Ab initio MO study on model compounds of malonyl-CoA: malonic acid and malonyl methyl sulfide

Lack of the 'long-distance' dynamical co-operative interactions due to low symmetry of hydrogen-bonded malonic acid aggregates in molecular crystals

The paper explains the relationship between the energy of hydrogen bonds and the distance between associated carboxyl groups of malonic acid (MA) molecules by means of infrared spectroscopic studies of crystals of its four isotopic varieties [CH₂(COOH)₂, h₄-MA; CH₂(COOD)₂, d₂^c-MA; CD₂(COOH)₂, d₂^m-MA; CD₂(COOD)₂, d₄-MA]. The effects associated with impact on the isotopic dilution and changes in the temperature of spectrum registration on the fine structures of the ν_O-H and ν_O-D bands were analyzed. MA molecular crystals are characterized by a tendency to spontaneous H/D isotopic exchange both within centrosymmetric hydrogen bond cycles and methylene groups. The mono- and polycrystalline spectra obtained in the infrared range of isotopically neat and isotopically diluted by deuterons do not indicate the occurrence of anomalous temperature evolution in the course of lowering their registration temperature to 77 K. Theoretical calculations did not give clear confirmation of the nature of the phenomena analyzed.

Exploring Intramolecular Reactions in Complex Systems with Metadynamics: The Case of the Malonate Anions

We have determined the optimized structures, relative energies and intramolecular reactions for two anionic forms of malonic acid, anion malonate(-1) (HO(2)CCH(2)CO(2)(-)) and malonate(-2) ((-)O(2)CCH(2)CO(2)(-)). For this purpose we employed accurate quantum chemistry calculations using second-order Möller-Plesset perturbation theory and Density Functional Theory with an aug'-cc-p-VTZ basis set to determine the structures and energies, and a novel metadynamics method based on Car-Parrinello molecular dynamics for the thermal reactions. For both malonates, we found new isomers (keto and enol structures) characterized by CO(2) rotations and intramolecular proton transfers. These proton transfers characterize the keto-enol tautomerism that takes place both in the monoanion and dianion. In all cases, the keto tautomer is the more stable configuration. The metadynamics method allows the system to explore the potential energy surface in a few picoseconds, crossing activation barriers of 20-50 kcal/mol.