This research work has assessed many Minnesota density functionals to find their molecular structure and electronic properties possessed by SYBR green I (SYBRGI) and ethidium bromide (EtBr) nucleic acid stains. In the determination of the global descriptors that come up from conceptual density functional theory (CDFT), the processes include: Self-Consistent Field Energy Differences (∆SCF) and higher occupied molecular orbital (HOMO) and lower unoccupied molecular orbital (LUMO) frontier orbitals energies. Regarding the deduced outcomes for the conceptual DFT indices, many of the descriptors have been adjusted to achieve the “Koopmans in DFT (KID)” process. It has also been shown that the only density functionals that confirm this approximation are the range-separated hybrids (RSH).
Part of the book: Density Functional Calculations
The molecular docking of tamoxifen’s metabolites, 4-hydroxy-tamoxifen, N-desmethyl-tamoxifen, and 4-hydroxy-N-desmethyl-tamoxifen, in estrogen and progesterone hormone receptors was studied in aqueous solution. The metabolites 4-hydroxy-tamoxifen, N-desmethyl-tamoxifen, and 4-hydroxy-N-desmethyl-tamoxifen exhibit a binding energy in the estrogen receptor cavity of −10.69 kcal/mol, −10.9 kcal/mol, and −11.35 kcal/mol, respectively, and −1.45 kcal/mol, −9.29 kcal/mol, and −0.38 kcal/mol in the progesterone receptor. This indicates a spontaneous interaction between the metabolites and the active sites in the hormone receptors. Docking has an adequate accuracy for both receptors, and from this calculation the active site residues were defined for the different metabolites and the estrogen and progesterone receptors. Also, the chemical reactivity of the amino acids of the active sites of each metabolite was determined. These reactivity properties were obtained within the framework of density functional theory, using the functional M06 with the basis set 6-31G (d). The results indicate that in the estrogen receptor, the highest charge transfer of the three analyzed metabolites is in the union of the metabolite and the Leu346-Thr347 residue. The progesterone receptor shows minor tendency to react with higher hardness values than the estrogen receptor. The hydrogen bonds are three for the estrogen receptor in two different metabolites, while in progesterone only one is formed with the N-desmethyl-tamoxifen metabolite.
Part of the book: Molecular Docking
Eight density functionals, CAM-B3LYP, LC-ωPBE, M11, MN12SX, N12SX, ωB97, ωB97X, and ωB97XD, in connection with the Def2TZVP basis set were assessed together with the SMD solvation model for the calculation of the molecular and chemical reactivity properties of the angiotensin II vasoconstrictor octapeptide in the presence of water. All the chemical reactivity descriptors for the systems were calculated via conceptual density functional theory (CDFT). The potential bioavailability and druggability as well as the bioactivity scores for angiotensin II were predicted through different methodologies already reported in the literature which have been previously validated during the study of different peptidic systems.
Part of the book: Cheminformatics and its Applications
A well-behaved model chemistry previously validated for the study of the chemical reactivity of peptides was considered for the calculation of the molecular properties and structures of the clavanin family of antimicrobial marine peptides. A methodology based on conceptual density functional theory (CDFT) was chosen for the determination of the reactivity descriptors. The molecular active sites were associated with the active regions of the molecules related to the nucleophilic and electrophilic Fukui functions. Finally, the drug-likenesses and the bioactivity scores for the clavanin peptides were predicted through a homology methodology relating them with the calculated reactivity descriptors, while other properties like the pKas were determined following a methodology developed by our group.
Part of the book: Density Functional Theory Calculations