Although the existence of Cα−H···OC hydrogen bonds in protein structures recently has been established, little is known about their strength and, therefore, the relative importance of these interactions. We have discovered that similar interactions occur in N,N-dimethylformamide dimers. High level ab initio calculations (MP2/aug-cc-pTZV) yield electronic association energies (D e) and association enthalpies (ΔH 298) for four dimer geometries. These data provide a lower limit of D e = −2.1 kcal mol-1 for the Cα−H···OC hydrogen bond. A linear correlation between C−H···O bond energies and gas-phase proton affinities is reported. The gas-phase anion proton affinity of a peptide Cα−H hydrogen was calculated (355 kcal mol-1) and used to estimate values of D e = −4.0 ± 0.5 kcal mol-1 and ΔH 298 = −3.0 ± 0.5 kcal mol-1 for the Cα−H···OC hydrogen bond. The magnitude of this interaction, roughly one-half the strength of the N−H···OC hydrogen bond, suggests that Cα−H···OC hydrogen bonding interactions represent a hitherto unrecognized, significant contribution in the determination of protein conformation.

The structures of the dimers of formamide and N-methylacetamide have been calculated at the ab initio electronic structure theory level, second-order Møller-Plesset perturbation theory (MP2) with augmented correlation consistent basis sets. Five unique structures were optimized for the formamide dimers at the MP2/ aug-cc-pVDZ and MP2/aug-cc-pVTZ levels. At the optimized geometries obtained with the aug-cc-pVTZ basis set, MP2 energies were evaluated with the aug-cc-pVQZ basis set, allowing an extrapolation of the energies to the complete basis set limit. Four structures were found for the N-methylacetamide dimer at the MP2/aug-cc-pVDZ level, and single-point energies were calculated at the MP2/aug-cc-pVTZ level. In both systems, the basis set superposition error was estimated with the counterpoise method. The strength of the NsH‚‚‚OdC bond has a mean value of 7.1 kcal/mol in the formamide dimers and a mean value of 8.6 kcal/mol in the N-methylacetamide dimers. The difference in hydrogen bond strengths is attributed to differences in basicity at the carbonyl oxygen receptor site. In several dimers CsH‚‚‚OdC hydrogen bonds play an important role in stabilizing these intermolecular complexes, increasing the interaction energy by 1.1-2.6 kcal/mol per interaction.

Conformations of an important model system, the alanine dipeptide, have been calculated by using high-level, ab initio electronic structure theory. A Ramachandran plot, with the angle φ in the range −180° to 90° and the angle ψ in the range −60° to 180°, was generated by using density functional theory with the generalized-gradient BLYP functional and a polarized triple-ζ basis set (TZVP+). Six conformers, C7eq, C5, C7ax, β2, αL, and α‘, have been identified in this region of the Ramachandran plot. A second derivative (frequency) analysis showed that all conformers are stable at this level of theory. These structures were used as starting points for geometry optimizations at the MP2/aug-cc-pVDZ level. Single-point energies were calculated at the MP2/aug-cc-pVTZ and MP2/aug-cc-pVQZ levels at the final MP2/aug-cc-pVDZ structures and together with the MP2/aug-cc-pVDZ results were used in extrapolations to the complete basis set limit. The N−H···O, N−H···N, and C−H···O hydrogen bond interactions that are key to the energetics are discussed. In general, the results obtained at the BLYP/TZVP+, MP2/aug-cc-pVDZ, MP2/aug-cc-pVTZ//aug-cc-pVDZ, and MP2/aug-cc-pVQZ//aug-cc-pVDZ levels are in reasonable agreement with each other, except for the β2 conformation for which there are significant differences in the structures. Although the same stability order is obtained at all levels of theory that were used, there are significant differences in the magnitude of the relative conformational energies.

Oxidative stress is related to the development of a large number of health disorders. Therefore, the study of molecular systems capable of preventing its onset by fighting free radicals is a crucial area of research. Carotenoids are one of the most efficient families of compounds fulfilling this purpose. In the present work, the free-radical-scavenger efficiency, expressed as the one-electron-donating capability, of different carotenoids has been studied using density functional theory. A large number of free radicals were considered, as well as environments of different polarity. A new donor-acceptor map is proposed that allows a rapid evaluation of full electron-transfer processes. Its efficiency for predicting the feasibility of electron transfer (ET) between carotenoids and free radicals was tested and validated through comparison with the corresponding Gibbs free energies of reaction. Our results demonstrate that ET reactions between carotenoids and free radicals are strongly influenced by the nature of the latter. Moreover, it is proposed that the electron affinity (EA) of the reacting free radical has an important effect on the viability of these reactions. The reactions were found to become exergonic when the EA of the free radical involved reaches a value of approximately 5 eV.

The electron transfer (ET) reaction between carotenoids and the superoxide radical anion is found to be not only a viable process but also a very unique one. The nature of the O(2) (-) inverts the direction of the transfer, with respect to ET involving other ROS: the O(2) (-) becomes the electron donor and carotenoids (CAR) the electron acceptor. Therefore the "antioxidant" activity of CAR when reacting with O(2) (-) lies in their capacity to prevent the formation of oxidant ROS. This peculiar charge transfer is energetically feasible in non-polar environments but not in polar media. In addition the relative reactivity of CAR towards O(2) (-) is drastically different from their reactivity to other ROS. Asthaxanthin (ASTA) is predicted to be a better O(2) (-) quencher than LYC and the other CAR. The CAR + O(2) (-) reactions were found to be diffusion controlled. The agreement with available experimental data supports the density functional theory results from the present work.

In this work a comparison between redox potentials, obtained by constructing current-potential plots from chronoamperometric measurements, and the parameter sigma(x), as proposed by Zuman in terms of the Hammett substituent parameters, was performed for several quinone compounds. This study shows the limitations of this approach and proves that methods based on quantum chemistry can be used to study the substituent effect in quinone systems. By using the Density Functional Theory, in the Kohn-Sham context with three exchange-correlation functionals, BLYP, B3LYP, and BHLYP, it was found that the electron affinity is good enough to give a useful relationship with experimental redox potentials of quinone systems. This conclusion is reached when the basis set functions involve diffuse functions, and also when the Hartree-Fock exchange energy is included in the exchange-correlation functional. The Fukui function, to describe preferential sites involved at initial stages of a system that bind an electron, is analyzed when electron donor and electron acceptor groups are present as substituents in quinone systems. The methods applied in this work are valid for any kind of quinone compound and will be used in further analysis of the electron reorganization in semiquinone species.

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A large number of crystal structures are analyzed to characterize the structural aspects of hydrogen bonding interactions with the NO(3)(-) anion. Further insight is provided by the use of electronic structure calculations to determine stable geometries and interaction energies for NO(3)(-) complexes with several simple hydrogen bond donor groups, including water, methanol, N-methylform-amide, and methane. The results establish the existence of a clear set of structural criteria for the rational design of molecular receptors that complex the NO(3)(-) anion through hydrogen bonding interactions.