational analytics suggested in the current paper. The latter presents extended virtual experiments aimed at determining the specific features of the optical spectra of the studied molecules that provide reliable express analysis of the body spatial structure and chemical content. Reduced graphene oxide was selected as the virtual experiment goal. A set of nanosize necklaced graphene molecules, based on the same graphene domain but differing by the necklace contents, were selected as the relevant DTs. As shown, the Raman spectra signatures contained information concerning the spatial structure of the graphene domains, while the molecule necklaces were responsible for the IR spectra. Suggested sets of general frequency kits facilitate the detailed chemical analysis. Express analysis of a shungite carbon, composed of rGO basic structural units, revealed the high ability of the approach. Full article
(This article belongs to the Special Issue Simple Substances of Non-metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry)
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14 pages, 3622 KiB  
Article
Twelve-Nitrogen-Atom Cyclic Structure Stabilized by 3d-Element Atoms: Quantum Chemical Modeling
by Oleg V. Mikhailov and Denis V. Chachkov
Int. J. Mol. Sci. 2022, 23(12), 6560; https://doi.org/10.3390/ijms23126560 - 12 Jun 2022
Cited by 2 | Viewed by 1394
Abstract
Using various versions of density functional theory (DFT), DFT M06/TZVP, DFT B3PW91/TZVP, DFT OPBE/TZVP, and, partially, the MP2 method, the possibility of the existence of 3d-element (M) compounds with nitrogen having unusual M: nitrogen ratio 1:12, unknown for these elements at [...] Read more.
Using various versions of density functional theory (DFT), DFT M06/TZVP, DFT B3PW91/TZVP, DFT OPBE/TZVP, and, partially, the MP2 method, the possibility of the existence of 3d-element (M) compounds with nitrogen having unusual M: nitrogen ratio 1:12, unknown for these elements at the present, was shown. Structural parameter data were presented. It was shown that all MN4 groupings have tetragonal-pyramidal structure. It was noted that the bond lengths formed by nitrogen atoms and an M atom were equal to each other only in the case of M = Ti, V, Cr and Co, whereas for other Ms, they were slightly different; moreover, the bond angles formed by nitrogen atoms and an M atom were equal to 90.0°, or practically did not differ from this value. Thermodynamic parameters, NBO analysis data and HOMO/LUMO images for this compound were also presented. Good agreement between the calculated data obtained using the above three quantum chemical methods was also noted. Full article
(This article belongs to the Special Issue Simple Substances of Non-metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry)
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11 pages, 1373 KiB  
Article
DFT Quantum-Chemical Calculation of Thermodynamic Parameters and DSC Measurement of Thermostability of Novel Benzofuroxan Derivatives Containing Triazidoisobutyl Fragments
by Elena Chugunova, Timur Shaekhov, Ayrat Khamatgalimov, Vladimir Gorshkov and Alexander Burilov
Int. J. Mol. Sci. 2022, 23(3), 1471; https://doi.org/10.3390/ijms23031471 - 27 Jan 2022
Cited by 2 | Viewed by 1789
Abstract
New derivatives of benzofuroxan containing triazidoisobutyl fragments, opening the way for the creation of highly effective compositions with an increased value of energy characteristics, were synthesized for the first time. Such compounds are also an excellent platform for further modification and for the [...] Read more.
New derivatives of benzofuroxan containing triazidoisobutyl fragments, opening the way for the creation of highly effective compositions with an increased value of energy characteristics, were synthesized for the first time. Such compounds are also an excellent platform for further modification and for the preparation of new biologically-active compounds containing tetrazole and triazole fragments. Calculations of heats of formation performed with the DFT (density functional theory) method showed that the studied compounds are high-energetic density ones, the enthalpies of formation of which are comparable to the enthalpies of formation of similar benzofuroxan derivatives and exceeds experimental enthalpy of formation of CL-14 (5,7-diamino-4,6-dinitrobenzofuroxan). The analysis of DSC indicates a sufficiently high thermal stability of the synthesized azidobenzofuroxans, which are acceptable for their use as components in the creation of highly efficient compositions with an increased value of energy characteristics. Full article
(This article belongs to the Special Issue Simple Substances of Non-metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry)
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11 pages, 1177 KiB  
Communication
Cubic Octa-Carbon: Quantum-Chemical Design of Molecular Structure and Potential Way of Its Synthesis from Cubane
by Denis V. Chachkov and Oleg V. Mikhailov
Int. J. Mol. Sci. 2021, 22(21), 12067; https://doi.org/10.3390/ijms222112067 - 08 Nov 2021
Viewed by 2135
Abstract
Quantum-chemical calculation of most important parameters of molecular and electronic structures of octa-carbon C8 having cubic form (bond lengths, bond and torsion angles) using CCSD(T)/QZVP and DFT B3PW91/QZVP methods, has been carried out. NBO analysis data and HOMO/LUMO images for this compound [...] Read more.
Quantum-chemical calculation of most important parameters of molecular and electronic structures of octa-carbon C8 having cubic form (bond lengths, bond and torsion angles) using CCSD(T)/QZVP and DFT B3PW91/QZVP methods, has been carried out. NBO analysis data and HOMO/LUMO images for this compound are presented, too. Good agreement was found between the structural data obtained using the above two quantum-chemical methods and, also, with corresponding experimental data. Also, the standard thermodynamic parameters of formation of cubic C8 considered here, and namely standard enthalpy ΔfH0(298K), entropy Sf0(298K) and Gibbs’ energy ΔfG0(298K) of formation for this compound were calculated. By using this data, a theoretically possible variant of the synthesis of this compound by dehydrogenation of cubane C8H8 is considered, and the thermodynamic characteristics of each of the four stages of this process have been calculated. It is noted that each of the four stages of this process is characterized by a very high (about 500 kJ/mol) enthalpy of activation, as a result of that, for their realization within a sufficiently short time, the use of appropriate catalysts is necessary. Full article
(This article belongs to the Special Issue Simple Substances of Non-metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry)
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Review

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24 pages, 4513 KiB  
Review
Molecular and Electronic Structures of Neutral Polynitrogens: Review on the Theory and Experiment in 21st Century
by Oleg V. Mikhailov
Int. J. Mol. Sci. 2022, 23(5), 2841; https://doi.org/10.3390/ijms23052841 - 04 Mar 2022
Cited by 6 | Viewed by 1852
Abstract
The data on the existence and physicochemical characteristics of uncharged single element chemical compounds formed by nitrogen atoms and containing more than two nuclides of this element (from N4 to N120, oligomeric and polymeric polynitrogens) have been systematized and generalized. [...] Read more.
The data on the existence and physicochemical characteristics of uncharged single element chemical compounds formed by nitrogen atoms and containing more than two nuclides of this element (from N4 to N120, oligomeric and polymeric polynitrogens) have been systematized and generalized. It has been noticed that these data have a predominantly predictive character and were obtained mainly using quantum chemical calculations of various levels (HF, DFT, MP, CCSD etc.). The possibility of the practical application of these single element compounds has been considered. The review mainly covers articles published in the last 25 years. The bibliography contains 128 references. Full article
(This article belongs to the Special Issue Simple Substances of Non-metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry)
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23 pages, 3010 KiB  
Review
Substructural Approach for Assessing the Stability of Higher Fullerenes
by Ayrat R. Khamatgalimov and Valeri I. Kovalenko
Int. J. Mol. Sci. 2021, 22(7), 3760; https://doi.org/10.3390/ijms22073760 - 04 Apr 2021
Cited by 10 | Viewed by 2475
Abstract
This review describes the most significant published results devoted to the study of the nature of the higher fullerenes stability, revealing of correlations between the structural features of higher fullerene molecules and the possibility of their producing. A formalization of the substructure approach [...] Read more.
This review describes the most significant published results devoted to the study of the nature of the higher fullerenes stability, revealing of correlations between the structural features of higher fullerene molecules and the possibility of their producing. A formalization of the substructure approach to assessing the stability of higher fullerenes is proposed, which is based on a detailed analysis of the main structural features of fullerene molecules. The developed substructure approach, together with the stability of the substructures constituting the fullerene molecule, helps to understand deeper the features of the electronic structure of fullerenes. Full article
(This article belongs to the Special Issue Simple Substances of Non-metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry)
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