FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of biomolecule 5-aminouracil

A DFT study of vibrational spectra of 5-chlorouracil with molecular structure, HOMO-LUMO, MEPs/ESPs and thermodynamic properties

The density functional theory calculation has been carried out for the analysis of 5-chlorouracil using DFT/Gaussian 09 with GAR2PED. Recorded experimental spectra for Raman and IR of 5-chlorouracil have been analyzed all fundamental vibrational modes using the outcome results of DFT at 6-311++G** of Gaussian 09 calculations and the GaussView 5.09. To help the analysis of vibrational modes, GAR2PED program has been used in the calculation of PEDs. The charge transfer properties of 5-chlorouracil have been analyzed using HOMO and LUMO level energy analysis. HOMO and LUMO energy gap study supports the charge transfer possibility in molecule. These have been made to study for reactivity and stability of heterocyclic molecules for the analysis of antiviral drugs against the new corona virus: COVID-19. Here, the smaller energy gap of 5-chlorouracil is more responsible for charge transfer interaction in the heterocyclic drug molecules and a reason of more bioactivity. The electron density mapping within molecular electrostatic potential plot and electrostatic potential plotting within iso-surface plot have been evaluated the charge distribution concept in the molecule as the nucleophilic reactions and electrophilic sites. These computations have been used to produce the molecular charges, structure and thermodynamic functions of biomolecule. This study has been made to all internal modes of chloro group substituent at pyrimidine ring of C₅ atom. The splitting of frequencies has arisen in the two species for the normal distribution modes.

Graphical abstract

DFT Study and Antiparasitic Activity of Some Azo Dyes Containing Uracil

In this study, for the first time, molecular modeling and antiparasitic activity studies were carried out on some azo dyes containing uracil, 6-amino-5-[(4-nitrophenyl) diazenyl] pyrimidine-2,4 (1H, 3H)-dione (dye I) and 6-amino-5-[(4-bromophenyl) diazenyl] pyrimidin-2,4 (1H, 3H)-dione (dye II), which were resynthesized using the same method in the literature and whose molecular structures were confirmed using FTIR and 1H-NMR methods. In molecular modeling study, all calculations were performed using DFT/B3LYP/6-311++G(d,p) method. The molecular structures of the possible tautomeric forms of dyes I and II were optimized, and their molecular total energies were calculated in the gas phase and DMSO solvent. IR and 1H-NMR spectral data of the possible tautomeric forms of dyes were obtained, and theoretical spectral data were compared with experimental ones. The evaluations show that, for both dyes, the spectral data of the imine-diketo-hydrazone form, which has the lowest energy and is hence determined to be the most stable form, are in agreement with the experimental ones. In antiparasitic activity study, dyes I and II were tested for the first time against parasites Leishmania infantum, Leishmania major, Leishmania tropica promastigotes, and Trichomonas vaginalis trophozoites. In vitro antileishmanial activities against Leishmania promastigotes were tested by microdilution broth assay with Alamar Blue in RPMI 1640 medium, and in vitro trichomonacidal activities against Trichomonas vaginalis parasite were tested using TYM medium. In tests, antileishmanial and trichomonacidal effects were determined by comparing the obtained minimum inhibitory concentration (MIC) and minimum lethal concentration (MLC) values with those obtained for standard drugs (amphotericin B and metronidazole, respectively).

DFT study on tautomerism and natural bond orbital analysis of 4-substituted 1,2,4-triazole and its derivatives: solvation and substituent effects

Density functional theory investigations at the DFT-B3LYP/6-311++G^** theoretical level employed to determine the tautomerism, substituent effects of 4-substituted 4-amino-5-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, and its derivatives (4-R-H, 4-R-CH₃, 4-R-F, 4-R-NO₂) in the selected solvent (acetone, acetonitrile, and dichloromethane) and gas phases using the polarizable continuum method (PCM) model. The substituted 1,2,4-triazoles have two main different tautomers namely N₂-H and S₇-H. For considered derivatives, thione forms are more energetically stable and dominant form in the studied solvent and gas phases. In addition, geometrical parameters, charges on atoms, dipole moments, energetic properties, and the nucleus-independent chemical shifts (NICS) are investigated. It has been seen that these molecular features of the studied compound and its derivatives are mostly solvent dependent. For electron-releasing and -withdrawing derivatives in the solution and gas phases, 2-H forms are the more stable and dominant form. The relative stability of the C₄-substituted 1,2,4-triazole tautomerism is influenced by the possibility for intramolecular interactions between substituent and electron-donor or electron-acceptor centers of the triazole ring.

Thermodynamic functions with other properties and vibrational spectra of pyrimidine ring of uracil for RNA and bio-molecule 5-aminouracil

Vibrational spectra (Infra Red and Raman) of uracil and 5-aminouracil have been recorded as well as reproduced in solid phase for the pyrimidinal region (200-2000 cm⁻¹) and the internal modes were analyzed especially for pyrimidine ring of bio-molecules theoretically by using the density functional theory (DFT) calculations on the different basis sets for Restricted Hartree–Fock (RHF) by employing the Gaussian-03 program. These quantum chemical calculations have been employed to yield the Mulliken atomic charges, atomic polarizability tensor (APT) charges and thermodynamic functional properties of these bio-molecules. These DFT calculations have been computed for the some important internal ring modes especially to pyrimidine ring of uracil with a substituent amino-group (NH₂) at site of C₅ atom on pyrimidine ring.

FT-IR and FT-Raman spectra of 5-chlorocytosine: Solid state simulation and tautomerism. Effect of the chlorine substitution in the Watson-Crick base pair 5-chlorodeoxycytidine-deoxyguanosine

The laser Raman and IR spectra of 5-chlorocytosine have been recorded and accurately assigned in the solid state using Density functional calculations (DFT) together with the linear scaling equation procedure (LSE) and the solid state simulation of the crystal unit cell through a tetramer form. These results remarkably improve those reported previously by other authors. Several new scaling equations were proposed to be used in related molecules. The six main tautomers of the biomolecule 5-chlorocytosine were determined and optimized at the MP2 and CCSD levels, using different basis sets. The relative stabilities were compared with those obtained in cytosine and their 5-halo derivatives. Several relationships between energies, geometric parameters and NBO atomic charges were established. The effect of the chlorine substitution in the fifth position was evaluated through the stability of the Watson-Crick (WC) base pair of 5-chlorodeoxycytidine with deoxyguanosine, and through their vibrational spectra.

2,4-Ditellurouracil and its 5-fluoro derivative: Theoretical investigations of structural, energetics and ADME parameters

2,4-Ditellurouracil exhibits keto-enol tautomerism via different pathways resulting in seven tautomers. These pathways were studied in the gas phase using density functional theory method. The functionals used were BLYP, B3LYP and BHLYP and the basis sets were 6-311++G(d,p) for all atoms except that LanL2DZ ECP was used for tellurium atom only. The results indicate that the diketo form is more stable as observed for uracil and its sulfur and selenium analogues. The effect of introducing fluorine at position 5 was also investigated and the energy difference between the diketo and dienol forms is reduced. 2,4-Ditellurouracil and its 5-fluoro analogue are expected to exist exclusively as the diketo form due to the high interconversion energy barrier. We extended the investigation to predict ADME parameters of the most stable diketo and dienol tautomers in view of understanding their biological properties. This research enlightens keto-enol tautomerism of 2,4-ditellurouracil and its 5-fluoro derivative with additional insights to biological functions.

Spectrometric measurements and DFT studies on new complex of copper (II) with 2-((E)-9-ethyl-3-(2-(6-(4-methylpyridin-2-yl)pyridin-3-yl)vinyl)-9H-carbazole

The molecular structure of a new complex of copper (II) with (E)-9-ethyl-3-(2-(6-(4-methylpyridin-2-yl)pyridin-3-yl)vinyl)-9H-carbazole ([Cu2(emppc)2Cl2]Cl2) was optimized with B3LYP/LanL2DZ, PBE1PBE/LanL2DZ and M062X/LanL2DZ theoretical level. The ligand, (E)-9-ethyl-3-(2-(6-(4-methylpyridin-2-yl)pyridin-3-yl)vinyl)-9H-carbazole (emppc), binds to Cu(II) ions with a bi-dentate mode, two Cl(-) serve as bridging ligand, each Cu(II) ion has a highly distorted tetrahedron coordination geometry. With M062X/LanL2DZ theoretical level, the calculated interaction energies of Cu(II) with coordination atoms N are between 183.3-200.0kJmol(-1) for α spin and 319.4-324.9kJmol(-1) for β spin, and interaction energies of Cu(II) with coordination atoms Cl atom are 248.0-252.4kJmol(-1) for α spin and 332.6-333.6kJmol(-1) for β spin. The experimental Fourier transform infrared spectrum was assigned. The calculated IR based on B3LYP/LanL2DZ, PBE1PBE/LanL2DZ and M062X/LanL2DZ methods were performed and compared with experimental results. The UV-Vis experimental spectra of [Cu2(emppc)2Cl2]Cl2 was measured in methanol solution. The calculated electronic spectrum was performed with TD/M062X and PCM-TD/M062X methods with LanL2DZ basis set. The nature bond orbital analysis and temperature dependence of the thermodynamic properties were calculated with the same methods.

Indole-containing new types of dyes and their UV-vis and NMR spectra and electronic structures: Experimental and theoretical study

Indole containing dyes were synthesized via a simple method with high yield. These molecules have different colors and UV-vis spectra of them were recorded. Impact of solvents on absorbances was investigated and it was observed that basic solvent such as DMF and pyridine have blue shift. TD-DFT calculations were done and results were compared with experimental data. NMR data of molecules were analyzed and tautomeric forms of colorants and their ratio were determined. It was find out that two tautomers might be formed in solution, called indole and indolenine form. HOMO-LUMO and energy gaps were calculated and plotted. Furthermore, molecular electrostatic potentials were simulated to find out electrophilic and nucleophilic regions.

Synthesis, structural characterization and theoretical approach of the tri(2-(2,6-dichlorophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline) cobalt(II)

The crystal structure of a new coordination compound tri(2-(2,6-dichlorophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline) Co(II) complex ([Co(dcpip)3]Cl2) was measured with X-ray diffraction measurements. The compound is crystallizes triclinic, Pī space group. The ligand, 2-(2,6-dichlorophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline(dcpip), binds to Co(II) ions with a bis-dentate mode, and each Co(II) ion with a distorted octahedral coordination geometry. The calculated interaction energies of Co(II) with coordination atoms N are between 101.7-206.5 kJ/mol and 115.3-230.9 kJ/mol for B3LYP/6-31+G(∗) and PBE1PBE/6-31+G(∗) theoretical methods, respectively. The experimental Fourier transform infrared spectrum was assigned. The calculated IR based on B3LYP/6-31+G(∗) and PBE1PBE/6-31+G(∗) methods were performed and compared with experimental results. The UV-Vis experimental spectrum of [Co(dcpip)3]Cl2 was measured in methanol solution. The calculated electronic spectrum was performed with TD/B3LYP and TD/PBE1PBE methods with 6-31+G(∗) basis set. The first and second order hyperpolarizability for the compound was calculated. The calculated values of γtot are -1.5551344 × 10(-33) esu for B3LYP method and -1.3323259 × 10(-33) esu for PBE1PBE method. The nature bond orbital analysis and temperature dependence of the thermodynamic properties were calculated with the same methods.

Quantum chemical calculation (electronic and topologic) and experimental (FT-IR, FT-Raman and UV) analysis of isonicotinic acid N-oxide

In this work, the molecular conformation, vibrational and electronic analysis of isonicotinic acid N-oxide (iso-NANO) were presented in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. The geometry optimization and energies associated possible two conformers (Rot-I and Rot-II) were computed. The vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The obtained structures were analyzed with the Atoms in Molecules (AIMs) methodology. The computational results diagnose the most stable conformer of iso-NANO as the Rot-I form. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (OPDOS) diagrams analysis for the most stable conformer (Rot-I) were calculated using the same method. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated. As a result, the optimized geometry and calculated spectroscopic data show a good agreement with the experimental results.

FT-IR, Laser-Raman spectra and computational analysis of 5-Methyl-3-phenylisoxazole-4-carboxylic acid

In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor, antiviral, hypoglycemic, antifungal and anti-HIV agent namely, 5-Methyl-3-phenylisoxazole-4-carboxylic acid has been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parametrized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated by using the same theoretical calculations.

The spectroscopic (FT-IR, UV-vis), Fukui function, NLO, NBO, NPA and tautomerism effect analysis of (E)-2-[(2-hydroxy-6-methoxybenzylidene)amino]benzonitrile

A new o-hydroxy Schiff base, (E)-2-[(2-hydroxy-6-methoxybenzylidene)amino]benzonitrile was isolated and investigated by experimental and theoretical methodologies. The solid state molecular structure was determined by X-ray diffraction method. The vibrational spectral analysis was carried out by using FT-IR spectroscopy in the range of 4000-400cm(-)(1). Theoretical calculations were performed by density functional theory (DFT) method using 6-31G(d,p) basis set. The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The UV-vis spectrum of the compound was recorded in the region 200-800 nm in several solvents and electronic properties such as excitation energies, and wavelengths were calculated by TD-DFT/B3LYP method. The most prominent transitions were corresponds to π→π∗. Hybrid density functional theory (DFT) was used to investigate the enol-imine and keto-amine tautomers of titled compound. The titled compound showed the preference of enol form, as supported by X-ray and spectroscopic analysis results. The geometric and molecular properties were compaired for both enol-imine and keto-amine forms. Additionally, geometry optimizations in solvent media were performed with the same level of theory by the integral equation formalism polarizable continuum (IEF-PCM). Stability of the molecule arises from hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed using natural bond orbital (NBO) analysis. Mulliken population method and natural population analysis (NPA) have been studied. Also, condensed Fukui function and relative nucleophilicity indices calculated from charges obtained with orbital charge calculation methods (NPA). Molecular electrostatic potential (MEP) and non linear optical (NLO) properties are also examined.

Synthesis and DFT calculation of a novel 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene

In this study, 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene has been synthesized from 2-aminoantracene and 25,27-dihydroxy-26,28-diethylacetate calix[4]arene. In order to identify the molecular structure and vibrational features of the prepared azocalix[4]arene, FT-IR and (1)H NMR spectral data have been used. FT-IR spectrum of the studied molecule is recorded in the region 4000-400 cm(-1). (1)H NMR spectrum is recorded for 0.1-0.2 M solutions in DMSO-d6 solution. The molecular geometry, infrared spectrum are calculated by the density functional method employing B3LYP level with different basis sets, including 6-31G(d) and LanL2DZ. The chemical shifts calculation for (1)H NMR of the title molecule is calculated by using by Gauge-Invariant Atomic Orbital method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via GaussSum 3.0 program. Frontier molecular orbital (HOMO-LUMO) and molecular electrostatic potential surface on the title molecule are carried out for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical calculations have been compared, and they are found to be in good agreement.

Quantum chemical and spectroscopic (FT-IR and FT-Raman) investigations of 3-methyl-3h-imidazole-4-carbaldehyde

FT-IR and FT-Raman spectra of 3-methyl-3h-imidazole-4-carbaldehyde (3M3HI4C) were recorded in the region 4000-400cm(-1) and 3500-50cm(-1), respectively. Optimized geometric parameters, conformational equilibria, normal mode frequencies, and corresponding vibrational assignments of 3M3HI4C were theoretically examined by quantum chemical methods for the first time. All vibrational frequencies were assigned in detail with the help of total energy distribution (TEDs). The experimental wavenumbers were compared with the scaled vibrational frequencies determined by DFT/B3LYP method. The results showed that the B3LYP/6-311++G(d,p) method predicts vibrational frequencies and the structural parameters effectively. The most stable conformer of the title compound was determined. The total electron density and molecular electrostatic potential surfaces of the molecule were constructed by using B3LYP/6-311++G(d,p) method to display electrostatic potential (electron+nuclei) distribution. The electronic properties HOMO and LUMO energies were measured. The lower energy band was assigned to the HOMO→LUMO transition. Natural bond orbital analysis of title molecule has been performed to indicate the presence of intramolecular charge transfer. Energies, relative stabilities, and dipole moments of title molecule were also compared and analyzed in the gas phase and in solvents. Furthermore, solvent effects on the geometry and vibrational frequency of 3M3HI4C were studied theoretically at the DFT/B3LYP level in combination with the conductor polarizable continuum model (C-PCM).

FT-IR and FT-Raman spectra of 5-fluoroorotic acid with solid state simulation by DFT methods

FT-Raman and FT-IR studies of the biomolecule 5-fluoroorotic acid in the solid state were carried out. The unit cell found in the crystal was simulated as a tetramer form by density functional calculations. They were performed to clarify wavenumber assignments of the experimental observed bands in the spectra. Correlations with the molecule of uracil were made, and specific scale equations were employed to scale the wavenumbers of 5-fluoroorotic acid. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of the bands. This fact confirms our simplified solid state model. The molecular structure was fully optimized using DFT and MP2 methods. The relative stability of both the syn and anti conformations was investigated, and the anti-form was found to be slightly more stable, by 7.49 kJ/mol at the MP2 level. The structures of all possible tautomeric forms were determined. The keto-form appeared as the most stable one. The NBO atomic charges and several thermodynamic parameters were also calculated.

Experimental (FT-IR, NMR and UV) and theoretical (M06-2X and DFT) investigation, and frequency estimation analyses on (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile

The spectroscopic properties of (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile have been investigated by FT-IR, UV, (1)H and (13)C NMR techniques. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parameterized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been carried out by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies were in good agreement with the corresponding experimental data, and with the results in the literature. (1)H and (13)C NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength wavelengths were performed by B3LYP methods. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.

IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-aminouracil

Infrared (IR) and Raman spectra of uracil and 5-aminouracil have been recorded and analyzed between the region 200-4000 cm(-1). The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-aminouracil by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, the most of B3LYP/6-311++G** vibrational frequencies are in the excellent agreement with available experimental assignments and helped in the reassignments of some fundamental vibrational modes. On the basis of calculated results, the assignments of some missing frequencies in the experimental study are proposed. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a') and non-planar (a″) are given by 25a'+11a″, of which 30 modes (21a'+9a″) correspond to the uracil moiety and 6 modes (4a'+2a″) to the NH2 group. Kekule ring stretching mode is found to be comparatively higher frequency magnitude than the mode of uracil due to the involvement of hydrogen bonding of amino group. But, the ring breathing is found to be lower frequency magnitude compared to those for uracil which could be due to mass effect of the NH2 group in place of the hydrogen atom. All other bands have also been assigned different fundamentals/overtones/combinations.

FT-IR and FT-Raman spectra of 6-chlorouracil: molecular structure, tautomerism and solid state simulation. A comparison between 5-chlorouracil and 6-chlorouracil

A Raman and IR study of the biomolecule 6-chlorouracil was carried out in the solid state. The unit cell found in the crystal was simulated as a tetramer form by density functional calculations. Specific scale factors and scaling equations deduced from uracil molecule were employed in the predicted wavenumbers of 6-chlorouracil. The scaled wavenumbers were used in the reassignment of the IR and Raman experimental bands. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. A comparison between the molecular structure and charge distribution of 6-chlorouracil and 5-chlorouracil molecules was presented. The effect of the hydration with the PCM model in the molecular structure and charges was discussed. The optimum tautomers of 6-chlorouracil were optimized and analyzed. Six of them were related to those of uracil molecule. The effect of the halogen substitution in the sixth position of the pyrimidine ring in the stability of the different tautomers was evaluated. HOMO and LUMO orbital energy analysis were carried out.

Vibrational spectroscopy (FT-IR and Laser-Raman) investigation, and computational (M06-2X and B3LYP) analysis on the structure of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone

In this study, the experimental and theoretical vibrational spectral analysis of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone have been carried out. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) have been recorded for the solid state samples. The theoretical vibrational frequencies and the optimized geometric parameters (bond lengths and angles) have been calculated for gas phase using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set. The diversity in molecular geometry of fluorophenyl substituted thiosemicarbazones has been discussed based on the X-ray crystal structure reports and theoretical calculation results from the literature. The assignments of the vibrational frequencies have been done on the basis of potential energy distribution (PED) analysis by using VEDA4 software. A good correlation was found between the computed and experimental geometric and vibrational data. In addition, the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbital energy levels and other related molecular energy values of the compound have been determined using the same level of theoretical calculations.

Vibrational spectroscopy investigation using M06-2X and B3LYP methods analysis on the structure of 2-Trifluoromethyl-10H-benzo[4,5]-imidazo[1,2-a]pyrimidin-4-one

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized bioactive agent namely, 2-Trifluoromethyl-10H-benzo[4,5]-imidazo[1,2-a]pyrimidin-4-one (TIP) have been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and the optimized geometric parameters (bond lengths and bond angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.

Experimental FT-IR, Laser-Raman and DFT spectroscopic analysis of 2,3,4,5,6-Pentafluoro-trans-cinnamic acid

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized 2,3,4,5,6-Pentafluoro-trans-cinnamic acid have been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parameterized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.

Experimental and theoretical spectroscopic analysis, HOMO-LUMO, and NBO studies of cyanuric chloride

The vibrational spectral analysis of cyanuric chloride was carried out by using FT-Raman and FT-IR spectra in the range 100-4000cm(-1) and 400-4000cm(-1) respectively. The structure optimization was done and structural characteristics were determined by Density Functional Theory (B3LYP) method with 6-31G(d,p) and 6-311++G(d,p) basis sets. The vibrational wavenumbers have been calculated and scaled values are compared with experimental FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED). The Natural bonding orbital (NBO) analysis performed to confirm the stability of the molecule arising from hyper conjugation and delocalization. The Mulliken atomic charges were also calculated. The computed HOMO-LUMO energy gap shows that charge transfer occurs within the molecule. The thermodynamic properties at different temperatures have been calculated from the vibrational analysis.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-1)) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

Isolation, Identification, Molecular and Electronic Structure, Vibrational Spectroscopic Investigation, and Anti-HIV-1 Activity of Karanjin Using Density Functional Theory

“Karanjin” (3-methoxy furano-2,3,7,8-flavone) is an anti-HIV drug, and it is particularly effective in the treatment of gastric problems. The method of isolation of “Karanjin” followed the Principles of Green Chemistry (eco-friendly and effortless method). The optimized geometry of the “Karanjin” molecule has been determined by the method of density functional theory (DFT). Using this optimized structure, we have calculated the infrared wavenumbers and compared them with the experimental data. The calculated wavenumbers are in an excellent agreement with the experimental values. On the basis of fully optimized ground-state structure, TDDFT//B3LYP/LANL2DZ calculations have been used to determine the low-lying excited states of Karanjin. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of “Karanjin.” A complete assignment is provided for the observed FTIR spectra. This is the first report of the isolation, molecular and electronic structure using vibrational spectroscopic investigation, density functional theory, and anti-HIV-1 activity of “Karanjin.”

Investigation of solvent polarity effect on molecular structure and vibrational spectrum of xanthine with the aid of quantum chemical computations

The main scope of this study is to determine the effects of 8 solvents on the geometric structure and vibrational spectra of the title compound, xanthine, by means of the DFT/B3LYP level of theory in the combination with the polarizable conductor continuum model (CPCM) for the first time. After determination of the most-steady state (favored structure) of the xanthine molecule, the role of the solvent polarity on the SCF energy (for the molecule stability), atomic charges (for charge distribution) and dipole moments (for molecular charge transfer) belonging to tautomer is discussed in detail. The results obtained indicate not only the presence of the hydrogen bonding and strong intra-molecular charge transfer (ICT) in the compound but the increment of the molecule stability with the solvent polarity, as well. Moreover, it is noted that the optimized geometric parameters and the theoretical vibrational frequencies are in good agreement with the available experimental results found in the literature. In fact, the correlations between the experimental and theoretical findings for the molecular structures improve with the enhancement of the solvent polarity. At the same time, the dimer forms of the xanthine compound are simulated to describe the effect of intermolecular hydrogen bonding on the molecular geometry and vibrational frequencies. It is found that the CO and NH stretching vibrations shift regularly to lower frequency value with higher IR intensity as the dielectric medium enhances systematically due to the intermolecular NH⋯O hydrogen bonds. Theoretical vibrational spectra are also assigned based on the potential energy distribution (PED) using the VEDA 4 program.

The biomolecule, 2-[(2-methoxyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile: FT-IR, Laser-Raman spectra and DFT

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized potential chemotherapeutic agent namely, 2-[(2-methoxyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile have been investigated. The experimental FT-IR (4000-400cm(-1)) and Laser-Raman spectra (4000-100cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.

FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-halogenated uracils (5-X-uracils; X=F, Cl, Br, I)

Raman (200-4000 cm(-1)) and FT-IR (400-4000 cm(-1)) spectra of uracil and 5-halogenated uracils (5-X-uracils; X=F, Cl, Br, I) have been recorded and analyzed in the range 200-4000 cm(-1). The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Ab initio and DFT calculations [using Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP)] were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-halogenated uracils by employing Gaussian-03 program. Gauss View software was used to make the vibrational analysis. Raman and IR spectra have been computed theoretically for the uracil and 5-halogenated molecules. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. Quantum chemical calculations helped in the reassignments of some fundamental vibrational modes. Most of the B3LYP/6-311++G(**) vibrational frequencies are in excellent agreement with available experimental assignments. The ring breathing and kekule stretching modes are found to lower magnitudes compared to those for uracil which could be due to mass effect of halogen atom in place of the hydrogen atom. The C-X (X=F, Cl, Br, I) stretching frequency is distinctly separated from the CH/NH ring stretching frequencies on the pyrimidine ring. All other bands have also been assigned different fundamentals/overtones/combinations.