Artur Ratkiewicz

Many‐body perturbation theory of electrostatic interactions between molecules: Comparison with full configuration interaction for four‐electron dimers

Many‐body perturbation theory for a direct calculation of the electrostatic interaction energy is developed. Since no multipole expansion is used, the obtained electrostatic energy includes the short‐range contributions resulting from the overlap (penetration) of monomers’ charge distributions. The influence of intramonomer electronic correlation is accounted for by the perturbation expansion in terms of the Mo/ller–Plesset type fluctuation potentials for the interacting molecules. Two types of expansions are introduced: one based on the standard Mo/ller–Plesset expansion of the electron density, and the second accounting for the perturbation induced modifications of the monomer’s Fock operators, i.e., for the so‐called response or orbital relaxation effects. Explicit orbital expressions for the terms through the fourth order in the intramonomer fluctuation potentials are derived. In this way the leading three‐particle correlation contribution to the electrostatic energy is taken into account. Numerical r...

Kinetics of 1,4-Hydrogen Migration in the Alkyl Radical Reaction Class

The kinetics of the 1,4-intramolecular hydrogen migration in the alkyl radicals reaction class has been studied using reaction class transition-state theory combined with the linear energy relationship (LER) and barrier height grouping (BHG) approach. The rate constants for the reference reaction of n-C(4)H(9) were obtained by canonical variational transition-state theory (CVT) with the small curvature tunnelling (SCT) correction in the temperature range 300-3000 K with potential-energy surface information computed at the CCSD(T)/cc-pVDZ//BH&HLYP/cc-pVDZ level of theory. Error analyses indicate that RC-TST/LER, where only reaction energy is needed, and RC-TST/BHG, where no other information is needed, can predict rate constants for any reaction in this reaction class with excellent accuracy. Specifically, for this reaction class the RC-TST/LER method has less than 65% systematic errors in the predicted rate constants, while the RC-TST/BHG method has less than 80% error when compared to explicit rate calculations.

Kinetics of the C–C Bond Beta Scission Reactions in Alkyl Radical Reaction Class

Kinetics of the β-scission in alkyl radical reaction class was studied using the reaction class transition state theory (RC-TST) combined with the linear energy relationship (LER) and the barrier height grouping (BHG) approach. All necessary parameters were derived from first-principle density functional calculations for a representative set of 21 reactions. Different error analyses and comparisons with available literature data were made. Direct comparison with available experimental data indicates that the RC-TST/LER, where only reaction energy is needed, can predict rate constants for any reaction in this reaction class with excellent accuracy. Specifically for this reaction class, the RC-TST/LER method has less than 60% systematic errors on average in the predicted rate constants when compared to explicit rate calculations.

Kinetics of the hydrogen abstraction C2H3* + alkane --> C2H4 + alkyl radical reaction class.

This paper presents an application of the reaction class transition state theory (RC-TST) to predict thermal rate constants for hydrogen abstraction reactions of the type C(2)H(3) + alkane --> C(2)H(4) + alkyl radical. The linear energy relationship (LER) was proven to hold for both noncyclic and cyclic hydrocarbons. We have derived all parameters for the RC-TST method from rate constants of 19 representative reactions, coupling with LER and the barrier height grouping (BHG) approach. Both the RC-TST/LER, where only reaction energy is needed, and the RC-TST/BHG, where no other information is needed, can predict rate constants for any reaction in this reaction class with satisfactory accuracy for combustion modeling. Our analysis indicates that less than 90% systematic errors on the average exist in the predicted rate constants using the RC-TST/LER or RC-TST/BHG method, while in comparison to explicit rate calculations, the differences are within a factor of 2 on the average.

Kinetics of 1,5-hydrogen migration in alkyl radical reaction class.

Kinetics of the 1,5-intramolecular hydrogen migration in the alkyl radicals reaction class has been studied using the reaction class transition state theory combined with the linear energy relationship (LER) and the barrier height grouping (BHG) approach. The high pressure limits of the rate constants for the reference reaction of 1-pentyl → 1-pentyl, calculated by the Canonical Variational Transition State Theory (CVT) with the Small Curvature Tunneling (SCT), are taken from the literature. Direct comparison with available experimental data indicates that the RC-TST/LER, where only reaction energy is needed, can predict rate constants for any reaction in this reaction class with excellent accuracy. Specifically for this reaction class, the RC-TST/LER method has less than 65% systematic errors in the predicted rate constants when compared to explicit rate calculations.

Mechanism and Kinetics of Low-Temperature Oxidation of a Biodiesel Surrogate: Methyl Propanoate Radicals with Oxygen Molecule

This paper presents a computational study on the low-temperature mechanism and kinetics of the reaction between molecular oxygen and alkyl radicals of methyl propanoate (MP), which plays an important role in low-temperature oxidation and/or autoignition processes of the title fuel. Their multiple reaction pathways either accelerate the oxidation process via chain branching or inhibit it by forming relatively stable products. The potential energy surfaces of the reactions between three primary MP radicals and molecular oxygen, namely, C(•)H2CH2COOCH3 + O2, CH3C(•)HCOOCH3 + O2, and CH3CH2COOC(•)H2 + O2, were constructed using the accurate composite CBS-QB3 method. Thermodynamic properties of all species as well as high-pressure rate constants of all reaction channels were derived with explicit corrections for tunneling and hindered internal rotations. Our calculation results are in good agreement with a limited number of scattered data in the literature. Furthermore, pressure- and temperature-dependent rate constants for all reaction channels on the multiwell-multichannel potential energy surfaces were computed with the quantum Rice-Ramsperger-Kassel (QRRK) and the modified strong collision (MSC) theories. This procedure resulted in a thermodynamically consistent detailed kinetic submechanism for low-temperature oxidation governed by the title process. A simplified mechanism, which consists of important reactions, is also suggested for low-temperature combustion at engine-like conditions.

First-principles kinetics of n-octyl radicals

Kinetics of the isomerisation and unimolecular degradation of n-octyl radicals have been studied with the reaction class transition state theory (RC-TST) method. To explore the kinetics of the 1,7-H migration reactions family, the accurate high-pressure limits of the rate constants for the reference reaction of this class (1-heptyl → 1-heptyl) have been calculated. Finally, both the achievements reported in this paper and previous developments are employed to obtain theoretical branching ratios of intramolecular H-transfers and unimolecular degradations of all possible n-octyl radicals; the results are in satisfactory agreement when compared to experiment. The application of the rates obtained to the simulation of a simple reactor is also reported.

Non-adiabatic effects in ion/molecule reactions

Abstract The non-adiabatic effects in the capture of an ion by a linear dipole were examined over a wide range of energies and temperatures. While typical ion/molecule systems do not exhibit any sensitivity towards such effects, some atypical systems, such as thermal electron/dipole, do, to the extent that the real capture rate constant may be lower by 10% or more than that estimated using the Born-Oppenheimer approximation.

Thiamine and selected thiamine antivitamins - biological activity and methods of synthesis

Thiamine plays a very important coenzymatic and non-coenzymatic role in the regulation of basic metabolism. Thiamine diphosphate is a coenzyme of many enzymes, most of which occur in prokaryotes. Pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes as well as transketolase are the examples of thiamine-dependent enzymes present in eukaryotes, including human. Therefore, thiamine is considered as drug or diet supplement which can support the treatment of many pathologies including neurodegenerative and vascular system diseases. On the other hand, thiamine antivitamins, which can interact with thiamine-dependent enzymes impeding their native functions, thiamine transport into the cells or a thiamine diphosphate synthesis, are good propose to drug design. The development of organic chemistry in the last century allowed the synthesis of various thiamine antimetabolites such as amprolium, pyrithiamine, oxythiamine, or 3-deazathiamine. Results of biochemical and theoretical chemistry research show that affinity to thiamine diphosphate-dependent enzymes of these synthetic molecules exceeds the affinity of native coenzyme. Therefore, some of them have already been used in the treatment of coccidiosis (amprolium), other are extensively studied as cytostatics in the treatment of cancer or fungal infections (oxythiamine and pyrithiamine). This review summarizes the current knowledge concerning the synthesis and mechanisms of action of selected thiamine antivitamins and indicates the potential of their practical use.

ISOTOPE EFFECTS IN THE ION/MOLECULE CAPTURE

Abstract Calculations indicate that ion–molecule reactions in gases exhibit marked kinetic isotope effects. Whereas at high temperatures the effects are normal (the lighter molecule reacts faster than the heavier one), at low temperatures the reversed isotope effect is predicted: a heavier isotopomeric molecule reacts with an ion faster than the lighter one.