Calculations Of Wavenumbers Research Articles

A COMPREHENSIVE ELECTRONIC, VIBRATIONAL, NATURAL BOND ORBITAL AND REACTIVITY DESCRIPTOR ANALYSIS OF PHARMACOLOGICALLY IMPORTANT MOLECULE MIGALASTAT: A THEORETICAL STUDY

Migalastat (Galafold) is a pharmacological chaperone indicated for the long term treatment for fabry disease a rare genetic disorder in adults. Quantum chemical calculations of energy, geometrical shape and vibrational wavenumbers of Migalastat have been accomplished by the usage of DFT method. The specific exploration of the infrared spectra of the compound underneath have a look at is centered on potential energy distribution (PED). Dipole moment, polarizability and first order static hyperpolarizability calculation using DFT/B3LYP/6-311G(d,p) level of theory outlined the nonlinear optical behavior of the underlying molecule. The frontier molecular orbitals and molecular electrostatic potential map were additionally given to clarify the molecular characteristics of the compound. To show the chemical activity of the chemical compound, reactivity descriptors and thermodynamic properties were also calculated utilizing 6-311G(d,p) basis set. Electron density distribution on atoms and bonds of given molecule was interpreted by its complete NBO analysis.

Structural insights, spectral, flourescence, Z-scan, C-H…O/N-H…O hydrogen bonding and AIM, RDG, ELF, LOL, FUKUI analysis, NLO activity of N-2(Methoxy phenyl) acetamide

Quantum chemical calculations of geometries and vibrational wavenumbers of N-2(methoxy phenyl)acetamide(N2MPA) in the ground state were carried out by using density functional theory (DFT/B3LYP) method with 6-31G (d,p) basis set. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using MOLVIB program. The experimental 1H and 13C NMR chemical shifts were investigated and then compared with computed NMR data using the gauge – invariant atomic orbital (GIAO) method. The optical nature of the grown crystal was evaluated by using the UV-Vis optical transmittance spectrum. The lower wavelength absorption range and various optical constant for instance, energy band gap, absorption and extinction coefficient, refractive index, susceptibility and Urbach energy values were evaluated. The colourless crystal of N2MPA was grown by slow-evaporation technique. The nonlinear optical (NLO) properties of N2MPA have been investigated using Z-scan technique. The emission behavior of N2MPA was analyzed by fluorescence spectral analysis. Thermal stability of N2MPA was studied by TG-DTA analysis. The HOMO and LUMO energy levels are constructed and the corresponding frontier energy gaps are determined to realize the charge transfer within the molecule. The molecular electrostatic potential(MESP), natural bond orbital(NBO) analysis and topological analysis such as electron localization function(ELF), reduced density gradient(RDG), localized orbital locator(LOL), atoms in molecule(AIM) and FUKUI function analysis have been used to evaluate the intermolecular interaction, especially the hydrogen bonds. Fingerprint plots of Hirshfeld surfaces were used to locate and analyze the percentage of hydrogen bonding interactions.

Experimental Spectroscopic, Structural (Monomer and Dimer), Molecular Docking, Molecular Dynamics Simulation and Hirshfeld Surface Analysis of 2-Amino-6-Methylpyridine

2-Amino-6-methylpyridine (2-AMP) was investigated experimentally using FT-IR, 1H, NMR, and UV-Vis spectra, as well as theoretically using DFT calculations. The quantum computational calculations (the optimized structure, FT-IR, NMR and UV-Vis.) to support experimental data were performed by DFT approach at B3LYP functional and 6–311 + +G(d,p) basis set. The optimized molecular geometry and wavenumber calculations were done in the gas phase, while theoretical NMR was performed in Chloroform (CHCL3) solvation. The “Potential Energy Distribution analysis” (PED) of the title compound was performed with VEDA analysis and these assignments were compared with the experimental FT-IR spectrum. Hirshfeld analysis was also performed and analyzed intermolecular interactions on the surface of crystal, However, the most significant contributions to the Hirshfeld surface come from N···H (17.3%), C···H/H···C (23%) and H···H (68.8%). Chemical reactivity studies, Molecular Electrostatic Potential (MEP) maps, and surface area maps were also conducted. To show electron delocalization in the molecule, researchers used the electron localization function (ELF). Other topics included topological and mulliken charge distribution studies. Natural Bond Order Analysis (NBO) was performed to interpret intermolecular charge transfer.The effect of temperature on thermodynamical parameters such as Gibbs free energy, enthalpy, and entropy was examined. TD-DFT analysis was also used to shed more light on how the electronic transitions in the UV–Vis spectra were estimated. For different solvents, the estimated maximum wavelength (λ) absorbance and the band-gap energy of 2-AMP were calculated and compared to experimental results. The molecule's bioactivity is described theoretically using the Electrophilicity index and the interaction between the ligand-protein is depicted using Molecular docking. The proteins 3DQS, 4UX6, 5ADF, 5TUD, and 6E9L were studied via molecular docking. The nature of the molecule was determined by its drug-likeness. A molecular dynamics simulation was used to explore biomolecular stability.

Synthesis, X-ray Crystallography, Hirshfeld Surface Analysis, Spectral Analysis, and Molecular Docking Studies on (E)–2–(1–(4–Fluorophenyl)Ethylidene) Hydrazine Carbothioamide

Synthesis, X-ray crystallography, spectral analysis, and molecular docking analysis on (E)–2–(1–(4–fluorophenyl) ethylidene) hydrazine carbothioamide (EFEHC) are performed. Thiosemicarbazones are a class of small molecules used as anticancer therapeutics. The FT–IR and FT-Raman spectra of EFEHC have been recorded in 4000–400 and 4000–100 cm–1, respectively. The present communication deals with the quantum chemical calculations of energies, geometrical structure, and vibrational wavenumbers of EFEHC using the density functional (DFT/B3LYP) method with 6–31G (d, p) basis set. The conformational analysis gives the energy values based on the change in the position of atoms in the EFEHC molecule. Hirshfeld surface analysis (HSs) is used to discuss the evaluation of intermolecular interactions. Molecular docking analysis of the small molecule EFEHC with macromolecule HMG–CoA protein showed that this is a good molecule and is suitable for anti-cholesterol targets.

DFT Studies on Molecular Structure, Thermodynamics Parameters, HOMO-LUMO and Spectral Analysis of Pharmaceuticals Compound Quinoline (Benzo[b]Pyridine)

Advances in computational chemistry have greatly increased its effectiveness and attractiveness as an emerging adjunct to experimental chemistry but also as an independent research field. This work studied some basic bonding Parameters, geometry, Uv-Visible spectra, HOMO-LUMO and harmonic vibrational frequencies of Quinoline were investigated by using density functional theory (DFT/6-31+ (d, p)) methods. The calculated wave numbers (B3LYP) agree properly with the determined wave numbers. The results obtained are then as compared with experimental statistics in which available. The structural parameters; thermochemistry, rotational constants, IR spectra and frequencies, bond distances, angles and dipole moment were obtained from the optimized stable geometries of the compound. The computed optimized geometric bond lengths and bond angles show good agreement with experimental data of the title compound. The calculated HOMO and LUMO energies indicate that charge transfer occurs within the molecule.

Structure and optical properties of 3-bromo-4-methylthio-2,6-lutidine N-oxide and its eight-coordinate europium(III) and terbium(III) aqua complexes

New europium and terbium [LnCl3L3(H2O)2] polycrystalline complexes were synthesized with the ligand L = 3-bromo-4-methylthio-2,6-lutidine N-oxide. IR, Raman, electron absorption UV-VIS and emission spectra measurements were carried out for these compounds. Re-crystallization of these materials led to formation of single crystals with another composition [LnL(H2O)7]Cl3∙L3, they were characterized by X-ray diffraction technique and spectroscopic measurements. Both types of the materials consist of eight coordinated LnCl3O3O’2 or LnOO’7 polyhedrons containing O - oxygen atoms of the N-oxide group, chlorine atoms or O’ - oxygen atoms of the water units. The crystal structure was solved for two complexes of the formula [Ln(L)(H2O)7]Cl3∙(L)3 where Ln = Eu and Tb. X-ray diffraction analysis reveals that these complexes are isostructural with P21/m space group. The optimization of the molecular system and frequency calculations were carried out using density functional theory (DFT). The DFT quantum chemical calculations of the vibrational wavenumbers were performed for the ligands used for the Eu3+ and Tb3+ ions complexation. The emission measurements were carried out with the femtosecond excitation. The effective ligand-to-metal energy transfer was discovered in the [LnCl3L3(H2O)2] complexes formed in the polycrystalline state.

Spectroscopic investigation, Hirshfeld surface analysis and molecular docking studies on mebendazole and its derivatives

In the present study, structural properties of mebendazole have been studied extensively by different spectral methods. Quantum chemical calculations of energies, geometries, vibrational wavenumbers and nuclear magnetic resonance analysis have been carried out by density functional theory using B3LYP (Becke 3-parameter Lee Yang Parr) functional combined with 6-311++G(D,P) basis set. Natural bond orbital (NBO) analysis and frontier molecular orbitals analysis are performed at the same level of theory. Hirshfeld surface analysis of mebendazole has been carried out and the intramolecular interactions within the compound are revealed by finger print plots. Molecular docking studies have been performed for mebendazole and its five related compounds with different proteins and showed best binding affinity with 2MBC.

Experimental approach, theoretical investigation and molecular docking of 2- chloro-5-fluoro phenol antibacterial compound

The molecular structural dimerization of biologically potent 2-chloro-5-fluoro phenol (2C5FP) is optimized. A combined experimental and theoretical characteristics of vibrational spectral determinations (NMR, FT-IR and Raman) on 2-chloro-5-fluoro phenol (2C5FP) were used at DFT-B3LYP/6–31++G (d,p) level of computation. A close coherence is achieved when experimentally observed wave numbers are compared with calculated wave numbers by refinement of the scale factors. Calculated values of global chemical descriptors of the present molecule reveal significant molecular stability and chemical reactivity. Non-Linear optical (NLO) property of the present molecule is investigated by determining the second order non linear parameter of first hyperpolarizability β. Moreover, hydrogen bond and thermodynamic parameters at various temperatures are determined and discussed. Investigated compound 2C5FP possesses a better antibacterial activity against Echerichia coli, Streptococcus aureus, Pseudomonas aureus,and Staphylococcus aureus, respectively. The title molecule is subjected to molecular docking studies with two different proteins, namely Staphylococcus aureus Tyrosyl-tRNA synthetase (PDB ID: 1JIL) and human dihydroorotate dehydrogenase (hDHODH) (PDB ID: 6CJF). The results of molecular docking analysis support the antibacterial activity and demonstrate a strong interaction with the DHODH inhibitor.

Diethyl (2-Amino-3-Cyano-4H-Chromen-4-yl)Phosphonate and Its Halogenated Derivatives as Effective Drug: A Theoretical and an Experimental Spectroscopic Study

Theoretical calculations of geometrical structure and vibrational wavenumbers, nuclear magnetic behavior and natural bond orbital (NBO) analysis were carried out using density functional (DFT/B3LYP) method with 6-311++G(d, p) as basis set for diethyl (2-amino-3-cyano-4H-chromen-4-yl)phosphonate (DACHP; 1), diethyl (2-amino-6-chloro-3-cyano-4H-chromen-4-yl)phosphonate (CDACHP; 2) and diethyl (2-amino-6-bromo-3-cyano-4H-chromen-4-yl)phosphonate (BDACHP; 3). The global reactivity descriptors are also calculated and compared at same level of theory for all the three molecules. The FT-IR spectra of the compounds under study were measured in their condensed state. The calculated scaled vibrational wavenumbers were found in good agreement with the experimental wavenumbers. Hyper-conjugative interactions and charge delocalization within the molecules were studied using NBO analysis to explore their stability. 1H NMR and 13C NMR chemical shifts of the title molecules were calculated by the GIAO method and compared with experimental results, and good correlations were accomplished. Molecular docking studies were performed for all the three molecules (1–3) to elicit their possible potential as an effective drug.

Spectroscopic (FTIR, UV-Vis and NMR), theoretical investigation and molecular docking of substituted 1,8-dioxodecahydroacridine derivatives

Recently, substituted 1,8-dioxodecahydroacridine derivatives have been investigated and found to possess a wide variety of biological and pharmacological activities. Two of these biologically relevant N-heterocyclic scaffolds, 2-(9-(4-methoxyphenyl)-3,3,6,6-tetramethyl-1,8-dioxo-1,2,3,4,5,6,7,8- -octahydroacridin-10(9H)-yl)succinic acid (MTDOSA) and 2-(3,3,6,6-tetramethyl- 9-(4-nitrophenyl)-1,8-dioxo-1,2,3,4,5,6,7,8-octahydroacridin-10(9H)-yl)- succinic acid (NTDOSA), have been studied in ground and first excited state using DFT method employing B3LYP/6-311++G(d,p) level of theory. Quantum chemical calculations of geometrical structure and vibrational wavenumbers of MTDOSA and NTDOSA were carried out using DFT method. The experimental FT-IR spectra of the compounds were recorded in the range 4000?400 cm-1 and comprehensively interpreted on the basis of potential energy distribution. The global reactivity descriptors are calculated and discussed. Moreover, 1H- and 13C-NMR spectral data have been calculated using the gauge independent atomic orbital method and compared with experimental spectra. The docking studies reveal that the compounds MTDOSA and NTDOSA have strong binding affinity toward the target protein 5KLH. Thus, the compounds have a possible use as an antileishmanial drug.

The coupling of localised, vibrational modes - Probing OH-bands of organic molecules via a two dimensional Numerov approach.

In this article the extension of the grid-based Numerov approach to probe two coupled, localised vibrational modes is assessed. The theoretically obtained wave numbers are compared to experimental results for five increasingly complex organic molecules carrying two OH groups measured in gas-phase as well as carbon tetrachloride. By using an appropriate spacing of the associated potential energy grid a deviation of the predicted wave numbers with experiment of ≤1% is achieved for both the fundamental and the first overtone bands. In particular the calculated wave numbers of aliphatic species in vacuum underline the versatility of this approach. In addition, it is demonstrated that bicubic interpolation is a viable strategy to greatly reduce the required data points and thus, the computational effort. Comparison of predicted wave numbers obtained for different conformers with experimental data enables the identification of the most relevant conformer present in solution. Since especially the accurate calculation of overtone vibrations is known to be challenging in case of strongly anharmonic potentials such as OH bonds, the presented approach provides a particularly efficient route to study the properties of the associated overtone contribution under the influence of inter-mode coupling. This is due to the fact that the Numerov approach requires no assumption about form and composition of the vibrational wave functions. In addition, the presented method also provides one of the simplest routes to access combined excitations of the considered vibrational modes.

Anisotropic bidispersive convection.

This paper investigates thermal convection in an anisotropic bidisperse porous medium. A bidisperse porous medium is one which possesses the usual pores, but in addition, there are cracks or fissures in the solid skeleton and these give rise to a second porosity known as micro porosity. The novelty of this paper is that the macro permeability and the micro permeability are each diagonal tensors but the three components in the vertical and in the horizontal directions may be distinct in both the macro and micro phases. Thus, there are six independent permeability coefficients. A linear instability analysis is presented and a fully nonlinear stability analysis is inferred. Several Rayleigh number and wavenumber calculations are presented and it is found that novel cell structures are predicted which are not present in the single porosity case.

Synthesis, characterization and biological investigation of glycine-based sulfonamide derivative and its complex: Vibration assignment, HOMO – LUMO analysis, MEP and molecular docking

A combined experimental and theoretical investigation has been reported on N-(glycine)-para styrene sulfonamide (abbreviated as GSS). The GSS and its complex were synthesized for first time in two steps. The GSS was synthesized from the reaction of para styrene sulfonyl chloride and glycine in the mild condition. The palladium complex was prepared from the reaction of PdCl2, CH3CN and GSS as a ligand. The GSS and its complex was confirmed using FT-IR and 1H-NMR spectra. The data obtained from wave number calculations are used to assign vibrational bands obtained in infrared and Raman spectra recorded. Potential energy distribution was done using GAR2PED program. HOMO-LUMO analysis, and Molecular Electrostatic Potential studies of the GSS and its complex have been investigated using DFT method. The GSS is investigated against Staphylococcus aureus and Escherichia coli. Molecular Docking study of GSS is also reported.

Synthesis, molecular structure analyses and DFT studies on new asymmetrical azines based Schiff bases

In this paper, we report the synthesis of new unsymmetrical azines Schiff bases. These compounds were prepared by condensation of hydrazine with different aldehydes and ketones to give (E) -2-hydroxynaphthalene-1-carbaldehyde [(1E) -2-thienylmethylene] hydrazone compound (I) and (Z) - 2 - [(E) -1- (2-hydroxyphenyl) ethylidenehydrazin-1-ylidene] -1,2-diphenylethanone compound (II). The method adopted consists in reacting the two different carbonyl compounds simultaneously in one step in a stepwise manner reported which is practical and cost-effective. The reaction with a minor modification in operating conditions proceeded efficiently and with excellent performance. The structure of each of the two compounds (I) and (II) was determined by the X-ray diffraction technique performed on single crystals. The asymmetric unity of the two molecules consists of one asymmetry-independent molecule. In addition, hydrogen bonds CH … π are observed in the compound (II). We then present a detailed DFT study based on B3LYP/6-31G (d, p) geometric structures of compounds (I); (II) and another compound (III) also another asymmetric azine (Z) -2 - [(E) -2-benzylidenehydrazine-1-ylidene] -1,2-diphenylethanone whose crystal structure is reported. The fundamental vibration wave numbers are calculated and a good agreement between the observed and calculated wave numbers is obtained. The study was extended to the HOMO-LUMO analysis to calculate the energy gap. The calculated HOMO and LUMO energy reveals that the charge is transferred into the molecule.

Vibrational spectroscopic (FT-IR, FT-Raman), anti-inflammatory, docking and molecular characteristic studies of Ni(II) complex of 2-aminonicotinaldehyde using theoretical and experimental methods

Fourier transform infrared (FT-IR) and Raman (FT-Raman) spectra of the nickel(II) complex of 2-aminonicotinaldehyde (Ni(II)CANA) have been recorded and analyzed. The experimental work has been complemented by density functional theory (DFT) computations.The most optimized structure of the titled compound and their minimum energies were analyzed by using B3LYP functional with 6-31G(d,p) basis set. The calculated wave numbers from density functional theory method was scaled down to coincide with the experimentally recorded values and results were reported. The RMS error between the scaled calculated and observed fundamentals is 5.42 cm−1. All the vibrational modes of the compound under studied were ascribed and the structural properties predicted and analyzed. The first hyperpolarizability (β), polarizability (α) and dipole moment (μ) of the compound was computed and the results were reported. The thermo dynamical parameters and HOMO-LUMO energy gap were calculated. To obtain the electronic transitions from UV–Visible spectra have been calculated using the TD-DFT method. NBO analysis was executed to know the transfer of electrons within the molecule, MESP analysis also performed for (Ni(II)CANA). The in vivo anti-inflammatory activity was done by using the carrageenan-induced rat paw edema method in Albino rats (Wister strain). The results revealed that it possesses a significant anti-inflammatory activity. The docking studies were carried out to identify the potential COX-2 inhibitor. In order to understand the binding mode of the titled compound to the cell line, molecular docking studies were also carried out and it was found to have a binding energy of −8.67 kcal/mol.

Structural, Spectroscopic, Antimicrobial Activity and DFT Studies on 4-Methyl-N-(4-methylphenylsulfonyl)-N-phenylbenzenesulfonamide

This study reports the structural characterization of a disulfonimide derivative, 4-methyl-N-(4-methylphenylsulfonyl)-N-phenylbenzenesulfonamide (MPBSA), using spectroscopic and quantum chemical methods. The molecule was characterized with FT-IR, 1H 13C NMR and UV-Vis spectroscopies. Quantum chemical calculations of molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO) 1H and 13C-NMR chemical shifts of the compound were carried out by using density functional method (DFT) at B3LYP/6−311++G(d,p) level of theory. Electronic absorption spectra of the compound have been computed using the time-dependent density functional theory (TD-DFT) method at the same level. A satisfactory consistency between the experimental and theoretical findings was obtained. The antimicrobial activity screening of the compound was performed on some bacteria and fungus species using microdilution method. The results showed that the title molecule have noteworthy antibacterial and antifungal activities.

A Theoretical Study on N′-[(Z)-(4-Methylphenyl)Methylidene]-4-Nitrobenzohydrazide (NMPMN)

Quantum mechanical calculations of ground state energy, vibration wavenumbers, and electronic absorption wavelengths of N′-[(Z)-(4-methylphenyl)methylidene]-4-nitrobenzohydrazide with C15H13N3O3 empirical formula was performed by using Gaussian 09 program. Becke’s three-parameter exchange functional in conjunction with the Lee-Yang-Parr correlation functional and Heyd-Scuseria-Ernzerhof functional levels of density functional theory (DFT) with the 6-311++G(d,p) basis set were used in the performing of above mentioned calculations. The highest occupied and lowest unoccupied molecular orbital (HOMO and LUMO) energies have been also calculated at the same levels. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) behavior of the title molecule has been examined by the determining of electric dipole moment (μ), polarizability (α), and static first-order hyperpolarizability (β). Finally, molecular electrostatic potential (MEP) surface as well as Mulliken and NBO atomic charges were calculated by using Gaussian 09 program.

FT-IR, UV–visible, and NMR Spectral Analyses, Molecular Structure, and Properties of Nevadensin Revealed by Density Functional Theory and Molecular Docking

ABSTRACTNevadensin 2-(4-methoxyphenyl)-5,7-dihydroxy-6,8-dimethoxy-4H-1-benzo-pyran-4-one] is a natural bioactive flavonoid compound that has the potential to become a novel “natural lead” in the field of drug discovery program. The molecular structure, vibrational frequencies, and corresponding vibrational assignment of nevadensin have been investigated experimentally and theoretically by employing the B3PW91/6–311++G(d,p) method. The fundamental vibrational wave numbers as well as their intensities were calculated, and a good correlation between experimental and scaled calculated wave numbers had been accomplished. The ultraviolet spectrum of the studied molecule was recorded in the region 200–500 nm, and the electronic properties were predicted by the time-dependent density functional theory approach. 1H and 13C NMR spectra have been calculated by employing the gauge-independent atomic orbital method. Nevadensin has been reported to exhibit antimicrobial activities against both Gram-positive and Gram-negative bacteria and also against the fungal pathogens, highlighting the pharmacological importance of the molecule.

Vibrational (FT-IR and FT-Raman), electronic (UV–vis) and quantum chemical investigations on pyrogallol: A study on benzenetriol dimers

Pyrogallol was identified for the first time from the natural extract of Abrus precatorius Linn seeds using GC–MS technique. The vibrational analysis of pyrogallol was investigated in solid phase by FT-IR and FT-Raman spectroscopic techniques in the region 4000–400 cm−1 and 4000–40 cm−1, respectively. The optimized molecular geometry, wave number and intensity of the vibrational bands of pyrogallol and its isomers were obtained by DFT method with different basis sets. The electronic transition energy and intensities, HOMO-LUMO energy gap have been computed with the ZINDO, CIS, TDDFT theory for isomers and the differences were compared with UV–vis absorption spectra. The observed wave numbers in FT-IR, FT-Raman and UV–vis spectra were analyzed and assigned to various fundamental modes of vibration in the molecules. Experimentally observed vibrational frequencies and electronic transitions were assigned with the help of theoretical vibrational and electronic spectra, respectively. The differences between observed and calculated wave number values of most of the fundamental modes are very small. The calculated parameters were found to be in best agreement with experimental findings, thereby confirming the monomer and dimer structure of the identified molecule as well as its isomers.

Normal coordinate analysis of pyridine and its C2v2H-isotopomers. A new approach

The vibrational spectra of pyridine and its C2v deuterated isotopomers were reconsidered by means of density functional theory (DFT) methods. The B3LYP level, with 6–311++G** and cc-pVTZ basis sets, is used for geometrical optimization and calculations of harmonic vibrational wavenumbers. Furthermore, the anharmonic vibrational wavenumbers were also calculated at the B3LYP/6-311++G** level. The calculated internal coordinates were used to perform complete normal coordinate analysis (NCA) and potential energy distribution (PED) calculations for pyridine and its 2H-isotpomers.