Theoretical Study of the Reactivity and Selectivity of Various Free Radicals with Cysteine Residues

BH9, a New Comprehensive Benchmark Data Set for Barrier Heights and Reaction Energies: Assessment of Density Functional Approximations and Basis Set Incompleteness Potentials

The calculation of accurate reaction energies and barrier heights is essential in computational studies of reaction mechanisms and thermochemistry. To assess methods regarding their ability to predict these two properties, high-quality benchmark sets are required that comprise a reasonably large and diverse set of organic reactions. Due to the time-consuming nature of both locating transition states and computing accurate reference energies for reactions involving large molecules, previous benchmark sets have been limited in scope, the number of reactions considered, and the size of the reactant and product molecules. Recent advances in coupled-cluster theory, in particular local correlation methods like DLPNO-CCSD(T), now allow the calculation of reaction energies and barrier heights for relatively large systems. In this work, we present a comprehensive and diverse benchmark set of barrier heights and reaction energies based on DLPNO-CCSD(T)/CBS called BH9. BH9 comprises 449 chemical reactions belonging to nine types common in organic chemistry and biochemistry. We examine the accuracy of DLPNO-CCSD(T) vis-a-vis canonical CCSD(T) for a subset of BH9 and conclude that, although there is a penalty in using the DLPNO approximation, the reference data are accurate enough to serve as a benchmark for density functional theory (DFT) methods. We then present two applications of the BH9 set. First, we examine the performance of several density functional approximations commonly used in thermochemical and mechanistic studies. Second, we assess our basis set incompleteness potentials regarding their ability to mitigate basis set incompleteness errors. The number of data points, the diversity of the reactions considered, and the relatively large size of the reactant molecules make BH9 the most comprehensive thermochemical benchmark set to date and a useful tool for the development and assessment of computational methods.

Theoretical Study of the Iron Complexes with Lipoic and Dihydrolipoic Acids: Exploring Secondary Antioxidant Activity

The thermodynamic stability of twenty-nine Fe(III) complexes with various deprotonated forms of lipoic (LA) and dihydrolipoic (DHLA) acids, with coordination numbers 4, 5 and 6, is studied at the M06(SMD)/6-31++G(d,p) level of theory in water under physiological pH conditions at 298.15 K. Even though the complexes with LA- are more stable than those with DHLA-, the most thermodynamically stable Fe(III) complexes involve DHLA2-. The twenty-four exergonic complexes are used to evaluate the secondary antioxidant activity of DHLA and LA relative to the Fe(III)/Fe(II) reduction by O2•- and ascorbate. Rate constants for the single-electron transfer (SET) reactions are calculated. The thermodynamic stability of the Fe(III) complexes does not fully correlate with the rate constant of their SET reactions, but more exergonic complexes usually exhibit smaller SET rate constants. Some Cu(II) complexes and their reduction to Cu(I) are also studied at the same level of theory for comparison. The Fe(III) complexes appear to be more stable than their Cu(II) counterparts. Relative to the Fe(III)/Fe(II) reduction with ascorbate, DHLA can fully inhibit the formation of •OH radicals, but not by reaction with O2•-. Relative to the Cu(II)/Cu(I) reduction with ascorbate, the effects of DHLA are moderate/high, and with O2•- they are minor. LA has minor to negligible inhibition effects in all the cases considered.

Modelling the repair of carbon-centred protein radicals by the antioxidants glutathione and Trolox

GSH can repair carbon-centred protein radicals with rate constants in the diffusion limit, but Trolox repairs are much slower.