Biomedical subjects

Igor V Tokmakov

Publications and source records attributed to Igor V Tokmakov.

4 recordsLinked to original sources

PubMed2006

Urea and urea nitrate decomposition pathways: a quantum chemistry study.

Electronic structure calculations have been performed to investigate the initial steps in the gas-phase decomposition of urea and urea nitrate. The most favorable decomposition pathway for an isolated urea molecule leads to HNCO and NH3. Gaseous urea nitrate formed by the association of urea and HNO3 has two isomeric forms, both of which are acid-base complexes stabilized by the hydrogen-bonding interactions involving the acidic proton of HNO3 and either the O or N atoms of urea, with binding energies (D0(o), calculated at the G2M level with BSSE correction) of 13.7 and 8.3 kcal/mol, respectively, and with estimated standard enthalpies of formation (delta(f)H298(o) of -102.3 and -97.1 kcal/mol, respectively. Both isomers can undergo relatively facile double proton transfer within cyclic hydrogen-bonded structures. In both cases, HNO3 plays a catalytic role for the (1,3) H-shifts in urea by acting as a donor of the first and an acceptor of the second protons transferred in a relay fashion. The double proton transfer in the carbonyl/hydrogen bond complex mediates the keto-enol tautomerization of urea, and in the other complex the result is the breakdown of the urea part to the HNCO and NH3 fragments. The enolic form of urea is not expected to accumulate in significant quantities due to its very fast conversion back to H2NC(O)NH2 which is barrierless in the presence of HNO3. The HNO3-catalyzed breakdown of urea to HNCO and NH3 is predicted to be the most favorable decomposition pathway for gaseous urea nitrate. Thus, HNCO + NH3 + HNO3 and their association products (e.g., ammonium nitrate and isocyanate) are expected to be the major initial products of the urea nitrate decomposition. This prediction is consistent with the experimental T-jump/FTIR data [Hiyoshi et al. 12th Int. Detonation Symp., Aug 11-16, San Diego, CA, 2002].

Journal Article↗

PubMed2006

Interpolating moving least-squares methods for fitting potential-energy surfaces: further improvement of efficiency via cutoff strategies.

In standard applications of interpolating moving least squares (IMLS) for fitting a potential-energy surface (PES), all available ab initio points are used. Because remote ab initio points negligibly influence IMLS accuracy and increase IMLS time-to-solution, we present two methods to locally restrict the number of points included in a particular fit. The fixed radius cutoff (FRC) method includes ab initio points within a hypersphere of fixed radius. The density adaptive cutoff (DAC) method includes points within a hypersphere of variable radius depending on the point density. We test these methods by fitting a six-dimensional analytical PES for hydrogen peroxide. Both methods reduce the IMLS time-to-solution by about an order of magnitude relative to that when no cutoff method is used. The DAC method is more robust and efficient than the FRC method.

Journal Article↗

PubMed2005

Experimental and computational studies of the phenyl radical reaction with propyne.

The kinetics for the gas-phase reaction of phenyl radical with propyne has been measured by cavity ring-down spectrometry (CRDS), and the mechanism and initial product branching have been elucidated with the help of quantum chemical calculations. Absolute rate constants measured by the CRDS technique can be expressed by the following Arrhenius equation: (k/cm(3) mol(-1) s(-1)): k(propyne)(T=301-428 K)=(3.68+/-0.92) x 10(11)exp[-(1685+/-80)/T]. The experiment is unable to distinguish between the possible reactive channels, but theory indicates that phenyl radicals preferably add to the unsaturated terminal carbon atom in propyne under our experimental conditions. Theoretical kinetic calculations, employing high-level G2M(RCC, RMP2) and G3 energetic and IRCMax(RCCSD(T)//B3LYP-DFT) molecular parameters, reproduce the total experimental rate constants within a factor of three. Calculated total and branching rate constants are provided for high-T kinetic modeling. Addition reactions of phenyl to C3H4 are estimated to be less important molecular-growth pathways in high-T conditions (T>1000 K) in comparison to the C6H5 + C2H2 reaction.

Journal Article↗

PubMed2005

The reaction of phenyl radical with molecular oxygen: a G2M study of the potential energy surface.

Ab initio G2M calculations have been performed to investigate the potential energy surface for the reaction of C6H5 with O2. The reaction is shown to start with an exothermic barrierless addition of O2 to the radical site of C6H5 to produce phenylperoxy (1) and, possibly, 1,2-dioxaspiro[2.5]octadienyl (dioxiranyl, 8) radicals. Next, 1 loses the terminal oxygen atom to yield the phenoxy + O products (3) or rearranges to 8. The dioxiranyl can further isomerize to a seven-member ring 2-oxepinyloxy radical (10), which can give rise to various products including C5H5 + CO2, pyranyl + CO, o-benzoquinone + H, and 2-oxo-2,3-dihydrofuran-4-yl + C2H2. Once 10 is produced, it is unlikely to go back to 8 and 1, because the barriers separating 10 from the products are much lower than the reverse barrier from 10 to 8. Thus, the branching ratio of C6H5O + O against the other products is mostly controlled by the critical transition states between 1 and 3, 1 and 8, and 8 and 10. According to the calculated barriers, the most favorable product channel for the decomposition of 10 is C5H5 + CO2, followed by pyranyl + CO and o-benzoquinone + H. Since C6H5O + O and C5H5 + CO2 are expected to be the major primary products of the C6H5 + O2 reaction and thermal decomposition of C6H5O leads to C5H5 + CO, cyclopentadienyl radicals are likely to be the major product of phenyl radical oxidation, and so it results in degradation of the six-member aromatic ring to the five-member cyclopentadienyl ring. Future multichannel RRKM calculations of reaction rate constants are required to support these conclusions and to quantify the product branching ratios at various combustion conditions.

Benzene↗