Sergey G. Molodtsov

Structure Elucidator: a versatile expert system for molecular structure elucidation from 1D and 2D NMR data and molecular fragments.

StrucEluc is an expert system that allows the computer-assisted elucidation of chemical structures based on the inputs of a series of spectral data including 1D and 2D NMR and mass spectra. The system has been enabled to allow a chemist to utilize fragments stored in a fragment database as well as user-defined fragments submitted by the chemist in the structure elucidation process. The association of fragments in this way has been shown to dramatically speed up the process of structure generation from 2D NMR data and has helped to minimize or eliminate the need for user intervention thereby further enabling the vision of automated elucidation. The use of fragments has frequently transformed very difficult 2D NMR elucidation challenges into easily solvable tasks. A strategy to utilize molecular fragments has been developed and optimized based on specific challenging examples. This strategy will be described here using real world examples. Experience gained by solving more than 150 structure elucidation problems from a variety of literature sources is also reviewed in this work.

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

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. Copyright

Are deterministic expert systems for computer-assisted structure elucidation obsolete?

Expert systems for spectroscopic molecular structure elucidation have been developed since the mid-1960s. Algorithms associated with the structure generation process within these systems are deterministic; that is, they are based on graph theory and combinatorial analysis. A series of expert systems utilizing 2D NMR spectra have been described in the literature and are capable of determining the molecular structures of large organic molecules including complex natural products. Recently, an opinion was expressed in the literature that these systems would fail when elucidating structures containing more than 30 heavy atoms. A suggestion was put forward that stochastic algorithms for structure generation would be necessary to overcome this shortcoming. In this article, we describe a comprehensive investigation of the capabilities of the deterministic expert system Structure Elucidator. The results of performing the structure elucidation of 250 complex natural products with this program were studied and generalized. The conclusion is that 2D NMR deterministic expert systems are certainly capable of elucidating large structures (up to about 100 heavy atoms) and can deal with the complexities associated with both poor and contradictory spectral data.

Structure revision of asperjinone using computer-assisted structure elucidation methods.

The elucidated structure of asperjinone (1), a natural product isolated from thermophilic Aspergillus terreus, was revised using the expert system Structure Elucidator. The reliability of the revised structure (2) was confirmed using 180 structures containing the (3,3-dimethyloxiran-2-yl)methyl fragment (3) as a basis for comparison and whose chemical shifts contradict the suggested structure (1).

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

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

Reconstruction of a graph from 2-vicinities of its vertices

We prove that a connected graph of diameter at least 4 and of girth 7 or more (in particular, a tree) can be exactly reconstructed from metric balls of radius 2 of all its vertices. On the other hand, there exist graphs of diameter 3 and of girth 6 which are not reconstructible. This new graph theory problem is motivated by reconstruction of chemical compounds.

New computer-assisted methods for the elucidation of molecular structure from 2-D spectra

General principles of the construction of expert systems for the elucidation of the structure of molecules from their spectra were considered. The principal attention was focused on systems based on the use of 2-D NMR spectra. The structural information extracted from 2D NMR spectra was characterized, and the strategy was outlined for structure elucidation under the conditions when the analyzed spectrostructural information is incomplete, fuzzy, and contradictory. The most advanced expert system ACD/Structure Elucidator, which is capable of determining the structure and stereochemistry of large molecules, in particular, those typical in the chemistry of natural compounds, is described as an example.

Reconstruction of a graph from 2–vicinities of its vertices

Abstract We prove that a connected graph of diameter at least 4 and of girth 7 or more (in particular, a tree) can be exactly reconstructed from metric balls of radius 2 of all its vertices. On the other hand, there exist graphs of diameter 3 and of girth 6 which are not reconstructible. This new graph theory problem is motivated by reconstruction of chemical compounds.

Largest Graphs of Diameter 2 and Maximum Degree 6

Abstract The results of computer generation of the largest graphs of diameter 2 and maximum degree 6 are presented. The order of such graphs is equal 32. There are exactly 6 graphs of diameter 2 and maximum degree 6 on 32 vertices including one vertex-transitive graph.