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Structure and Conformational Analysis of Heterocyclic Compounds
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Structure and Conformational Analysis of Heterocyclic Compounds

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Organic Chemistry".

Deadline for manuscript submissions: closed (30 May 2020) | Viewed by 19934

Special Issue Editor

Prof. Dr. Bagrat A. Shainyan

E-Mail Website
Guest Editor
Siberian Branch of Russian Academy of Sciences, A.E. Favorsky Irkutsk Institute of Chemistry, Irkutsk, Russia
Interests: stereochemistry; organosilicon chemistry; conformational analysis; chemistry of triflates; reaction mechanisms
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As early as in the first half of the 20th century, the structural and conformational analysis of cyclohexanes and, to a lesser extent, their five- and seven-membered analogues has become a classical part of modern organic synthetic and theoretical chemistry. Since then, a wealth of information has accumulated regarding the structure and conformational behavior, and their influence on the reactivity of numerous heteroanalogues of these carbocycles. The knowledge available nowadays, on the one hand, has revealed common features of heterocyclic compounds and their carbocycle predecessors and, on the other hand, interesting specific behavior determined by and depending on the nature of the heteroatom in the ring. Therefore, the planned Special Issue seeks contributions which will illustrate the most recent developments and trends for the future of this field. The investigated molecules in this Special Issue will include oxanes, dioxanes, thianes, dithianes, piperidines, silacyclohexanes, and phosphacyclohexanes, as well as cyclohexanes containing other heteroatoms and/or their combinations, either as isolated species or incorporated in more complex structures. Other 5–7-membered heterocycloalkanes will also be considered. Special attention will be paid to the influence of heteroatoms on the molecular structure, conformational properties, and reactivity of the studied molecules, whether existing or theoretically designed.

Communications, full papers, and reviews on the abovementioned topics are particularly welcome.

Prof. Bagrat A. Shainyan
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at mdpi.longhoe.net 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. 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 2700 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

  • enantioselective synthesis
  • physical methods
  • computational chemistry
  • mechanistic studies
  • conformational analysis
  • stereochemistry
  • mechanistic studies

Published Papers (7 papers)

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Editorial

Jump to: Research, Review

2 pages, 164 KiB  
Editorial
Structural and Conformational Aspects in the Chemistry of Heterocycles
by Bagrat A. Shainyan
Molecules 2020, 25(15), 3461; https://doi.org/10.3390/molecules25153461 - 30 Jul 2020
Cited by 1 | Viewed by 1449
Abstract
Heterocyclic compounds represent more than half of all known organic compounds, so the growing interest in this field of chemistry is not surprising [...] Full article
(This article belongs to the Special Issue Structure and Conformational Analysis of Heterocyclic Compounds)

Research

Jump to: Editorial, Review

16 pages, 6164 KiB  
Article
Mechanism of Reactions of 1-Substituted Silatranes and Germatranes, 2,2-Disubstituted Silocanes and Germocanes, 1,1,1-Trisubstituted Hyposilatranes and Hypogermatranes with Alcohols (Methanol, Ethanol): DFT Study
by Denis Chachkov, Rezeda Ismagilova and Yana Vereshchagina
Molecules 2020, 25(12), 2803; https://doi.org/10.3390/molecules25122803 - 17 Jun 2020
Cited by 7 | Viewed by 2383
Abstract
The mechanism of reactions of silatranes and germatranes, and their bicyclic and monocyclic analogues with one molecule of methanol or ethanol, was studied at the Density Functional Theory (DFT) B3PW91/6-311++G(df,p) level of theory. Reactions of 1-substituted sil(germ)atranes, 2,2-disubstituted sil(germ)ocanes, and 1,1,1-trisubstituted hyposil(germ)atranes with [...] Read more.
The mechanism of reactions of silatranes and germatranes, and their bicyclic and monocyclic analogues with one molecule of methanol or ethanol, was studied at the Density Functional Theory (DFT) B3PW91/6-311++G(df,p) level of theory. Reactions of 1-substituted sil(germ)atranes, 2,2-disubstituted sil(germ)ocanes, and 1,1,1-trisubstituted hyposil(germ)atranes with alcohol (methanol, ethanol) proceed in one step through four-center transition states followed by the opening of a silicon or germanium skeleton and the formation of products. According to quantum chemical calculations, the activation energies and Gibbs energies of activation of reactions with methanol and ethanol are close, their values decrease in the series of atranes–ocanes–hypoatranes for interactions with both methanol and ethanol. The reactions of germanium-containing derivatives are characterized by lower activation energies in comparison with the reactions of corresponding silicon-containing compounds. The annular configurations of the product molecules with electronegative substituents are stabilized by the transannular N→X (X = Si, Ge) bond and different intramolecular hydrogen contacts with the participation of heteroatoms of substituents at the silicon or germanium. Full article
(This article belongs to the Special Issue Structure and Conformational Analysis of Heterocyclic Compounds)
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Graphical abstract

6 pages, 348 KiB  
Article
Enthalpies of Combustion and Formation of Severely Crowded Methyl-Substituted 1,3-dioxanes. The Magnitudes of 2,4- and 4,6-diaxial Me,Me-Interactions and the Chair–2,5-twist Energy Difference
by Kalevi Pihlaja, Henri Kivelä, Pirjo Vainiotalo and William V. Steele
Molecules 2020, 25(12), 2762; https://doi.org/10.3390/molecules25122762 - 15 Jun 2020
Cited by 5 | Viewed by 2068
Abstract
Enthalpies of combustion of 2,2-trans-4,6- (1) and 4,4,6,6-tetramethyl- (2) and 2,4,4,6,6- (3) and 2,2,4,4,6-pentamethyl-1,3-dioxanes (4) were determined to estimate their enthalpies of formation in the gas phase. By comparing the latter with the [...] Read more.
Enthalpies of combustion of 2,2-trans-4,6- (1) and 4,4,6,6-tetramethyl- (2) and 2,4,4,6,6- (3) and 2,2,4,4,6-pentamethyl-1,3-dioxanes (4) were determined to estimate their enthalpies of formation in the gas phase. By comparing the latter with the corresponding enthalpies estimated based on the various bond–bond interactions allowed to determine the chair–2,5-twist energy difference (ΔHCT = 29.8 kJ mol–1) for 1 since C-13 shift correlations indicate that it escapes to the 2,5-twist form where the 2-methyl groups are isoclinal and 4- and 6-methyl groups pseudoequatorial to avoid syn-axial interactions. Compounds 2 and 3 in turn give the values 21.0 and 21.6 kJ mol–1 for the 4,6-diaxial Me,Me-interaction. Finally compound 4, which retains the chair conformation to avoid pseudoaxial interactions in the twist forms gives the value 19.5 kJ mol–1 for the 2,4-diaxial Me,Me-interaction indicating that its chair form appears to be somewhat deformed. Full article
(This article belongs to the Special Issue Structure and Conformational Analysis of Heterocyclic Compounds)
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Scheme 1

15 pages, 1805 KiB  
Article
Synthesis and Conformational Analysis of Naphthoxazine-Fused Phenanthrene Derivatives
by Khadija Belasri, Leila Topal, Matthias Heydenreich, Andreas Koch, Erich Kleinpeter, Ferenc Fülöp and István Szatmári
Molecules 2020, 25(11), 2524; https://doi.org/10.3390/molecules25112524 - 28 May 2020
Cited by 2 | Viewed by 2189
Abstract
The synthesis of new phenanthr[9,10-e][1,3]oxazines was achieved by the direct coupling of 9-phenanthrol with cyclic imines in the modified aza-Friedel–Crafts reaction followed by the ring closure of the resulting bifunctional aminophenanthrols with formaldehyde. Aminophenanthrol-type Mannich bases were synthesised and transformed [...] Read more.
The synthesis of new phenanthr[9,10-e][1,3]oxazines was achieved by the direct coupling of 9-phenanthrol with cyclic imines in the modified aza-Friedel–Crafts reaction followed by the ring closure of the resulting bifunctional aminophenanthrols with formaldehyde. Aminophenanthrol-type Mannich bases were synthesised and transformed to phenanthr[9,10-e][1,3]oxazines via [4 + 2] cycloaddition. Detailed NMR structural analyses of the new polyheterocycles as well as conformational studies including Density Functional Theory (DFT) modelling were performed. The relative stability of ortho-quinone methides (o-QMs) was calculated, the geometries obtained were compared with the experimentally determined NMR structures, and thereby, the regioselectivity of the reactions has been assigned. Full article
(This article belongs to the Special Issue Structure and Conformational Analysis of Heterocyclic Compounds)
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Graphical abstract

14 pages, 3390 KiB  
Article
Synthesis and Thermal Investigations of Eleven-Membered Ring Systems Containing One of the Heavier Group 14 Element Atoms Si, Ge, and Sn
by Nadi Eleya, Clement Appiah, Enno Lork, Mathias Gogolin, Thorsten M. Gesing, Tim Stauch and Anne Staubitz
Molecules 2020, 25(2), 283; https://doi.org/10.3390/molecules25020283 - 10 Jan 2020
Cited by 2 | Viewed by 2795
Abstract
Unique eleven-membered rings containing silicon, germanium, and tin were synthesized in good yields by the reactions of the corresponding 1,2-bis((2-bromothiophen-3-yl)methoxy)benzenes with (C6H5)2ECl2 where E = Sn, Ge, Si. The Sn and Ge congeners were crystallized, but [...] Read more.
Unique eleven-membered rings containing silicon, germanium, and tin were synthesized in good yields by the reactions of the corresponding 1,2-bis((2-bromothiophen-3-yl)methoxy)benzenes with (C6H5)2ECl2 where E = Sn, Ge, Si. The Sn and Ge congeners were crystallized, but the conformers that these rings crystallized in, were quite different. As confirmed by Density Functional Theory (DFT) calculations, (C28H22O2S2Sn) assumes a unique crystal structure that leaves more room around the tetrel atom as compared to the crystal structure of the corresponding Ge compound. In the latter, the central cavity is quite open, whereas in the former, one of the methylene groups can fold inwards. Another consequence is the influence on the planes of the aromatic rings flanking the heterocycle. In the Ge case, the benzene ring is folded away from the central cavity, whereas in the Sn case, it is almost parallel to the imaginary axis through the center of the ring. Thermal analysis investigations (TGA and DSC methods) of these eleven-membered rings suggested the loss of a phenyl group in the first decomposition step. The decomposition temperature decreased from the Si containing heterocycle to Ge and was lowest for the Sn containing heterocycle. Full article
(This article belongs to the Special Issue Structure and Conformational Analysis of Heterocyclic Compounds)
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Figure 1

Review

Jump to: Editorial, Research

37 pages, 11335 KiB  
Review
Stereochemistry of Simple Molecules inside Nanotubes and Fullerenes: Unusual Behavior of Usual Systems
by Valerij Kuznetsov
Molecules 2020, 25(10), 2437; https://doi.org/10.3390/molecules25102437 - 23 May 2020
Cited by 16 | Viewed by 5240
Abstract
Over the past three decades, carbon nanotubes and fullerenes have become remarkable objects for starting the implementation of new models and technologies in different branches of science. To a great extent, this is defined by the unique electronic and spatial properties of nanocavities [...] Read more.
Over the past three decades, carbon nanotubes and fullerenes have become remarkable objects for starting the implementation of new models and technologies in different branches of science. To a great extent, this is defined by the unique electronic and spatial properties of nanocavities due to the ramified π-electron systems. This provides an opportunity for the formation of endohedral complexes containing non-covalently bonded atoms or molecules inside fullerenes and nanotubes. The guest species are exposed to the force field of the nanocavity, which can be described as a combination of electronic and steric requirements. Its action significantly changes conformational properties of even relatively simple molecules, including ethane and its analogs, as well as compounds with C−O, C−S, B−B, B−O, B−N, N−N, Al−Al, Si−Si and Ge−Ge bonds. Besides that, the cavity of the host molecule dramatically alters the stereochemical characteristics of cyclic and heterocyclic systems, affects the energy of pyramidal nitrogen inversion in amines, changes the relative stability of cis and trans isomers and, in the case of chiral nanotubes, strongly influences the properties of R- and S-enantiomers. The present review aims at primary compilation of such unusual stereochemical effects and initial evaluation of the nature of the force field inside nanotubes and fullerenes. Full article
(This article belongs to the Special Issue Structure and Conformational Analysis of Heterocyclic Compounds)
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Figure 1

22 pages, 9104 KiB  
Review
Silacyclohexanes, Sila(hetero)cyclohexanes and Related Compounds: Structure and Conformational Analysis
by Bagrat A. Shainyan
Molecules 2020, 25(7), 1624; https://doi.org/10.3390/molecules25071624 - 1 Apr 2020
Cited by 5 | Viewed by 2938
Abstract
Conformational analysis of Si-mono- and Si,Si-disubstituted silacyclohexanes as well as their analogues with a heteroatom(s) in the ring is reviewed with the focus on the recent results. Experimental measurements in the gas phase (gas electron diffraction, GED) and low temperature NMR spectroscopy (LT [...] Read more.
Conformational analysis of Si-mono- and Si,Si-disubstituted silacyclohexanes as well as their analogues with a heteroatom(s) in the ring is reviewed with the focus on the recent results. Experimental measurements in the gas phase (gas electron diffraction, GED) and low temperature NMR spectroscopy (LT NMR) on 1H, 13C and 29Si nuclei are described along with theoretical calculations at the DFT and MP2 levels of theory. Structural and conformational specific features are shown to be principally different from those of the carbon predecessors—the corresponding cyclohexanes, oxanes, thianes and piperidines. The role of various effects (steric, hyperconjugation, stereoelectronic, electrostatic) is demonstrated. Full article
(This article belongs to the Special Issue Structure and Conformational Analysis of Heterocyclic Compounds)
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