Comparative assessment of some benzodiazepine drugs based on Density Functional Theory, molecular docking, and ADMET studies

Benzodiazepines are widely used to treat anxiety, insomnia, agitation, seizures, and muscle spasms. It works through the GABAA receptors to promote sleep by inhibiting brainstem monoaminergic arousal pathways. It is safe and effective for short-term use, and arises some crucial side effects based on dose and physical condition. In this investigation, physicochemical properties, molecular docking, and ADMET properties have been studied. Density functional theory with B3LYP/6-311G+(d,p) level of theory was set for geometry optimization and elucidate their thermodynamic, orbital, dipole moment, and electrostatic potential properties. Molecular docking and interaction calculations have performed against human GABAA receptor protein (PDB ID: 4COF) to search the binding affinity and effective interactions of drugs with the receptor protein. ADMET prediction has performed to investigate their absorption, metabolism, and toxic properties. Thermochemical data suggest the thermal stability; the docking result predicts effecting bindings and ADMET calculation disclose non-carcinogenic and relatively harmless phenomena for oral administration of all drugs.

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Computational Study of the Electron Spectra of Vapor-Phase Indole and Four Azaindoles

Molecules ◽

10.3390/molecules26071947 ◽

2021 ◽

Vol 26 (7) ◽

pp. 1947

Author(s):

Delano P. Chong

Keyword(s):

Density Functional Theory ◽

Vapor Phase ◽

Density Functional ◽

Computational Study ◽

Geometry Optimization ◽

The Other ◽

Functional Theory ◽

Electron Spectra

After geometry optimization, the electron spectra of indole and four azaindoles are calculated by density functional theory. Available experimental photoemission and excitation data for indole and 7-azaindole are used to compare with the theoretical values. The results for the other azaindoles are presented as predictions to help the interpretation of experimental spectra when they become available.

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Analytic gradients for multiconfiguration pair-density functional theory with density fitting: Development and application to geometry optimization in the ground and excited states

The Journal of Chemical Physics ◽

10.1063/5.0039258 ◽

2021 ◽

Vol 154 (7) ◽

pp. 074108

Author(s):

Thais R. Scott ◽

Meagan S. Oakley ◽

Matthew R. Hermes ◽

Andrew M. Sand ◽

Roland Lindh ◽

...

Keyword(s):

Density Functional Theory ◽

Excited States ◽

Density Functional ◽

Geometry Optimization ◽

Functional Theory ◽

Pair Density ◽

Density Fitting

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Molecular docking and molecular dynamics simulation studies to identify potent AURKA inhibitors: assessing the performance of density functional theory, MM-GBSA and mass action kinetics calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1674695 ◽

2019 ◽

Vol 38 (14) ◽

pp. 4325-4335 ◽

Cited By ~ 6

Author(s):

Sathishkumar Chinnasamy ◽

Gurudeeban Selvaraj ◽

Aman Chandra Kaushik ◽

Satyavani Kaliamurthi ◽

Selvaraj Chandrabose ◽

...

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Mass Action ◽

Dynamics Simulation ◽

Simulation Studies ◽

Functional Theory ◽

Mass Action Kinetics

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Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one

Molecules ◽

10.3390/molecules26123631 ◽

2021 ◽

Vol 26 (12) ◽

pp. 3631

Author(s):

Ahmed M. Deghady ◽

Rageh K. Hussein ◽

Abdulrahman G. Alhamzani ◽

Abeer Mera

Keyword(s):

Density Functional Theory ◽

Antibacterial Activity ◽

Molecular Docking ◽

Carbonyl Group ◽

Active Sites ◽

Density Functional ◽

Chemical Reactivity ◽

Basis Set ◽

Molecular Docking Study ◽

Functional Theory

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).

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Molecular docking and density functional theory studies on creatine, guanidinoacetic acid, and their phosphorylated analogues binding to muscle creatine kinase

Journal of Chemical Research ◽

10.1177/1747519820978583 ◽

2020 ◽

pp. 174751982097858

Author(s):

M Vraneš ◽

S Ostojić ◽

Č Podlipnik ◽

A Tot

Keyword(s):

Density Functional Theory ◽

Creatine Kinase ◽

Molecular Docking ◽

Density Functional ◽

Creatine Phosphate ◽

Docking Studies ◽

Muscle Creatine Kinase ◽

Functional Theory ◽

Guanidinoacetic Acid ◽

Muscle Creatine

Comparative molecular docking studies on creatine and guanidinoacetic acid, as well as their phosphorylated analogues, creatine phosphate, and phosphorylated guanidinoacetic acid, are investigated. Docking and density functional theory studies are carried out for muscle creatine kinase. The changes in the geometries of the ligands before and after binding to the enzyme are investigated to explain the better binding of guanidinoacetic acid and phosphorylated guanidinoacetic acid compared to creatine and creatine phosphate.

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Density functional theory investigation of the effect of axial coordination and annelation on the absorption spectroscopy of nickel(II) and vanadyl porphyrins relevant to bitumen and crude oils

Canadian Journal of Chemistry ◽

10.1139/cjc-2012-0532 ◽

2013 ◽

Vol 91 (9) ◽

pp. 872-878 ◽

Cited By ~ 16

Author(s):

Stanislav R. Stoyanov ◽

Cindy-Xing Yin ◽

Murray R. Gray ◽

Jeffrey M. Stryker ◽

Sergey Gusarov ◽

...

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Polyaromatic Hydrocarbons ◽

Geometry Optimization ◽

Soret Band ◽

Heavy Oils ◽

Visible Absorption ◽

Functional Theory ◽

Axial Coordination ◽

Td Dft

The vanadium and nickel components in heavy oils and bitumen are important impurities in catalytic processing and form aggregates with other asphaltene components. Metalloporphyrins are commonly analyzed using the characteristic Soret band in the UV–vis absorption spectrum. However, the Soret band of metalloporphyrins in petroleum is broadened and weaker than expected based on the concentration of Ni and V in heavy oils and the extinction coefficients of isolated porphyrins. We hypothesize that the low intensity and broadening of the Soret band could be due to axial coordination of the metal center or fusion (annelation) of aromatic rings on the porphyrin π-system. This hypothesis is examined using the density functional theory for geometry optimization and time-dependent density functional theory (TD-DFT) for calculation of excited states of nickel(II) and vanadyl porphyrins with axially coordinated ligands and annelated polyaromatic hydrocarbons. Predictions of the excited electronic states performed using the tandem of TD-DFT and conductor-like polarizable continuum model of solvation support this hypothesis and provide insight into the extent of Soret band broadening and intensity decrease due to coordination and annelation. These computational results, validated with respect to visible absorption spectra, are important for understanding asphaltene aggregation and spectroscopic characterization and suggest methods for removal of transition metals from heavy oil.

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DENSITY FUNCTIONAL THEORY STUDY OF H2O ADSORPTION AND DISSOCIATION ON Al (111) SURFACE

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633613500351 ◽

2013 ◽

Vol 12 (05) ◽

pp. 1350035 ◽

Cited By ~ 1

Author(s):

LIXIA YANG ◽

XIAOLI LEI ◽

JUN FENG ◽

YUXIN ZHANG ◽

MINGXING LIU

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Catalytic Effect ◽

Geometry Optimization ◽

Vacancy Defect ◽

Hydroxyl Group ◽

Dissociation Pathway ◽

Functional Theory ◽

Lower Activation ◽

Adsorption And Dissociation

Comparative study about the adsorption and dissociation behaviors of H2O molecule on clean and vacancy defective Al (111) surface was conducted by extensive density functional theory (DFT) calculations, the interaction mechanisms between H2O molecule and Al (111) surface were also figured out. Geometry optimization results indicated that H2O molecule was apt to be adsorbed at top site on these two kinds of surfaces, whereas, the adsorption configurations, the adsorption type and inclination of H2O molecule planes away from the normal were different. The calculated adsorption energies demonstrated that the adsorption of H2O molecule occurred more readily on vacancy defective Al (111) surface. The electron density distribution indicated that the vacancy defect enhanced the interactions between H2O molecule and surface Al atoms. Further analysis of the density of states (DOS) showed that the vacancy defect increased the number of bonding electrons between H2O molecule and surface Al atoms. The detailed exploration of dissociation pathways demonstrated that the dissociation of H2O molecule on these two kinds of surfaces was a two-step process: (1) H2O → H + OH , (2) OH → H + O . However, for each step the dissociation pathway variations on vacancy defective Al (111) surface were different with those on clean Al (111) surface. Compared with the first step, the dissociation of hydroxyl group into O atom and H atom was kinetically difficult. The calculated lower activation energy barriers on vacancy defective Al (111) surface showed that the vacancy defect had catalytic effect for the dissociation of H2O molecule to some extent, especially for the first step.

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