Base pairs with 5-chloroorotic acid and comparison with the natural nucleobase. Structural and spectroscopic study, and three suggested antiviral modified nucleosides

A structural and spectroscopic study of 5-chloroorotic acid (5-ClOA) biomolecule was carried out by IR and FT-Raman and the results obtained were compared to those achieved in 5-fluoroorotic acid and 5-aminoorotic acid compounds. The structures of all possible tautomeric forms were determined using DFT and MP2 methods. To know the tautomer form present in the solid state, the crystal unit cell was optimized through dimer and tetramer forms in several tautomeric forms. The keto form was confirmed through an accurate assignment of all the bands. For this purpose, an additional improvement in the theoretical spectra was carried out using linear scaling equations (LSE) and polynomic equations (PSE) deduced from uracil molecule. Base pairs with uracil, thymine and cytosine nucleobases were optimized and compared to the natural Watson-Crick (WC) pairs. The counterpoise (CP) corrected interaction energies of the base pairs were also calculated. Three nucleosides were optimized based on 5-ClOA as nucleobase, and their corresponding WC pairs with adenosine. These modified nucleosides were inserted in DNA:DNA and RNA:RNA microhelices, which were optimized. The position of the -COOH group in the uracil ring of these microhelices interrupts the DNA/RNA helix formation. Because of the special characteristic of these molecules they can be used as antiviral drugs.Communicated by Ramaswamy H. Sarma.

Base pairs with 4-amino-3-nitrobenzonitrile: comparison with the natural WC pairs. Dimer and tetramer forms, Infrared and Raman spectra, and several proposed antiviral modified nucleosides

Base pairs of 4-amino-3-nitrobenzonitrile (4A-3NBN) molecule with uracil, thymine and cytosine nucleobases were optimized and compared to natural Watson-Crick (WC) pairs. The slightly greater flexibility of the -NO₂ group of 4A-3NBN than the N3-H group of the natural nucleobases together with a noticeable higher dipole moment of its pairs can facilitate disruption of the DNA/RNA helix formation. Several new mutagenic modified nucleosides with 4A-3NBN and 3-amino-2-nitrobenzonitrile (3A-2NBN) were proposed as antiviral prodrugs and their base pairs optimized. The special characteristics of these prodrugs appear appropriated for their clinical use. The counterpoise (CP) corrected interaction energies of the base pairs were calculated and compared to the natural ones. The M06-2X DFT method was used for this purpose. The molecular structure of 4A-3NBN was analyzed in detail and the crystal unit cell was simulated by a tetramer form and eight dimer forms. The performance of the B3LYP, X3LYP and M06-2X methods was tested on the vibrational wavenumbers in the monomer, dimer and tetramer forms of 4A-3NBN. The observed IR and Raman bands were assigned according to the optimum dimer II form determined by B3LYP and by the tetramer form calculated by M06-2X, which is the expected unit cell that forms the crystal net. The two best scaling procedures were used.Communicated by Ramaswamy H. Sarma.

Inactivation of Bacillus anthracis and Bacillus atrophaeus spores on different surfaces with ultraviolet light produced with a low-pressure mercury vapor lamp or light emitting diodes

AIMS

To obtain quantitative efficacy data of two ultraviolet light (UVC) technologies for surface inactivation of Bacillus anthracis Ames and Bacillus atrophaeus spores.

METHODS AND RESULTS

Spores were deposited onto test coupons and controls of four different materials, via liquid suspension or aerosol deposition. The test coupons were then exposed to UVC light from either a low-pressure mercury vapor lamp or a system comprised of light emitting diodes, with a range of dosages. Positive controls were held at ambient conditions and not exposed to UVC light. Following exposure to UVC, spores were recovered from the coupons and efficacy was quantified in terms of log₁₀ reduction (LR) in the number of viable spores compared to that from positive controls.

CONCLUSIONS

Decontamination efficacy varied by material and UVC dosage (efficacy up to 5·7 LR was demonstrated). There was no statistical difference in efficacy between the two species or between inoculation methods. Efficacy improved for the LED lamp at lower relative humidity, but this effect was not observed with the mercury vapor lamp.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study will be useful in determining whether UVC could be used for the inactivation of B. anthracis spores on different surface types.

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.

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.

Density Functional Computations on 6-Aminouracil: Effect of Amino Group in the 6th Position on the Watson–Crick Base Pair Uridine–Adenosine

The predicted infrared and Raman spectra of 6-aminouracil in the solid state by density functional theory methods were analyzed and compared with the experimental spectra. The effect of amino substitution in the sixth position of uridine on the stability of the Watson–Crick (WC) base pairs with deoxyadenosine was evaluated. Different WC pairs of 5-aminouridine, 6-aminouridine, and uridine with deoxyadenosine were simulated, and the counterpoise-corrected interaction energies were determined. 6-Aminouridine produces a stronger WC pair than that involving uridine, and its high dipole moment facilitates interaction with water molecules.

Quantum chemical computations, vibrational spectroscopic analysis and antimicrobial studies of 2,3-Pyrazinedicarboxylic acid

Density Functional Theory (DFT) calculations at B3PW91 level with 6-311G (d) basis sets were carried out for 2,3-Pyrazinedicarboxylic acid (PDCA) to analyze in detail the equilibrium geometries and vibrational spectra. Calculations reveal that the optimized geometry closely resembles the experimental XRD data. Vibrational spectra were analyzed on the basis of potential energy distribution (PED) of each vibrational mode, which provides quantitative as well as qualitative interpretation of IR and Raman spectra. Information about size, shape, charge density distribution and site of chemical reactivity of the molecule were obtained by mapping electron density isosurface with the electrostatic potential surface (ESP). Based on optimized ground state geometries, NBO analysis was performed to study donor-acceptor (bond-antibond) interactions. TD-DFT analysis was also performed to calculate energies, oscillator strength of electronic singlet-singlet transitions and the absorption wavelengths. The (13)C and (1)H nuclear magnetic resonance (NMR) chemical shifts of the molecule in the ground state were calculated by gauge independent atomic orbital (GIAO) method and compared with the experimental values. PDCA was screened for its antimicrobial activity and found to exhibit antifungal and antibacterial effects. Molecular docking was also performed for the different receptors.

FT-IR and FT-Raman spectra, MEP and HOMO-LUMO of 2,5-dichlorobenzonitrile: DFT study

The experimental FT-IR and FT-Raman spectra of 2,5-dichlorobenzonitrile molecule were recorded at room temperature, and the results compared with quantum chemical theoretical values using MP2 and DFT methods. Molecular geometry, vibrational wavenumbers and thermodynamic parameters were calculated. With the help of specific scaling procedures for the computed wavenumbers, the experimentally observed FTIR and FT-Raman bands were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range and the error obtained was in general very low. Several general conclusions were deduced. The NBO analysis has been done and Molecular Electrostatic Potential (MEP) has been plotted.

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.

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 spectroscopic studies and DFT computation of the nonlinear optical molecule L-Valinium formate

The Fourier Transform Infrared and Raman spectra of the L-Valinium formate have been recorded and analyzed. The assignments of the bands of the vibrational spectra have been carried out with the aid of Normal Coordinate Analysis following the calculated quantum mechanical force field methodology. Optimized geometry of the molecule has computed using of Density Functional Theory method. Natural Bond Orbital Analysis, Mulliken's net charges and the atomic natural charges are also predicted. HOMO and LUMO energy gap value suggest the possibility of charge transfer within the molecule. The thermodynamic properties at different temperatures are also calculated.

FT-IR, FT-Raman spectra and other molecular properties of 2,4- dichlorobenzonitrile: a interpretation by a DFT study

FT-IR and FT-Raman spectra of 2,4-dichlorobenzonitrile at room temperature have been recorded in the regions 200-3500cm(-)(1) and 0-3400cm(-)(1), respectively. The observed vibrational bands were analyzed and assigned to different normal modes of the molecule according to the Wilson's notation. Density functional calculations were performed to support our frequency assignments. Specific scale equations deduced from the benzene molecule were employed to improve the calculated values. For the majority of the normal modes, the deviations between the corresponding experimental and scaled theoretical wavenumbers are located in the expected range. A correct characterization of each normal mode is of vital importance in the assignment of the observed bands, and the same has been successfully done by the aid of Potential Energy Distributions (PEDs) calculated separately for each normal mode of 2,4-dichlorobenzonitrile. The molecular structure was optimized and several thermodynamic parameters were determined. HOMO and LUMO orbital energy analysis were carried out.

Structural features of the 2-amino-5-nitrobenzophenone by means of vibrational spectroscopy HF and DFT, first order hyperpolarizability, NBO, HOMO-LUMO and theromodynamic properties

The FT-IR and Raman spectra of 2-amino-5-nitrobenzophenone (ANBP) molecule have been recorded using Brucker IFS 66 V spectrometer in the range of 4000-100 cm(-1). The molecular geometry and vibrational frequencies in the ground state are calculated using the Hartree-Fock (HF) and B3LYP with 6-311+G(d) basis set. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. The isotropic HF and DFT analysis showed good agreement with experimental observations comparison of the fundamental vibrational frequencies with calculated results by HF and B3LYP methods indicates that B3LYP/6-311+G(d) is superior to HF/6-311+G(d) for molecular vibrational problems. The electric dipole moment (μ) and first hyper polarizability (β) values of the investigated molecule were computed using density functional theory calculations. Stability of the molecule arising from hyperconjucative interactions leading to its bioactivity, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The calculated HOMO-LUMO energies shows that charge transfer occur within the molecule. The thermodynamic functions (heat capacity, internal heat energy, Gibbs energy and entropy) from spectroscopic data by statistical methods were obtained for the range of temperature 100-1000 K. The observed and calculated frequencies are found to be in good agreement.

FT-IR, FT-Raman spectra and other molecular properties of 3,5-dichlorobenzonitrile: a DFT study

The IR and Raman spectra of 3,5-dichlorobenzonitrile (3,5-DCBN) molecule were recorded at room temperature and then the assignment of the observed fundamental bands were achieved by the aid of the theoretical vibrational spectral data obtained from a quantum chemical study carried out for the free molecule case. In the calculations performed to determine the molecular geometry, vibrational spectral data and thermodynamic parameters, Møller-Plesset second order perturbation theory (MP2) and hybrid Density Functional Theory (DFT) types of electronic structure methods, B3LYP and B3PW91, were used. The overestimations of the calculated harmonic wavenumbers were efficiently corrected by the aid of a specific scaling procedure. This empirical scaling process significantly increased the reliability of our assignments and analyses on the observed bands due to different vibrational normal modes of the molecule. For the majority of the normal modes, the deviations between the corresponding experimental and scaled theoretical wavenumbers have located in the expected range. A correct characterization of the normal modes is of vital importance in the assignment of the observed bands, and this was successfully done by the aid of the Potential Energy Distributions (PEDs) separately calculated for each normal mode of 3,5-DCBN.

Normal coordinate analysis and Nonlinear Optical Response of cross-conjugated system 4,4-Dimethyl Benzophenone

FT-Raman and IR spectra of the nonlinear optical active crystal, 4,4-Dimethyl Benzophenone (4DMBP) have been recorded and analyzed The equilibrium geometry, harmonic vibrational wavenumbers of 4DMBP investigated with the help of density functional theory (DFT) method. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The calculated hyperpolarizability value shows the nonlinear optical activity of the molecule. The value of HOMO-LUMO energy, Mulliken and the natural charges are calculated and analyzed. The Natural bond orbital analysis confirms the occurrence of intramolecular charge transfer interaction.

Theoretical investigations on the molecular structure, vibrational spectra, thermodynamics, HOMO-LUMO, NBO analyses and paramagnetic susceptibility properties of p-(p-hydroxyphenoxy)benzoic acid

The experimental FT-IR (4000-400 cm(-1)) and FT-Raman (3500-100 cm(-1)) spectra of p-(p-hydroxyphenoxy) benzoic acid have been recorded. Quantum chemical calculations of energies, geometries, and vibrational wavenumbers of p-(p-hydroxyphenoxy) benzoic acid (PPHPBA) are carried out using HF and DFT/B3LYP methods with 6-311G (d,p) basis set. The optimized geometrical parameters obtained by B3LYP method show a good agreement with experimental data. The difference between the observed and scaled wave number values of most of the fundamentals is very small. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated with scaled quantum mechanical method. The calculated HOMO and LUMO energies allow the calculation of atomic and molecular properties and they also show that charge transfer occurs in the molecule. A detailed molecular picture of PPHPBA and its intermolecular interactions were obtained from NBO analysis. The temperature dependence of various thermodynamic parameters was also studied. The paramagnetic behavior of the molecule under consideration has been investigated and the variation of paramagnetic susceptibility with temperature has been studied.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented.

Vibrational spectral investigations and density functional theory study of 4-Formylbenzoic acid

An accurate assignment of the vibrational spectra of 4-Formylbenzoic acid in solid state was carried out. For this purpose density functional calculations (DFT) were performed to clarify wavenumber assignments of the experimentally observed bands for the first time. A scaling of the wavenumbers was carried out to improve the calculated values. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. The NBO analysis was carried out, and it reveals hyper conjugative interaction, ICT and stabilization of molecules.

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.

Simulation of a tetramer form of 5-chlorouracil: the vibrational spectra and molecular structure in the isolated and in the solid state by using DFT calculations

A Raman and FT-IR study of the biomolecule 5-chlorouracil in the solid state was carried out. The unit cell found in the crystal was simulated as a tetramer form by density functional calculations. They were performed to clarify the assignments of the experimentally observed bands in the spectra. Calculations in the monomer form and comparisons with the experimental data in Ar matrix were also carried out. The error in the calculated frequencies was analyzed and reduced by using scaling equations and scaling factors deduced from the uracil molecule. The calculations with the B3LYP method and with the 6-31G(d,p) and 6-311+G(2d,p) basis set, appear in general to be useful, when combining with a scaling equation procedure or with the specific scale factors, for interpretation of the general features of the IR and Raman spectra. The scaled values were used in the reassignment of the IR and Raman experimental bands. Comparison of the results with those determined in uracil and 5-halogenated derivatives were performed. The substitution at 5-position of the uracil ring by a chlorine atom has a little effect on the geometric parameters.

2-Amino-3,5-dichlorobenzonitrile: DFT calculations in the monomer and dimer forms, FT-IR and FT-Raman spectra, molecular geometry, atomic charges and thermodynamical parameters

The experimental IR and Raman spectra of 2-amino-3,5-dichlorobenzonitrile molecule were recorded, and the results compared with theoretical values. Molecular geometry, vibrational wavenumbers and thermodynamic parameters were calculated using MP2 and DFT quantum chemical methods. With the help of specific scaling procedures for the computed wavenumbers, the experimentally observed FTIR and FT-Raman bands were analyzed and assigned to different normal modes of vibrations of the molecule. Simulations in the dimer form were carried out to improve the assignment of the bands in the solid state experimental spectra. The error obtained was in general very low. Using PED's were determined the contributions of the different modes to each wavenumber. Several general conclusions were also deduced.

Growth and vibrational spectral investigation of nonlinear optical crystal L-Argininum Perchlorate-DFT study

Nonlinear optical active L-Argininum Perchlorate single crystals are grown by slow evaporation technique. The second-order NLO properties of the molecule are studied by Kurtz-Perry powder technique. FT-IR, FT-Raman spectra have been recorded and analyzed. The equilibrium geometry, vibrational wavenumbers and the first order hyperpolarizability have been calculated with the aid of density functional theoretical method. The NBO analysis explains the intramolecular interactions, electron densities within the molecule. It also confirms the presence of weak intermolecular C-H···O hydrogen bonding in the molecule. The blue-shift in CH stretching wavenumbers is due to the C-H···O hydrogen bonding. The Mulliken population analysis on atomic charges and the HOMO, LUMO energies were also calculated.

Molecular structure and vibrational spectral investigation of charge transfer NLO crystal naphthalene picrate for THz application

Molecular structure and the vibrational spectra of Naphthalene Picrate have been calculated using density functional theoretical computation and compared with the experimental. The dipole moments (μ), polarizability (α), first hyperpolarizabilities (β) second hyperpolarizability (γ) and frontier molecular orbital energies are computed at the DFT level. The frontier molecular orbital calculation shows the inverse relationship of HOMO-LUMO gap with the total static hyperpolarizability. The hyperpolarizability value reveals that these classes of organic compounds show very large non-linear optical properties. Natural Bond Orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. Terahertz time-domain spectroscopy has been used to detect the absorption spectra in the frequency range from 0.2 to 1.5 THz.

Solid state simulation of tetramer form of 5-aminoorotic acid: the vibrational spectra and molecular structure study by using MP2 and DFT calculations

The Raman and IR spectra of the biomolecule 5-aminoorotic acid in the solid state were simulated by a dimer and tetramer forms, with the special interest in the interactions that involve the NH and NH(2) groups. The unit cell expected in the crystal was simulated as a tetramer form by density functional calculations. They were performed to clarify wavenumber assignments of the experimentally observed bands in the spectra. Correlations with the molecule of uracil were made, and accurate scaling procedures deduced by us were employed in the calculated wavenumbers of 5-aminoorotic acid. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. This fact confirms our simplified solid state model. The scaling leads to a reassignment of the IR and Raman experimental bands. The NBO atomic charges and several thermodynamic parameters were also calculated.

Analysis of vibrational spectra and nonlinear optical properties of organic molecule L-alaninium formate

Vibrational and electronic spectra of the crystallized nonlinear optical molecule L-alaninium formate have been recorded and analyzed. The equilibrium geometry, vibrational wavenumbers, and the first order hyperpolarizability of the crystal have been calculated with the help of density functional theory computations. The N-H···O bond distance shows the presence of intramolecular hydrogen bonding and the result is confirmed by the natural bond orbital analysis. The HOMO-LUMO energy gap and the first order hyperpolarizability was calculated and it supports the nonlinear optical activity of the L-alaninium formate crystal.

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.

Density functional theory calculations and vibrational spectral analysis of 3,5-(dinitrobenzoic acid)

The FT-IR and Raman spectra of 3,5-dinitrobenzoic acid (DNBA) have been recorded and analyzed. The equilibrium geometry, various bonding and harmonic vibrational wavenumbers have been calculated with the help of density functional theory (DFT) method. Most of the vibrational modes are observed in the expected range. Mulliken population analysis shows the interactions C-N-O⋯H-C and C-O⋯H-C. The most possible interaction is explained using natural bond orbital (NBO) analysis. The strengthening and polarization of the CO bond increases due to the degree of conjugation. HOMO-LUMO energy and the thermodynamic properties are also evaluated.

Relationships observed in the structure and spectra of uracil and its 5-substituted derivatives

The effects on the geometry structure, atomic charges and vibrational wavenumbers of the main different substituents in the 5th position of the uracil ring were analysed, and relationships were established. The 5-monosubstituted derivatives studied were 5-XU (X=F, Cl, Br, I, CH(3), NH(2), NO(2)). The geometry and vibrational wavenumbers were determined in these molecules. The FT-IR and Raman spectra were studied with the support of B3LYP calculations using several basis sets. Several general conclusions were underlined.

Effect of organophosphorus hydrolysing enzymes on obidoxime-induced reactivation of organophosphate-inhibited human acetylcholinesterase

The reactivation of organophosphate (OP)-inhibited acetylcholinesterase (AChE) by oximes results inevitably in the formation of highly reactive phosphyloximes (POX), which may re-inhibit the enzyme. An impairment of net reactivation by stable POX was found with 4-pyridinium aldoximes, e.g. obidoxime, and a variety of OP compounds. In this study the effect of organophosphorus hydrolase (OPH), organophosphorus acid anhydrolase (OPAA) and diisopropylfluorophosphatase (DFPase) on obidoxime-induced reactivation of human acetylcholinesterase (AChE) inhibited by different OPs was investigated. Reactivation of paraoxon-, sarin-, soman- and VX-inhibited AChE by obidoxime was impaired by POX-induced re-inhibition whereas no deviation of pseudo first-order kinetics was observed with tabun, cyclosarin and VR. OPH prevented (paraoxon) or markedly reduced the POX-induced re-inhibition (VX, sarin, soman), whereas OPAA and DFPase were without effect. Additional experiments with sarin-inhibited AChE indicate that the POX hydrolysis by OPH was concentration-dependent. The activity of OP-inhibited AChE was not affected by OPH in the absence of obidoxime. In conclusion, OPH may be a valuable contribution to the therapeutic regimen against OP poisoning by accelerating the degradation of both the parent compound, OP, and the reaction product, POX.

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

Vibrational study of the biomolecule 2-thiouracil was carried out. Ab initio and density functional calculations were performed to assign the experimental spectra. A comparison with the uracil molecule was made, and specific scale factors were deduced and employed in the predicted frequencies of 2-thiouracil. Several scaling procedures were used. The geometry structure of the molecule was determined. The effect of sulfur substitution at C2 position in the uracil molecule, on the N1-H and N3-H frequencies and intensities reflects changes in proton donor abilities of these groups. Calculations with the 6-31 G** basis set with HF and DFT methods appear in general to be useful for interpretation of the general features of the IR and Raman spectra of the molecule. Using specific scale factors a very small error was obtained. The use of these specific scale factors resolve and correct some of the controversial assignments in the literature.

3,5-Difluorobenzonitrile: ab initio calculations, FTIR and Raman spectra

Geometry, vibrational wavenumbers and several thermodynamic parameters were calculated using ab initio quantum chemical methods for the 3,5-difluorobenzonitrile molecule. The results were compared with the experimental values. With the help of three specific scaling procedures, the observed vibrational wavenumbers in FTIR and Raman spectra were analysed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range and the error obtained was in general very low. Using PEDs the contributions were determined for the different modes to each wavenumber. From the PED, it is apparent that the frequency corresponding to C[triple bond]N stretching contains 87% contribution from the C[triple bond]N stretching force constant and it mixes with the C-CN stretching mode 13 to the extent of 12%. Other general conclusions were also deduced.

Quantum chemical predictions of the vibrational spectra of polyatomic molecules. The uracil molecule and two derivatives

This work describes the different scaling procedures used to correct the quantum-chemical theoretical predictions of the IR and Raman vibrational wavenumbers. Examples of each case are shown, with special attention to the uracil molecule and some derivatives. The results obtained with different semiempirical and ab initio methods, and basis sets, are compared and discussed. A comprehensive compendium of the main scale factors and scaling equations available to obtain the scaled wavenumbers is also shown.

Ab initio calculations, FTIR and raman spectra of 2,3-difluorobenzonitrile

Geometry, vibrational frequencies, atomic charges and several thermodynamic parameters (the total energy, the zero point energy, the rotational constants and the room temperature entropy) were calculated using ab initio quantum chemical methods for 2,3-difluorobenzonitrile molecule. The results were compared with experimental values. With the help of two specific scaling procedures, observed FTIR and Raman vibrational frequencies were analysed and assigned to different normal modes of the molecule. The error obtained was in general very low. Other general conclusions have also been deduced.

Laser Raman and IR spectra and force fields for 2,4-dichlorobenzonitrile

Raman spectrum of 2,4-dichlorobenzonitrile (2,4-DCBN) in powder form has been recorded in the region 50-4000 cm(-1) on a Jasco K-500 Raman spectrophotometer using the 488.0 nm radiation from an argon laser. FTIR spectra in the region 200-4000 cm(-1) have been recorded in KBr pellet and nujol mull on a Nicolet DX spectrometer. Using the observed Raman and IR frequencies, normal co-ordinate analysis has been carried out to support the vibrational analysis and to determine the planar and non-planar force fields.

Structural changes linked to proton translocation by subunit c of the ATP synthase

F1F0 ATP synthases use a transmembrane proton gradient to drive the synthesis of cellular ATP. The structure of the cytosolic F1 portion of the enzyme and the basic mechanism of ATP hydrolysis by F1 are now well established, but how proton translocation through the transmembrane F0 portion drives these catalytic changes is less clear. Here we describe the structural changes in the proton-translocating F0 subunit c that are induced by deprotonating the specific aspartic acid involved in proton transport. Conformational changes between the protonated and deprotonated forms of subunit c provide the structural basis for an explicit mechanism to explain coupling of proton translocation by F0 to the rotation of subunits within the core of F1. Rotation of these subunits within F1 causes the catalytic conformational changes in the active sites of F1 that result in ATP synthesis.

Alteromonas prolidase for organophosphorus G-agent decontamination

Enzymes catalyzing the hydrolysis of highly toxic organophosphorus compounds (OPs) are classified as organophosphorus acid anhydrolases (OPAA; EC 3.1.8.2). Recently, the genes encoding OPAA from two species of Alteromonas were cloned and sequenced. Sequence and biochemical analyses of the cloned genes and enzymes have established Alteromonas OPAAs to be prolidases (E.C. 3.4.13.9), a type of dipeptidase hydrolyzing dipeptides with a prolyl residue in the carboxyl-terminal position (X-Pro). Alteromonas prolidases hydrolyze a broad range of G-type chemical warfare (CW) nerve agents. Efforts to over-produce a prolidase from A. sp.JD6.5 with the goal of developing strategies for long-term storage and decontamination have been successfully achieved. Large-scale production of this G-agent degrading enzyme is now feasible with the availability of an over-producing recombinant cell line. Use of this enzyme for development of a safe and non-corrosive decontamination system is discussed.

Solution structure of the transmembrane H+-transporting subunit c of the F1F0 ATP synthase

Subunit c is the H+-translocating component of the F1F0 ATP synthase complex. H+ transport is coupled to conformational changes that ultimately lead to ATP synthesis by the enzyme. The properties of the monomeric subunit in a single-phase solution of chloroform-methanol-water (4:4:1) have been shown to mimic those of the protein in the native complex. Triple resonance NMR experiments were used to determine the complete structure of monomeric subunit c in this solvent mixture. The structure of the protein was defined by >2000 interproton distances, 64 (3)JN alpha, and 43 hydrogen-bonding NMR-derived restraints. The root mean squared deviation for the backbone atoms of the two transmembrane helices was 0.63 A. The protein folds as a hairpin of two antiparallel helical segments, connected by a short structured loop. The conserved Arg41-Gln42-Pro43 form the top of this loop. The essential H+-transporting Asp61 residue is located at a slight break in the middle of the C-terminal helix, just prior to Pro64. The C-terminal helix changes direction by 30 +/- 5 degrees at the conserved Pro64. In its protonated form, the Asp61 lies in a cavity created by the absence of side chains at Gly23 and Gly27 in the N-terminal helix. The shape and charge distribution of the molecular surface of the monomeric protein suggest a packing arrangement for the oligomeric protein in the F0 complex, with the front face of one monomer packing favorably against the back face of a second monomer. The packing suggests that the proton (cation) binding site lies between packed pairs of adjacent subunit c.

Role of allosteric: zinc interdomain region of the regulatory subunit in the allosteric regulation of aspartate transcarbamoylase from Escherichia coli

The hydrophobic interface between the allosteric and the zinc domains of the regulatory subunit of aspartate transcarbamoylase has previously been implicated in the heterotropic ATP activation of the enzyme. The present work shows that this interface also affects CTP and CTP-UTP inhibition and proposes a structural explanation for the effects. Mutant enzymes derived from nonselective mutagenesis of residues r101-r106 (residues that contribute part of the interface) displayed a variety of homotropic and heterotropic effects. The cooperative behavior of the enzymes was affected, as indicated by reduced aspartate S0.5 values and apparent Hill coefficient values for V106L, V106L/N105S, and I103F/R102C. In addition, both ATP activation and CTP inhibition were significantly reduced and CTP+UTP synergistic inhibition was decreased in these mutants. The D104G mutant enzyme was subject to inhibition by CTP andCTP+UTP, but was not activated by ATP. Finally, the I103T mutant enzyme had an increased S0.5 value of 11.5 mM and displayed altered effector responses: ATP acted as an inhibitor, and the CTP+UTP synergistic inhibition was reduced. Most of these allosteric variations can be explained in terms of perturbations to the "tongue and groove" hydrophobic interface between the allosteric and the zinc domains and a consequent impact on a second interface ("reg1:cat4") between regulatory and catalytic subunits.

Biotransformation patterns of 2,4,6-trinitrotoluene by aerobic bacteria

2,4,6-Trinitrotoluene (TNT), a toxic nitroaromatic explosive, accumulates in the environment, making necessary the remediation of contaminated areas and unused materials. Although bioremediation has been utilized to detoxify TNT, the metabolic processes involved in the metabolism of TNT have proven to be complex. The three aerobic bacterial strains reported here (Pseudomonas aeruginosa, Bacillus sp. , and Staphylococcus sp.) differ in their ability to biotransform TNT and in their growth characteristics in the presence of TNT. In addition, enzymatic activities have been identified that differ in the reduction of nitro groups, cofactor preferences, and the ability to eliminate-NO2 from the ring. The Bacillus sp. has the most diverse bioremediation potential owing to its growth in the presence of TNT, high level of reductive ability, and capability of removing-NO2 from the nitroaromatic ring.

Enzymatic hydrolysis of Russian-VX by organophosphorus hydrolase

The Russian-VX (R-VX) is the principle V-type nerve agent in the chemical warfare (CW) arsenal of the Former Soviet Union. We here report the enzymatic hydrolysis of the P-S bond of Russian-VX by organophosphorus hydrolase (OPH) from Pseudomonas diminuta. While the Michaelis constant, K(m) for R-VX (474 microM), was similar to that for VX (434 microM), the Vmax for R-VX (2.1 mumoles/mg/min) was about four-fold higher compared to that for VX (0.56 mumoles/mg/min). A 50% inhibition in the rate of the enzymatic hydrolysis of R-VX was observed in the presence of 0.5% ethanol, isoamyl-alcohol, or isopropanol. The presence of acetonitrile, diethylene glycol, or methanol had marginal effects. These results comprise the first demonstration of enzymatic detoxification of R-VX.

NMR structural characterisation of a hairpin DNA with two-base loop: solution conformation of d-GGTACIAGTACC

An inosine-adenosine mismatched base-pair oligonucleotide, d-GGTACIAGTACC has been studied by 1H and 31P NMR spectroscopy. Almost complete 1H and 31P resonance assignments of the oligomer at 0.90 mM concentration and 310 K have been achieved. NMR results demonstrate that the oligomer adopts a hairpin conformation, which has a structure with two purines I6 and A7 forming a two-base loop on a B-DNA stem. Stacking is continued on the 5'-side of the loop, with the I6 stacked upon C5. The base A7, on the 3'-side of the loop stacks partially with I6. All the bases are in anti conformation with respect to their respective sugar moiety.

Nucleotide sequence of a gene encoding an organophosphorus nerve agent degrading enzyme from Alteromonas haloplanktis

Organophosphorus acid anhydrolases (OPAA) catalyzing the hydrolysis of a variety of toxic organophosphorus cholinesterase inhibitors offer potential for decontamination of G-type nerve agents and pesticides. The gene (opa) encoding an OPAA was cloned from the chromosomal DNA of Alteromonas haloplanktis ATCC 23821. The nucleotide sequence of the 1.7 -kb DNA fragment contained the opa gene (1.3 kb) and its flanking region. We report structural and functional similarity of OPAAs from A. haloplanktis and Alteromonas sp JD6.5 with the enzyme prolidase that hydrolyzes dipeptides with a prolyl residue in the carboxyl-terminal position. These results corroborate the earlier conclusion that the OPAA is a type of X-Pro dipeptidase, and that X-Pro could be the native substrate for such an enzyme in Alteromonas cells.

An improved method of plant megabase DNA isolation in agarose microbeads suitable for physical mapping and YAC cloning

The isolation of high quality megabase DNA from plant cells that is susceptible to a variety of molecular reagents is a critical first step in the physical analysis of complex genomes. A method for the isolation of such DNA by encapsulating plant protoplasts in agarose microbeads is presented. In comparison with the conventional agarose plug method, microbeads provide a dramatic increase in the surface area yielding megabase DNA that can be treated essentially as an aqueous DNA solution. Examples of the utility of DNA prepared by this technique for physical mapping, partial restriction enzyme digestion and cloning of large inserts as YACs are presented.

Cloning and nucleotide sequencing of Rhizobium meliloti aminotransferase genes: an aspartate aminotransferase required for symbiotic nitrogen fixation is atypical

In Rhizobium meliloti, an aspartate aminotransferase (AspAT) encoded within a 7.3-kb HindIII fragment was previously shown to be required for symbiotic nitrogen fixation and aspartate catabolism (V. K. Rastogi and R.J. Watson, J. Bacteriol. 173:2879-2887, 1991). A gene coding for an aromatic aminotransferase located within an 11-kb HindIII fragment was found to complement the AspAT deficiency when overexpressed. The genes encoding these two aminotransferases, designated aatA and tatA, respectively, have been localized by subcloning and transposon Tn5 mutagenesis. Sequencing of the tatA gene revealed that it encodes a protein homologous to an Escherichia coli aromatic aminotransferase and most of the known AspAT enzymes. However, sequencing of the aatA gene region revealed two overlapping open reading frames, neither of which encoded an enzyme with homology to the typical AspATs. Polymerase chain reaction was used to selectively generate one of the candidate sequences for subcloning. The cloned fragment complemented the original nitrogen fixation and aspartate catabolism defects and was shown to encode an AspAT with the expected properties. Sequence analysis showed that the aatA protein has homology to AspATs from two thermophilic bacteria and the eukaryotic tyrosine aminotransferases. These aminotransferases form a distinct class in which only 13 amino acids are conserved in comparison with the well-known AspAT family. DNA homologous to the aatA gene was found to be present in Agrobacterium tumefaciens and other rhizobia but not in Klebsiella pneumoniae or E. coli.