Vibrational analysis of free and hydrogen bonded complexes of nicotinamide and picolinamide

Harmonic and anharmonic vibrations of free nicotinamide (NIA) and picolinamide (PIA) molecules together with their hydrogen bonded complexes H₂O–NIA and H₂O–PIA have been studied by means of density functional method. The calculation results of the vibrational spectra of free molecules have been investigated and are compared to the available experimental spectra. The vibrational wavenumbers of both molecules have also been calculated by polarizable continuum model (PCM) that represents the solvent as a polarizable continuum and places the solute in a cavity within the solvent (water is chosen as the solvent in this study). The results of PCM calculations and the H₂O–NIA, H₂O–PIA complexes, are used to investigate the H-bonding interactions of both molecules with the water molecule. The harmonic wavenumbers have been scaled by proper factors obtained by comparing the observed versus calculated wavenumbers and it is shown that anharmonic corrections on the vibrational spectra provided a better agreement between the observed and calculated wavenumbers compared to the results obtained by scaling factor method.     

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.     

Vibrational spectra and assignments of 5-amino-2-chlorobenzoic acid by ab initio Hartree-Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra of 5-amino-2-chlorobenzoic acid (5A2CBA) were recorded in the solid phase. Geometry opitimizations were done without any constraint and harmonic-vibrational wavenumber and several thermodynamic parameters were calculated for the minimum energy conformer at ab initio and DFT levels invoking 6-311G(d,p) basis set and the results are compared with the experimental values with the help of three specific scaling procedures, the observed vibrational wavenumbers in FTIR and FT-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range, the error obtained was in general very low. The appropriate theoretical spectrograms for the FTIR spectra of the title molecule were also constructed.     

IR and Raman spectra,density functional computations of vibrational spectrum,molecular geometry,atomic charges,and some molecular properties of 3‐aminobenzonitrile molecule

Geometry, vibrational wavenumbers, and several thermodynamic parameters have been calculated using ab initio quantum chemical methods for the 3‐aminobenzonitrile molecule for the first time. The results were compared with experimental values. With the help of specific scaling procedures, the observed vibrational wavenumbers were analyzed and assigned to different normal modes of the molecule. In general, the error obtained was very low. Using potential energy distribution (PED), the contributions of the different modes to each wavenumber were determined. Other general conclusions were also deduced. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

FT-Raman and FTIR spectra, assignments and ab initio calculations of 2-aminobenzyl alcohol

The Fourier transform Raman and Fourier transform infrared spectra of 2-aminobenzyl alcohol (2ABA) were recorded in the solid phase. Geometry optimizations were done with out any constraint and harmonic vibrational wave numbers and several thermodynamic parameters were calculated for the minimum energy conformer at ab initio and DFT levels invoking 6-31g** and 6-311+g(2d, p) basis sets and the results were compared with the experimental values. With the help of three specific scaling procedures, the observed vibrational wavenumbers in FTIR and FT-Raman spectra 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. The appropriate theoretical spectrograms for the Raman and IR spectra of 2ABA were also constructed.     

FTIR and FT Raman, molecular geometry, vibrational assignments, ab initio and density functional theory calculations for 1,5-methylnaphthalene

The FTIR and FT Raman vibrational spectra of 1,5-methylnaphthalene (1,5-MN) have been recorded using Brunker IFS 66 V Spectrometer in the range 3600-10 cm(-1) in the solid phase. A detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The Optimized molecular geometry, harmonic frequencies, electronic polarizability, atomic charges, dipole moment, rotational constants and several thermodynamic parameters in the ground state were calculated using ab initio Hartree Fock (HF) and density functional B3LYP methods (DFT) with 6-311++ G(d) basis set. With the help of different scaling factors, the observed vibrational wavenumbers in FTIR and FT Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range. The results of the calculations were applied to simulated infrared and Raman spectra of the title compound which showed excellent agreement with the observed spectra.     

FT-IR, NIR-FT-Raman and gas phase infrared spectra of 3-aminoacetophenone by density functional theory and ab initio Hartree-Fock calculations

The gas phase infrared spectrum of 3-aminoacetophenone (3AAP) was measured in the range 5000-500cm(-1) and with a resolution of 0.5cm(-1). The Fourier transform Raman (FT-Raman) and Fourier transform infrared (FT-IR) spectra of 3AAP were recorded in the solid phase. Geometry optimizations were done without any constraint and several thermodynamic parameters were calculated for the minimum energy conformer at ab initio and density functional theory (DFT) levels invoking 6-311G(2df 2p) basis set and the results are compared with the experimental values. Harmonic-vibrational wavenumber was also calculated for the minimum energy conformer at ab initio and DFT levels using 6-31G(d,p) basis set and the results are compared with related molecules. With the help of specific scaling procedures, the observed vibrational wavenumbers in gas phase, FT-IR and FT-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range, the error obtained was in general very low. The appropriate theoretical spectrogram for the FT-IR spectra of the title molecule is also constructed.     

Vibrational assignments and theoretical calculations of 1-phenyl-5-mercaptotetrazole and 1-phenyl-5-mercaptotetrazolate

The infrared and Raman spectra of 1-phenyl-5-mercaptotetrazole (PMT) and 1-phenyl-5-mercaptotetrazole sodium salt in the solid state and in solution have been measured. Detailed vibrational assignments of PMT and 1-phenyl-5-mercaptotetrazolate (PMTA) have been performed. In order to give a firmer basis to the interpretation of the vibrational spectra, harmonic wavenumbers of PMT and PMTA have been calculated by means of MP2 and DFT/BPW91 calculations. The DFT calculations provide a satisfactory agreement between the calculated and observed wavenumbers without using scaling factors. Experimental evidence shows that PMT is present in the thione tautomer both in the solid state and in solution of polar solvents.     

Vibrational assignment, <Emphasis Type="Italic">ab initio</Emphasis> calculation and normal coordinate analysis of 2,2′-biquinoline

The vibrational wavenumbers and the fundamental modes of 2,2′-biquinoline were obtained by density functional theory (DFT) with the B3LYP functional using the 6-31G(d,p) basis set. The calculated wavenumbers were scaled by a single factor of 0.965 to correct them for vibrational anharmonicity, but the force constants were overestimated. Normal coordinate analysis of the molecule was also carried out by using the force field of the quinoline molecule and the force field parameters of quinoline are shown to be transferable to 2,2′-biquinoline. The potential energy distribution associated with the normal modes is also given. The theoretical wavenumbers are found to be in good agreement with the experimental data.     

Vibrational markers of structural distortion in adenine nucleobases upon DNA damage

Oxidation is one of the common causes of chemical damage of DNA. Among the oxidized nucleobases in DNA, 8-oxoadenine (8-oxoA) and 4,6-diamino-5-formamidoadenine (FaPyA) are two of the most commonly found lesions. Relatively little information has been published so far on these lesions compared to the more mutagenic modified purines like 8-oxoguanine. In this study, we investigate the structure and vibrational spectra of these two lesions using Density Functional Theory relative to the parent compound adenine. In addition, we have incorporated a solvent environment through the Polarizable Continuum Model (PCM), as well as explicit solvent model calculations to test for the best prediction of the vibrational wavenumbers of adenine. We find that, while the explicit solvent model predicts the structure of the lesions better with respect to published X-ray diffraction structures, they do not reproduce the vibrational wavenumbers as accurately. In comparison, PCM predicts the wavenumbers better with less of the typical overestimation seen in the absence of solvent effects. Intriguingly, uniform linear scaling of the 'gas phase' calculations provides the best agreement with published experimental spectra. Finally, we demonstrate that 8-oxoA and FaPyA have unique spectral features compared to adenine by characterizing the differences in their normal modes. We propose the use of their distinct spectra as site-specific Raman probes of systems such as base-specific local probing of a DNA strand and DNA-enzyme active site interactions where the substrate can be used as an in situ probe.     

Vibrational spectra and quantum chemical calculations of 3,4-diaminobenzoic acid.

The Fourier Transform Raman and Fourier Transform infrared spectra of 3,4-diaminobenzoic acid (3,4-DABA) were recorded in the solid phase. Geometry optimizations were done without any constraint and harmonic-vibrational wave numbers and several thermodynamic parameters were calculated for the minimum energy conformer at ab initio and DFT levels invoking 6-311++G(d,p) basis set. The results were compared with the experimental values with the help of specific scaling procedures, the observed vibrational wavenumbers in FT-IR and FT-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range, the error obtained was in general very low. The appropriate theoretical spectrograms for the IR and Raman spectra of the title molecule were also constructed.     

Classification of commercial apple beverages using a minimum set of mid-IR wavenumbers selected by Procrustes rotation

When infrared spectral data are used in classification and/or multivariate regression methods there can be problems related to both chemical understanding and computation speed due to the large number of wavenumbers in each spectrum. Here, it is shown that the Procrustes rotation technique can be used to select a minimum set of spectral variables (wavenumbers) to perform classification and regression. Procrustes rotation was coupled to several multivariate methods as PLS, SIMCA and potential curves (a maximum likelihood classification method). The practical problem of implementing a screening methodology for classifying apple juice-based beverages according to their contents of "pure" apple juice was addressed using attenuated total reflectance, mid-IR spectroscopy. It is found that two of the original wavenumbers are almost as good predictors as all the 176 initial ones.     

Scaling behavior of adsorption on patchwise bivariate surfaces revisited

The adsorption of gases on patchwise heterogeneous bivariate surfaces is studied. These surfaces are characterized by a collection of strong and weak adsorbing patches with a typical length scale l. Different forms and spatial arrangements of these patches determine different topographies characterized by an effective length, l(eff) = sigmal, where sigma takes values from 1 to 4 for the different topographies considered here. Previous studies showed that the mean square deviation between isotherms corresponding to different values of l(eff) scaled as a power law with exponent alpha, without providing any physical interpretation of such behavior. In the present work, we introduce a different scaling function, chi(l), which is shown to be twice the difference in free energy per site between a reference isotherm and the given isotherm, at half coverage. With this function the scaling behavior and the value of the scaling exponent alpha are determined over the whole range of interparticles interaction energy and adsorptive energy, and for different temperatures, through Monte Carlo simulations. The results are similar to those obtained in previous studies, with a value of alpha which is half the one obtained before due to the different definition of the scaling function, but the present analysis provides a full understanding of the scaling behavior based on the physical significance of the scaling function and the scaling exponent.     

The harmonic force fields of dimethyl zinc,cadmium and mercury: A joint theoretical and experimental study

The harmonic force fields of the title compounds have been calculated at the ab initio SCF level using effective core potentials and polarized double-zeta basis sets. After scaling, the theoretical wavenumbers are in good agreement with experiment both for the parent compounds and the perdeuterated isotopomers, and the ¹²C→¹³C shifts are well reproduced. Constraining all but three off-diagonal force constants to their ab initio values in a least squares refinement, semi-empirical harmonic force fields have been derived which account well for all available experimental data. The CH stretching motions are analyzed in terms of an harmonic local mode approach.     

Comparative vibrational spectroscopic study of 1,3-diacetylbenzene and 2,6-diacetylpyridine aided with density functional calculation

Comparative studies of the Raman and infrared spectra of 1,3-diacetylbenzene and 2,6-diacetylpyridine have been made. The spectra are interpreted with the aid of normal mode analysis following full structure optimization based on the density functional method using different levels of theories and various basis sets combination. The unscaled DFT LSDA frequencies approximate the experimental ones in much more uniform fashion than B3LYP or B3PW91 theories do. Nevertheless the use of overall scale factor leads to further significant improvement with less than 2% error. The scaled B3PW91 6-31G result is best, even though LSDA 6-311G frequencies are superior to the B3PW91 ones before scaling. While making complete assignments of vibrational wavenumbers on the basis of potential energy distribution, some interesting observation in the vibrational spectra of these two molecules have been noticed. Instances of Fermi resonances between fundamentals and some combination modes of vibration have also been ascertained. Following the quantum chemical calculation optimized geometries of the both molecules are predicted. The theoretical global minimum energy calculation helps to find the structural symmetries of the molecules.     

Density functional theory study of the fourier transform infrared and Raman spectra of dichloro-bis(2,4-pentanedionate)tin(IV).

Fourier transform infrared and Fourier transform Raman spectra of dichloro-bis(2,4-pentanedionate)tin(IV) have been obtained. Density functional theory (DFT) BLYP calculations, have been carried out with the purpose of understanding the metal-ligand region spectra of this compound. Vibrational wavenumbers calculated by BLYP/6-31G* force fields are closed with the experimental results. The percentage of deviation of the bond lengths and bond angles gives a good picture of the normal modes, and serves as a basis for the assignment of the wavenumbers. The calculated geometrical parameters show slight differences compared with the experimental ones, and these differences can be explained by the different physical state of Sn(acac)2Cl2. The DFT-BLYP calculations assumed a free molecule in the gas phase. The experimental wavenumbers are obtained from the spectra of solid samples.     

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

FT-IR and FT-Raman spectra of the biomolecule 5-aminouracil were recorded in the regions 400–4000 cm⁻¹ and 10–3500 cm⁻¹, respectively. The observed vibrational wavenumbers were analyzed and assigned to different normal modes of vibration of the molecule. Density functional calculations were performed to support wavenumber assignments of the observed bands. A comparison with the molecule of uracil was made, and specific scale factors were employed in the predicted wavenumbers of 5-aminouracil. With the purpose of study the important molecule 5-aminouracil, its equilibrium geometry and harmonic wavenumbers were calculated for the first time by the B3LYP DFT method. The vibrational wavenumbers were compared with IR and Raman experimental data. Also good reproduction of the experimental wavenumbers is obtained and the % error is very small. All the tautomeric forms of 5-aminouracil were determined and optimized. The dimer forms were also simulated. The energy, atomic charges and dipole moments were discussed and several general conclusions were underlined.     

Solvent dependence of absorption intensities and wavenumbers of the fundamental and first overtone of NH stretching vibration of pyrrole studied by near-infrared/infrared spectroscopy and DFT calculations

Near-infrared (NIR) and IR spectra were measured for pyrrole in CCl(4), CHCl(3), and CH(2)Cl(2) to study solvent dependence of absorption intensities and wavenumbers of the fundamental and first overtone of NH stretching vibration. It was found that the wavenumbers of the NH fundamental and its first overtone decrease in the order of CCl(4), CHCl(3), and CH(2)Cl(2), which is the increasing order for of the dielectric constant of the solvents. Their absorption intensities increase in the same order, and the intensity increase is more significant for the fundamental than the overtone. These results for the solvent dependence of the wavenumbers and absorption intensities of NH stretching bands of pyrrole are quite different from those due to the formation of hydrogen bonds. Quantum chemical calculations of the wavenumbers and absorption intensities of NH stretching bands by using the 1D Schr?dinger equation based on the self-consistent reaction field (SCRF)/isodensity surface polarized continuum model (IPCM) suggest that the decreases in the wavenumbers of both the fundamental and the overtone of the NH stretching mode with the increase in the dielectric constant of the solvents arise from the anharmonicity of vibrational potential and their intensity increases come from the gradual increase in the slope of the dipole moment function.     

Density functional theory and ab initio studies of geometry, electronic structure and vibrational spectra of novel benzothiazole and benzotriazole herbicides

The ground-state geometries, electronic structures and vibrational wavenumbers of S-1,3-benzothiazolyl-4-bromobenzenecarbothioate and S-(5,7-dimethyl-3H-4lambda-5-[1,2,4]triazolo[1,5-a]pyridinyl)4-chlorobenzenecarbothioate were studied by DFT-B3LYP, BLYP and ab initio RHF method with different basis sets. The comparison was performed for optimized geometries, thermodynamic parameters and electronic structures at different levels of theory. Because of the larger repulsion effect in triazole ring, the vibrational wavenumbers of skeleton vibration of triazole ring are significantly lower than that of thiazole ring.     

Comments on the assignment of the out-of-plane vibrations of the trans-buta-1,3-diene molecule

An assignment of the out-of-plane vibrations of the trans-buta-1,3-diene molecule was performed by analysis of the isotopic shifts of wavenumbers in the methylene moieties =CHX, where X = H, D or T. A suggestion for the mutual reassignment of the wavenumbers belonging to the twisting vibration of the methylene moiety =CH₂ and the out-of-plane vibration of the methine moiety =CH— was shown to be incorrect.