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A Themed Issue in Honor of Professor Mikhail Elyashberg on the Occasion of His 85th Birthday

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

Deadline for manuscript submissions: closed (1 September 2021) | Viewed by 12637

Special Issue Editor


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Guest Editor
US Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, NC-27711, USA
Interests: cheminformatics; chemistry databases; chemistry software; QSPR/QSAR modeling; systematic nomenclature; computer-assisted structure elucidation

Special Issue Information

Dear colleagues,

I am honored to have the opportunity to serve as Guest Editor for this Special Issue of Molecules in honor of Professor Dr. Mikhail Elyashberg’s 85th birthday to celebrate his many contributions to science. During my decade-long tenure at ACD/Labs, a chemistry software company specializing in analytical chemistry software solutions, I had the opportunity to work alongside Mikhail in the development of a computer-assisted structure elucidation (CASE) software program. As a PhD NMR spectroscopist by training and having worked in a government laboratory in academia as well as in a Fortune 500 chemical company as an NMR spectroscopist, I had seen the promise of applying computational techniques to structure elucidation. Working alongside ACD/Labs’ scientists and developers, and with Mikhail as one of my favorite company collaborators, the promise of CASE was delivered to the community in the form of the ACD/Structure Elucidator software application, a program used in chemical and pharmaceutical companies and university labs all over the world.

Mikhail was born on 7 May 1936 in Minsk in the former USSR. In 1959, he graduated from the Faculty of Physics, Tomsk State University as a specialist in physical optics and spectroscopy. He started his scientific work as a research engineer in Institute No. 4 of the USSR Ministry of Defense, Moscow, where he investigated radio wave propagation through the ionosphere. While he was promoted to a senior research engineer position, he decided to pursue his passion for molecular spectroscopy, and in 1963, he transferred to the All-Union Institute of Organic Synthesis in Moscow. Despite not registering as a PhD student, Mikhail identified the topic for a dissertation and performed his research in his private time, encouraged by Prof. L.A. Gribov. He was the first person to suggest the application of mathematical logic to model the reasoning process of a spectroscopist during the structural group analysis (SGA) of organic molecules from infrared spectroscopy and 1D nuclear magnetic resonance. He received a PhD (in phys. math.) from the Moscow Pedagogical University in 1970, and in 1984, he obtained a Doctor of Sciences (habilitation) degree in chemistry from the Vernadsky Institute of Geochemistry and Analytical Chemistry, Moscow.

In 1981, Mikhail assumed a leadership role and headed up the Laboratory of Molecular Spectroscopy at his institute. The laboratory was equipped with modern spectrometers (NMR, GC–FTIR, Raman, UV–VIS, GC–HRMS) and focused on the development and analysis of new high-energy polycyclic hydrocarbons of interest in space engineering. Mikhail’s personal interests remained on the development of computational methods for molecular structure elucidation, and he made great progress in this domain. In collaboration with co-workers, he created four generations of the expert system “RASTR” for the structure elucidation of organic molecules from IR and NMR spectra over about 15 years (up to 1990). From 1993–96, his group worked with Bruker to develop the X-PERT system based, again, on IR and NMR data. His research included the development of mathematical methods and programs for the generation of all stereoisomers corresponding to a given structural formula and building their 3D models with symmetry, calculation of associated vibrational spectra, development of referenceless quantitative molecular spectral analysis, methods of computer-aided molecular design of high-energy content polycyclic organic compounds, and other related topics.

Mikhail saw the opportunity to couple his research efforts in structure elucidation with the efforts of ACD/Labs, a software company with development offices in Moscow. The company had become one of the pre-eminent commercial software companies providing PC-based NMR prediction tools for both proton and carbon NMR and had initiated an investigation into the reverse problem of structure elucidation from spectral data. When Mikhail joined the venture in 1997, they then had the opportunity to integrate infrared spectroscopy for functional group recognition and continued to enhance the system. Under Mikhail’s guidance, they extended their efforts into the analysis of various forms of 2D NMR spectroscopy initiated with 1H–1H correlation spectroscopy and direct and long-range hetereonuclear 1H–13C spectroscopy. The resulting software product, ACD/Structure Elucidator, has continued to develop in functionality and capability and with the support of advanced spectroscopic data for a period of almost two decades. The application is now installed in chemical and pharmaceutical companies across the world and has had its performance validated a number of times in the elucidation of complex chemical structures, especially natural products with exotic connectivities and stereochemistry.

Mikhail remains active in the development of the Structure Elucidator CASE system and especially in pushing the technology to the limits. His profound contributions to science are represented in over 130 research publications and 5 books as well as the number of laboratories in the world that are using the software that he has been pivotal in guiding through its development. In 1999, Mikhail was made a laureate of the State Prize of the Russian Federation in the field of science and engineering, the highest scientific award in Russia.

I am honored to organize this Special Issue to celebrate Professor Mikhail Elyashberg’s 85th birthday and to dedicate this issue to his enormous contributions to molecular spectroscopy and computer-assisted structure elucidation. We encourage and welcome manuscripts in molecular spectroscopy, analysis of stereochemistry, applications of computers to the processing and analysis of spectroscopic data and, of course, computer-assisted structure elucidation, including the applications of DFT.

Dr. Antony J. Williams
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. 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

  • molecular spectroscopy
  • expert systems
  • structure elucidation

Published Papers (5 papers)

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Research

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23 pages, 6340 KiB  
Article
Sampling CASE Application for the Quality Control of Published Natural Product Structures
by Lorena Martins Guimarães Moreira and Jochen Junker
Molecules 2021, 26(24), 7543; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26247543 - 13 Dec 2021
Cited by 1 | Viewed by 1693
Abstract
Structure elucidation with NMR correlation data is dicey, as there is no way to tell how ambiguous the data set is and how reliably it will define a constitution. Many different software tools for computer assisted structure elucidation (CASE) have become available over [...] Read more.
Structure elucidation with NMR correlation data is dicey, as there is no way to tell how ambiguous the data set is and how reliably it will define a constitution. Many different software tools for computer assisted structure elucidation (CASE) have become available over the past decades, all of which could ensure a better quality of the elucidation process, but their use is still not common. Since 2011, WebCocon has integrated the possibility to generate theoretical NMR correlation data, starting from an existing structural proposal, allowing this theoretical data then to be used for CASE. Now, WebCocon can also read the recently presented NMReDATA format, allowing for uncomplicated access to CASE with experimental data. With these capabilities, WebCocon presents itself as an easily accessible Web-Tool for the quality control of proposed new natural products. Results of this application to several molecules from literature are shown and demonstrate how CASE can contribute to improve the reliability of Structure elucidation with NMR correlation data. Full article
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12 pages, 10873 KiB  
Article
Incorporation of 4J-HMBC and NOE Data into Computer-Assisted Structure Elucidation with WebCocon
by Matthias Köck, Thomas Lindel and Jochen Junker
Molecules 2021, 26(16), 4846; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26164846 - 11 Aug 2021
Cited by 5 | Viewed by 1968
Abstract
Over the past decades, different software programs have been developed for the Computer-Assisted Structure Elucidation (CASE) with NMR data using with various approaches. WebCocon is one of them that has been continuously improved over the past 20 years. Here, we present the inclusion [...] Read more.
Over the past decades, different software programs have been developed for the Computer-Assisted Structure Elucidation (CASE) with NMR data using with various approaches. WebCocon is one of them that has been continuously improved over the past 20 years. Here, we present the inclusion of 4JCH correlations (4J-HMBC) in the HMBC interpretation of Cocon and NOE data in WebCocon. The 4J-HMBC data is used during the structure generation process, while the NOE data is used in post-processing of the results. The marine natural product oxocyclostylidol was selected to demonstrate WebCocon’s enhanced HMBC data processing capabilities. A systematic study of the 4JCH correlations of oxocyclostylidol was performed. The application of NOEs in CASE is demonstrated using the NOE correlations of the diterpene pyrone asperginol A known from the literature. As a result, we obtained a conformation that corresponds very well to the existing X-ray structure. Full article
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17 pages, 2772 KiB  
Article
The DEPTQ+ Experiment: Leveling the DEPT Signal Intensities and Clean Spectral Editing for Determining CHn Multiplicities
by Peter Bigler, Camilo Melendez and Julien Furrer
Molecules 2021, 26(12), 3490; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123490 - 08 Jun 2021
Cited by 1 | Viewed by 2143
Abstract
We propose a new 13C DEPTQ+ NMR experiment, based on the improved DEPTQ experiment, which is designed to unequivocally identify all carbon multiplicities (Cq, CH, CH2, and CH3) in two experiments. Compared to this improved DEPTQ experiment, [...] Read more.
We propose a new 13C DEPTQ+ NMR experiment, based on the improved DEPTQ experiment, which is designed to unequivocally identify all carbon multiplicities (Cq, CH, CH2, and CH3) in two experiments. Compared to this improved DEPTQ experiment, the DEPTQ+ is shorter and the different evolution delays are designed as spin echoes, which can be tuned to different 1JCH values; this is especially valuable when a large range of 1JCH coupling constants is to be expected. These modifications allow (i) a mutual leveling of the DEPT signal intensities, (ii) a reduction in J cross-talk in the Cq/CH spectrum, and (iii) more consistent and cleaner CH2/CH3 edited spectra. The new DEPTQ+ is expected to be attractive for fast 13C analysis of small-to medium sized molecules, especially in high-throughput laboratories. With concentrated samples and/or by exploiting the high sensitivity of cryogenically cooled 13C NMR probeheads, the efficacy of such investigations may be improved, as it is possible to unequivocally identify all carbon multiplicities, with only one scan, for each of the two independent DEPTQ+ experiments and without loss of quality. Full article
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17 pages, 4861 KiB  
Article
The Advantage of Automatic Peer-Reviewing of 13C-NMR Reference Data Using the CSEARCH-Protocol
by Wolfgang Robien
Molecules 2021, 26(11), 3413; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26113413 - 04 Jun 2021
Cited by 11 | Viewed by 1942
Abstract
A systematic investigation of the experimental 13C-NMR spectra published in Molecules during the period of 1996 to 2015 with respect to their quality using CSEARCH-technology is described. It is shown that the systematic application of the CSEARCH-Robot-Referee during the peer-reviewing process prohibits [...] Read more.
A systematic investigation of the experimental 13C-NMR spectra published in Molecules during the period of 1996 to 2015 with respect to their quality using CSEARCH-technology is described. It is shown that the systematic application of the CSEARCH-Robot-Referee during the peer-reviewing process prohibits at least the most trivial assignment errors and wrong structure proposals. In many cases, the correction of the assignments/chemical shift values is possible by manual inspection of the published tables; in certain cases, reprocessing of the original experimental data might help to clarify the situation, showing the urgent need for a public domain repository. A comparison of the significant key numbers derived for Molecules against those of other important journals in the field of natural product chemistry shows a quite similar level of quality for all publishers responsible for the six journals under investigation. From the results of this study, general rules for data handling, data storage, and manuscript preparation can be derived, helping to increase the quality of published NMR-data and making these data available as validated reference material. Full article
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Review

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34 pages, 6880 KiB  
Review
ACD/Structure Elucidator: 20 Years in the History of Development
by Mikhail Elyashberg and Antony Williams
Molecules 2021, 26(21), 6623; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26216623 - 01 Nov 2021
Cited by 10 | Viewed by 3296
Abstract
The first methods associated with the Computer-Assisted Structure Elucidation (CASE) of small molecules were published over fifty years ago when spectroscopy and computer science were both in their infancy. The incredible leaps in both areas of technology could not have been envisaged at [...] Read more.
The first methods associated with the Computer-Assisted Structure Elucidation (CASE) of small molecules were published over fifty years ago when spectroscopy and computer science were both in their infancy. The incredible leaps in both areas of technology could not have been envisaged at that time, but both have enabled CASE expert systems to achieve performance levels that in their present state can outperform many scientists in terms of speed to solution. The computer-assisted analysis of enormous matrices of data exemplified 1D and 2D high-resolution NMR spectroscopy datasets can easily solve what just a few years ago would have been deemed to be complex structures. While not a panacea, the application of such tools can provide support to even the most skilled spectroscopist. By this point the structures of a great number of molecular skeletons, including hundreds of complex natural products, have been elucidated using such programs. At this juncture, the expert system ACD/Structure Elucidator is likely the most advanced CASE system available and, being a commercial software product, is installed and used in many organizations. This article will provide an overview of the research and development required to pursue the lofty goals set almost two decades ago to facilitate highly automated approaches to solving complex structures from analytical spectroscopy data, using NMR as the primary data-type. Full article
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