Database retrieval techniques for carbon-13 nuclear magnetic resonance spectrum simulation

J. Chem. Inf. Comput. Sci.

1996

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An enhanced version of an algorithm is discussed which encodes a description of the chemical environment of carbon atoms in a manner that correlates to carbon-13 nuclear magnetic resonance (13C NMR) chemical shifts. The encoding algorithm uses a vector-based approach in which the first dimension of the vector represents the chemical shift of the carbon atom, the second dimension represents the collective influence of atoms one bond away from the carbon on its chemical shift, and each successive dimension represents the influence of the atoms one bond further away. This encoding algorithm is a key component of a 13C NMR spectrum simulation procedure in which each of the carbons in a large database of known structures and spectra is represented as a vector. Database search methods based on vector comparisons are used to find the closest matching chemical environments and associated chemical shifts for each of the carbons in a structure input by a user. Enhancements to the original algorithm include an expansion of the number of atom classes treated, the addition of a scheme to treat aromatic systems as a special case, and the use of an expanded vector format to regain some of the information lost by collapsing the molecular structure to a vector representation. To test this algorithm, a database of structures and spectra is split into training and test sets consisting of 16 959 and 4240 structures, respectively. Experiments performed to optimize several parameters associated with the encoding algorithm are followed by comparing the retrieved (i.e., predicted) and actual chemical shifts for the structures in the test set. For the optimal parameter settings found, the median of the mean absolute deviations in chemical shifts for the structures in the test set was 1.30 ppm and was obtained with an expanded vector representation based on 15 dimensions.

Section: Resultsmentioning

confidence: 99%

Enhanced Structural Encoding Algorithm for Database Retrievals of Carbon-13 Nuclear Magnetic Resonance Chemical Shifts

and

J. Chem. Inf. Comput. Sci.

1996

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“…The algorithm used in this work was developed by Small and Jurs 18 and has been used previously to implement chemical shift retrievals. 15 In this scheme, the environment of carbon atom a is represented as an n+1 dimensional vector of the form where the first dimension, e 0 , characterizes atom a, the second dimension, e 1 , describes the influence of atoms one bond removed from atom a on its chemical shift, and each successive dimension describes the collective influence of the atoms one bond further from atom a on the chemical shift of that atom. Experimental chemical shifts of small molecules were used to define a set of parameters for use in computing the elements of e a .…”

Section: Resultsmentioning

confidence: 99%

“…The purpose of this scheme is to represent the chemical environment of carbon atoms in a manner that relates to the chemical shift and in a way that facilitates quantitative comparisons between environments. The algorithm used in this work was developed by Small and Jurs and has been used previously to implement chemical shift retrievals . In this scheme, the environment of carbon atom a is represented as an n+1 dimensional vector of the form where the first dimension, e 0 , characterizes atom a , the second dimension, e 1 , describes the influence of atoms one bond removed from atom a on its chemical shift, and each successive dimension describes the collective influence of the atoms one bond further from atom a on the chemical shift of that atom.…”

Section: Resultsmentioning

confidence: 99%

“…In our work, this database searching procedure is based on encoding carbon atom environments in a multidimensional vector format and then employing a conventional vector-based search system to retrieve the most closely matching environments to a desired target carbon. 15 A limitation of this method is the significant computational overhead associated with the requirement to perform potentially hundreds of thousands of Euclidean distance calculations to implement the vector comparisons. There are several strategies which could be used to speed up this vector-based search.…”

Section: Introductionmentioning

confidence: 99%

“…Since the database retrieval step must be performed for each carbon atom in the input structure and the closest matches are drawn from the entire atom-based database, the retrieval algorithm used must be as efficient as possible. In our work, this database searching procedure is based on encoding carbon atom environments in a multidimensional vector format and then employing a conventional vector-based search system to retrieve the most closely matching environments to a desired target carbon . A limitation of this method is the significant computational overhead associated with the requirement to perform potentially hundreds of thousands of Euclidean distance calculations to implement the vector comparisons.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Performance Enhancement of Vector-Based Search Systems: Application to Carbon-13 Nuclear Magnetic Resonance Chemical Shift Prediction

Schweitzer

J. Chem. Inf. Comput. Sci.

1996

Self Cite

A database partitioning algorithm is described for use in increasing the speed of vector-based search systems. When implemented with a library of n-dimensional vectors to be searched, the algorithm subdivides the n-dimensional data space into multiple levels of n-dimensional boxes. The vectors lying within each box are catalogued, and the search for the nearest matches to a target vector is reduced to a search of only the box in the data space containing the target vector and the immediate neighboring boxes. The use of multiple layers of boxes serves to reduce the computer memory requirements for implementing the partitioning scheme while still allowing the number of vector comparisons in the search to be minimized. In the work presented, this algorithm is applied to the prediction of carbon-13 nuclear magnetic resonance chemical shifts. A database retrieval system for chemical shifts is implemented based on encoding the chemical environments of carbon atoms into a seven-dimensional vector representation. The chemical shifts of target carbon atoms are estimated by performing a search of the database for carbon environments that match the targets. The performance enhancement afforded by the partitioning algorithm as well as the search accuracy is found to depend on three design variables. Employing a library of 133 533 environment vectors, these variables are optimized for the chemical shift prediction application by performing searches on sets of 39 074 and 3900 test carbons. Based on the relative number of vector comparisons required to implement the searches with and without partitioning, speed increases by factors of 34.1 and 19.9 are realized for searches in which the 5 and 200 nearest matches are found, respectively.

ChemInform Abstract: Database Retrieval Techniques for 13C NMR Spectrum Simulation.

1992

ChemInform