Chemical Reactivity of Supported ZnO Clusters: Undercoordinated Zinc and Oxygen Atoms as Active Sites

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule’s chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule’s stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol).

Download Full-text

Escherichia coli and herpes-simplex-virus ribonucleotide reductase R2 subunit. Compared reactivities of the redox centres

Biochemical Journal ◽

10.1042/bj2900807 ◽

1993 ◽

Vol 290 (3) ◽

pp. 807-810 ◽

Cited By ~ 10

Author(s):

M Atta ◽

N Lamarche ◽

J P Battioni ◽

B Massie ◽

Y Langelier ◽

...

Keyword(s):

Escherichia Coli ◽

Herpes Simplex Virus ◽

Herpes Simplex ◽

Ribonucleotide Reductase ◽

Active Sites ◽

Hydrophobic Interactions ◽

Chemical Reactivity ◽

Small Subunit ◽

Tyrosyl Radical ◽

Simplex Virus

Protein R2, the small subunit of ribonucleotide reductase, contains a diferric centre and a tyrosyl radical absolutely required for enzyme activity. The reduction of the tyrosyl radical and the mobilization of the iron centre result in the inhibition of the enzyme and thus of DNA synthesis. The chemical reactivity of the iron-radical centre of Escherichia coli and herpes simplex virus has been studied by u.v.-visible and e.p.r. spectroscopies. The tyrosyl radical is efficiently scavenged by hydroxamic acids and phenols during reactions controlled by steric hindrance and hydrophobic interactions. The reaction with o-disubstituted phenols yields the corresponding diphenoquinones. The reactivity of the bacterial radical greatly contrasts with that of the viral radical, and the iron centre in herpes-simplex-virus R2 is much more labile than that in E. coli R2, as shown from the facile mobilization of iron by chelators such as catechol. These results suggest that the active sites of the two enzymes are significantly different and might be useful for designing new antiviral agents.

Download Full-text

Calculation of the Global and Local Conceptual DFT Indices for the Prediction of the Chemical Reactivity Properties of Papuamides A–F Marine Drugs

Molecules ◽

10.3390/molecules24183312 ◽

2019 ◽

Vol 24 (18) ◽

pp. 3312 ◽

Cited By ~ 2

Author(s):

Norma Flores-Holguín ◽

Juan Frau ◽

Daniel Glossman-Mitnik

Keyword(s):

Density Functional Theory ◽

Active Sites ◽

Density Functional ◽

Chemical Reactivity ◽

Active Regions ◽

Conceptual Density Functional Theory ◽

Functional Theory ◽

Reactivity Descriptors ◽

Global And Local

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 Papuamide family of 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 Parr functions. Finally, the drug-likenesses and the bioactivity scores for the Papuamide peptides were predicted through a homology methodology relating them with the calculated reactivity descriptors, while other properties such as the pKas were determined following a methodology developed by our group.

Download Full-text

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

Journal of Chemistry ◽

10.1155/2013/850297 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 12

Author(s):

Jorge Ignacio Martínez-Araya ◽

Guillermo Salgado-Morán ◽

Daniel Glossman-Mitnik

Keyword(s):

Active Sites ◽

Chemical Reactivity ◽

Fukui Function ◽

Conceptual Dft ◽

Density Functionals ◽

Structure And Properties ◽

Dual Descriptor ◽

Reactivity Descriptors ◽

Koopmans Theorem ◽

Chemical Reactivity Descriptors

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 descriptorf(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.

Download Full-text

Active sites residues of beef liver carnitine octanoyltransferase (COT) and carnitine palmitoyltransferase (CPT-II)

Biochemical Journal ◽

10.1042/bj3301029 ◽

1998 ◽

Vol 330 (2) ◽

pp. 1029-1036 ◽

Cited By ~ 6

Author(s):

Nóirin NIC a'BHÁIRD ◽

Victoria YANKOVSKAYA ◽

R. Rona RAMSAY

Keyword(s):

Active Sites ◽

Chemical Reactivity ◽

Fatty Acyl ◽

Carnitine Palmitoyltransferase ◽

Inactivation Kinetics ◽

Beef Liver ◽

First Order Kinetics ◽

Carnitine Acyltransferases ◽

Carnitine Palmitoyltransferase Ii ◽

Selective Reagent

The carnitine acyltransferases which catalyse the reversible transfer of fatty acyl groups between carnitine and coenzyme A have been proposed to contain a catalytic histidine. Here, the chemical reactivity of active site groups has been used to demonstrate differences between the active sites of beef liver carnitine octanoyltransferase (COT) and carnitine palmitoyltransferase-II (CPT-II). Treatment of CPT-II with the histidine-selective reagent, diethyl pyrocarbonate (DEPC), resulted in simple linear pseudo-first-order kinetics. The reversal of the inhibition by hydroxylamine and the pKa (7.1) of the modified residue indicated that the residue was a histidine. The order of the inactivation kinetics showed that 1 mol of histidine was modified per mol of CPT-II.

Download Full-text

Understanding the Chemical Reactivity of Dihydroxyfumaric Acid and its Derivatives through Conceptual DFT

Revista de Chimie ◽

10.37358/rc.21.4.8465 ◽

2020 ◽

Vol 72 (4) ◽

pp. 162-174

Author(s):

Gheorghe Duca ◽

Natalia Bolocan

Keyword(s):

Active Sites ◽

Chemical Reactivity ◽

Conceptual Dft ◽

Total Hardness ◽

Hydroxyl Groups ◽

Reactivity Descriptors ◽

Local Reactivity ◽

Koopmans Theorem ◽

Chemical Reactivity Descriptors ◽

Homo And Lumo

The chemical reactivity descriptors have been calculated through Molecular Electron Density Theory encompassing Conceptual DFT. The validity of �Koopmans� theorem in DFT� (KID) has been assessed by a comparison between the global descriptors (electronegativity, total hardness, and global electrophilicity) calculated through vertical energy values and those arising from the HOMO and LUMO values. These results suggest that the KID procedure is valid and may be used, in conjunction with the B3LYP/3-611G(d, p) level of theory in further studies of related compounds in the aqueous medium. The active sites for nucleophilic and electrophilic attacks have been identified and verified using the local reactivity descriptors: the dual descriptor, the electrophilic and nucleophilic Parr functions, the local reactivity difference index Rk and MEP maps. Obtained results suggest that the antioxidant/antiradical power of investigated compounds may be explained by the highest ambiphilic activation of the oxygen atoms of the hydroxyl groups in the ene-diol moiety.

Download Full-text

Seeking a Structure-Function Relationship for γ-Al2O3 Surfaces

10.26434/chemrxiv.6789974.v1 ◽

2018 ◽

Author(s):

Muhammed Acikgoz ◽

Jaren Harrell ◽

Michele Pavanello

Keyword(s):

Structure Function ◽

Active Sites ◽

Chemical Reactivity ◽

Surface Oxidation ◽

Morphological Variations ◽

Structure Function Relationship ◽

Interesting Correlation ◽

Surface Dipole ◽

New Perspective ◽

Function Relationship

<p>The subject of this work is gamma alumina surfaces. We show that surface morphological variations can induce significant changes in work function and surface dipole particularly in regards of the surface oxidation level.</p> <p>Our results offer a new perspective on the structure-function relationship between surface morphology and electronic properties. For example, and for the first time in the literature, we uncover an interesting correlation between surface dipole and chemical reactivity of the surface active sites.</p>

Download Full-text

Computational Nanochemistry Study of the Molecular Structure and Properties of Chlorophyll a

International Journal of Photoenergy ◽

10.1155/2013/424620 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 4

Author(s):

Mónica Alvarado-González ◽

Norma Flores-Holguín ◽

Daniel Glossman-Mitnik

Keyword(s):

Molecular Structure ◽

Chlorophyll A ◽

Active Sites ◽

Chemical Reactivity ◽

Molecular Structures ◽

Structure And Properties ◽

Reactivity Descriptors ◽

Koopmans Theorem ◽

Td Dft ◽

Chemical Reactivity Descriptors

The M06 family of density functionals has been assessed for the calculation of the molecular structure and properties of the chlorophyll a molecule. Besides the determination of the molecular structures, the UV-Vis spectra have been computed using TD-DFT in the presence of a solvent, and the results were compared with the experimental data available. 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. A comparison between the descriptors calculated through vertical energy values and those arising from the Koopmans' theorem approximation have been performed in order to check for the validity of the last procedure.

Download Full-text

Chemical-Reactivity Properties, Drug Likeness, and Bioactivity Scores of Seragamides A–F Anticancer Marine Peptides: Conceptual Density Functional Theory Viewpoint

Computation ◽

10.3390/computation7030052 ◽

2019 ◽

Vol 7 (3) ◽

pp. 52 ◽

Cited By ~ 2

Author(s):

Norma Flores-Holguín ◽

Juan Frau ◽

Daniel Glossman-Mitnik

Keyword(s):

Density Functional Theory ◽

Active Sites ◽

Density Functional ◽

Chemical Reactivity ◽

Drug Repurposing ◽

Chemical Hardness ◽

Conceptual Density Functional Theory ◽

Functional Theory ◽

Fukui Functions ◽

Reactivity Descriptors

A methodology based on concepts that arose from Density Functional Theory (CDFT) was chosen for the calculation of global and local reactivity descriptors of the Seragamide family of marine anticancer peptides. Determination of active sites for the molecules was achieved by resorting to some descriptors within Molecular Electron Density Theory (MEDT) such as Fukui functions. The pKas of the six studied peptides were established using a proposed relationship between this property and calculated chemical hardness. The drug likenesses and bioactivity properties of the peptides considered in this study were obtained by resorting to a homology model by comparison with the bioactivity of related molecules in their interaction with different receptors. With the object of analyzing the concept of drug repurposing, a study of potential AGE-inhibition abilities of Seragamides peptides was pursued by comparison with well-known drugs that are already available as pharmaceuticals.

Download Full-text

Hydrothermal Carbon/Carbon Nanotube Composites as Electrocatalysts for the Oxygen Reduction Reaction

Journal of Composites Science ◽

10.3390/jcs4010020 ◽

2020 ◽

Vol 4 (1) ◽

pp. 20 ◽

Cited By ~ 1

Author(s):

Rafael G. Morais ◽

Natalia Rey-Raap ◽

Rui S. Costa ◽

Clara Pereira ◽

Alexandra Guedes ◽

...

Keyword(s):

Carbon Nanotubes ◽

Electrical Conductivity ◽

Oxygen Reduction Reaction ◽

Oxygen Reduction ◽

Ball Milling ◽

Active Sites ◽

Chemical Reactivity ◽

Carbon Composite ◽

Reduction Reaction ◽

Limiting Current

The oxygen reduction reaction is an essential reaction in several energy conversion devices such as fuel cells and batteries. So far, the best performance is obtained by using platinum-based electrocatalysts, which make the devices really expensive, and thus, new and more affordable materials should be designed. Biomass-derived carbons were prepared by hydrothermal carbonization in the presence of carbon nanotubes with different oxygen surface functionalities to evaluate their effect on the final properties. Additionally, nitrogen functional groups were also introduced by ball milling the carbon composite together with melamine. The oxygen groups on the surface of the carbon nanotubes favor their dispersion into the precursor mixture and the formation of a more homogenous carbon structure with higher mechanical strength. This type of structure partially avoids the crushing of the nanotubes and the carbon spheres during the ball milling, resulting in a carbon composite with enhanced electrical conductivity. Undoped and N-doped composites were used as electrocatalysts for the oxygen reduction reaction. The onset potential increases by 20% due to the incorporation of carbon nanotubes (CNTs) and nitrogen, which increases the number of active sites and improves the chemical reactivity, while the limiting current density increases by 47% due to the higher electrical conductivity.

Download Full-text