Matevž Pompe

Prediction of rate constants for the reaction of O3 with different organic compounds

Abstract Volatile organic compounds (VOCs) of anthropogenic and biogenic origin play an important role in different photochemical processes in the atmosphere. In order to evaluate the lifetime of individual VOCs in the atmosphere and their impact on the photochemical processes, a detailed knowledge about their abundance in the atmosphere as well as kinetic parameters for the reactions with reactive species are required. Coding capabilities of different structural descriptors for the prediction of reactive rate constants of VOCs with ozone were studied. A diverse data set of 117 compounds with known reaction rate constants was taken from the literature. A 6-parameter MLR model was selected based on prediction capabilities of the model. The final prediction ability of the model was evaluated by 10-fold cross-validation procedure. The average root-mean squared error value for the prediction of log k O 3 was 0.99.

Modelling of gas chromatographic retention indices using counterpropagation neural networks

Abstract Unspecific fragmentation of organic substances in the ion source of MS detector hinders identification of organic substances in gas chromatographic separation. In such instances theoretical prediction of the retention indices could be a useful tool. A new method for theoretical prediction of gas chromatographic retention indices is described. Artificial neural networks were trained in counterpropagation mode to predict retention data. Extensive data sets of simple organic compounds with known retention indices taken from the literature were serving for training and test sets. The structure of molecules was described with a 12-dimensional vector the components of which were topological and chemical parameters. Various geometries of artificial neural networks were tested and different divisions into training and testing sets tried. The ANN with the configuration of 15 × 15 neurons has been chosen for routine work. The average RMS value was 36.6 retention time units.

Using variable and fixed topological indices for the prediction of reaction rate constants of volatile unsaturated hydrocarbons with OH radicals.

Volatile organic compounds (VOCs) play an important role in different photochemical processes in the troposphere. In order to predict their impact on ozone formation processes a detailed knowledge about their abundance in the atmosphere as well as their reaction rate constants is required. The QSPR models were developed for the prediction of reaction rate constants of volatile unsaturated hydrocarbons. The chemical structure was encoded by constitutional and topological indices. Multiple linear regression models using CODESSA software was developed with the RMS(CV) error of 0.119 log units. The chemical structure was encoded by six topological indices. Additionally, a regression model using a variable connectivity index was developed. It provided worse cross-validation results with an RMS(CV) error of 0.16 log units, but enabled a structural interpretation of the obtained model. We differentiated between three classes of carbon atoms: sp2-hybridized, non-allylic sp3-hybridized and allylic sp3-hybridized. The structural interpretation of the developed model shows that most probably the most important mechanisms are the addition to multiple bonds and the hydrogen atom abstraction at allylic sites.

Variable Connectivity Index as a Tool for Modeling Structure- Property Relationships

We report on the calculation of normal boiling points for a series of n = 58 aliphatic alcohols using the variable connectivity index in which variables x and y are used to modify the weights on carbon (x) and oxygen atoms (y) in molecular graphs, respectively. The optimal regressions are found for x = 0.80 and y = -0.90. Comparison is made with available regressions on the same data reported previously in the literature. A refinement of the model was considered by introducing different weights for primary, secondary, tertiary, and quaternary carbon atoms. The standard error in the case of the normal boiling points of alcohols was slightly reduced with optimal weights for different carbon atoms from s = 4.1 degrees C (when all carbon atoms were treated as alike) to s = 3.9 degrees C.

π-Electron Partitions, Signatures, and Clar Structures of Selected Benzenoid Hydrocarbons

It is shown for a representative set of isomeric benzenoids that pi-electron partitions and signatures can serve for characterizing and ordering benzenoids. Benzenoid signatures (sequences s6 through s1 where the subscripts correspond to numbers of pi electrons in all rings) are obtained by examining the numbers of assigned pi electrons ranging from 6 to 1 for each ring in all resonance structures. The pi-electron partitions and signatures of all 33 non-isoarithmic peri-condensed benzenoid hydrocarbons with eight rings and four contiguous internal carbon atoms allow an ordering of these benzenoids that agrees fairly well with increasing numbers of Kekulé valence structures and Clar sextets. Interestingly, an excellent correlation (R2 > 0.99) is observed between s6 + s5 + s2 + s1 and s4 + s3, and an explanation for this observation is provided: the number P of pi electrons is divided unequally between two components: s34 = s4 + s3 and s1256 = s6 + s5 + s2 + s1 so that s1256 or the quotient s1256/s34 = Q can serve as a new metric for perfect matchings of polyhexes and a criterion for ordering and for evaluating the complexity of isomeric benzenoids quantitatively.

Calibration of mass selective detector in non-target analysis of volatile organic compounds in the air.

Volatile organic compounds (VOCs) play an important role in the chemistry of the atmosphere and in biogeochemistry. They contribute to the oxidative capacity of the atmosphere, particle and air pollutants, as well as to the production of greenhouse gases (for instance ozone). Among analytical techniques for their determination in the atmosphere gas chromatography coupled with mass spectrometry (GC-MS) offers several advantages. However, for an accurate quantification calibration with standard substances is necessary. A quantitative structure-property relationship (QSPR) model for the prediction of MS response factors was developed on basis of our experimental measurements for the quantification of ozone precursors present in the atmosphere. A linear correlation between chemical structures and response factors was established by using a 7-parameter MLR model. The average error in the prediction of response factors was calculated by cross-validation procedure and was below 20%, which is sufficient for the determination of VOCs in the air. The proposed procedure is time consuming so it is more suited for the quantification of tentatively identified organic compounds during the reprocessing of MS chromatograms in cases when the original sample is no longer available.

Study of sorptive properties of trap systems for selective enrichment of volatile organic compounds from tobacco smoke samples

Currently for compound detection the most difficult are sampling steps and sample preparation for analysis of highly volatile compounds (VOC) and their derivatives, such as ethylene, propylene, acetaldehyde and acetone. For this purpose single- and multibed sorbent tubes were prepared, filled with the following materials: Tenax TA, Carbotrap, Carbopack C, Carbosieve SIII, Carboxen 569. The linear relationship between the mass of analysed compounds and decreased recovery from carbon molecular sieve was determined. The highest desorption recovery (∼100%) for C2–C5 hydrocarbons from multibed sorption traps contained Tenax TA/Carbotrap/Carbosieve SIII. Sorbent traps were also used to determine selected VOC (acetone, acetaldehyde, 2-butanone, benzene, toluene, m,p-xylene) in gas phase of tobacco smoke from single 1R5F reference cigarette. Quantitative analysis of selected compounds was done by standard addition method with r 2 = 0.9931 for 2-butanone and 0.9773 for acetaldehyde. The best combination of sorbent materials included Tenax TA/Carbotrap/Carboxen 569 allowing for VOC determination at low level: 0.31 µg L−1 for m,p-xylene and 40.24 µg L−1 for acetaldehyde. This composition of multibed sorption trap also gave the highest recovery for acetone and 2-butanone as well as the lowest RSD (9.81%, and 9.14%, respectively).

Application of variable anti-connectivity index to active sites. Modelling pK a values of aliphatic monocarboxylic acids

A partial distance-weighted variable anti-connectivity topological index was introduced for modelling pK a values of 31 aliphatic carboxylic acids and haloalkyl-carboxylic acids. The partial distance-weighted variable anti-connectivity index showed superior modelling capabilities compared with the index calculated from the complete graph, because it is capable of accounting correctly for the intramolecular interactions of unconnected vertices to specific bond strengths (active site), thereby improving the RMSCV error by about 30% (0.221 pK a units).

NMR spectral properties of the tetramantanes - nanometer-sized diamondoids.

Tetramantanes, and all diamondoid hydrocarbons, possess carbon frameworks that are superimposable upon the cubic diamond lattice. This characteristic is invaluable in assigning their 1H and 13C NMR spectra because it translates into repeating structural features, such as diamond‐cage isobutyl moieties with distinctively complex methine to methylene signatures in COSY and HMBC data, connected to variable, but systematic linkages of methine and quaternary carbons. In all tetramantane C22H28 isomers, diamond‐lattice structures result in long‐range 4JHH, W‐coupling in COSY data, except where negated by symmetry; there are two highly symmetrical and one chiral tetramantane (showing seven 4JHH). Isobutyl‐cage methines of lower diamondoids and tetramantanes are the most shielded resonances in their 13C spectra (<29.5 ppm). The isobutyl methylenes are bonded to additional methines and at least one quaternary carbon in the tetramantanes. W‐couplings between these methines and methylenes clarify spin‐network interconnections and detailed surface hydrogen stereochemistry. Vicinal couplings of the isobutyl methylenes reveal positions of the quaternary carbons: HMBC data then tie the more remote spin systems together. Diamondoid 13C NMR chemical shifts are largely determined by α and β effects, however γ‐shielding effects are important in [123]tetramantane. 1H NMR chemical shifts generally correlate with numbers of 1,3‐diaxial H–H interactions. Tight van der Waals contacts within [123]tetramantanes molecular groove, however, form improper hydrogen bonds, deshielding hydrogen nuclei inside the groove, while shielding those outside, indicated by Δδ of 1.47 ppm for geminal hydrogens bonded to C‐3,21. These findings should be valuable in future NMR studies of diamondoids/nanodiamonds of increasing size. Copyright

Development of a calibration system to evaluate VOC losses in a branch enclosure

Considerable uncertainties are associated with the experimental estimates of emission rates of different volatile organic compound (VOC) species from the biosphere to the atmosphere. Some of this uncertainty derives from the sampling and analytical procedures used in emission rate measurements. A calibration system was developed in order to evaluate possible errors in the measurements of biogenic emission rates using a branch enclosure system. Two types of calibration procedures were tested, a standard additions technique and an internal standard procedure. Both techniques were used to evaluate possible losses while sampling isoprene and monoterpenes, which are the most abundant VOCs of biogenic origin. The losses to Teflon lines and the empty sampling system were tested and losses to the branch enclosure system installed on two VOC emitting plant species were evaluated. A considerable loss of isoprene (approximately 18% of inflow concentration 65 ng l(-1)) to the empty enclosure system and to the system installed on the plant was measured, but no losses of monoterpenes were observed.