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Search Results: 1 - 10 of 32724 matches for " Daniel Glossman-Mitnik "
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Comparative Study of the Chemical Reactivity of Helical Peptide Models for Protein Glycation  [PDF]
Juan Frau, Daniel Glossman-Mitnik
Computational Chemistry (CC) , 2017, DOI: 10.4236/cc.2017.52006
Abstract: Non-enzymatic glycation of proteins has been implicated as an important cause of the complications associated with diabetes and Alzheimer disease. It is well known that glycation involves the reactivity of, primarily, the ε-amino group of the lysines present in the protein. The immediate chemical environment of an amino group modulates the glycation reaction. In this work, several model helical peptides for protein glycation has been studied by resorting to QM:MM calculations through the ONIOM methodology. Some Conceptual DFT descriptors have been calculated that allowed the comparison of the chemical reactivity between the different model peptides in terms of the position of the Lys group and other spatially proximate amino acid residues.
Computational Study of 3,4-Diphenyl-1,2,5-Thiadiazole 1-Oxide for Organic Photovoltaics
Daniel Glossman-Mitnik
International Journal of Photoenergy , 2009, DOI: 10.1155/2009/806714
Abstract: We make use of a model chemistry within Density Functional Theory (DFT) recently presented, which is called CHIH-DFT, to calculate the molecular structure of 3,4-diphenyl-1,2,5-thiadiazole 1-oxide (TSO), as well to predict its infrared (IR), ultraviolet (UV-Vis) and fluorescence (Fluo) spectra, the dipole moment and polarizability, the free energy of solvation in different solvents as an indication of solubility, and the chemical reactivity parameters that arise from Conceptual DFT. The calculated values are compared with the available experimental data for this molecule as a means of validation of our proposed model chemistry.
Chemical Reactivity Theory (CRT) Study of the Melanoidin M8: Local Conceptual Density Functional Theory Descriptors  [PDF]
Juan Frau, Norma Flores-Holguín, Daniel Glossman-Mitnik
Computational Molecular Bioscience (CMB) , 2018, DOI: 10.4236/cmb.2018.82004
Abstract: This study evaluated a fixed long-range corrected range-separated hybrid (RSH) density functional associated with the Def2TZVP basis set alongside the Solvation Model based on Density (SMD) for the computation of the structure, molecular properties and chemical reactivity of the M8 intermediate melanoidin pigment. The preference of the active sites pertinent to radical, nucleophilic and electrophilic attacks is made through linking them with the electrophilic and nucleophilic Parr functions, Fukui function indices, and condensed Dual Descriptor. This study showed that the MN12SX density functional is the most suitable one for predicting the chemical reactivity of this system.
Conceptual Density Functional Theory Study of the Chemical Reactivity Properties and Bioactivity Scores of the Leu-Enkephalin Opioid Peptide Neurotransmitter  [PDF]
Juan Frau, Norma Flores-Holguín, Daniel Glossman-Mitnik
Computational Molecular Bioscience (CMB) , 2019, DOI: 10.4236/cmb.2019.91002
Abstract: The SMD solvation model (Solvation Model based on the Density) and eight density functionals, CAM-B3LYP, LC-ωPBE, M11, MN12SX, N12SX, ωB97, ωB97X, and ωB97XD, were assessed in link with the Def2TZVP basis set for the calculation of the structure of the Leu-Enkephalin Opioid Peptide Neurotransmitter as well as their molecular properties. Through the Conceptual Density Functional Theory (CDFT), the entire chemical descriptors for the system were calculated. The active regions of the molecules necessary for electrophilic, nucleophilic and radical attacks were chosen through linking them with the corresponding Fukui functions. Furthermore, the prediction of the pKa value for the peptide is done with great accuracy as well as the ability of the studied molecule in acting as an efficient inhibitor of the formation of Advanced Glycation Endproducts (AGEs), which comprises of a useful knowledge for the development of drugs for preventing Alzheimer, Diabetes and Parkinson diseases. Lastly, the bioactivity scores for the studied peptides are predicted via various methodologies.
DFT study of the effect of substituents on the absorption and emission spectra of Indigo
Francisco Cervantes-Navarro, Daniel Glossman-Mitnik
Chemistry Central Journal , 2012, DOI: 10.1186/1752-153x-6-70
Abstract: Calculations were performed based on the framework of density functional theory (DFT) with the Becke 3- parameter-Lee-Yang-Parr (B3LYP) functional, where the 6-31 G(d,p) basis set was employed. The configuration interaction singles (CIS) method with the same basis set was employed for the analysis of excited states and for the acquisition of the emission spectra.The presented absorption and emission spectra were affected by the substitution position. When a hydrogen atom of the molecule was substituted by Cl or Br, practically no change in the absorbed and emitted energies relative to those of the indigo molecule were observed; however, when N was substituted by S or Se, the absorbed and emitted energies increased.Substituent effects on molecules have always been a subject of study because it is our goal to modify molecules based on our needs. A way in which to study this phenomenon is to analyze the effects of substituents on the spectra of molecules. Solvent [1], substituent [2] and synthesis effects [3], as well as combinations of these effects [4], have been shown.In the present study, the indigo molecule was employed as the base molecule, with Chlorine (Cl), Bromine (Br), Sulfur (S) and Selenium (Se) as substituents [5]. The Hemi-Indigo molecule [6,7] was also studied because its properties have been shown to be similar to those of the Indigo molecule; we also thought it would be interesting to compare its properties with those of the rest of the investigated molecules.Theoretical studies of the effects of substituents on absorption and emission spectra [8-16] have been performed, including studies on the indigo molecule [17]. The present work attempts to explain, perhaps vaguely but completely based on the obtained results, the effects observed when the absorption and emission spectra of indigo are compared.GAUSSVIEW 03 software was used to generate the molecular structures, and calculations were performed using GAUSSIAN 03?W. Density functional theory (DFT) w
Natural Carotenoids as Nanomaterial Precursors for Molecular Photovoltaics: A Computational DFT Study
Teresita Ruiz-Anchondo,Norma Flores-Holguín,Daniel Glossman-Mitnik
Molecules , 2010, DOI: 10.3390/molecules15074490
Abstract: In this work several natural carotenoids were studied as potential nanomaterial precursors for molecular photovoltaics. M05-2X/6-31+G(d,p) level of theory calculations were used to obtain their molecular structures, as well as to predict the infrared (IR) and ultraviolet (UV-Vis) spectra, the dipole moment and polarizability, the pKa, and the chemical reactivity parameters (electronegativity, hardness, electrophilicity and Fukui functions) that arise from Conceptual DFT. The calculated values were compared with the available experimental data for these molecules and discussed in terms of their usefulness in describing photovoltaic properties.
Docking Studies of Binding of Ethambutol to the C-Terminal Domain of the Arabinosyltransferase from Mycobacterium tuberculosis
Guillermo Salgado-Moran,Rodrigo Ramirez-Tagle,Daniel Glossman-Mitnik,Samuel Ruiz-Nieto
Journal of Chemistry , 2013, DOI: 10.1155/2013/601270
Abstract:
Chemical Reactivity Properties, Drug-Likeness Features and Bioactivity Scores of the Cholecystokinin Peptide Hormone  [PDF]
Norma Flores-Holguín, Juan Frau, Daniel Glossman-Mitnik
Computational Molecular Bioscience (CMB) , 2019, DOI: 10.4236/cmb.2019.92004
Abstract: Five density functionals, CAM-B3LYP, LC-ωPBE, MN12SX, N12SX 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 Cholecystokinin peptide hormone (CCK-8) 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 scoresfor CCK-8 were predicted through different methodologies already reported in the literature which have been previously validated during the study of different peptidic systems. The conclusion was that the CCK-8 peptide will be moderately bioactive regarding all the interactions.
Computational Study of the Chemical Reactivity and Bioactivity Rates of Marine Peptides Hemiasterlin and Its A and B Derivatives Used in the Cancer Treatment through Conceptual Density Functional Theory  [PDF]
Norma Flores-Holguín, Juan Frau, Daniel Glossman-Mitnik
Computational Molecular Bioscience (CMB) , 2019, DOI: 10.4236/cmb.2019.94008
Abstract: This study involved the assessment of the MNI2SX/Def2TZVP/H2O model chemistry to enhance the understanding of the structural composition of the marine peptide Hemiasterlin and its derivatives A and B used in cancer treatment. The Conceptual Density Functional theory was used in the calculation of molecular properties of the system chemical descriptors during the study. Integration of the active molecular regions into their respective Fukui functions was used in the selection of electrophilic and nucleophilic attacks. Additionally, the proposed correlation between global hardness and the pKa was used as the basis of deriving accurate predictions for the pKa values while a homology technique was used in the prediction of bioactivity and bioavailability scores of the peptides under investigation.
Density Functional Theory (DFT) Study of Triphenylamine-Based Dyes for Their Use as Sensitizers in Molecular Photovoltaics
Jesús Baldenebro-López,José Castorena-González,Norma Flores-Holguín,Jorge Almaral-Sánchez,Daniel Glossman-Mitnik
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms13044418
Abstract: 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 p K a values were calculated with the semi-empirical PM6 method.
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