scholarly journals Computational Study of Novel 2,3-Bis[(1-methyl-1H-imidazole-2-yl)sulfanyl]quinoxaline: Structural Aspects, Spectroscopic Investigation, HOMO-LUMO, MESP, NLO, ADMET Predictions and Molecular Docking Studies as Potential Biotin Carboxylase and Antibiotics Resistant Aminoglycoside Phosphotransferase APH(2")IVA Enzyme Inhibitor

2020 ◽  
Vol 32 (3) ◽  
pp. 706-726
Author(s):  
Ashutosh Kumar ◽  
Anjali Pandey ◽  
Anil Mishra
Keyword(s):  
Gas Phase ◽  
13C Nmr ◽  
Function Analysis ◽  
Basis Set ◽  
Chemical Calculation ◽  
Biotin Carboxylase ◽  
Reference Drug ◽  
Aminoglycoside Phosphotransferase ◽  
Title Molecule ◽  
Structural Aspects

In this paper, a complete quantum chemical calculation has been done to describe the relevant structural aspects of novel 2,3-bis[(1-methyl-1H-imidazole-2-yl)sulfanyl]quinoxaline with combination of DFT/B3LYP method 6-311++G(d,p) basis set in gas phase and in solvent phase. The molecular structure was examined by using IR, 1H & 13C NMR and UV-visible techniques and solvent effect on spectroscopic properties are also discussed. The vibrational assignments are analyzed by PED using Gauss View 5.0 and VEDA 4.0 program. The 1H NMR and 13C NMR chemical shifts are calculated using the gauge-independent atomic orbital method (GIAO method) in gas phase and in solvents (water, DMSO and chloroform). The UV spectrum is calculated by using TD-DFT/6-311++G(d,p) method in gas phase and in solvent (water, DMSO and chloroform) using IEF-PCM model. With the help of theoretical calculations chemical activities, electrophilic/nucleophilic nature and sites in the molecule, molecular and chemical properties that cannot be obtained by experimental way are obtained. Accordingly, molecular electrostatic potential (MESP), hardness (η)/softness (S) parameters, net charges analyses are investigated to gain electrophilic and nucleophilic nature. Also the sites in molecule and Fukui function analysis are discussed. The dipole moment (μ), polarizability (αtot), anisotropic polarizability (Δα) and first-order hyperpolarizability (βtot) of the title compound are reported and results shows that the material is capable to generate non-linear effect (NLO). The in silico study of all th e biological and ADMET properties of title molecule are also discussed and compared with reference drug ciprofloxacin antibiotics. The title molecule and reference drug ciprofloxacin docked with biotin carboxylase enzyme (PDB ID: 2V59) of E. coli and aminoglycoside phosphotransferase APH(2")IVA (PDB ID: 4DFU) of Enterococcus casseliflavus receptor with the help of Molegro molecular viewer 2.5 program and binding affinity (ΔG) were determined by ParDock server.

scholarly journals Computational Design, Spectral, NBO, DOS, Bioactivity Evaluation, ADMET Analysis, Third-Order non-linear Optical and Quantum Chemical Investigations on Hydrogen Bonded Novel Organic Molecular Complex of 4-[Bis[2-(acetyloxy)ethyl]amino]benzaldehyde (4B2AEAB) Derivatives for Opto-Electronic Applications

2020 ◽  
Vol 32 (11) ◽  
pp. 2793-2820
Author(s):  
Ashutosh Kumar ◽  
Anil Mishra
Keyword(s):  
Gas Phase ◽  
Function Analysis ◽  
Chemical Reactivity ◽  
Computational Design ◽  
Basis Set ◽  
Mulliken Charge ◽  
Water Solvent ◽  
Non Linear ◽  
Linear Optical ◽  
Vibrational Wavenumbers

In this paper, the authors reported a theoretical investigation on molecular structure, geometry optimization, global and local chemical reactivity descriptors calculations, NBO study, DOS, non-linear optical behaviour and vibrational wavenumbers of the novel 4-[bis[2- (acetyloxy)ethyl]amino]benzaldehyde (4B2AEAB) were carried out by DFT (B3LYP and B3PW91) methods with 6-31+G (d, p) basis set in water solvent. The calculated vibrational wavenumbers are found to be in good agreement with experimental FT-IR spectra and PED analysis using GaussView 5.0 and VEDA 4 program. The UV-Vis absorption spectrum of 4B2AEAB was calculated by using TD-DFT/B3LYP/6-31+G(d,p) in gas phase, water, CHCl3, DMSO and CH2Cl2 solvents using CPCM model and λmax in range of 354.16, 341.35, 343.74, 342.18 and 342.64 nm, respectively. The density of state (DOS spectrum) of the compound in term of HOMOs and LUMOs and MESP were calculated and analyzed. The temperature effects on the thermodynamic properties are also discussed. The calculated 1H NMR and 13C NMR chemical shift using GIAO method and solvent effect are investigated by B3LYP/6-31+G(d,p) in gas phase, chloroform, water, DMSO and CH2Cl2 solvents and correlate with experimental chemical shifts. The dipole moment, polarizability and the first static hyperpolarizability values show that the 4B2AEAB molecule is active non-linear optical (NLO) material. The nucleophilic and electrophilic reactive sites in the 4B2AEAB and its derivatives were analyzed by Fukui function analysis using Mulliken charge. The charge transfer, conjugative interactions and delocalization of electron density are analyzed by natural bond orbital (NBO) analysis. The biological properties and ADMET study of 4B2AEAB and its derivatives are also discussed.

Structural aspects of the hisingerite-neotocite series

Clay Minerals ◽  
1983 ◽  
Vol 18 (1) ◽  
pp. 21-31 ◽  
Author(s):  
R. A. Eggleton ◽  
J. H. Pennington ◽  
R. S. Freeman ◽  
I. M. Threadgold
Keyword(s):  
Function Analysis ◽  
Pore Space ◽  
Hollow Spheres ◽  
X Ray ◽  
Broken Hill ◽  
Transmission Electron ◽  
X Ray Absorption ◽  
Interconnected Pore ◽  
Intermediate Member ◽  
Structural Aspects

AbstractTransmission electron microscopy, X-ray radial distribution function analysis, chemical analysis, X-ray absorption edge spectroscopy, and Mössbauer spectroscopy combine to confirm an amorphous or gel structure for minerals of the hisingerite-neotocite series: (Fe,Mn)0.8SiO3.1.2H2O. A framework of (Fe,Mn)O6 octahedra and [SiO4] tetrahedra form hollow spheres, 50–100 Å in diameter, cross-bonded into a physically isotropic solid with as much as 10% interconnected pore space. The outer 10–20 Å of the spheres has a rudimentary structure, possibly marking the onset of segregation into Si-rich and (Fe,Mn)-rich layers. The Broken Hill mineral ‘sturtite’ is an intermediate member of the hisingerite-neotocite series.

scholarly journals Absorption mechanism, structural and electronic properties of MC19 (M = B and Si) fullerenes with 1-acetylpiperazine

2017 ◽  
Vol 36 (1-2) ◽  
pp. 797-804
Author(s):  
Özgür Alver ◽  
Cemal Parlak ◽  
Mohamed I Elzagheid ◽  
Ponnadurai Ramasami
Keyword(s):  
Electronic Properties ◽  
Gas Phase ◽  
Basis Set ◽  
Stable Complex ◽  
Absorption Mechanism ◽  
Boron Doped ◽  
Structural And Electronic Properties ◽  
Influence Of Water ◽  
Vibrational Bands ◽  
Silicon Doped

The interaction mechanisms of undoped, silicon- and boron-doped C20 fullerenes and 1-acetylpiperazine (1-ap) were investigated. Stability, electronic properties, influence of water on the solubility and stability, molecular parameters, descriptive vibrational bands and nuclear magnetic resonance shielding values are reported. The quantum mechanical calculations were carried out using the M06-2X functional and the 6-31G(d) basis set. It is observed that all the complexes are more stabilized in water compared to the gas phase. The most stable complex was found as silicon-doped fullerene interacting with the carbonyl edge of 1-ap releasing energy of 64.13 kcal/mol in water.

scholarly journals Geometric and energetic data from quantum chemical calculations of halobenzenes and xylenes

2020 ◽  
Author(s):  
Sopanant Datta ◽  
Taweetham Limpanuparb
Keyword(s):  
Ab Initio ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical Calculation ◽  
Quantum Chemical ◽  
Software Package ◽  
Geometry Optimization ◽  
Theoretical Data ◽  
Basis Set ◽  
Chemical Calculation ◽  
Custom Made

<p>This article presents theoretical data on geometric and energetic features of halobenzenes and xylenes. Data were obtained from <i>ab initio</i> geometry optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 1504 structures of halobenzenes, three structures of xylenes and one structure of benzene were generated and processed by custom-made codes in Mathematica. The quantum chemical calculation was completed in Q-Chem software package. Geometric and energetic data of the compounds are presented in this paper as supplementary tables. Raw output files as well as codes and scripts associated with production and extraction of data are also provided.</p>

scholarly journals Unknown Knowns: Case Studies in Uncertainties in the Computation of Thermochemical Parameters

2020 ◽  
Author(s):  
John Simmie
Keyword(s):  
Heat Capacity ◽  
Gas Phase ◽  
Basis Set ◽  
Statistical Thermodynamic ◽  
Vibrational Modes ◽  
Heavy Atoms ◽  
New Methods ◽  
Formation Enthalpies ◽  
Thermochemical Parameters

<div>Both the computation of, and the uncertainties associated, with gas-phase molar formation enthalpies are now quite well established for systems comprised of tens of ‘heavy’ atoms chosen from the commonest elements. The same cannot be said for derived thermochemical quantities such as entropy, heat capacity and an enthalpy function. Whilst the application of well known statistical thermodynamic relations is mostly understood, the determination of the uncertainty with which such values can be obtained has been little studied — apart, that is, for a general protocol devised by Goldsmith et al. [J. Phys. Chem. A, 2012, 116, 9033–9057]. Specific examples from that work are explored here and it is shown that their estimates are overly pessimistic. It is also evident that for some species the calculated thermochemical parameters show very little variation with either the level of theory, or basis set, or treatment of vibrational modes — this renders the inclusion of such species in databases designed to validate new methods of limited value.<br></div>

scholarly journals Modeling organic aerosols in a megacity: comparison of simple and complex representations of the volatility basis set approach

2010 ◽  
Vol 10 (12) ◽  
pp. 30205-30277 ◽  
Author(s):  
M. Shrivastava ◽  
J. Fast ◽  
R. Easter ◽  
W. I. Gustafson ◽  
R. A. Zaveri ◽  
...  
Keyword(s):  
Gas Phase ◽  
Secondary Organic Aerosol ◽  
Computational Cost ◽  
Organic Aerosols ◽  
Field Measurements ◽  
Organic Aerosol ◽  
Basis Set ◽  
Aerosol Formation ◽  
Secondary Organic Aerosol Formation ◽  
The City

Abstract. The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) is modified to include a volatility basis set (VBS) treatment of secondary organic aerosol formation. The VBS approach, coupled with SAPRC-99 gas-phase chemistry mechanism, is used to model gas-particle partitioning and multiple generations of gas-phase oxidation of organic vapors. In addition to the detailed 9-species VBS, a simplified mechanism using 2 volatility species (2-species VBS) is developed and tested for similarity to the 9-species VBS in terms of both mass and oxygen-to-carbon ratios of organic aerosols in the atmosphere. WRF-Chem results are evaluated against field measurements of organic aerosols collected during the MILAGRO 2006 campaign in the vicinity of Mexico City. The simplified 2-species mechanism reduces the computational cost by a factor of 2 as compared to 9-species VBS. Both ground site and aircraft measurements suggest that the 9-species and 2-species VBS predictions of total organic aerosol mass as well as individual organic aerosol components including primary, secondary, and biomass burning are comparable in magnitude. In addition, oxygen-to-carbon ratio predictions from both approaches agree within 25%, providing evidence that the 2-species VBS is well suited to represent the complex evolution of organic aerosols. Model sensitivity to amount of anthropogenic semi-volatile and intermediate volatility (S/IVOC) precursor emissions is also examined by doubling the default emissions. Both the emission cases significantly under-predict primary organic aerosols in the city center and along aircraft flight transects. Secondary organic aerosols are predicted reasonably well along flight tracks surrounding the city, but are consistently over-predicted downwind of the city. Also, oxygen-to-carbon ratio predictions are significantly improved compared to prior studies by adding 15% oxygen mass per generation of oxidation; however, all modeling cases still under-predict these ratios downwind as compared to measurements, suggesting a need to further improve chemistry parameterizations of secondary organic aerosol formation.

scholarly journals Structural and spectroscopic characterization and DFT studies of 2-amino-1,10-phenanthrolin-1-ium chloride

2019 ◽  
Vol 10 (2) ◽  
pp. 95-101
Author(s):  
Sebile Işık Büyükekşi ◽  
Namık Özdemir ◽  
Abdurrahman Şengül
Keyword(s):  
Density Functional Theory ◽  
Electronic Absorption ◽  
13C Nmr ◽  
Density Functional ◽  
Electronic Absorption Spectra ◽  
Chemical Shifts ◽  
Atomic Orbital ◽  
Basis Set ◽  
Functional Theory ◽  
1H And 13C Nmr

A versatile synthetic building block, 2-amino-1,10-phenanthrolin-1-ium chloride (L∙HCl) was synthesized and characterized by IR, 1H and 13C NMR DEPT analysis, UV/Vis and single-crystal X-ray diffraction technique. The molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO), 1H and 13C NMR chemical shifts values of the title compound in the ground state were obtained by using density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set and compared with the experimental data. Electronic absorption spectrum of the salt was determined using the time-dependent density functional theory (TD-DFT) method at the same level. In the NMR and electronic absorption spectra calculations, the effect of solvent on the theoretical parameters was included using the default model with DMSO as solvent. The obtained theoretical parameters agree well with the experimental findings.

scholarly journals Crystal structure, computational study and Hirshfeld surface analysis of ethyl (2S,3R)-3-(3-amino-1H-1,2,4-triazol-1-yl)-2-hydroxy-3-phenylpropanoate

2019 ◽  
Vol 75 (12) ◽  
pp. 1919-1924
Author(s):  
Abdelkader Ben Ali ◽  
Youness El Bakri ◽  
Chin-Hung Lai ◽  
Jihad Sebhaoui ◽  
Lhoussaine El Ghayati ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Gas Phase ◽  
Surface Analysis ◽  
Computational Study ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Dft Methods ◽  
Important Interaction ◽  
The Mean ◽  
Title Molecule

In the title molecule, C13H16N4O3, the mean planes of the phenyl and triazole rings are nearly perpendicular to one another as a result of the intramolecular C—H...O and C—H...π(ring) interactions. In the crystal, layers parallel to (101) are generated by O—H...N, N—H...O and N—H...N hydrogen bonds. The layers are connected by inversion-related pairs of C—H...O hydrogen bonds. The experimental molecular structure is close to the gas-phase geometry-optimized structure calculated by DFT methods. Hirshfeld surface analysis indicates that the most important interaction involving hydrogen in the title compound is the H...H contact. The contribution of the H...O, H...N, and H...H contacts are 13.6, 16.1, and 54.6%, respectively.

Donor Functionalized Perylene and Different π-Spacers Based Sensitizers for DSSC Applications - A Theoretical Approach

2021 ◽  
Author(s):  
D. Nicksonsebastin ◽  
P. Pounraj ◽  
Prasath M
Keyword(s):  
Density Functional Theory ◽  
Solar Cell ◽  
Gas Phase ◽  
Density Functional ◽  
Basis Set ◽  
Dye Sensitized Solar Cell ◽  
Functional Theory ◽  
Dye Sensitized ◽  
Td Dft ◽  
Organic Sensitizers

Abstract Perylene based novel organic sensitizers for the Dye sensitized solar cell applications are investigated by using Density functional theory (DFT) and time dependant density functional theory (TD-DFT).The designed sensitizers have perylene and dimethylamine (DM) and N-N-dimethylaniline(DMA) functionalized perylene for the dssc applications.π-spacers are thiophene andcyanovinyl groups and cyanoacrylic acid is chosen as the acceptor for the designed sensitizers. The studied sensitizers were fully optimized by density functional theory at B3LYP/6-311G basis set on gas phase and DMF phase. The electronic absorption of the sensitizers is analyzed by TD-DFT at B3LYP/6-311G basis set in both gas and DMF phase.

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