Mikhail Elyashberg

Publications

• 1.61

  Impact points

  Elucidating 'undecipherable' chemical structures using computer-assisted structure elucidation approaches.

  Mikhail Elyashberg, Kirill Blinov, Sergey Molodtsov, Antony Williams

  Magnetic resonance in chemistry : MRC. 01/2012; 50(1):22-7.

  Structure elucidation using 2D NMR data and application of traditional methods of structure elucidation are known to fail for certain problems. In this work, it is shown that computer-assisted structure elucidation methods are capable of solving such problems. We conclude that it is now impossible t... [more] Structure elucidation using 2D NMR data and application of traditional methods of structure elucidation are known to fail for certain problems. In this work, it is shown that computer-assisted structure elucidation methods are capable of solving such problems. We conclude that it is now impossible to evaluate the capabilities of novel NMR experimental techniques in isolation from expert systems developed for processing fuzzy, incomplete and contradictory information obtained from 2D NMR spectra. Copyright © 2012 John Wiley & Sons, Ltd.
• 9.20

  Impact points

  Structural revisions of natural products by Computer-Assisted Structure Elucidation (CASE) systems.

  Mikhail Elyashberg, Antony J Williams, Kirill Blinov

  Natural product reports. 09/2010; 27(9):1296-328.
• 1.61

  Impact points

  Enhanced automated structure elucidation by inclusion of two-bond specific data.

  Steve F Cheatham, Mike Kline, Ryan R Sasaki, Kirill A Blinov, Mikhail E Elyashberg, Sergey G Molodtsov

  Magnetic resonance in chemistry : MRC. 08/2010; 48(8):571-4.

  The availability of cryogenically cooled probes permits routine acquisition of data from low sensitivity pulse sequences such as inadequate and 1,1-adequate. We demonstrate that the use of cryo-probe generated 1,1-adequate data in conjunction with HMBC dramatically improves computer-assisted structu... [more] The availability of cryogenically cooled probes permits routine acquisition of data from low sensitivity pulse sequences such as inadequate and 1,1-adequate. We demonstrate that the use of cryo-probe generated 1,1-adequate data in conjunction with HMBC dramatically improves computer-assisted structure elucidation (CASE) both in terms of speed and accuracy of structure generation. In this study data were obtained on two dissimilar natural products and subjected to CASE analysis with and without the incorporation of two-bond specific data. Dramatic improvements in both structure calculation times and structure candidates were observed by the inclusion of the two-bond specific data.
• 1.61

  Impact points

  Empirical and DFT GIAO quantum-mechanical methods of (13)C chemical shifts prediction: competitors or collaborators?

  Mikhail Elyashberg, Kirill Blinov, Yegor Smurnyy, Tatiana Churanova, Antony Williams

  Magnetic resonance in chemistry : MRC. 03/2010; 48(3):219-29.

  The accuracy of (13)C chemical shift prediction by both DFT GIAO quantum-mechanical (QM) and empirical methods was compared using 205 structures for which experimental and QM-calculated chemical shifts were published in the literature. For these structures, (13)C chemical shifts were calculated usin... [more] The accuracy of (13)C chemical shift prediction by both DFT GIAO quantum-mechanical (QM) and empirical methods was compared using 205 structures for which experimental and QM-calculated chemical shifts were published in the literature. For these structures, (13)C chemical shifts were calculated using HOSE code and neural network (NN) algorithms developed within our laboratory. In total, 2531 chemical shifts were analyzed and statistically processed. It has been shown that, in general, QM methods are capable of providing similar but inferior accuracy to the empirical approaches, but quite frequently they give larger mean average error values. For the structural set examined in this work, the following mean absolute errors (MAEs) were found: MAE(HOSE) = 1.58 ppm, MAE(NN) = 1.91 ppm and MAE(QM) = 3.29 ppm. A strategy of combined application of both the empirical and DFT GIAO approaches is suggested. The strategy could provide a synergistic effect if the advantages intrinsic to each method are exploited.
• 1.61

  Impact points

  The application of empirical methods of (13)C NMR chemical shift prediction as a filter for determining possible relative stereochemistry.

  Mikhail E Elyashberg, Kirill A Blinov, Antony J Williams

  Magnetic resonance in chemistry : MRC. 03/2009;

  The reliable determination of stereocenters contained within chemical structures usually requires utilization of NMR data, chemical derivatization, molecular modeling, quantum-mechanical (QM) calculations and, if available, X-ray analysis. In this article, we show that the number of stereoisomers wh... [more] The reliable determination of stereocenters contained within chemical structures usually requires utilization of NMR data, chemical derivatization, molecular modeling, quantum-mechanical (QM) calculations and, if available, X-ray analysis. In this article, we show that the number of stereoisomers which need to be thoroughly verified, can be significantly reduced by the application of NMR chemical shift calculation to the full stereoisomer set of possibilities using a fragmental approach based on HOSE codes. The applicability of this suggested method is illustrated using experimental data published for a series of complex chemical structures. Copyright (c) 2009 John Wiley & Sons, Ltd.
• 1.61

  Impact points

  A systematic approach for the generation and verification of structural hypotheses.

  Mikhail Elyashberg, Kirill Blinov, Antony Williams

  Magnetic resonance in chemistry : MRC. 02/2009;

  During the process of molecular structure elucidation the selection of the most probable structural hypothesis may be based on chemical shift prediction. The prediction is carried out using either empirical or quantum-mechanical (QM) methods. When QM methods are used, NMR prediction commonly utilize... [more] During the process of molecular structure elucidation the selection of the most probable structural hypothesis may be based on chemical shift prediction. The prediction is carried out using either empirical or quantum-mechanical (QM) methods. When QM methods are used, NMR prediction commonly utilizes the GIAO option of the DFT approximation. In this approach the structural hypotheses are expected to be investigated by scientist. In this article we hope to show that the most rational manner by which to create structural hypotheses is actually by the application of an expert system capable of deducing all potential structures consistent with the experimental spectral data and specifically using 2D NMR data. When an expert system is used the best structure(s) can be distinguished using chemical shift prediction, which is best performed either by an incremental or neural net algorithm. The time-consuming QM calculations can then be applied, if necessary, to one or more of the 'best' structures to confirm the suggested solution. Copyright (c) 2009 John Wiley & Sons, Ltd.

• Computer-assisted methods for molecular structure elucidation: realizing a spectroscopist's dream.

  Mikhail Elyashberg, Kirill Blinov, Sergey Molodtsov, Yegor Smurnyy, Antony J Williams, Tatiana Churanova

  Journal of cheminformatics. 01/2009; 1:3.

  This article coincides with the 40 year anniversary of the first published works devoted to the creation of algorithms for computer-aided structure elucidation (CASE). The general principles on which CASE methods are based will be reviewed and the present state of the art in this field will be descr... [more] This article coincides with the 40 year anniversary of the first published works devoted to the creation of algorithms for computer-aided structure elucidation (CASE). The general principles on which CASE methods are based will be reviewed and the present state of the art in this field will be described using, as an example, the expert system Structure Elucidator. The developers of CASE systems have been forced to overcome many obstacles hindering the development of a software application capable of drastically reducing the time and effort required to determine the structures of newly isolated organic compounds. Large complex molecules of up to 100 or more skeletal atoms with topological peculiarity can be quickly identified using the expert system Structure Elucidator based on spectral data. Logical analysis of 2D NMR data frequently allows for the detection of the presence of COSY and HMBC correlations of "nonstandard" length. Fuzzy structure generation provides a possibility to obtain the correct solution even in those cases when an unknown number of nonstandard correlations of unknown length are present in the spectra. The relative stereochemistry of big rigid molecules containing many stereocenters can be determined using the StrucEluc system and NOESY/ROESY 2D NMR data for this purpose. The StrucEluc system continues to be developed in order to expand the general applicability, provide improved workflows, usability of the system and increased reliability of the results. It is expected that expert systems similar to that described in this paper will receive increasing acceptance in the next decade and will ultimately be integrated directly to analytical instruments for the purpose of organic analysis. Work in this direction is in progress. In spite of the fact that many difficulties have already been overcome to deliver on the spectroscopist's dream of "fully automated structure elucidation" there is still work to do. Nevertheless, as the efficiency of expert systems is enhanced the solution of increasingly complex structural problems will be achievable.

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• 3.16

  Impact points

  Applying computer-assisted structure elucidation algorithms for the purpose of structure validation: revisiting the NMR assignments of hexacyclinol.

  A J Williams, M E Elyashberg, K A Blinov, D C Lankin, G E Martin, W F Reynolds, J A Porco, C A Singleton, S Su

  Journal of natural products. 05/2008; 71(4):581-8.

  Computer-assisted structure elucidation (CASE) using a combination of 1D and 2D NMR data has been available for a number of years. These algorithms can be considered as "logic machines" capable of deriving all plausible structures from a set of structural constraints or "axioms",... [more] Computer-assisted structure elucidation (CASE) using a combination of 1D and 2D NMR data has been available for a number of years. These algorithms can be considered as "logic machines" capable of deriving all plausible structures from a set of structural constraints or "axioms", defined by the spectroscopic data and associated chemical information or prior knowledge. CASE programs allow the spectroscopist not only to determine structures from spectroscopic data but also to study the dependence of the proposed structure on changes to the set of axioms. In this article, we describe the application of the ACD/Structure Elucidator expert system to help resolve the conflict between two different hypothetical hexacyclinol structures derived by different researchers from the NMR spectra of this complex natural product. It has been shown that the combination of algorithms for both structure elucidation and structure validation delivered by the expert system enables the identification of the most probable structure as well as the associated chemical shift assignments.
• 3.88

  Impact points

  Performance validation of neural network based (13)c NMR prediction using a publicly available data source.

  K A Blinov, Y D Smurnyy, M E Elyashberg, T S Churanova, M Kvasha, C Steinbeck, B A Lefebvre, A J Williams

  Journal of chemical information and modeling. 04/2008; 48(3):550-5.

  The validation of the performance of a neural network based 13C NMR prediction algorithm using a test set available from an open source publicly available database, NMRShiftDB, is described. The validation was performed using a version of the database containing ca. 214,000 chemical shifts as well a... [more] The validation of the performance of a neural network based 13C NMR prediction algorithm using a test set available from an open source publicly available database, NMRShiftDB, is described. The validation was performed using a version of the database containing ca. 214,000 chemical shifts as well as for two subsets of the database to compare performance when overlap with the training set is taken into account. The first subset contained ca. 93,000 chemical shifts that were absent from the ACD\CNMR DB, the "excluded shift set" used for training of the neural network and the ACD\CNMR prediction algorithm, while the second contained ca. 121,000 shifts that were present in the ACD\CNMR DB training set, the "included shift set". This work has shown that the mean error between experimental and predicted shifts for the entire database is 1.59 ppm, while the mean deviation for the subset with included shifts is 1.47 and 1.74 ppm for excluded shifts. Since similar work has been reported online for another algorithm we compared the results with the errors determined using Robien's CNMR Neural Network Predictor using the entire NMRShiftDB for program validation.
• 3.88

  Impact points

  Toward more reliable 13C and 1H chemical shift prediction: a systematic comparison of neural-network and least-squares regression based approaches.

  Yegor D Smurnyy, Kirill A Blinov, Tatiana S Churanova, Mikhail E Elyashberg, Antony J Williams

  Journal of chemical information and modeling. 02/2008; 48(1):128-34.

  The efficacy of neural network (NN) and partial least-squares (PLS) methods is compared for the prediction of NMR chemical shifts for both 1H and 13C nuclei using very large databases containing millions of chemical shifts. The chemical structure description scheme used in this work is based on indi... [more] The efficacy of neural network (NN) and partial least-squares (PLS) methods is compared for the prediction of NMR chemical shifts for both 1H and 13C nuclei using very large databases containing millions of chemical shifts. The chemical structure description scheme used in this work is based on individual atoms rather than functional groups. The performances of each of the methods were optimized in a systematic manner described in this work. Both of the methods, least-squares and neural network analyses, produce results of a very similar quality, but the least-squares algorithm is approximately 2--3 times faster.
• 1.61

  Impact points

  Automated structure elucidation of two unexpected products in a reaction of an alpha,beta-unsaturated pyruvate.

  Gary J Sharman, Ian C Jones, Mark P Parnell, Michael C Willis, Mary F Mahon, Dean V Carlson, Antony Williams, Mikhail Elyashberg, Kirill Blinov, Sergey G Molodtsov

  Magnetic resonance in chemistry : MRC. 08/2004; 42(7):567-72.

  The reaction between an alpha,beta-unsaturated pyruvate and ethyl diazoacetate (EDA) yielded two unexpected products. The structures of these products were determined by automated elucidation of the chemical structures using spectroscopic inputs of a series of 1D and 2D NMR data using the computer p... [more] The reaction between an alpha,beta-unsaturated pyruvate and ethyl diazoacetate (EDA) yielded two unexpected products. The structures of these products were determined by automated elucidation of the chemical structures using spectroscopic inputs of a series of 1D and 2D NMR data using the computer program ACD/Structure Elucidator, StrucEluc. The formation of these products is rationalised. Their structures were also confirmed by x-ray crystallography.

• Structure Elucidation from 2D NMR Spectra Using the

  Sergey G. Molodtsov, Mikhail E. Elyashberg, Kirill A. Blinov, Antony J. Williams, Eduard R. Martirosian, Gary E. Martin, Brent Lefebvre

  Journal of Chemical Information and Modeling. 01/2004; 44:1737-1751.

• net.researchgate.refind.jaxb.schema.dblp.I@7dd971a9

  Mikhail E. Elyashberg, Kirill A. Blinov, Antony J. Williams, Sergey G. Molodtsov, Gary E. Martin, Eduard R. Martirosian

  Journal of Chemical Information and Modeling. 01/2004; 44:771-792.
• 3.16

  Impact points

  Application of a new expert system for the structure elucidation of natural products from their 1D and 2D NMR data.

  Mikhail E Elyashberg, Kirill A Blinov, Antony J Williams, Eduard R Martirosian, Sergey G Molodtsov

  Journal of natural products. 06/2002; 65(5):693-703.

  Described herein are applications of the latest version of the StrucEluc expert software system, enhanced to use 2D NMR data, to the structure elucidation of 60 recently isolated natural products. In this study, selected molecules containing between 15 and 65 skeletal atoms and having molecular mass... [more] Described herein are applications of the latest version of the StrucEluc expert software system, enhanced to use 2D NMR data, to the structure elucidation of 60 recently isolated natural products. In this study, selected molecules containing between 15 and 65 skeletal atoms and having molecular masses ranging from 200 to 900 amu have been investigated. The correct structure was determined unambiguously for 58 of these molecules. The structures for 75% of the data sets were determined in less than one minute, while 90% of the analyses required no more than 30 minutes. The strategy of structure elucidation by this expert system is described, and several examples are discussed. These illustrate that StrucEluc is a powerful and versatile analytical tool for the structure elucidation of natural products.

• An expert system for automated structure elucidation utilizing 1H-1H, 13C-1H and 15N-1H 2D NMR correlations.

  K A Blinov, M E Elyashberg, S G Molodtsov, A J Williams, E R Martirosian

  Fresenius' journal of analytical chemistry. 05/2001; 369(7-8):709-14.

  A software program for the automated structure elucidation of complex organic molecules using an expert system and utilizing 2D homo- and heteronuclear correlation 1H, 13C and 15N NMR spectroscopy is described. The methodology is illustrated on the basis of the automated structure determination of s... [more] A software program for the automated structure elucidation of complex organic molecules using an expert system and utilizing 2D homo- and heteronuclear correlation 1H, 13C and 15N NMR spectroscopy is described. The methodology is illustrated on the basis of the automated structure determination of strychnine and some other examples.
• 3.29

  Impact points

  Artificial intelligence systems for molecular spectral analysis.

  M E Elyashberg, V V Serov, L A Gribov

  Talanta. 02/1987; 34(1):21-30.

  A brief survey is given of the most recent publications on development of artificial-intelligence systems for molecular spectral analysis. A new approach to solution of the problems of qualitative molecular spectral analysis is based on an applied logical calculus developed by the authors for fuzzy ... [more] A brief survey is given of the most recent publications on development of artificial-intelligence systems for molecular spectral analysis. A new approach to solution of the problems of qualitative molecular spectral analysis is based on an applied logical calculus developed by the authors for fuzzy predicates. It is suggested that spectral-structural knowledge should be specified in the language of fuzzy predicates, and mechanical theorem-proving procedures used for solving qualitative problems of spectral analysis, the initial information being considered as a set of axioms. System-oriented matters are given consideration. The formalism suggested is a basis for the development of an artificial-intelligence dialogue system capable of solving various problems in molecular spectral analysis while maintaining a dialogue with a research worker using a professionally-restricted natural language.

• Solution of spectral problems by methods of symbolic logic

  L.A. Gribov, M.E. Elyashberg, L.A. Moscovkina

  Journal of Molecular Structure.

  Examples of the practical use of the methods of mathematical logic in structural-group analysis of polyatomic molecules and establishment of ir frequencies characteristic of functional groups are described.Four concrete problems of the first type and three problems of the second type are considered ... [more] Examples of the practical use of the methods of mathematical logic in structural-group analysis of polyatomic molecules and establishment of ir frequencies characteristic of functional groups are described.Four concrete problems of the first type and three problems of the second type are considered in detail. The possibility of using formal logic methods for planning spectral investigations is also studied. A short description is given of a block diagram of the program for a computer of the M-20 type.

• Automation of spectrochemical investigations

  L.A. Gribov, V.A. Dementyev, M.E. Elyashberg, E.Z. Yakupov

  Journal of Molecular Structure.

  An automated system of simultaneous treatment of IR, Raman, UV, NMR and mass spectra is described and used to establish probable molecular structures satisfying the spectra and additional information. Then the vibrational and UV spectra of these structures are calculated and compared with experiment... [more] An automated system of simultaneous treatment of IR, Raman, UV, NMR and mass spectra is described and used to establish probable molecular structures satisfying the spectra and additional information. Then the vibrational and UV spectra of these structures are calculated and compared with experimental data. On the basis of this calculation the most probable structure is singled out and its parameters are determined more exactly.

• Mathematical synthesis and analysis of molecular structures

  V.V. Serov, M.E. Elyashberg, L.A. Gribov

  Journal of Molecular Structure.

  A system of algorithms and programs permitting mathematical synthesis and comprehensive analysis of a complete set of isomeric structural formulae which satisfy a given empirical formula is described. The system offers the possibility of structure- generation control which enables structures belongi... [more] A system of algorithms and programs permitting mathematical synthesis and comprehensive analysis of a complete set of isomeric structural formulae which satisfy a given empirical formula is described. The system offers the possibility of structure- generation control which enables structures belonging to specified classes of compounds to be generated and their topological characteristics to be investigated. For example, all cyclic compounds can be detected and their structural details (such as dimensions, the number of bonds of various multiplicity, the sequence of vertices, etc.) determined. Examples are given illustrating the applicability of the system. The possibility of using this system in prognosticating structures with specified properties is shown.

• Expert systems as a tool for the molecular structure elucidation by spectral methods. Strategies of solution to the problems

  M.E. Elyashberg, Yu.Z. Karasev, E.R. Martirosian, H. Thiele, H. Somberg

  Analytica Chimica Acta.

  A great number of spectral tasks were solved to elaborate strategies of molecular structure elucidation by expert systems based on the spectrum-structure correlations. The X-PERT system was used for this purpose. The main assumptions of the structural-group spectral analysis and the main consequence... [more] A great number of spectral tasks were solved to elaborate strategies of molecular structure elucidation by expert systems based on the spectrum-structure correlations. The X-PERT system was used for this purpose. The main assumptions of the structural-group spectral analysis and the main consequences of their violation are considered. The typical difficult situations met with, while problem solving, are investigated. A method for quality estimation of solutions to spectrum-structure problems is suggested. The capacity of 13C NMR chemical shift prediction by the additivity rules for selection the true structure was verified. Strategies of the solution to a problem are suggested. The main feature of the offered approach is in a series of reiterations accompanied by gradual growth of severity of the constraints which are imposed on the answer structural file. It is concluded that X-PERT can be successfully used for the structure elucidation of medium-sized molecules as well as for teaching spectral methods to students.