Critical evaluation of the potential energy surface of the CH3 + HO2 reaction system.

The CH3 + HO2 reaction system was studied theoretically by a newly developed, HEAT345-(Q) method based CHEAT1 protocol and includes the combined singlet and triplet potential energy surfaces. The main simplification is based on the CCSDT(Q)/cc-pVDZ calculation which is computationally inexpensive. Despite the economic and black-box treatment of higher excitations, the results are within 0.6 kcal/mol of the highly accurate literature values. Furthermore, the CHEAT1 surpassed the popular standard composite methods such as CBS-4M, CBS-QB3, CBS-APNO, G2, G3, G3MP2B3, G4, W1U, and W1BD mainly due to their poor performance in characterizing transition states (TS). For TS structures, various standard DFT and MP2 method have also been tested against the resulting CCSD/cc-pVTZ geometry of our protocol. A fairly good agreement was only found in the cases of the B2PLYP and BHandHLYP functionals, which were able to reproduce the structures of all TS studied within a maximum absolute deviation of 7%. The complex reaction mechanism was extended by three new low lying reaction channels. These are indirect water elimination from CH3OOH resulted formaldehyde, H2 elimination yielded methylene peroxide, and methanol and reactive triplet oxygen were formed via H-shift in the third channel. CHEAT1 protocol based on HEAT345-(Q) method is a robust, general, and cheap alternative for high accurate kinetic calculations.

The effect of oxidative stress on the bursopentin peptide structure: a theoretical study.

Bursopentin (BP(5), H-Cys(1)-Lys(2)-Arg(3)-Val(4)-Tyr(5)-OH), found in the bursa Fabricius of the chicken, is a pentapeptide that protects the organism from oxidative stress by reducing the intracellular generation of reactive oxygen species. Hydrogen abstraction, a common oxidative reaction occurring in proteins, often results in the formation of d amino acid residues. To study the effect of this phenomenon on the structure of bursopentin, each of its residues were converted from the l configuration to the d configuration, and the structures of these peptide epimers were compared to that of the wild-type bursopentin. The conformations, secondary structures, compactness and hydrogen bonding of bursopentin were compared to its epimers using molecular dynamics simulations and first principles quantum chemical computations. It was discovered that the repulsion between the side chains of Lys(2) and Arg(3) influenced the conformation of the peptide regardless of the configuration of these residues. Epimerisation of the Val(4) and Tyr(5) caused a reduction in the compactness of bursopentin. In all cases, the occurrence of a turn structure was relatively high, especially when Arg(3) was in the d configuration. Thermodynamic analysis of the epimerisation process showed that the formation of d amino acid residues is favourable.