scholarly journals Density Functional Theory, Chemical Reactivity, Pharmacological Potential and Molecular Docking of Dihydrothiouracil-Indenopyridopyrimidines with Human-DNA Topoisomerase II

2020 ◽  
Vol 21 (4) ◽  
pp. 1253 ◽  
Author(s):  
Mohamed E. Elshakre ◽  
Mahmoud A. Noamaan ◽  
Hussein Moustafa ◽  
Haider Butt
Keyword(s):  
Density Functional Theory ◽  
Molecular Docking ◽  
Density Functional ◽  
Topoisomerase Ii ◽  
Chemical Reactivity ◽  
Antitumor Drug ◽  
Binding Energies ◽  
Basis Sets ◽  
Chemical Hardness ◽  
Functional Theory

In this work, three computational methods (Hatree-Fock (HF), Møller–Plesset 2 (MP2), and Density Functional Theory (DFT)) using a variety of basis sets are used to determine the atomic and molecular properties of dihydrothiouracil-based indenopyridopyrimidine (TUDHIPP) derivatives. Reactivity descriptors of this system, including chemical potential (µ), chemical hardness (η), electrophilicity (ω), condensed Fukui function and dual descriptors are calculated at B3LYP/6-311++ G (d,p) to identify reactivity changes of these molecules in both gas and aqueous phases. We determined the molecular electrostatic surface potential (MESP) to determine the most active site in these molecules. Molecular docking study of TUDHIPP with topoisomerase II α and β is performed, predicting binding sites and binding energies with amino acids of both proteins. Docking studies of TUDHIPP versus etoposide suggest their potential as antitumor candidates. We have applied Lipinski, Veber’s rules and analysis of the Golden triangle and structure activity/property relationship for a series of TUDHIPP derivatives indicate that the proposed compounds exhibit good oral bioavailability. The comparison of the drug likeness descriptors of TUDHIPP with those of etoposide, which is known to be an antitumor drug, indicates that TUDHIPP can be considered as an antitumor drug. The overall study indicates that TUDHIPP has comparable and even better descriptors than etoposide proposing that it can be as effective antitumor drug, especially 2H, 6H and 7H compounds.

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

Molecules ◽  
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).

A Quantum Theory of Atoms-in-Molecules Perspective and DFT Study of Two Natural Products: Trans-Communic Acid and Imbricatolic Acid

2017 ◽  
Vol 70 (3) ◽  
pp. 328 ◽  
Author(s):  
Sarvesh Kumar Pandey ◽  
Mohammad Faheem Khan ◽  
Shikha Awasthi ◽  
Reetu Sangwan ◽  
Sudha Jain
Keyword(s):  
Density Functional Theory ◽  
Quantum Theory ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Atoms In Molecules ◽  
Reactivity Index ◽  
Chemical Hardness ◽  
Functional Theory ◽  
Bond Path ◽  
Topological Features

The topological features of the charge densities, ρ(r), and the chemical reactivity of two most biologically relevant and chemically interesting scaffold systems i.e. trans-communic acid and imbricatolic acid have been determined using density functional theory. To identify, characterize, and quantify efficiently, the non-covalent interactions of the atoms in the molecules have been investigated quantitatively using Bader's quantum theory of atoms-in-molecules (QTAIM) technique. The bond path is shown to persist for a range of weak H···H as well as C···H internuclear distances (in the range of 2.0–3.0 Å). These interactions exhibit all the hallmarks of a closed-shell weak interaction. To get insights into both systems, chemical reactivity descriptors, such as HOMO–LUMO, ionization potential, and chemical hardness, have been calculated and used to probe the relative stability and chemical reactivity. Some other useful information is also obtained with the help of several other electronic parameters, which are closely related to the chemical reactivity and reaction paths of the products investigated. Trans-communic acid seems to be chemically more sensitive when compared with imbricatolic acid due to its experimentally observed higher half-maximal inhibitory concentration (bioactivity parameter) value, which is in accordance with its higher chemical reactivity as theoretically predicted using density functional theory-based reactivity index. The quantum chemical calculations have also been performed in solution using different solvents, and the relative order of their structural and electronic properties as well as QTAIM-based parameters show patterns similar to those observed in gas phase only. This study further exemplifies the use and successful application of the bond path concept and the quantum theory of atoms-in-molecules.

Fluorescent styryl chromophores with rigid (pyrazole) donor and rigid (benzothiophenedioxide) acceptor – complete density functional theory (DFT), TDDFT and nonlinear optical study

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Sulochana Bhalekar ◽  
Archana Bhagwat ◽  
Nagaiyan Sekar
Keyword(s):  
Density Functional Theory ◽  
Dipole Moment ◽  
Density Functional ◽  
Nonlinear Optical ◽  
Absolute Error ◽  
Basis Sets ◽  
Chemical Hardness ◽  
Styryl Dyes ◽  
Functional Theory ◽  
Hybrid Functionals

Abstract Density functional theory (DFT) and time-dependent DFT computations were employed to examine linear and nonlinear optical (NLO) characteristics of (E)-4-((1,1-dioxido-3-oxobenzo[b]thiophen-2(3H)-ylidene) ethyl)-1-phenyl-1H-pyrazol-5(4H)-one derived styryl dyes. NLO properties were computed using the two different global hybrid functionals B3LYP, BHandHLYP and three range separated hybrid functionals CAM B3LYP, wB97, wB97X and wB97XD with the basis sets 6–311++G(d,p), cc-pVDZ and cc-pVTZ. The compounds shows higher values of dipole moment around 8–9 Debye than the other compounds. They show higher values of α 0, ß 0 and γ 0 values. The values of γ 0 are around 204–544 × 10−36 e.s.u. with the method, B3LYP/6–311++G(d, p). We have calculated the mean absolute error (MAE) for dipole moment, α 0, ß 0 and γ 0 values. It is observed that MAE is less (0.89) for wB97/6–311++G(d,p) which indicates that wB97 is the most suited functional for all three compounds. Chemical stability and reactivity of these dyes were studied using electrophilicity index and chemical hardness and hyperhardness.

Density functional theory study of structural, magnetic and spectral properties of the CrmFen (m + n = 6) and CrmFenCu (m + n = 5) clusters

2019 ◽  
Vol 9 (6) ◽  
pp. 570-577
Author(s):  
Yunlong Chen ◽  
Zhenghua Tang ◽  
Chong He ◽  
Yong Sheng
Keyword(s):  
Density Functional Theory ◽  
Infrared Spectroscopy ◽  
Density Functional ◽  
Energy Gap ◽  
Binding Energies ◽  
Chemical Hardness ◽  
Lumo Energy ◽  
Functional Theory ◽  
Homo Lumo ◽  
Original Cluster

Using Density functional theory (DFT) to study the geometries, stability, magnetic properties and infrared spectroscopy of CrmFen (m + n = 6) and CrmFenCu (m + n = 5) clusters at the BP86/SDD level. The ground state structures of CrmFen (m + n = 6) and CrmFenCu (m + n = 5) clusters are determined according to the principles of lowest energy and no virtual frequency. On this basis, the structural and chemical stabilities are obtained by the average binding energies (Eb), chemical hardness (η) and HOMO-LUMO energy gap (Eg). The average binding energies show the substitution of a copper atom is beneficial to improve the structural stability; It can be seen Cr4Fe2 and Cr3Fe2Cu have the best chemical stability in the two cluster series from the chemical hardness and HOMO-LUMO energy gap. By calculating the magnetic moment, it is shown that Cr5Fe and CrFe4Cu have large magnetic moments, which can be understood by the spin distribution. Finally, infrared spectroscopy of the clusters are calculated, we find a copper atom substitutes the CrmFen (m + n = 6) does not change the range of vibration frequency a lot because it does not significantly change the molecular structure of the original cluster, but it changes the vibration mode of the original cluster, resulting in the strongest infrared absorption peak intensity of Cr3Fe2Cu being lower than that of Cr3Fe3.

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

Computation ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 52 ◽  
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.

scholarly journals Theoretical Study of the Effect of π-Bridge on Optical and Electronic Properties of Carbazole-Based Sensitizers for DSSCs

Molecules ◽  
2020 ◽  
Vol 25 (16) ◽  
pp. 3670
Author(s):  
Tomás Delgado-Montiel ◽  
Jesús Baldenebro-López ◽  
Rody Soto-Rojo ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Molecular Orbital ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Energy Levels ◽  
Dye Sensitized Solar Cells ◽  
Geometry Optimization ◽  
Oscillator Strengths ◽  
Chemical Hardness ◽  
Functional Theory

Eight novel metal-free organic sensitizers were proposed for dye-sensitized solar cells (DSSCs), theoretically calculated and studied via density functional theory with D-π-A structure. These proposals were formed to study the effect of novel π-bridges, using carbazole as the donor group and cyanoacrylic acid as the anchorage group. Through the M06/6-31G(d) level of theory, ground state geometry optimization, vibrational frequencies, the highest occupied molecular orbital, the lowest unoccupied molecular orbital, and their energy levels were calculated. Further, chemical reactivity parameters were obtained and analyzed, such as chemical hardness (η), electrophilicity index (ω), electroaccepting power (ω+) and electrodonating power (ω-). Free energy of electron injection (ΔGinj) and light-harvesting efficiency (LHE) also were calculated and discussed. On the other hand, absorption wavelengths, oscillator strengths, and electron transitions were calculated through time-dependent density functional theory with the M06-2X/6-31G(d) level of theory. In conclusion, the inclusion of thiophene groups and the Si heteroatom in the π-bridge improved charge transfer, chemical stability, and other optoelectronic properties of carbazole-based dyes.

π–π INTERACTION IN BENZENE DIMER STUDIED USING DENSITY FUNCTIONAL THEORY AUGMENTED WITH AN EMPIRICAL DISPERSION TERM

2010 ◽  
Vol 09 (supp01) ◽  
pp. 109-123 ◽  
Author(s):  
CHAO FENG ◽  
CHENSHENG LIN ◽  
XIAOHONG ZHANG ◽  
RUIQIN ZHANG
Keyword(s):  
Density Functional Theory ◽  
Long Range ◽  
Density Functional ◽  
Theoretical Method ◽  
Binding Energies ◽  
Basis Sets ◽  
Functional Theory ◽  
Π Interactions ◽  
Benzene Dimer ◽  
Dispersion Term

The π–π interactions in various configurations of benzene dimers were studied using a density functional theoretical method augmented with an empirical dispersion term (acronym DFT-D) which is capable of describing long-range dispersive interaction. Compared with the previous CCSD(T) calculations, our approach using PBE functional and polarized triple-ζ quality basis sets provides reasonably accurate binding energies and equilibrium intermolecular geometries of the considered benzene dimer configurations, although the calculations are not counterpoisely corrected. It is expected that our approach can be utilized to evaluate the π–π interactions in large complex systems.

Benchmark of Simplified Time-Dependent Density Functional Theory for UV-Vis Spectral Properties of Porphyrinoids

2019 ◽  
Author(s):  
Kamal Batra ◽  
Stefan Zahn ◽  
Thomas Heine
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Large Scale ◽  
Absolute Error ◽  
Time Dependent ◽  
Basis Set ◽  
Basis Sets ◽  
Functional Theory ◽  
Framework Materials ◽  
Dependent Density

<p>We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV). </p>

A DFT study of spherands containing five anisyl groups — Highly preorganized to bind the alkali metal

2006 ◽  
Vol 84 (8) ◽  
pp. 1045-1049 ◽  
Author(s):  
Shabaan AK Elroby ◽  
Kyu Hwan Lee ◽  
Seung Joo Cho ◽  
Alan Hinchliffe
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Ionic Radius ◽  
Binding Energies ◽  
Cavity Size ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Good Agreement

Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygens during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. We used standard B3LYP/6-31G** (5d) density functional theory (DFT) to investigate the complexation between spherands containing five anisyl groups, with CH2–O–CH2 (2) and CH2–S–CH2 (3) units in an 18-membered macrocyclic ring, and the cationic guests (Li+, Na+, and K+). Our geometric structure results for spherands 1, 2, and 3 are in good agreement with the previously reported X-ray diffraction data. The absolute values of the binding energy of all the spherands are inversely proportional to the ionic radius of the guests. The results, taken as a whole, show that replacement of one anisyl group by CH2–O–CH2 (2) and CH2–S–CH2 (3) makes the cavity bigger and less preorganized. In addition, both the binding and specificity decrease for small ions. The spherands 2 and 3 appear beautifully preorganized to bind all guests, so it is not surprising that their binding energies are close to the parent spherand 1. Interestingly, there is a clear linear relation between the radius of the cavity and the binding energy (R2 = 0.999).Key words: spherands, preorganization, density functional theory, binding energy, cavity size.

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