Chapters authored
Assessment of the Validity of Some Minnesota Density Functionals for the Prediction of the Chemical Reactivity of the SYBR Green I and Ethidium Bromide Nucleic Acid Stains
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
Chemical Reactivity Properties and Bioactivity Scores of the Angiotensin II Vasoconstrictor Octapeptide
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
Conceptual DFT as a Helpful Chemoinformatics Tool for the Study of the Clavanin Family of Antimicrobial Marine Peptides
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
Computational Chemistry Study of Natural Apocarotenoids and Their Synthetic Glycopeptide Conjugates as Therapeutic Drugs
The objective of the research to be presented in the chapter is the determination of the chemical reactivity properties of some natural apocarotenoids and their synthetic glycopeptide conjugates that could have the ability to inhibit SARS-CoV-2 replication. The study will be based on the consideration of the Conceptual DFT branch of Density Functional Theory (DFT) through the consideration of particular successful model chemistry which has been demonstrated as satisfying the Janak and Ionization Energy theorems within Generalized Gradient Approximation (GGA) theory. The research will be complemented by a report of the ADMET and pharmacokinetic properties hoping that this information could be of help in the development of new pharmaceutical drugs for fighting COVID-19.
Part of the book: Carotenoids