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

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

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

Exploring marine toxins: comparative analysis of chemical reactivity properties and potential for drug discovery

Marine toxins, produced by various marine microorganisms, pose significant risks to both marine ecosystems and human health. Understanding their diverse structures and properties is crucial for effective mitigation and exploration of their potential as therapeutic agents. This study presents a comparative analysis of two hydrophilic and two lipophilic marine toxins, examining their reactivity properties and bioavailability scores. By investigating similarities among these structurally diverse toxins, valuable insights into their potential as precursors for novel drug development can be gained. The exploration of lipophilic and hydrophilic properties in drug design is essential due to their distinct implications on drug distribution, elimination, and target interaction. By elucidating shared molecular properties among toxins, this research aims to identify patterns and trends that may guide future drug discovery efforts and contribute to the field of molecular toxinology. The findings from this study have the potential to expand knowledge on toxins, facilitate a deeper understanding of their bioactivities, and unlock new therapeutic possibilities to address unmet biomedical needs. The results showcased similarities among the studied systems, while also highlighting the exceptional attributes of Domoic Acid (DA) in terms of its interaction capabilities and stability

Density Functional Theory (DFT) Study of Triphenylamine-Based Dyes for Their Use as Sensitizers in Molecular Photovoltaics

In this work we studied three dyes which are proposed for potential photovoltaic applications and named Dye7, Dye7-2t and Dye7-3t. The Density Functional Theory (DFT) was utilized, using the M05-2X hybrid meta-GGA functional and the 6–31+G(d,p) basis set. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the absorption and emission spectra, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT. Also, the pKa values were calculated with the semi-empirical PM6 method

EL USO DE RECURSOS NATURALES LOCALES EN LA PRODUCCIÓN DE SUPERFICIES PICTÓRICAS DECORATIVAS EN TEMPLOS JESUITAS DE LA NUEVA VIZCAYA (CHIHUAHUA, MÉXICO).

De un inventario de 283 templos históricos establecidos durante la dominación española en la región de la Nueva Vizcaya (Chihuahua, México) se han identificado 23 templos que albergan pinturas murales y/o techumbres polícromas. En este atículo se presenta el estudio que se está llevando a cabo ennueve de ellos, todos fundados por misioneros Jesuitas entre 1640 y 1767. Recientes estudios (XRF, FORS, FTIR) han evidenciado que mientras que aquellas obras que presentan figuras y elementos decorativas puramente indígenas mantienen el estándar de pigmentos a base de óxido de hierro, aquellas que siguen cánones estilísticos europeos contienen (además de éstos) otros pigmentos y colorantes (ej. cochinilla, índigo) que, si bien pudieron haberse producido localmente, no forman parte de la paleta nativa de esta región. El proyecto Biblioteca de Recursos Culturales desarrollado desde el Laboratorio de Patrimonio Histórico – Tecnológico de Monterrey Campus Chihuahua tiene como objetivo identificar, documentar y analizar materiales naturales presentes en Patrimonio Cultural. Gracias a él se están identificando los materiales utilizados en las superficies decorativas objeto de estudio. El presente artículo muestra la investigación multidisciplinar e interinstitucional que se ha desarrollado para la documentación, recolección y el estudio de dichos materiales en colaboración con miembros de las comunidades locales. Ello ha permitido no sólo poner en valor el patrimonio artístico de Chihuahua, sino también diseñar las estrategias de conservación adecuadas que garanticen su preservación

EL USO DE RECURSOS NATURALES LOCALES EN LA PRODUCCIÓN DE SUPERFICIES PICTÓRICAS DECORATIVAS EN TEMPLOS JESUITAS DE LA NUEVA VIZCAYA (CHIHUAHUA, MÉXICO)

De un inventario de 283 templos históricos establecidos durante la dominación española en la región de la Nueva Vizcaya (Chihuahua, México) se han identificado 23 templos que albergan pinturas murales y/o techumbres polícromas. En este atículo se presenta el estudio que se está llevando a cabo ennueve de ellos, todos fundados por misioneros Jesuitas entre 1640 y 1767. Recientes estudios (XRF, FORS, FTIR) han evidenciado que mientras que aquellas obras que presentan figuras y elementos decorativas puramente indígenas mantienen el estándar de pigmentos a base de óxido de hierro, aquellas que siguen cánones estilísticos europeos contienen (además de éstos) otros pigmentos y colorantes (ej. cochinilla, índigo) que, si bien pudieron haberse producido localmente, no forman parte de la paleta nativa de esta región. El proyecto Biblioteca de Recursos Culturales desarrollado desde el Laboratorio de Patrimonio Histórico – Tecnológico de Monterrey Campus Chihuahua tiene como objetivo identificar, documentar y analizar materiales naturales presentes en Patrimonio Cultural. Gracias a él se están identificando los materiales utilizados en las superficies decorativas objeto de estudio. El presente artículo muestra la investigación multidisciplinar e interinstitucional que se ha desarrollado para la documentación, recolección y el estudio de dichos materiales en colaboración con miembros de las comunidades locales. Ello ha permitido no sólo poner en valor el patrimonio artístico de Chihuahua, sino también diseñar las estrategias de conservación adecuadas que garanticen su preservación.Los autores agradecen a todas las organizaciones e instituciones de México (Misiones Coloniales de Chihuahua AC, Tecnológico Monterrey Campus Chihuahua, Laboratorio de Patrimonio Histórico, Consejo Nacional de Ciencia y Tecnología - CONACYT, Centro de Investigación de Materiales Avanzados - CIMAV Chihuahua, Universidad Autónoma de Chihuahua, Instituto Nacional de Antropología e Historia - INAH, Chihuahua, CONACYT-Instituto de Física, Universidad Nacional Autónoma de México, Empresa minera Dia Bras, así como autoridades locales y comunidades de Santa María de Cuevas, Cusihuiriachi, La Joya, Satevó, Rosario, Coyachi, San Francisco de Borja), Estados Unidos (Museum Conservation Institute- Smithsonian Institution, Programa de Becas J. Paul Getty), España (Universidad Politécnica de Valencia) e Italia (Università Ca`Foscari, IFAC-CNR en Firenze, IVASACNR en Trento), que han contribuido al desarrollo de este estudio.Muñoz Alcocer, KM.; Fuster López, L.; Ruiz Checa, JR.; Vázquez De Agredos Pascual, ML.; Izzo, FC.; Vega Moctezuma, DL.; Flores Holguín, NR.... (2017). EL USO DE RECURSOS NATURALES LOCALES EN LA PRODUCCIÓN DE SUPERFICIES PICTÓRICAS DECORATIVAS EN TEMPLOS JESUITAS DE LA NUEVA VIZCAYA (CHIHUAHUA, MÉXICO). Arché. (11 - 12):71-78. http://hdl.handle.net/10251/101200717811 - 1