Automated structure elucidation — the benefits of a symbiotic relationship between the spectroscopist and the expert system

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

doi:10.1002/jhet.5570400610

Cited by 15 publications

(13 citation statements)

References 38 publications

(72 reference statements)

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“…In such cases, a fragment library containing about 1,000,000 fragments, as well as user-defined fragments introduced by chemists on the basis of prior knowledge, can be utilized. We provided the ability to embed fragments into the MCDs if they included carbon centers with the appropriate chemical shifts matching the experimental data [33][34][35]. The fragments from the library also include assigned carbon atoms transferred from the molecules used in the construction of the structure library databases.…”

Section: Methodology Of Applying Found Fragments In Acd/sementioning

confidence: 99%

“…This approach can utilize the symbiosis between the spectroscopist and the expert system as the scientist inputs user fragments and participates in the selection of relevant fragments, and this allows problems that seemed to be hopeless at the outset of the structure elucidation process to be solved. Our experiences accumulated as a result of elucidating the structures of 150 natural products were reported in our publications [33][34][35]. Structures 11-18, together with their assigned 13 C chemical shifts, were used for the creation of a user structure database.…”

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confidence: 99%

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ACD/Structure Elucidator: 20 Years in the History of Development

Elyashberg¹,

Williams²

2021

Molecules

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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.

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Section: Methodology Of Applying Found Fragments In Acd/sementioning

confidence: 99%

mentioning

confidence: 99%

ACD/Structure Elucidator: 20 Years in the History of Development

Elyashberg¹,

Williams²

2021

Molecules

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“…In this example, the MAX-ERR-LRDC value was set to zero. This did not hinder the identification of a correct result, since the two non-standard COSY correlations (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21) and (4-9), indicated by arrows in the structure 6.1, had been extended to 3-5 bonds.…”

Section: The Expert System Cisoc-sesmentioning

confidence: 97%

“…Numerous experiments have enabled workers [4][5][6][7][8][9][10] to outline general strategies for the solution of problems based on 2D NMR data. These strategies include the detection and elimination of contradictions in the input data and the usage of additional parameters that reduce uncertainty around the input data.…”

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confidence: 99%

CASE 2D NMR-based Expert Systems

2011

Contemporary Computer-Assisted Approaches to Molecular Structure Elucidation

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Modern expert systems utilize 1D and 2D NMR data. The 2D NMR expert systems described in the literature over the last two decades will be reviewed as these form the foundation of understanding from which modern systems have been developed. These systems include the SESAMI, CISOC-SES, LSD, COCON and LUCY systems. These systems have previously demonstrated the possibility of elucidating structures common to organic chemistry utilizing 1H-1H COSY-connectivities, one-bond and long-range 1H-13C correlations. These systems have paved the way for the development of the most effective strategies for the application of expert systems.

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“…If the dataset does not contain non-standard connectivities, then the program completes the process of structure generation and the further solution of the problem is carried out as described previously. 3,21,22 If an attempt with m ¼ 0 proves to be unsuccessful then the program automatically performs FSG starting with m ¼ 1, a ¼ 16, and continues problem solving in the manner described earlier for Mode 3. The merit of such an approach is that no assumption regarding the a value is necessary.…”

Section: Modes Of Fsgmentioning

confidence: 99%

The Challenge of Non-Standard Spectral Responses and the Role of Fuzzy Structure Generation

2011

Contemporary Computer-Assisted Approaches to Molecular Structure Elucidation

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Examples discussed in Chapters 6 and 9 lead us to conclude that the CASE 2D NMR methodology can provide solutions for computer-assisted structure elucidation tasks in a reasonable time if the 2D NMR and MS data are true, consistent and complete (i.e. the number of observed NMR correlations is large enough to sufficiently define the connectivities within a structure). If at least one of these conditions is violated the possibility to somehow find a correct solution to the problem decreases significantly. As was shown earlier in Chapter 8, methods to overcome the presence of contradictions in experimental data have been suggested and the corresponding algorithms have been developed and implemented in the StrucEluc system. In this Chapter we will consider the different StrucEluc-based strategies for molecular structure elucidation in those situations when 2D NMR spectra contain non-standard correlations (NSCs). These strategies were developed and tested using a series of more than 60 separate structure elucidations with deliberately contradictory 2D NMR data. 2D NMR literature data, as well as raw 2D NMR spectra, were used in this study. The spectral data were entered into the program and the structures were assumed to be unknown. Later, an attempt was made to elucidate the structures on the assumption that no information existed regarding the presence of contradictions in the 2D NMR data. These problems were used to perform numerous experiments to determine and remove the contradictions. This was feasible, since the 2D NMR data related to these problems were known to contain COSY and/or HMBC connectivities of non-standard length.It was shown that the program was capable of determining the presence of connectivities of non-standard length in 90% of all cases using the MCD New Developments in NMR No. 1

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Automated structure elucidation — the benefits of a symbiotic relationship between the spectroscopist and the expert system

Cited by 15 publications

References 38 publications

ACD/Structure Elucidator: 20 Years in the History of Development

ACD/Structure Elucidator: 20 Years in the History of Development

CASE 2D NMR-based Expert Systems

The Challenge of Non-Standard Spectral Responses and the Role of Fuzzy Structure Generation

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