Electrochemical and Structural Study of the Buried Tryptophan in Azurin: Effects of Hydration and Polarity on the Redox Potential of W48.

Tryptophan serves as an important redox-active amino acid in mediating electron transfer and mitigating oxidative damage in proteins. We previously showed a difference in electrochemical potentials for two tryptophan residues in azurin with distinct hydrogen-bonding environments. Here, we test whether reducing the side chain bulk at position Phe110 to Leu, Ser, or Ala impacts the electrochemical potentials (E°) for tryptophan at position 48. X-ray diffraction confirmed the influx of crystallographically resolved water molecules for both the F110A and F110L tyrosine free azurin mutants. The local environments of W48 in all azurin mutants were further evaluated by UV resonance Raman (UVRR) spectroscopy to probe the impact of mutations on hydrogen bonding and polarity. A correlation between the frequency of the ω17 mode─considered a vibrational marker for hydrogen bonding─and E° is proposed. However, the trend is opposite to the expectation from a previous study on small molecules. Density functional theory calculations suggest that the ω17 mode reflects hydrogen bonding as well as local polarity. Further, the UVRR data reveal different intensity/frequency shifts of the ω9/ω10 vibrational modes that characterize the local H-bonding environments of tryptophan. The cumulative data support that the presence of water increases E° and reveal properties of the protein microenvironment surrounding tryptophan.

Atmospheric Ring-Closure and Dehydration Reactions of 1,4-Hydroxycarbonyls in the Gas Phase: The Impact of Catalysts.

1,4-Hydroxycarbonyls can potentially undergo sequential reactions involving cyclization followed by dehydration to form dihydrofurans. As dihydrofurans contain a double bond, they are highly reactive toward atmospheric oxidants such as OH, O3, and NO3. In the present study, we use ab initio calculations to examine the impact of various atmospheric catalysts on the energetics and kinetics of the gas-phase cyclization and dehydration reaction steps associated with 4-hydroxybutanal, a prototypical 1,4-hydroxycarbonyl molecule. The cyclization step transforms 4-hydroxybutanal into 2-hydroxytetrahydrofuran, which can subsequently undergo dehydration to form 2,3-dihydrofuran. As the barriers associated with the cyclization and dehydration steps for 4-hydroxybutanal are, respectively, 34.8 and 63.0 kcal/mol in the absence of a catalyst, both reaction steps are inaccessible under atmospheric conditions in the gas phase. However, the presence of a suitable catalyst can significantly reduce the reaction barriers, and we have examined the impact of a single molecule of H2O, HO2 radical, HC(O)OH, HNO3, and H2SO4 on these reactions. We find that H2SO4 reduces the reaction barriers the greatest, with the barrier for the cyclization step being reduced to -13.1 kcal/mol and that for the dehydration step going down to 9.2 kcal/mol, measured relative to their respective separated starting reactants. Interestingly, our kinetic study shows that HNO3 gives the fastest rate due to the combined effects of a larger atmospheric concentration and a reduced barrier. Thus, our study suggests that, with acid catalysis, the cyclization reaction step can readily occur for 1,4-hydroxycarbonyls in the gas phase. Because the dehydration step exhibits a significant barrier even with acid catalysis, the 2-hydroxytetrahydrofuran products, once formed, are likely lost through their reaction with OH radicals in the atmosphere. We have investigated the reaction pathways and the rate constant for this bimolecular reaction in the presence of excess molecular oxygen (3O2), as it would occur under tropospheric conditions, using computational chemistry over the 200-300 K temperature range. We find that the main products from these OH-initiated oxidation reactions are succinaldehyde + HO2 and 2,3-dihydro-2-furanol + HO2.

A Computational Study Investigating the Energetics and Kinetics of the HNCO + (CH3)2NH Reaction Catalyzed by a Single Water Molecule.

High-level ab initio calculations are used to explore the energetics and kinetics for the formation of 1,1-dimethyl urea via the reaction of isocyanic acid (HNCO) with dimethyl amine (DMA) catalyzed by a single water molecule. Compared to the uncatalyzed HNCO + DMA reaction, the presence of a water molecule lowers the reaction barrier, defined here as the energy difference between the separated HNCO + DMA + H2O reactants and the transition state (TS), by ∼26 kcal/mol. In addition to the HNCO + DMA + H2O reaction, the energetics of the analogous reactions involving, respectively, ammonia and methyl amine were also investigated. Comparing the barriers for these three amine addition reactions, which can be represented as HNCO + R-NH-R' + H2O with R and R' being either -CH3 or -H, we find that the reaction barrier decreases with the degree of methylation on the amine nitrogen atom. The effective rate constants for the bimolecular reaction pathways HNCO··H2O + DMA and HNCO··DMA + H2O were calculated using canonical variational TS theory coupled with both small curvature and zero-curvature tunneling corrections over the 200-300 K temperature range. For comparison, we also calculated the rate constant for the HNCO + OH reaction. Our results suggest that the HNCO + H2O + DMA reaction can make a non-negligible contribution to the gas-phase removal of atmospheric HNCO under conditions where the HNCO and water concentrations are high and the temperature is low.