Modeling reaction pathways of low energy particle deposition on polymer surfaces via first principle calculations.

The chemical processes that lead to polystyrene surface modification via low energy deposition of C(2)H(+), C(2)F(+), CH(2), CH(2)(+), and H(+) radicals and ions are examined using first principles calculations. Specifically, the reaction mechanisms responsible for products identified in classical molecular dynamics with reactive empirical bond-order potentials are examined using density functional theory. In addition, these calculations consider how the presence of charges on the incident particles changes the result for the CH(2) system through the comparison of barriers, transition states, and final products for CH(2) and CH(2)(+). The structures of the reaction species and energy barriers are determined using the B3LYP hybrid functional. Finally, CCSD/6-31G(d,p) single point energy calculations are carried out to obtain optimized energy barriers. The results indicate that the large variety of reactions occurring on the polystyrene surface are a consequence of complex interactions between the substrate and the deposited particles, which can easily be identified and characterized using advanced computational methodologies, such as first principle calculations.

Experimental and theoretical study of the reaction of POCl(3) (-) with O(2).

The oxidation of the trichlorooxyphosphorus anion (POCl(3) (-)), which takes place in combustion flames, has been examined experimentally at a variety of temperatures and theoretically via ab initio and density functional methods. The reaction was examined in a turbulent ion flow tube and kinetics was measured between 300 and 626 K, estimating an overall reaction barrier of 1.23 kcal/mol. Calculations at the density functional, Moller-Plesset second order perturbation, and coupled cluster levels of theory with basis sets up to augmented triple-zeta quality point to a multistep reaction mechanism involving an initial [OP(Cl)(3)(OO)](-) intermediate, an adduct between triplet O(2) with POCl(3) (-), subsequent formation of a four-membered nonplanar P-O-O-Cl ring transition state, with concomitant breaking of the P-Cl and O-O bonds to provide a transient intermediate [OP(Cl)(2)OO...Cl](-), which, in turn, converts to the product complex (POCl(2) (-))(ClO) upon formation of the Cl-O bond without barrier. The calculated energy of the four-membered transition state is considered to be in good agreement with the small overall barrier found by experiment. The final step is responsible for the large exothermicity of the reaction.

Theoretical studies of proton-coupled electron transfer reactions.

A theoretical formulation for proton-coupled electron transfer (PCET) is described. This theory allows the calculation of rates and kinetic isotope effects and provides insight into the underlying fundamental principles of PCET reactions. Applications of this theory to PCET reactions in iron bi-imidazoline complexes, oxoruthenium polypyridyl complexes, osmium-benzoquinone systems, amidinium-carboxylate salt bridges, DNA-acrylamide complexes, and ruthenium polypyridyl-tyrosine systems are summarized. The mechanistic insight gained from theoretical calculations on these model systems is relevant to PCET in more complex biological processes such as photosynthesis and respiration.

Proton-coupled electron transfer in a model for tyrosine oxidation in photosystem II.

Theoretical calculations of a model for tyrosine oxidation in photosystem II are presented. In this model system, an electron is transferred to ruthenium from tyrosine, which is concurrently deprotonated. This investigation is motivated by experimental measurements of the dependence of the rates on pH and temperature (Sjödin et al. J. Am. Chem. Soc. 2000, 122, 3932). The mechanism is proton-coupled electron transfer (PCET) at pH < 10 when the tyrosine is initially protonated and is single electron transfer (ET) for pH > 10 when the tyrosine is initially deprotonated. The PCET rate increases monotonically with pH, whereas the single ET rate is independent of pH and is 2 orders of magnitude faster than the PCET rate. The calculations reproduce these experimentally observed trends. The pH dependence for the PCET reaction arises from the decrease in the reaction free energies with pH. The calculations indicate that the larger rate for single ET arises from a combination of factors, including the smaller solvent reorganization energy for ET and the averaging of the coupling for PCET over the reactant and product hydrogen vibrational wave functions (i.e., a vibrational overlap factor in the PCET rate expression). The temperature dependence of the rates, the solvent reorganization energies, and the deuterium kinetic isotope effects determined from the calculations are also consistent with the experimental results.

Theoretical investigation of large kinetic isotope effects for proton-coupled electron transfer in ruthenium polypyridyl complexes.

A theoretical investigation of proton-coupled electron transfer in ruthenium polypyridyl complexes is presented. The three reactions studied are as follows: (1) the comproportionation reaction of [(bpy)(2)(py)Ru(IV)O](2+) and [(bpy)(2)(py)Ru(II)OH(2)](2+) to produce [(bpy)(2)(py)Ru(III)OH](2+); (2) the comproportionation reaction of [(tpy)(bpy)Ru(IV)O](2+) and [(tpy)(bpy)Ru(II)OH(2)](2+) to produce [(tpy)(bpy)Ru(III)OH](2+); and (3) the cross reaction of [(tpy)(bpy)Ru(III)OH](2+) and [(bpy)(2)(py)Ru(II)OH(2)](2+) to produce [(tpy)(bpy)Ru(II)OH(2)](2+) and [(bpy)(2)(py)Ru(III)OH](2+). This investigation is motivated by experimental measurements of rates and kinetic isotope effects for these systems (Binstead, R. A.; Meyer, T. J. J. Am. Chem. Soc. 1987, 109, 3287. Farrer, B. T.; Thorp, H. H. Inorg. Chem. 1999, 38, 2497.). These experiments indicate that the second reaction is nearly one order of magnitude faster than the first reaction, and the third reaction is in the intermediate regime. The experimentally measured kinetic isotope effects for these three reactions are 16.1, 11.4, and 5.8, respectively. The theoretical calculations elucidate the physical basis for the experimentally observed trends in rates and kinetic isotope effects, as well as for the unusually high magnitude of the kinetic isotope effects. In this empirical model, the proton donor-acceptor distance is predicted to be largest for the first reaction and smallest for the third reaction. This prediction is consistent with the degree of steric crowding near the oxygen proton acceptor for the three reactions. The second reaction is faster than the first reaction since a smaller proton donor-acceptor distance leads to a larger overlap between the reactant and product proton vibrational wave functions. The intermediate rate of the third reaction is determined by a balance among several competing factors. The observed trend in the kinetic isotope effects arises from the higher ratio of the hydrogen to deuterium vibrational wave function overlap for larger proton donor-acceptor distances. Thus, the kinetic isotope effect increases for larger proton donor-acceptor distances. The unusually high magnitude of the kinetic isotope effects is due in part to the close proximity of the proton transfer interface to the electron donor and acceptor. This proximity results in strong electrostatic interactions that lead to a relatively small overlap between the reactant and product vibrational wave functions.