Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index.

MOTIVATION: Matching both the retention index (RI) and the mass spectrum of an unknown compound against a mass spectral reference library provides strong evidence for a correct identification of that compound. Data on retention indices are, however, available for only a small fraction of the compounds in such libraries. We propose a quantitative structure-RI model that enables the ranking and filtering of putative identifications of compounds for which the predicted RI falls outside a predefined window. RESULTS: We constructed multiple linear regression and support vector regression (SVR) models using a set of descriptors obtained with a genetic algorithm as variable selection method. The SVR model is a significant improvement over previous models built for structurally diverse compounds as it covers a large range (360-4100) of RI values and gives better prediction of isomer compounds. The hit list reduction varied from 41% to 60% and depended on the size of the original hit list. Large hit lists were reduced to a greater extend compared with small hit lists. AVAILABILITY: http://appliedbioinformatics.wur.nl/GC-MS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Quantum chemical calculation of infrared spectra of acidic groups in chabazite in the presence of water.

The changes in the spectra of the acidic group in chabazite are studied by quantum chemical calculations. The zeolite is modeled by two clusters consisting of eight tetrahedral atoms arranged in a ring and seven tetrahedral atoms coordinated around the zeolite OH group. The potential energy and dipole surfaces were constructed from the zeolite OH stretch, in-plane and out-of-plane bending coordinates, and the intermolecular stretch coordinate that corresponds to a movement of the water molecule as a whole. Both the anharmonicities of the potential energy and dipole were taken into account by calculation of the frequencies and intensities. The matrix elements of the vibrational Hamiltonian were calculated within the discrete variable representation basis set. We have assigned the experimentally observed frequencies at approximately 2900, approximately 2400, and approximately 1700 cm(-1) to the strongly perturbed zeolite OH vibrations caused by the hydrogen bonding with the water molecule. The ABC triplet is a Fermi resonance of the zeolite OH stretch mode with the overtone of the in-plane bending (the A band) and the overtone of the out-of-plane bending (the C band). In the B band the stretch is also coupled with the second overtone of the out-of-plane bending. The frequencies at approximately 3700 and approximately 3550 cm(-1) we have assigned to the OH stretch frequencies of a slightly perturbed water molecule.