Vibrational frequencies and structure of 2-thiouracil by Hartree-Fock, post-Hartree-Fock and density functional methods

CNT-based nanocarrier loaded with pyrimethamine for adipose mesenchymal stem cells differentiation and cancer treatment: The computational and experimental methods

Pyrimethamine is an effective drug in the cancer cell treatment and is a dihydrofolate reductase inhibitor. In this work, the amount of drug loading up on CNT and its cytotoxicity effect upon MCF-7 cell lines was surveyed. The novel applications of some drugs and nanocarriers can induce the differentiation of adipose mesenchymal cells into nerve cells. Hence carbon nanotube-pyrimethamine was used to differentiate mesenchymal stem cells into the neural category, for the first time. The results of NSE and NFM gene expression level were evaluated using the real-time PCR. A detailed study on the interaction between pyrimethamine anticancer drug and (6, 0) zigzag single-walled carbon nanotube was performed by DFT/B3LYP and DFT/M06-2X with 6-31G* basis set calculations in gas phase and in solvent using the PCM. Different configurations of the adsorbed pyrimethamine onto the CNT surface were studied. Based on the results, the process of pyrimethamine adsorption on diff ;erent sites on the outer wall of the nanotube was exothermic and configurations were stable. The adsorption energy values indicated that the pyrimethamine molecule could be physically adsorbed on the external surface of the SWCNT. The QTAIM was used for characterizing the nature of the interactions between the pyrimethamine and the selected nanocarrier.

Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes

The molecular structure of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil was analyzed under the effect of the first and second hydration shell by using the B3LYP density functional (DFT) method, and the results were compared to those obtained for the uracil molecule. A slight difference in the water distribution appears in these molecules. On the hydration of these molecules several trends in bond lengths and atomic charges were established. The ring in uracil molecule appears easier to be deformed and adapted to different environments as compared to that when it is thio-substituted. Molecular docking calculations of 2-thiouracil against three different pathogens: Bacillus subtilis, Escherichia coli and Candida albicans were carried out. Docking calculations of 2,4-dithiouracil ligand with various targeted proteins were also performed. Different DNA: RNA hybrid microhelixes with uridine, 2-thiouridine, 4-thiouridine and 2,4-dithiouridine nucleosides were optimized in a simple model with three nucleotide base pairs. Two main types of microhelixes were analyzed in detail depending on the intramolecular H-bond of the 2'-OH group. The weaker Watson-Crick (WC) base pair formed with thio-substituted uracil than with unsubstituted ones slightly deforms the helical and backbone parameters, especially with 2,4-dithiouridine. However, the thio-substitution significantly increases the dipole moment of the A-type microhelixes, as well as the rise and propeller twist parameters.

Experimental (FT-IR, Laser-Raman and NMR) and theoretical comparative study on 2-benzylsulfanyl-4-pentyl-6-(phenylsulfanyl)pyrimidine-5-carbonitrile, a potential bioactive agent

In this paper, the experimental and theoretical vibrational frequencies of a potential bioactive pyrimidine derivative molecule named 2-benzylsulfanyl-4-pentyl-6-(phenylsulfanyl)pyrimidine-5-carbonitrile has been investigated. The experimental FT-IR and Laser-Raman spectra of the studied molecule are in the region (4000–400[Formula: see text]cm[Formula: see text] and (4000–100[Formula: see text]cm[Formula: see text], respectively, in gas phase. The vibrational modes and optimized ideal structure parameters(bond lengths, bond angles and selected dihedral angles) were calculated by using DFT/B3LYP, DFT/BHandHLYP and DFT/PBE1PBE methods with 6-311[Formula: see text]G(d,p) basis set. The theoretical mode assignments have been obtained by using potential energy distribution (PED) with the VEDA4 software program. Additionally, infrared and Raman intensities, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) energies and their clouds, and other related molecular properties were calculated and evaluated. The proton (1H) and carbon-13 ([Formula: see text]C) nuclear magnetic resonance (NMR) chemical shifts have been investigated for the title molecule, both experimentally (in DMSO-d[Formula: see text] and theoretically (in vacuum and DMSO). The thermodynamic properties of the tile compound have been investigated using the mentioned theoretical computational methods. The results revealed that there isgood agreement between experimental and theoretical results and these results have supported the related literature.

A Promising Copper(II) Complex as Antifungal and Antibiofilm Drug against Yeast Infection

The high mortality rate of candidemia and the limited option for the treatment of Candida spp. infection have been driving the search for new molecules with antifungal property. In this context, coordination complexes of metal ions and ligands appear to be important. Therefore, this study aimed to synthesize two new copper(II) complexes with 2-thiouracil and 6-methyl-2-thiouracil ligands and to evaluate their mutagenic potential and antifungal activity against Candida. The complexes were synthesized and characterized by infrared vibrational spectroscopy, CHN elemental analysis, UV-Vis experiments and ESI-HRMS spectrometry studies. The antifungal activity was evaluated by broth microdilution against 21 clinical isolates of Candida species. The mutagenic potential was evaluated by the Ames test. The complexes were Cu(Bipy)Cl₂(thiouracil) (Complex 1) and Cu(Bipy)Cl₂(6-methylthiouracil) (Complex 2). Complex 1 showed fungicidal and fungistatic activities against all isolates. Furthermore, the Minimum Inhibitory Concentration (MIC) from 31 to 125 µg/mL and inhibition percentage of 9.9% against the biofilms of C. krusei and C. glabrata were demonstrated. At the concentrations tested, complex 1 exhibited no mutagenic potential. Complex 2 and the free ligands exhibited no antifungal activity at the concentrations evaluated. Since complex 1 presented antifungal activity against all the tested isolates and no mutagenic potential, it could be proposed as a potential new drug for anti-Candida therapy.

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.

Spectroscopic investigation of 2-(4-benzoyl-1,5-diphenyl-1H-pyrazol-3-yl)-4H-naphto[2,3-d][1,3]oxazin-4-one molecule

In this present study, the experimental and theoretical vibrational frequencies of an important pharmacological molecule 2-(4-benzoyl-1,5-diphenyl-1[Formula: see text]-pyrazol-3-yl)-4[Formula: see text]-naphto[2,3-[Formula: see text]][1,3]oxazin-4-one have been researched. The experimental FT-IR and laser-Raman spectra of the title compound have been taken in the region (4000–400[Formula: see text]cm[Formula: see text]) and (4000–100[Formula: see text]cm[Formula: see text]), respectively. The vibrational modes and optimized structure parameters have been computed by using DFT/B3LYP methods with 6-311[Formula: see text]G(d,p) basis set. In our calculations, Gaussian 09W software program has been used. Assignments of theoretical vibrations have been obtained by potential energy distribution analysis using VEDA 4 software program. This program is important because it performs assignments with 10% precision. We have obtained a fairly good agreement between experimental and theoretically obtained results, and these results have supported the literature. Additionally, we have examined the highest occupied molecular orbital and the lowest unoccupied molecular orbital energies, the other related molecular energy values, nuclear magnetic resonance ([Formula: see text]C and 1H-proton) chemical shifts, and UV–Vis wavelengths (electronic absorption wavelengths of the title compound) by using the mentioned calculation level. The nonlinear optical properties of the title compound have also been determined by using DFT/B3LYP/6-311[Formula: see text]G(d,p) level.

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

The trans-2-deoxyribosylation of 4-thiouracil (4SUra) and 2-thiouracil (2SUra), as well as 6-azauracil, 6-azathymine and 6-aza-2-thiothymine was studied using dG and E. coli purine nucleoside phosphorylase (PNP) for the in situ generation of 2-deoxy-α-D-ribofuranose-1-phosphate (dRib-1P) followed by its coupling with the bases catalyzed by either E. coli thymidine (TP) or uridine (UP) phosphorylases. 4SUra revealed satisfactory substrate activity for UP and, unexpectedly, complete inertness for TP; no formation of 2'-deoxy-2-thiouridine (2SUd) was observed under analogous reaction conditions in the presence of UP and TP. On the contrary, 2SU, 2SUd, 4STd and 2STd are good substrates for both UP and TP; moreover, 2SU, 4STd and 2'-deoxy-5-azacytidine (Decitabine) are substrates for PNP and the phosphorolysis of the latter is reversible. Condensation of 2SUra and 5-azacytosine with dRib-1P (Ba salt) catalyzed by the accordant UP and PNP in Tris∙HCl buffer gave 2SUd and 2'-deoxy-5-azacytidine in 27% and 15% yields, respectively. 6-Azauracil and 6-azathymine showed good substrate properties for both TP and UP, whereas only TP recognizes 2-thio-6-azathymine as a substrate. 5-Phenyl and 5-tert-butyl derivatives of 6-azauracil and its 2-thioxo derivative were tested as substrates for UP and TP, and only 5-phenyl- and 5-tert-butyl-6-azauracils displayed very low substrate activity. The role of structural peculiarities and electronic properties in the substrate recognition by E. coli nucleoside phosphorylases is discussed.

Silver colloid and film substrates in surface-enhanced Raman scattering for 2-thiouracil detection

Surface-enhanced Raman scattering-based silver substrates were designed and fabricated for the detection of 2-thiouracil (2-TU).

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.

Conformations of 2-thiouracil in the aqueous solution and its adsorption behavior on the gold substrates explored by DFT calculations and experimental methods

2-Thiouracil, a thio-derivative of uracil, may appear in various tautomeric forms due to the different positions of protons. In this paper, the adsorption behavior and conformations of 2-thiouracil on the gold substrates are inspected by means of surface-enhanced Raman scattering (SERS) and density functional theory (DFT) calculations. The results indicate that all the enhanced bands are assigned to in-plane vibration modes. Besides, most of the bands related to N and S atoms are significantly enhanced and have obvious shifts in the SERS spectra. Furthermore, the CO stretching band at 1695 cm(-1) also appears in the SERS spectra. The theoretical SERS spectra of 2TU-Au₄ and 2TU2-Au₄ complexes agree well with the experimental SERS spectra of 2-thiouracil at 0.04 mM. Meanwhile, we calculate that the binding energies for 2TU2-Au₄ and 2TU-Au₄ are ca. 70 and 50 kcal/mol, respectively. Those results above imply that the 2TU and 2TU2 conformers can exist stably in the aqueous solution and both of them are vertically chemisorbed on the gold surfaces. For the 2TU, it is adsorbed on the gold surfaces through N1H position and the sulfur atom. While the 2TU2 adsorbed on the gold substrates through the N1 site and its deprotonated sulfur atom.

Theoretical investigations on the molecular structure, vibrational spectra, HOMO-LUMO analyses and NBO study of 1-[(Cyclopropylmethoxy)methyl]-5-ethyl-6-(4-methylbenzyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione

The FT-IR and FT-Raman spectra of 1-[(Cyclopropylmethoxy)methyl]-5-ethyl-6-(4-methylbenzyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione were recorded. In this work, experimental and theoretical study on the molecular structure and vibrational wavenumbers of the title compound are presented. The vibrational wavenumbers were obtained theoretically at the DFT level and were compared with the experimental results. The study is extended to calculate the HOMO-LUMO energy gap, NBO, mapped molecular electrostatic potential and first hyperpolarizability. The calculated first hyperpolarizability of the title compound is 9.15 times that of urea and hence the title compound and the series of compounds it represents are attractive candidates for further studies in non linear optical applications. In the title compound, the HOMO of π nature is delocalized over the phenyl ring while the LUMO is located over the pyrimidine ring. The inter-molecular hydrogen bonding at O7 and N1H25 positions in each monomer give rise to a C2-symmetry dimer which is predicted to be about 10kcalmol(-1) more stable than the monomeric form.

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.

Mono- and binuclear copper(I) complexes of thionucleotide analogues and their catalytic activity on the synthesis of dihydrofurans

The reaction of copper(I) halides with 2-thiouracil (TUC), 6-methyl-2-thiouacil (MTUC), and 4-methyl-2-mercaptopyrimidine (MPMTH) in the presence of triphenylphosphine (tpp) in a 1:1:2 molar ratio results in a mixed-ligand copper(I) complex with the formulas [Cu2(tpp)4(TUC)Cl] (1), [Cu2(tpp)4(MTUC)Cl] (2), [Cu(tpp)2(MPMTH)Cl]·(1)/2CH3OH (3), [Cu(tpp)2(MTUC)Br] (4), and [Cu(tpp)2(MTUC)I]·(1)/2CH3CN (5). The complexes have been characterized by FT-IR, (1)H NMR, and UV-vis spectroscopic techniques and single-crystal X-ray crystallography. Complexes 1 and 2 are binuclear copper(I) complexes. Two phosphorus atoms from tpp ligands are coordinated to the copper(I) ions, forming two units that are linked to each other by a deprotonated TUC or MTUC chelating ligand through a sulfur bridge. A linear Cu-S-Cu moiety is formed. The tetrahedral geometry around the metal centers is completed by the nitrogen-donor atom from the TUC or MTUC ligand for the one unit, while for the other one, it is completed by the chloride anion. Two phosphorus atoms from two tpp ligands, one sulfur atom from MPMTH or MTUC ligand, and one halide anion (Cl, Br, and I) form a tetrahedron around the copper ion in 3-5 and two polymorphic forms of 4 (4a and 4b). In all of the complexes, either mono- or binuclear intramolecular O-H···X hydrogen bonds enhance the stability of the structures. On the other hand, in almost all cases of mononuclear complexes (with the exception of a symmetry-independent molecule in 4a), intermolecular NH···O hydrogen-bonding interactions lead to dimerization. Complexes 1-5 were studied for their catalytic activity for the intermolecular cycloaddition of iodonium ylides toward dihydrofuran formation by HPLC, (1)H NMR, and LC-HRMS spectroscopic techniques. The results show that the geometry and halogen and ligand types have a strong effect on the catalytic properties of the complexes. The highest yield of dihydrofurans was obtained when "linear" complexes 1 and 2 were used as the catalysts. The activity of the metal complexes on the copper(I)-catalyzed and uncatalyzed intramolecular cycloaddition of iodonium ylide is rationalized through electronic structure calculation methods, and the results are compared with the experimental ones.

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.

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.

Accurate molecular structure and spectroscopic properties of nucleobases: a combined computational-microwave investigation of 2-thiouracil as a case study

The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.

Experimental FT-IR, Laser-Raman and DFT spectroscopic analysis of a potential chemotherapeutic agent 6-(2-methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized potential chemotherapeutic agent namely, 6-(2-methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile 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 M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09 W 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.

The biomolecule of 5-bromocytosine: FT-IR and FT-Raman spectra and DFT calculations. Identification of the tautomers in the isolated state and simulation the spectra in the solid state

An accurate assignment of the IR spectrum in Ar matrix of 5-bromocytosine and of the IR and Raman spectra in the solid state was carried out. For this purpose Density functional calculations (DFTs) were performed to clarify wavenumber assignments of the experimental observed bands. The calculated values were scaled using scaling equations and they were compared with IR and Raman experimental data. Good reproduction of the experimental wavenumbers is obtained and the% error is very small in the majority of cases. In the isolated state all the tautomer forms of 5-bromocytosine were determined and optimized. The wavenumbers corresponding to C1 and C2b tautomers were identified and assigned in the IR experimental spectrum reported in Ar matrix. Our study confirms the existence of at least two tautomers, the amino-oxo and the amino-hydroxy in the isolated state. In the solid state the FT-IR and FT-Raman spectra of 5-bromocytosine in the powder form were recorded in the region 400-4000 cm(-1) and 50-3500 cm(-1), respectively. The unit cell found in the crystal was simulated as a tetramer form in three tautomers. Thus, it has been possible to assign all the 33 normal modes of vibration. The study indicates that the features, that are the characteristic of the vibrational spectra of cytosine, are retained by the spectra of 5-bromocytosine and it exists in the solid phase in the amino-oxo form.

Molecular structure analysis and spectroscopic characterization of 5-ethyl-5-phenyl-1,3-diazinane-4,6-dione with experimental (FT-IR and FT-Raman) techniques and quantum chemical calculations

In this work, the FT-IR and FT-Raman spectra of 5-ethyl-5-phenyl-1,3-diazinane-4,6-dione have been recorded. The optimum molecular geometry, normal mode wavenumbers, infrared and Raman intensities, Raman scattering activities, corresponding vibrational assignments and Mullikan atomic charges were investigated with the help of HF and B3LYP(DFT) methods using 6-31G(d,p) basis set. The assignments of vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The stability of molecule has been analyzed by NBO analysis. The calculated HOMO and LUMO energies show that charge transfer interactions take place within the molecule. Finally, the Mulliken population analysis on atomic charges of the title compound has been calculated.

Coordination modes, spectral, thermal and biological evaluation of hetero-metal copper containing 2-thiouracil complexes

Mononuclear copper complex [CuL(NH(3))(4)]Cl(2)·0.5H(2)O and three new hetero-metallic complexes: [Cu(2)Ni(L)(2)(NH(3))(2)Cl(2)·6H(2)O] 2H(2)O(,) [Cu(3)Co(L)(4)·8H2O]Cl·4(·)5H(2)O, and [Cu(4)Co(2)Ni(L)(3)(OH)(4)(NH(3))Cl(4)·3H(2)O]4H(2)O where L is 2-thiouracil, were prepared and characterized by elemental analyses, molar conductance, room-temperature magnetic susceptibility, spectral (IR, UV-Vis and ESR) studies and thermal analyses techniques (TG, DTG and DTA). The molar conductance data revealed that [CuL(NH(3))(4)]Cl(2)·0.5H(2)O and [Cu(3)Co(L)(4)·8H2O]Cl·4.5H(2)O are electrolytes, while, [Cu(2)Ni(L)(2)(NH(3))(2)Cl(2·)6H(2)O]·2H(2)O and [Cu(4)Co(2)Ni(L)(3)(OH)(4)(NH(3))Cl(4)·3H(2)O]4H(2)O are non-electrolytes. IR spectra showed, that 2-thiouracil ligand behaves as a bidentate or tetradentate ligand. The geometry around the metal atoms is octahedral in all the prepared complexes except in [Cu(4)Co(2)Ni(L)(3)(OH)(4)(NH(3))Cl(4)·3H(2)O]4H(2)O complex where square planar environment around Co(II), Ni(II) and Cu(II) were suggested. Thermal decomposition study of the prepared complexes was monitored by TG, DTG and DTA analyses under N(2) atmosphere. The decomposition course and steps were analyzed. The order of chemical reactions (n) was calculated via the peak symmetry method and the activation parameters of the non- isothermal decomposition were computed from the thermal decomposition data. The negative values of ΔS(∗) deduced the ordered structures of the prepared complexes compared to their starting reactants. The antimicrobial activity of the prepared complexes were screened in vitro against a Gram positive, a Gram negative bacteria, a filamentous fungi and a yeast. The antimicrobial screening data showed that the studied compounds exhibited a good level of activity against Escherichia coli, Staphylococcus aureus and Candida albicans but have no efficacy against Aspergillus flavus. It was observed that [Cu(4)Co(2)Ni(L)(3)(OH)(4)(NH(3))Cl(4)·3H(2)O]4H(2)O complex showed the most intensive activity against the tested microorganisms. Trials to prepare single crystals from complexes were failed.

Environmental effects on the lignin model monomer, vanillyl alcohol, studied by Raman spectroscopy

Structural analysis of plant materials, i.e., lignin, cellulose, hemicellulose, etc., supports the growing interest of their uses, e.g., as sources for biofuels or materials. Lignin is a main polymer formed from three phenolic presursors, containing none, one, or two OMe groups, i.e., H, G, and S units, respectively. Raman spectroscopy gives valuable knowledge on lignin and has a large potential for further developments. Thus in the present work we show how the use of electronic structure theory can support the study of environmental effects on lignin Raman bands. Raman spectra of the lignin model monomer, vanillyl alcohol (G type), dissolved in different solvents were compared to investigate such effects on the Raman band shapes and positions. Density functional theory combined with the polarizable continuum model were applied to assign the observed bands and tested for prediction accuracy. Two ring deformation modes at ∼1600 cm(-1) showed strong dependency on solvent ability to act as hydrogen bond donor, and this has to be considered in addition to substitutional effects on these modes.

Vibrational spectra, tautomerism and thermodynamics of anticarcinogenic drug: 5-fluorouracil

The FT-IR and FT-Raman spectra of 5-Fluorouracil were recorded in the solid phase in the regions 400-4000 cm(-1) and 50-4000 cm(-1), respectively. The vibrational spectra were analysed and the observed fundamentals were assigned to different normal modes of vibration. The experimental wavenumbers were compared with the scaled vibrational values using DFT methods: the Ar matrix data were related to gas phase calculations, while the values of the solid state spectra were compared to those with dimer simulations. The study indicates that some features that are characteristic of vibrational spectra of uracil and its derivatives are retained in the spectrum of 5-fluorouracil and it exists in ketonic form in the solid phase. The tautomerism was also studied and the spectra of the two most stable forms were simulated. The calculated wavenumbers have been employed to yield thermodynamic properties.

DFT study of molecular geometries and vibrational characteristics of uracil and its thio-derivatives and their radical cations

DFT calculations at the B3LYP/6-311++G** level have been carried out to study the vibrational characteristics of the neutral molecules, anionic and cationic radicals of uracil, 2-thiouracil and 4-thiouracil. In the U molecule, C=C bond loses its double bond character and magnitude of the C=C stretching frequency decreases significantly as a result of radicalization. Frequency for the in-plane deformation mode of C=O increases when a sulfur atom is substituted for the oxygen atom at the site C(2) in the uracil molecule but decreases when a sulfur atom is substituted for the oxygen atom at the site C(4). The magnitude of both the N-H stretching frequencies decreases in all the radical cations as compared to their neutral molecules. Radicalization leads to significant changes in the magnitudes and intensities corresponding to some of the normal modes for all the three cases. Removal of an electron leads to decrease in the electronic charge mainly from the sulfur atom in the case of 2-TU and 4-TU, whereas it is distributed over the sites N(1), C(5), O(8) and O(10) in case of the U molecule.

Experimental and Density Functional Theory Study of the Vibrational Properties of 2-Mercaptobenzimidazole in Interaction with Gold

The vibrational properties of the 2-mercaptobenzimidazole (MBI) molecule in interaction with gold were examined by a combined approach of FTIR measurements and density functional theory (DFT). A complete assignment of the 42 normal modes of MBI has been performed on the basis of DFT calculations at the B3PW91 level in complement to the Raman and FTIR spectra. Calculations demonstrated that, on the deprotonated MBI molecule, the negative charge is localized on the sulfur atom, favoring the formation of a gold-sulfur bond upon reaction of MBI with gold. This was confirmed by the very good agreement between the calculated spectrum and the experimental spectra of different gold-MBI compounds, indicating that the vibrational properties of adsorbed MBI are chiefly determined by the coordination through the sulfur atom.

Electrochemical oxidation of 2-thiouracil at pyrolytic graphite electrode

2-Thiouracil has been studied in phosphate buffers of pH 1.95-11.08 using linear and cyclic sweep voltammetry, coulometry, controlled potential electrolysis and spectral studies. One well-defined oxidation peak I(a) in the pH range 1.95-11.08 was noticed. The number of electrons involved in peak I(a) was found to be four in a thin layer cell whereas under exhaustive electrolysis condition oxidation was found to involve six electrons. A reduction peak II(c) (2e, 2H(+)) is noticed in the reverse sweep. Spectral studies during oxidation were carried out at different pH. Kinetic studies indicated that the decay of the UV-absorbing intermediate is a first order reaction. The products of the electrooxidation have been characterized and a tentative EC mechanism has been suggested for the oxidation of 2-thiouracil.