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Recent Advances in Computational Studies of Natural Products
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Recent Advances in Computational Studies of Natural Products

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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 7197

Special Issue Editors

Prof. Dr. Leonid B. Krivdin

E-Mail Website
Guest Editor
A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
Interests: computational NMR; natural compounds; stereochemical studies
Dr. Valentin Semenov

E-Mail Website
Guest Editor
A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
Interests: computational NMR; natural compounds; stereochemical studies

Special Issue Information

Dear Colleagues, 

The area of the quantum chemical calculations of natural products is rapidly developing in parallel with the growth of computing resources, which are becoming available at the leading chemical and biochemical research centers and universities around the world. We are currently witnessing unprecedented progress in this field, and notable advances in computational approaches to elucidating the structure of these extremely important biologically active compounds are at the forefront of modern chemical science. This Special Issue is devoted to the latest advances in the field of theoretical and stereochemical studies of natural products with paying special attention to the latest advances in the computational NMR results. For the publication in this issue, reviews, regular articles, and short communications are mostly welcome, the latter dealing with the stereochemical and conformational structure of different natural products, their structural elucidation including NMR computation and experiment. A particular emphasis of this issue is focused on the results that reveal the potential of a variety of modern computational protocols, which can be used for a structural survey of natural products.

Prof. Dr. Leonid B. Krivdin
Dr. Valentin Semenov
Guest Editors

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

  • natural products
  • computational studies
  • stereochemical and conformational structure

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Published Papers (3 papers)

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Research

12 pages, 593 KiB  
Article
A Theoretical Study of Hydrogen Abstraction Reactions in Guanosine and Uridine
by Kasper F. Schaltz and Stephan P. A. Sauer
Int. J. Mol. Sci. 2023, 24(9), 8192; https://doi.org/10.3390/ijms24098192 - 3 May 2023
Cited by 4 | Viewed by 2389 | Correction
Abstract
All the practically possible hydrogen abstraction reactions for guanosine and uridine have been investigated through quantum chemical calculations of energy barriers and rate constants. This was conducted at the level of density functional theory (DFT) with the ωB97X-D functional and the 6-311++G(2df,2pd) Pople [...] Read more.
All the practically possible hydrogen abstraction reactions for guanosine and uridine have been investigated through quantum chemical calculations of energy barriers and rate constants. This was conducted at the level of density functional theory (DFT) with the ωB97X-D functional and the 6-311++G(2df,2pd) Pople basis set. Transition state theory with the Eckart tunneling correction was used to calculate the rate constants. The results show that the reaction involving the hydrogen labeled C4′ in the ribofuranose part has the largest rate constant for guanosine with the value 6.856 × 1010 L s−1mol−1 and the largest for uridine with the value 3.655 × 109 L s−1mol−1. Based on the results for these two nucleosides, there is a noticeable similarity between the rate constants in the ribofuranose part of the molecule, even though they are bound to two entirely different nucleobases. Full article
(This article belongs to the Special Issue Recent Advances in Computational Studies of Natural Products)
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20 pages, 3995 KiB  
Article
Stereochemical Study of the Super Large Tetrakis Alkaloid Alasmontamine A by Means of an Advanced Computational NMR
by Valentin A. Semenov and Leonid B. Krivdin
Int. J. Mol. Sci. 2023, 24(6), 5572; https://doi.org/10.3390/ijms24065572 - 14 Mar 2023
Cited by 2 | Viewed by 1613
Abstract
1H and 13C NMR chemical shifts of the tetrakis monoterpene indole alkaloid alasmontamine A, with a molecular formula of C84H91N8O12, have been calculated within the DFT framework. Six minimum energy conformers of this [...] Read more.
1H and 13C NMR chemical shifts of the tetrakis monoterpene indole alkaloid alasmontamine A, with a molecular formula of C84H91N8O12, have been calculated within the DFT framework. Six minimum energy conformers of this alkaloid were identified, and three key configurations that contribute to its NMR shielding constants were established. Several ambiguities in the reported assignment of the NMR chemical shifts of alasmontamine A have been resolved. Full article
(This article belongs to the Special Issue Recent Advances in Computational Studies of Natural Products)
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17 pages, 1879 KiB  
Article
A Combined Experimental and Theoretical Study of ESR Hyperfine Coupling Constants for N,N,N’,N’-Tetrasubstituted p-Phenylenediamine Radical Cations
by Ronan Gleeson, Cecilie L. Andersen, Peter Rapta, Peter Machata, Jørn B. Christensen, Ole Hammerich and Stephan P. A. Sauer
Int. J. Mol. Sci. 2023, 24(4), 3447; https://doi.org/10.3390/ijms24043447 - 8 Feb 2023
Cited by 1 | Viewed by 2612
Abstract
A test set of N,N,N’,N’-tetrasubstituted p-phenylenediamines are experimentally explored using ESR (electron spin resonance) spectroscopy and analysed from a computational standpoint thereafter. This computational study aims to further aid structural characterisation by comparing experimental ESR hyperfine coupling constants (hfccs) with computed [...] Read more.
A test set of N,N,N’,N’-tetrasubstituted p-phenylenediamines are experimentally explored using ESR (electron spin resonance) spectroscopy and analysed from a computational standpoint thereafter. This computational study aims to further aid structural characterisation by comparing experimental ESR hyperfine coupling constants (hfccs) with computed values calculated using ESR-optimised “J-style” basis sets (6-31G(d,p)-J, 6-31G(d,p)-J, 6-311++G(d,p)-J, pcJ-1, pcJ-2 and cc-pVTZ-J) and hybrid-DFT functionals (B3LYP, PBE0, TPSSh, ωB97XD) as well as MP2. PBE0/6-31g(d,p)-J with a polarised continuum solvation model (PCM) correlated best with the experiment, giving an R2 value of 0.8926. A total of 98% of couplings were deemed satisfactory, with five couplings observed as outlier results, thus degrading correlation values significantly. A higher-level electronic structure method, namely MP2, was sought to improve outlier couplings, but only a minority of couples showed improvement, whilst the remaining majority of couplings were negatively degraded. Full article
(This article belongs to the Special Issue Recent Advances in Computational Studies of Natural Products)
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