Quantum Computational, Spectroscopic, NHO and Molecular Docking Studies on 1-Methyl-nicotinamide (MNA): An Antithrombotic, Anti-inflammatory, Gastroprotective and Vasoprotective Compound

2021 ◽  
Vol 6 (2) ◽  
pp. 128-140
Author(s):  
Mukesh Kumar ◽  
Satyavir Singh ◽  
Nazia Siddiqui ◽  
Saleem Javed
Keyword(s):  
Molecular Docking ◽  
Density Functional ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Binding Energies ◽  
Basis Set ◽  
Theory Approach ◽  
Fukui Functions ◽  
Donor And Acceptor ◽  
Ligand Interactions

In present work, 1-methylnicotinamide (1-MNA) has been investigated theoretically by density functional theory approach and investigated its vibrational spectroscopy. To complete the structure optimization, determination of vibrational frequencies and other valuable parameters, B3LYP method used with the 6-311++G(d,p) basis set. Atoms in molecules theory (AIM) had been used to evaluate ellipticity, isosurface projection by electron localization function and binding energies. The IR and Raman spectra have also been calculated computationally. NBO analysis employed to determine interactions of donor and acceptor. Fukui functions and molecular electrostatic potential (MEP) showed reactive regions of the molecule. UV-vis spectrum calculated using TD-DFT/PCM methods with different solvents. Thermodynamic properties like free energy, enthalpy and entropy with various temperature were calculated. By the use of the electrophilicity index, the probability of the bioactive nature of the molecule was proved theoretically. Protein-ligand interactions calculated and established by molecular docking. The biological investigations for druglikeness also employed for the (1-MNA).

Quantum Computational, Spectroscopic and Molecular Docking Studies on N-(4-Hydroxyphenyl)picolinamide

2021 ◽  
Vol 6 (3) ◽  
pp. 186-203
Author(s):  
Meenakshi Singh ◽  
Mukesh Kumar ◽  
Neha Singh ◽  
Shikha Sharma ◽  
Neha Agarwal ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Geometry ◽  
Energy Difference ◽  
Docking Studies ◽  
Basis Set ◽  
Fukui Functions ◽  
Homo And Lumo ◽  
Gibb’S Free Energy

In this work, the quantum computations of newly synthesized N-(4-hydroxyphenyl)picolinamide (4-HPP) is focused. Density functional theory (DFT) was used to perform the quantum calculations. The optimized molecular geometry was obtained using the B3LYP and MP2 methods employing 6-311++G(d,p) basis set, which served as the foundation for all subsequent calculations. The experimental data was compared with the calculated vibrational frequencies and NMR spectra. With the use of the molecular electrostatic potential surface (MEP) and the Fukui functions, the charge distribution, reactive regions and electrostatic potential were displayed. The chemical activity of the 4-HPP was evaluated by the energy difference between HOMO and LUMO. For better understanding of the intermolecular charge transfer (ICT), natural bond order analysis (NBO) was used. At various temperatures, thermodynamic parameters such as Gibb’s free energy, enthalpy and entropy were determined. The electrophilicity index was used to portray the molecule’s bioactivity and molecular docking was used to show the interaction between the ligand and the protein. The nature of the molecule was determined by drug similarity when expecting its application for medical purposes.

scholarly journals A Combined Experimental (FT-IR) and Computational Studies of 9-Chloroanthracene

2019 ◽  
Vol 31 (6) ◽  
pp. 1332-1342 ◽  
Author(s):  
KATTAESWAR SRIKANTH ◽  
RAMAIAH KONAKANCHI ◽  
JYOTHI PRASHANTH
Keyword(s):  
Density Functional ◽  
Minimum Energy ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Basis Set ◽  
Protein Targets ◽  
Charge Delocalization ◽  
Fukui Functions ◽  
Homo And Lumo ◽  
Ft Ir

The experimental FT-IR spectral analysis of 9-chloroanthracene has worked out by using density functional theory (DFT). The optimized molecular structure and minimum energy of 9-chloroanthracene has analyzed using DFT/B3LYP functional employing 6-311++G(d,p) basis set. The vibrational frequencies along with IR intensities were computed, scaling was used for a better fit between the experimental and computed frequencies, they agreed with rms error 8.48 cm-1 for 9-chloroanthracene. The NLO behaviour of the molecule is investigated from first-order hyperpolarizability. The HOMO and LUMO energies are evaluated to demonstrate the chemical stability, reactivity of molecule. The MESP over the molecules were plotted to evaluate electron density regions and thermodynamic parameters are calculated. Hyper conjugative interactions and charge delocalization of the molecule study from NBO analysis and Fukui functions are evaluated for 9-chloroanthracene. The molecular docking studies were performed against anticancer protein targets Tyrosinase and HER2.

Binding Energies of Organic Charge-Transfer Complexes Calculated by First-Principles Methods

1998 ◽  
Vol 63 (8) ◽  
pp. 1223-1244 ◽  
Author(s):  
Cordula Rauwolf ◽  
Achim Mehlhorn ◽  
Jürgen Fabian
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Ground State ◽  
Density Functional ◽  
Binding Energies ◽  
Basis Set ◽  
Dispersion Energy ◽  
Functional Theory ◽  
Basis Set Superposition Error ◽  
Donor And Acceptor

Weak interactions between organic donor and acceptor molecules resulting in cofacially-stacked aggregates ("CT complexes") were studied by second-order many-body perturbation theory (MP2) and by gradient-corrected hybrid Hartree-Fock/density functional theory (B3LYP exchange-correlation functional). The complexes consist of tetrathiafulvalene (TTF) and related compounds and tetracyanoethylene (TCNE). Density functional theory (DFT) and MP2 molecular equilibrium geometries of the component structures are calculated by means of 6-31G*, 6-31G*(0.25), 6-31++G**, 6-31++G(3df,2p) and 6-311G** basis sets. Reliable molecular geometries are obtained for the donor and acceptor compounds considered. The geometries of the compounds were kept frozen in optimizing aggregate structures with respect to the intermolecular distance. The basis set superposition error (BSSE) was considered (counterpoise correction). According to the DFT and MP2 calculations laterally-displaced stacks are more stable than vertical stacks. The charge transfer from the donor to the acceptor is small in the ground state of the isolated complexes. The cp-corrected binding energies of TTF/TCNE amount to -1.7 and -6.3 kcal/mol at the DFT(B3LYP) and MP2(frozen) level of theory, respectively (6-31G* basis set). Larger binding energies were obtained by Hobza's 6-31G*(0.25) basis set. The larger MP2 binding energies suggest that the dispersion energy is underestimated or not considered by the B3LYP functional. The energy increases when S in TTF/TCNE is replaced by O or NH but decreases with substitution by Se. The charge-transferred complexes in the triplet state are favored in the vertical arrangement. Self-consistent-reaction-field (SCRF) calculations predicted a gain in binding energy with solvation for the ground-state complex. The ground-state charge transfer between the components is increased up to 0.8 e in polar solvents.

scholarly journals Electron Donor and Acceptor Influence on the Nonlinear Optical Response of Diacetylene-Functionalized Organic Materials (DFOMs): Density Functional Theory Calculations

Molecules ◽  
2019 ◽  
Vol 24 (11) ◽  
pp. 2096 ◽  
Author(s):  
Muhammad Khalid ◽  
Riaz Hussain ◽  
Ajaz Hussain ◽  
Bakhat Ali ◽  
Farrukh Jaleel ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Electron Donor ◽  
Density Functional ◽  
Nbo Analysis ◽  
Basis Set ◽  
First Hyperpolarizability ◽  
Functional Theory ◽  
Parent Molecule ◽  
Donor And Acceptor

Herein, we report the quantum chemical results based on density functional theory for the polarizability (α) and first hyperpolarizability (β) values of diacetylene-functionalized organic molecules (DFOM) containing an electron acceptor (A) unit in the form of nitro group and electron donor (D) unit in the form of amino group. Six DFOM 1–6 have been designed by structural tailoring of the synthesized chromophore 4,4′-(buta-1,3-diyne-1,4-diyl) dianiline (R) and the influence of the D and A moieties on α and β was explored. Ground state geometries, HOMO-LUMO energies, and natural bond orbital (NBO) analysis of all DFOM (R and 1–6) were explored through B3LYP level of DFT and 6-31G(d,p) basis set. The polarizability (α), first hyperpolarizability (β) values were computed using B3LYP (gas phase), CAM-B3LYP (gas phase), CAM-B3LYP (solvent DMSO) methods and 6-31G(d,p) basis set combination. UV-Visible analysis was performed at CAM-B3LYP/6-31G(d,p) level of theory. Results illustrated that much reduced energy gap in the range of 2.212–2.809 eV was observed in designed DFOM 1–6 as compared to parent molecule R (4.405 eV). Designed DFOM (except for 2 and 4) were found red shifted compared to parent molecule R. An absorption at longer wavelength was observed for 6 with 371.46 nm. NBO analysis confirmed the involvement of extended conjugation and as well as charge transfer character towards the promising NLO response and red shift of molecules under study. Overall, compound 6 displayed large <α> and βtot, computed to be 333.40 (a.u.) (B3LYP gas), 302.38 (a.u.) (CAM-B3LYP gas), 380.46 (a.u.) (CAM-B3LYP solvent) and 24708.79 (a.u.), 11841.93 (a.u.), 25053.32 (a.u.) measured from B3LYP (gas), CAM-B3LYP (gas) and CAM-B3LYP (DMSO) methods respectively. This investigation provides a theoretical framework for conversion of centrosymmetric molecules into non-centrosymmetric architectures to discover NLO candidates for modern hi-tech applications.

POST HARTREE–FOCK AND DENSITY FUNCTIONAL THEORY STUDIES ON (BN)n=1–10 CLUSTERS

2005 ◽  
Vol 04 (03) ◽  
pp. 377-388 ◽  
Author(s):  
V. NIRMALA ◽  
P. KOLANDAIVEL
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Structural Parameters ◽  
Nbo Analysis ◽  
Simple Expression ◽  
Binding Energies ◽  
Basis Set ◽  
Functional Theory ◽  
Basis Set Superposition Error ◽  
Hartree Fock

Density functional theory and Møller–Plesset perturbation theory methods have been used to study the ring clusters of ( BN )n=1–10 employing 6-311++G** basis set. The binding energies have been corrected for the basis set superposition error (BSSE). Static polarizability of these ring clusters has been investigated. A simple expression for the size dependence of polarizability has been invoked, so that the same relation can be useful for predicting the polarizability of larger clusters. The topological properties were analyzed employing the Bader's atoms in molecules theory. A good correlation between the structural parameters and the properties of electron density is found. Localization and delocalization indices were also used for the analysis of molecular electronic structure by an electron pair perspective. The contribution of stereo electronic interactions to the molecular properties as a function of ring size is analyzed based on the natural bond orbital (NBO) analysis.

scholarly journals Antibacterial, Antifungal Chalcone Derivatives as EGFR Inhibitors-Molecular Docking and ADMET Studies

2021 ◽  
pp. 387-396
Author(s):  
Hemalatha Sattu ◽  
Indira rani Nerella ◽  
Saritha Jyostna Tangeda
Keyword(s):  
Molecular Docking ◽  
Growth Factor Receptor ◽  
Docking Simulation ◽  
Docking Studies ◽  
Binding Energies ◽  
Receptor Protein ◽  
Molecular Docking Studies ◽  
Chalcone Derivatives ◽  
Ligand Interactions ◽  
Protein Environment

Aim: In our earlier research, we have synthesized series of substituted 1-(2, 5-dimethyl thiophene-3yl)-(4-substituted phenyl)-2-propene-1-one derivatives and evaluated them for their anti-bacterial and antifungal activity. In recent years, chalcone derivatives are proved for their varied pharmacological effects ranging from antimicrobial activity to anti-cancer effects. In this study, we have hypothesized the efficiency of our earlier synthesized anti-bacterial and antifungal chalcone derivatives for their potential inhibition of epidermal growth factor receptor protein (EGFR), through molecular docking studies. Methodology: Molecular docking simulation studies are performed using the Glide XP module of Schrodinger Suite and ligand binding energies are also calculated. Results: Molecular docking studies of the selected compounds against EGFR revealed docking scores ranging from -6.746 (compound 5) to -5.681 (compound 3) and also provided insight into binding conformations of the ligands in the EGFR protein environment. Additionally, molecular property and Absorption, Distribution, Metabolism, and Excretion (ADME) predictor analysis is also performed for the dataset ligands, which further provided the probable explanation for the binding potentials. Conclusion: Among all the tested dataset ligands, compound 5 has shown the highest dock score (-6.746) with better ADME profiles. Binding energies in the protein-ligand interactions explain how fit the ligand binds with the target protein. Molecular docking studies of these anti-bacterial, antifungal chalcone derivatives provided deeper insights in understanding the probable conformations of these tested ligands in the EGFR protein environment.

scholarly journals Vibrational Spectroscopic Analysis of 10H-Dibenzo[b,e][2,4]oxazine and Investigate their Structural Reactivity by DFT Computations and Molecular Docking Analysis

2020 ◽  
Vol 32 (10) ◽  
pp. 2475-2485
Author(s):  
M. Latha Beatrice ◽  
S. Mary Delphine ◽  
M. Amalanathan ◽  
H. Marshan Robert
Keyword(s):  
Molecular Docking ◽  
Density Functional ◽  
Atomic Orbital ◽  
Nbo Analysis ◽  
Vibrational Frequencies ◽  
Basis Set ◽  
Functional Theory ◽  
Homo And Lumo ◽  
Ft Ir ◽  
Title Molecule

The molecular structure and vibrational spectra of 10H-dibenzo[b,e][2,4]oxazine was calculated with the help of B3LYP density functional theory (DFT) using 6-311G (d,p) basis set. The FT-IR and FT-Raman spectra of title compound were interpreted by comparing the experimental results with the theoretical B3LYP/6-311G (d,p) calculations. The experimental observed vibrational frequencies are compared with the calculated vibrational frequencies and they are in good agreement with each other. Natural bond orbital (NBO) analysis interprets the intramolecular contacts of title molecule. The 1H and 13C NMR chemical movements of the particle have been determined by the gauge independent atomic orbital (GIAO) strategy and contrasted with the experimental outcome. The deciphered HOMO and LUMO energies showed the chemical stability of the molecules. Fukui capacity and natural charge investigation on atomic charges of the title molecule have been discussed. Docking reads were performed for title molecule utilizing the molecular docking programming with fungicidal dynamic PDB’s.

scholarly journals Molecular Structure, Vibrational Spectra and Docking Studies of Abacavir by Density Functional Theory

2017 ◽  
Vol 72 ◽  
pp. 9-27 ◽  
Author(s):  
R. Solaichamy ◽  
J. Karpagam
Keyword(s):  
Title Compound ◽  
Density Functional ◽  
Molecular Geometry ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Basis Set ◽  
Vibrational Assignments ◽  
Molecular Stability ◽  
Homo And Lumo ◽  
Ft Ir

In this study, optimized geometry, spectroscopic (FT-IR, FT-Raman, UV) analysis, and electronic structure analysis of Abacavir were investigated by utilizing DFT/B3LYP with 6-31G(d,p) as a basis set. Complete vibrational assignments and correlation of the fundamental modes for the title compound were carried out. The calculated molecular geometry has been compared with available X-ray data of Abacavir. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The molecular stability and bond strength have been investigated by applying the Natural Bond Orbital (NBO) analysis. The computational molecular docking studies of title compound have been performed.

scholarly journals Comparative study of molecular docking, structural, electronic, vibrational and hydrogen bonding interactions on 4-hydroxy benzo hydrazide (4HBH) and its newly designed derivative [(E)–N′-((1H-Pyrrol-2-YL)methylene) –4-hydroxy benzo hydrazide and its isomers (I, II and III)] (potential inhibitors) for COVID-19 protease

2021 ◽  
pp. 1-21
Author(s):  
Anoop Kumar Pandey ◽  
Vijay Singh ◽  
Apoorva Dwivedi
Keyword(s):  
Hydrogen Bonding ◽  
Density Functional ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Basis Set ◽  
Hybrid Functional ◽  
Linear Optical Properties ◽  
Vibrational Bands ◽  
The One ◽  
Potential Inhibitors

Studies have shown that hydrazides and thier derivatives are used for pharmaceutical and medicinal purposes. At present, the whole world is suffering for COVID-19 virus. There are some vaccines or medicines available to treat this disease all over the world. Today the one fourth of the world’s population is under lockdown condition. In this scenario, scientists from the whole world are doing different types of research on this disease. Being a molecular modeller, this inspires us to design new types of species (may be drugs) which may be capable for COVID-19 Protease. In the present effort, we have performed docking studies of title compounds with COVID-19 protein (6LU7) for anti-COVID-19 activity. A comparative quantum chemical calculations of molecular geometries (bond lengths and bond angles) of 4-Hydroxy Benzo Hydrazide (4HBH) and its newly designed derivatve [(E)-N′-((1H-Pyrrol-2-YL)Methylene) –4-Hydroxy Benzo Hydrazide and its isomers (I, II and III)] in the ground state have also been carried out due to its biological importance and compared with the similer type of compound found in literature i.e. benzohydrazide. The optimized geometry and wavenumber of the vibrational bands of the molecules have been calculated by density functional theory (DFT) using Becke’s three-parameters hybrid functional (B3LYP/CAM-B3LYP) with 6–311G (d, p) as the basis set. Vibrational wavenumbers are compared with the observed FT-IR and FTRaman spectra of 4-Hydroxy Benzo Hydrazide. TDDFT calculations are also done on the same level of theory and a theoretical UV-vis spectrum of title molecules are also drawn. HOMO-LUMO analysis has been done to describe the way the molecule interacts with other species. Natural bond orbitals (NBO) analysis has been carried out to inspect the intra- and inter- molecular hydrogen-bonding, conjugative and hyper conjugative interactions and their second order stabilization energy. Nonlinear optical (NLO) analysis has been performed to study the non-linear optical properties of the molecule by computing the first hyperpolarizability. The variation of thermodynamic properties with temperature has been studied. QATIM analysis shows that hydrogen bonding occurs in 4HBH, isomer II and III respectively.

Density functional theory, Comparative vibrational spectroscopic studies, HOMO-LUMO, and NBO analysis of Trichloro isocyanuric acid and Trithio cyanuric acid

2015 ◽  
Vol 8 (3) ◽  
pp. 2197-2221
Author(s):  
Theraviyum Chithambarathanu ◽  
M. Darathi ◽  
J. DaisyMagdaline ◽  
S. Gunasekaran
Keyword(s):  
Density Functional ◽  
Cyanuric Acid ◽  
Nbo Analysis ◽  
Basis Set ◽  
Potential Energy Distribution ◽  
Point Energy ◽  
Isocyanuric Acid ◽  
Ft Ir ◽  
Homo Lumo ◽  
Ft Raman

The molecular vibrations of Trichloro isocyanuric acid (C3Cl3N3O3) and Trithio cyanuric acid (C3H3N3S3) have been investigated in polycrystalline sample at room temperature by Fourier Transform Infrared (FT-IR) and FT-Raman spectroscopies in the region 4000-450 cm-1 and 4000-50 cm-1 respectively, which provide a wealth of structural information about the molecules. The spectra are interpreted with the aid of normal co-ordinate analysis following full structure optimization and force field calculations based on density functional theory   (DFT) using standard B3LYP / 6-311++ G (d, p) basis set for investigating the structural and spectroscopic properties. The vibrational frequencies are calculated and the scaled values are compared with experimental FT-IR and FT-Raman spectra. The scaled theoretical wave numbers shows very good agreement with experimental ones. The complete vibrational assignments are performed on the basis of potential energy distribution (PED) of vibrational modes, calculated with scaled quantum (SQM) method. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that change in electron density (ED) in σ* and π* anti-bonding orbitals and second order delocalization   energy (E2) confirm the occurrence of Intra molecular Charge Transfer (ICT) within the molecule. The thermodynamic properties like heat capacity, entropy, enthalpy and zero point energy have been calculated for the molecule. The frontier molecular orbitals have been visualized and the HOMO-LUMO energy gap has been calculated. The Molecular Electrostatic Potential (MEP) analysis reveals the sites for electrophilic attack and nucleophilic reactions in the molecule.

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