ARTICLE | doi:10.20944/preprints202007.0742.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: KID protocol; Global Reactivity; Conceptual DFT; Kopmans’ Theorem; Mo–oxo Complexes; Hydrogen production
Online: 31 July 2020 (10:09:50 CEST)
The KID (Koopmans in DFT) procedure usually applies in organic molecules of the closed–shell type. We used the KID procedure in an open–shell system for the first time to choose the most suitable density functional to compute global and local reactivity descriptors coming from the Conceptual Density–Functional Theory. From a set of 18 density functionals spread from the second until the fourth rung of the Jacob’s ladder: BP86, B97-D, BLYP, CAM-B3LYP, M06-L, M11-L, MN12-L, B3LYP, PBE0, N12-SX, M06-2X, M11, MN12-SX, CAM-B3LYP, LC-ωHPBE, ωB97X-D, APFD, MN15 and MN15-L, we concluded that CAM-B3LYP provides the best outcome.
ARTICLE | doi:10.20944/preprints202008.0690.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: Theopapuamides A-D; Virtual Screening; Chemoinformatics; Conceptual DFT; Computational Peptidology; Bioavailability; Bioactivity Scores; ADMET
Online: 31 August 2020 (03:57:38 CEST)
This work presents the results of a computational study of the chemical reactivity and bioactivity properties of the members of the Theopapuamides A-D family of marine peptides by making use of our own proposed methodology named Computational Peptidology (CP) that has been successfully considered in previous studies of this kind of molecular systems. CP allowed for the determination of the global and local descriptors that come from Conceptual Density Functional Theory (CDFT) that can give an idea of the chemical reactivity properties of the marine natural products under study which are already known to be related to their bioactivity. At the same time, the validity of the procedure based on the adoption of the KID (Koopmans in DFT) technique as well as the MN12SX/Def2TZVP/H2O model chemistry has been successfully verified. Together with several Chemoinformatic tools that can be used for the improvement of process of Virtual Screening, some additional properties of these marine peptides were identified related to their ability to behave as useful drugs. With the further object of analyzing their bioactivity some parameters of usefulness for future QSAR studies, their predicted biological targets and the the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) parameters related to the Theopapuamides A-D pharmacokinetics are also reported.
ARTICLE | doi:10.20944/preprints202008.0351.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: discodermins A-H; chemical reactivity theory; conceptual DFT; global and local reactivity descriptors; pKa; bioavailability; bioactivity scores; ADME
Online: 17 August 2020 (04:45:58 CEST)
A methodology based on the concepts that arise from Density Functional Theory named Conceptual Density Functional Theory (CDFT) was chosen for the calculation of some global and local reactivity descriptors of the Discodermins A-H family of marine peptides through the consideration of the KID (Koopmans in DFT) technique that was successfully used in previous studies of this kind of molecular systems. The determination of active sites of the studied molecules for different kind of reactivities was achieved by resorting to some CDFT-based descriptors like the Fukui functions as well as the Parr functions derived from Molecular Electron Density Theory (MEDT). A few properties identified with their ability to behave as a drug and the bioactivity of the peptides considered in this examination were acquired by depending on a homology model by studying the correlation with the known bioactivity of related molecules in their interaction with various biological receptors. With the further object of analyzing their bioactivity some parameters of usefulness for future QSAR studies, their predicted biological targets and the the ADME (Absorption, Distribution, Metabolism, and Excretion) parameters related to the Discodermins A-H pharmacokinetics are also reported.
ARTICLE | doi:10.20944/preprints202309.0007.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: Talaloride A; Talaropeptides A-D; DFT; Conceptual DFT; KID; Cheminformatics; Pharmacokinetics
Online: 1 September 2023 (12:00:13 CEST)
Molecules sourced from marine environments hold immense promise for the development of novel therapeutic drugs, owing to their distinctive chemical compositions and valuable medicinal attributes. Notably, Talarolide A and Talaropeptides A-D have gained recent attention as potential candidates for pharmaceutical applications. This study aims to explore the chemical reactivity of Talarolide A and Talaropeptides A-D through the application of molecular modeling and computational chemistry techniques, specifically employing Conceptual Density Functional Theory (CDFT). By investigating their chemical behaviors, the study seeks to contribute to the understanding of the potential pharmacological uses of these marine-derived compounds. The investigation involves the utilization of molecular modeling and computational chemistry tools, with a specific focus on Conceptual DFT. These techniques are applied to examine the chemical reactivity of Talarolide A and Talaropeptides A-D, shedding light on their potential for interacting with various biological targets. The research reveals insights into the chemical reactivity of Talarolide A and Talaropeptides A-D, uncovering active reaction sites and potential biological targets. Talarolide A demonstrates robust anti-inflammatory properties and antitumor activity against diverse cancer cell lines, while Talaropeptide A displays antimicrobial efficacy against both bacteria and fungi. The study underscores the significance of comprehending the chemical reactivity of natural marine products for advancing pharmaceutical development. By employing computational tools such as Conceptual DFT, this research uncovers crucial information about the active sites and potential targets of Talarolide A and Talaropeptides A-D. The findings contribute to the broader understanding of marine-derived peptides and their prospects as pharmaceutical agents, though further investigations are necessary to fully elucidate their pharmacological attributes.
ARTICLE | doi:10.20944/preprints202308.1966.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: Drug discovery; computational chemistry; conceptual DFT; marine cyclopeptides; chemical reactivity properties; bioavailability scores
Online: 29 August 2023 (09:36:49 CEST)
Stellatolides are natural compounds that have shown promising biological activities, including antitumor, antimicrobial, and anti-inflammatory properties, making them potential candidates for drug development. Chemical Reactivity Theory (CRT) is a branch of chemistry that explains and predicts the behavior of chemical reactions based on the electronic structure of molecules. Conceptual Density Functional Theory (CDFT) and Computational Peptidology (CP) are computational approaches used to study the behavior of atoms, molecules, and peptides. In this study, we present the results of our investigation of the chemical reactivity and ADMET properties of Stellatolides A-H using a novel computational approach called Conceptual DFT-based Computational Peptidology (CDFT-CP). Our study uses CDFT and CP to predict the reactivity and stability of molecules and to understand the behavior of peptides at the molecular level. We also predict the ADMET properties of the Stellatolides A-H to provide insight into their effectiveness, potential side effects, and optimal dosage and route of administration. This study sheds light on the potential of Stellatolides A-H as promising candidates for drug development and highlights the potential of CDFT-CP for the study of other natural compounds and peptides.
ARTICLE | doi:10.20944/preprints202309.0204.v1
Subject: Chemistry And Materials Science, Applied Chemistry Keywords: copper (I); triazine, phosphine, crystal structure, theoretical calculations, co-sensitized.
Online: 4 September 2023 (14:59:22 CEST)
A new copper(I) complex, [Cu2(L)2dppm](PF6)2 (1) [L = 3-(2-Pyridyl)-5,6-diphenyl-1,2,4-triazine and dppm: Bis(diphenylphosphino)methane] was prepared and characterized by IR, 1H-NMR, 31P-NMR spectroscopy, elemental and thermogravimetric analysis, and single-crystal X-ray diffraction technique. Complex 1 is a dinuclear compound, showing that L and dppm act as tridentate and bidentate chelating ligands, respectively. The two Cu(I) atoms exhibit a distorted tetrahedral coordination sphere embedded in N3P environments. The supramolecular interactions in the solid-state structure are characterized by C−H···N, C−H···F, C-H···π and π···π intermolecular interactions that were analyzed by inspection of the Hirshfeld surface and fingerprint plots. Additionally, the complex was studied experimentally in solution by UV–Vis spectroscopy and cyclic voltammetry; also, theoretical studies with Time-Dependent Density Functional Theory (TD-DFT) were performed. Moreover, the optical and electrochemical properties have been studied, focusing on the band gap. Compound 1 has been used as a co-sensitizer in a dye-sensitized solar cell, showing good activity.