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)

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

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

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

A Combined Molecular Docking and Electronic Structure Study for a Breast Cancer Drug Design

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

Computational Nutraceutics: Chemical Reactivity Properties of the Flavonoid Naringin by Means of Conceptual DFT

The M06 family of density functionals has been assessed for the calculation of the molecular structure and properties of the Naringin molecule. The chemical reactivity descriptors have been calculated through Conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices and the dual descriptor f (2) (r). A comparison between the descriptors calculated through vertical energy values and those arising from the Koopmans' theorem approximation has been performed in order to check for the validity of the last procedure

Interaction of Tamoxifen Analogs With the Pocket Site of Some Hormone Receptors. A Molecular Docking and Density Functional Theory Study

In this paper, the antiestrogenic properties of Tamoxifen analogs have been investigated and a theoretical report of its analogs interaction with the pocket site of some hormone receptors are presented. Analogs were generated by modification of the hydrophilic functional group of Tamoxifen by hydroxyl, amide, carboxyl, and sulfhydryl functional groups, in an attempt to improve their activity and selectivity. The analogs exhibit a negative binding energy in the estrogen and progesterone receptors, which indicates a spontaneous interaction between the analogs and the pocket site in the hormone receptors. The values of the molecular polar surface area indicate that the analogs have good permeability and are strong electrophiles. The couplings showed electrostatic interactions such as hydrogen bond and π-π interactions. According with the Lipinsky Rule of Five, the four analogs presented a good biodistribution, permeability, and pharmacological action on the hormone receptors. The analysis of the charge transfer suggests a limited enhanced oxidative damage in the estrogen receptor that not takes place with the progesterone receptor

Theoretical Study of Copper Complexes: Molecular Structure, Properties, and Its Application to Solar Cells

We present a theoretical investigation of copper complexes with potential applications as sensitizers for solar cells. The density functional theory (DFT) and time-dependent DFT were utilized, using the M06 hybrid meta-GGA functional with the LANL2DZ (D95V on first row) and DZVP basis sets. This level of calculation was used to find the optimized molecular structure, the absorption spectra, the molecular orbitals energies, and the chemical reactivity parameters that arise from conceptual DFT. Solvent effects have been taken into account by an implicit approach, namely, the polarizable continuum model (PCM), using the nonequilibrium version of the IEF-PCM model

Electronic Structure of Carotenoids in Natural and Artificial Photosynthesis

This chapter is about a theoretical study applied to six carotenoids present in vegetables containing carotenes and xanthophylls. Electronic properties are analyzed such as energy in frontier orbitals and the first molecular orbitals to work in the UV-Vis absorption spectroscopy. Electronic structure methodologies were used within the frame of the density functional theory (DFT) using the theoretical methods B3LYP/6-31G(d)//B3LYP/6-31G+(d,p) for ground states and B3LYP/6-31G(d)//CAM-B3LYP/6-31G+(d,p) for excited states. Results for the main absorption peak are in agreement with experimental results with a difference between zeaxanthin and violaxanthin results of 0.1 eV, approximately. The UV-Vis absorption spectra obtained for carotenoids are in good agreement with the experimental results. The possible use in energy generation systems is discussed for these systems. Diade chlorophyllide a-zeaxanthin was formed, and calculation results predicted energy transfer for these photosynthetic systems

Experimental and quantum chemical studies of a novel synthetic prenylated chalcone

BACKGROUND: Chalcones are ubiquitous natural compounds with a wide variety of reported biological activities, including antitumoral, antiviral and antimicrobial effects. Furthermore, chalcones are being studied for its potential use in organic electroluminescent devices; therefore the description of their spectroscopic properties is important to elucidate the structure of these molecules. One of the main techniques available for structure elucidation is the use of Nuclear Magnetic Resonance Spectroscopy (NMR). Accordingly, the prediction of the NMR spectra in this kind of molecules is necessary to gather information about the influence of substituents on their spectra. RESULTS: A novel substituted chalcone has been synthetized. In order to identify the functional groups present in the new synthesized compound and confirm its chemical structure, experimental and theoretical (1)H-NMR and (13)C-NMR spectra were analyzed. The theoretical molecular structure and NMR spectra were calculated at both the Hartree-Fock and Density Functional (meta: TPSS; hybrid: B3LYP and PBE1PBE; hybrid meta GGA: M05-2X and M06-2X) levels of theory in combination with a 6-311++G(d,p) basis set. The structural parameters showed that the best method for geometry optimization was DFT:M06-2X/6-311++G(d,p), whereas the calculated bond angles and bond distances match experimental values of similar chalcone derivatives. The NMR calculations were carried out using the Gauge-Independent Atomic Orbital (GIAO) formalism in a DFT:M06-2X/6-311++G(d,p) optimized geometry. CONCLUSION: Considering all HF and DFT methods with GIAO calculations, TPSS and PBE1PBE were the most accurate methods used for calculation of (1)H-NMR and (13)C-NMR chemical shifts, which was almost similar to the B3LYP functional, followed in order by HF, M05-2X and M06-2X methods. All calculations were done using the Gaussian 09 software package. Theoretical calculations can be used to predict and confirm the structure of substituted chalcones with good correlation with the experimental data