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The optimum geometries and binding energies of the complexes formed by AMPA and Kainic acid, as well as their anions with tyrosine, proline and some tripeptides are investigated with quantum chemical calculations (HF/6-31G**). It was found that receptors featuring the Tyr-Ala-Pro sequence exhibit stronger binding energies to the substrates than the Tyr-Ser-Pro and Tyr-Ser-Ser. As expected, the anions are more bound than the neutral species. This work can lead to investigations on the effect of AMPA receptors mutations on the brain functions, possibly related to criminal tendencies.

Energies corresponding to optimum geometries of ninhydrin, some of its analogs, the corresponding Ruhemann's Purple analogs and some of the intermediates of the reaction between ninhydrin analogs and amino acids are calculated at Hartree-Fock/6-31G** level of theory. Such a study is significant from a forensic science point of view because of the strong interest in the forensic chemistry and law enforcement communities in developing alternatives to the current generation of ninhydrin-like chemicals for the detection and development of latent fingerprints. In examining our new predictions for the net energetics of the reactions in the formation of substituted Ruhemann's Purples, we find that a fluorine-containing analog is the most thermodynamically feasible reaction. In light of this finding, we suggest further experimental studies to determine the kinetic feasibility of synthesizing the fluorine-containing analog, as well as other similar molecules and to determine their spectroscopic properties.

The complex formed by isopentane, as a model for the isoleucine residue present in the wild-type thymidylate synthase, with 4-mercaptopyridine as a fragment of the thymidylate synthase inhibitor Thymitaq (AG337) is investigated with ab initio quantum chemical calculations at Hartree-Fock and MP2 levels, using the 3-21G* basis set. The binding energy is compared with the binding energies of 4-mercaptopyridine with amino acid residues found in mutant thymidylate synthase enzymes. As compared with isoleucine, alanine and glycine do not show binding, in agreement with enzyme-inhibition results.

Ab initio calculations (Hartree-Fock) using the 3-21G and the STO-3G Gaussian basis sets were performed on the sequence selective minor groove binding bis-benzimidazole Hoechst 33258. Geometry optimized conformations, energies and distribution of electrostatic charges within the molecule were derived. The binding of the optimized conformations of the drug to both alternating and non-alternating (AT)n sequences was studied.