Absolute configurations, predominant conformations, and tautomeric structures of enantiomeric tert-butylphenylphosphinothioic acid.

Vibrational absorption and circular dichroism spectra of dextrorotatory, levorotatory, and racemic mixture of tert-butylphenylphosphinothioic acid have been measured in CCl(4) solutions in the 2000-900 cm(-1) region. The conformations for both tautomeric structures of (S)-tert-butylphenylphosphinothioic acid are investigated using the B3LYP functional with the 6-31G* basis set. For the most stable conformation, the absorption and VCD spectra are predicted ab initio using the B3LYP functional with 6-31G*, 6-311G(2d, 2p), 6-31+G, and 6-311G(3df, 3pd) basis sets. A different functional, B3PW91, was also used with the 6-31G* basis set. The predicted spectra are compared to the experimental spectra. The comparison indicates that (-)-tert-butylphenylphosphinothioic acid is of the (S)-configuration and exists in only one tautomeric structure and one conformation in CCl(4) solution.     

Theoretical study on the geometry and vibration of 1-[6-(4-Chlorophenyl)-1-[(6-chloropyridin-3-yl)methyl]-2-[(6-chloropyridin-3-yl)methylsulfanyl]-4-methyl-1,6-dihydropyrimidin-5-yl]ethanone

The solid phase FT-IR and FT-Raman spectra of 1-[6-(4-chlorophenyl)-1-[(6-chloropyridin-3-yl)methyl]-2-[(6-chloropyridin-3-yl)methylsulfanyl]-4-methyl-1,6-dihydropyrimidin-5-yl]ethanone (C25H21Cl3N4OS) were recorded in the region 4000-400 and 3500-100cm(-1), respectively. The vibrational spectra have been computed using density functional theory (B3LYP) and ab initio molecular orbital calculation (HF) with 6-31G(d, p) basis sets. A close agreement was achieved between the observed and calculated frequency by employing normal coordinate calculations. The observed and simulated spectra were found to be well comparable.     

FTIR, FT-Raman spectra and ab initio DFT vibrational analysis of 2,4-dichloro-6-nitrophenol

The FTIR and FT-Raman spectra of 2,4-dichloro-6-nitrophenol (2,4-DC6NP) has been recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of (2,4-DC6NP) were obtained by the ab initio and DFT levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311+G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.     

Theoretical study of absorption and fluorescence spectra of firefly luciferin in aqueous solutions

The absorption and fluorescence spectra of firefly luciferin, which is an analog of oxyluciferin, are investigated by performing the density functional theory (DFT) calculations, especially focusing on the experimentally unassigned peaks. Time-dependent DFT calculations are performed for the excited states of firefly luciferin and its conjugate acids and bases. We find that (1) the peaks in the experimental absorption spectra correspond to the excited states of not only (6'O(-), 4COO(-)) and (6'OH, 4COO(-)), but also (6'OH, 4COOH) and (6'OH, 3H(+), 4COOH); (2) the peaks in the experimental fluorescence spectra correspond to the excited states of not only (6'O(-), 4COO(-)), but also (6'OH, 4COO(-)), (6'O(-), 4COOH), (6'OH, 4COOH) and (6'OH, 3H(+), 4COOH); (3) the unassigned peak near 400 nm in the experimental absorption spectra at pH 1 is assigned to the absorption from the equilibrium ground state to the first excited state of (6'OH, 3H(+), 4COOH); and (4) the unassigned peak at 610 nm in the experimental fluorescence spectra corresponds to the transition from the equilibrium first excited state to the ground state of (6'OH, 4COO(-)).     

Structures and vibrational frequencies of 2-naphthoic acid and 6-bromo-2-naphthoic acid based on density functional theory calculations

The solid phase mid FTIR and FT Raman spectra of 2-naphthoic acid (NA) and 6-bromo-2-naphthoic acid (BNA) have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The fundamental vibrational frequencies and intensities of the vibrational bands were evaluated using density functional theory (DFT) using standard B3LYP method and 6-311+G** basis set combinations. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical force field. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.     

Density functional theory studies on tautomeric stability and infrared and Raman spectra of some purine derivatives

The molecular vibrations of 6-hydroxy-purine (6HP) and 6-amino-purine (6AP) were investigated in polycrystalline sample, at room temperature by Fourier transform infrared (FTIR) and FT-Raman spectroscopy. The spectra of the above compounds have been recorded in the region 4000-50, 3500-100 cm(-1), respectively. They were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on density functional theory (DFT) using HF/6-31G* and B3LYP/6-311+G** methods and basis set combinations. The results of the calculations were applied to simulated infrared and Raman spectra of the title compounds, which showed excellent agreement with the observed spectra. The dipole moment and the tautometric stability of purine derivatives were also studied.     

Nanostructural organization and anion effects in the optical Kerr effect spectra of binary ionic liquid mixtures

This article reports a study of the effect of anions on the optical Kerr effect (OKE) spectra of binary ionic liquid mixtures with one mixture comprising the 3-methyl-1-pentylimidazolium ([C 5mim] (+)) cation and the anions PF 6 (-) and CF 3CO 2 (-) (TFA (-)), and another mixture comprising the [C 5mim] (+) cation and the anions Br (-) and bis(trifluomethanesulfonyl)imide (NTf 2 (-)). The spectra were obtained by the use of optical heterodyne-detected Raman-induced Kerr Effect Spectroscopy at 295 K. The OKE spectra of the mixtures are compared with the calculated mole-fraction weighted sum of the normalized OKE spectra of the neat liquids. The OKE spectra are nearly additive for [C 5mim]Br/[C 5mim][NTf 2] mixtures, but nonadditive for [C 5mim][PF 6]/[C 5mim][TFA] mixtures. In the case of the equimolar [C 5mim][PF 6]/[C 5mim][TFA] mixture, the nonadditivity is such that the experimental OKE spectrum is narrower than the calculated OKE spectrum. The additivity or nonadditivity of OKE spectra for IL mixtures can be explained by assuming ionic liquids are nanostructurally organized into nonpolar regions and ionic networks. The ionic networks in mixtures will be characterized by "random co-networks" for anions that are nearly the same in size (PF 6 (-) and TFA (-)) and by "block co-networks" for anions that differ greatly in size (Br (-) and NTf 2 (-)).     

FT-Raman and FT-IR spectra, ab initio and density functional studies of 2-amino-4,5-difluorobenzoic acid

The Fourier transform Raman and Fourier transform infrared spectra of 2-amino-4,5-difluorobenzoic acid (2A45DFBA) were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, depolarization ratios were calculated by HF and density functional B3LYP method with the 6-31+G(d, p) and 6-311+G(d, p) basis sets. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-31+G(d, p)/6-311+G(d, p) and B3LYP/6-31+G(d, p)/6-311+G(d, p) levels of theory. A detailed interpretations of the infrared and Raman spectra of 2-amino-4,5-difluorobenzoic acid is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.     

Structures and vibrational frequencies of 2-hydroxy-3-methoxy-5-nitrobenzaldehyde and 2-methoxy-1-naphthaldehyde based on density functional theory calculations

FT-IR and FT-Raman spectra of 2-hydroxy-3-methoxy-5-nitrobenzaldehyde (HMN) and 2-methoxy-1-naphthaldehyde (MN) have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The molecular structure, conformational stability, geometry optimization, vibrational frequencies have been investigated. The total energy calculations of HMN and MN were tried for various possible conformers. The spectra were interpreted with the aid of normal coordinate analysis based on density functional theory (DFT) using B3LYP/6-31G* and B3LYP/6-311+G** level and basis set combinations and was scaled using various scale factors yielding good agreement between observed and calculated frequencies. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.     

Scaled quantum chemical calculations and FT-IR, FT-Raman spectral analysis of 2-methyl piperazine

The vibrational spectra of 2-methyl piperazine (2MPZ) have been computed using B3LYP methodology and 6-31G* and 6-31G** basis sets. The solid phase FT-IR and FT-Raman spectra were recorded in the region 4000-400 and 3500-100 cm(-1), respectively. A close agreement was achieved between the observed and calculated frequencies by employing normal coordinate calculations. The observed and simulated spectra were found to be well comparable.     

Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 3-aminobenzotrifluoride

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of 3-aminobenzotrifluoride. The FT-Raman and Fourier transform infrared spectra of 3-aminobenzotrifluoride (3ABTF) were recorded in the liquid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, depolarization ratios, reduced masses were calculated by HF and density functional B3LYP method with the 6-31G(d,p) and 6-311G(d,p) basis sets. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-31G(d,p)/6-311G(d,p) and B3LYP/6-31G(d,p)/6-311G(d,p) levels of theory. A detailed interpretations of the infrared and Raman spectra of 3ABTF is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.     

Spectroscopic analysis of small organic molecules: a comprehensive near-edge x-ray-absorption fine-structure study of C6-ring-containing molecules

We report high-resolution C 1s near-edge x-ray-absorption fine-structure (NEXAFS) spectra of the C6-ring-containing molecules benzene (C6H6), 1,3- and 1,4-cyclohexadiene (C6H8), cyclohexene (C6H10), cyclohexane (C6H12), styrene (C8H8), and ethylbenzene (C8H10) which allow us to examine the gradual development of delocalization of the corresponding pi electron systems. Due to the high experimental resolution, vibrational progressions can be partly resolved in the spectra. The experimental spectra are compared with theoretical NEXAFS spectra obtained from density-functional theory calculations where electronic final-state relaxation is accounted for. The comparison yields very good agreement between theoretical spectra and experimental results. In all cases, the spectra can be described by excitations to pi*- and sigma*-type final-state orbitals with valence character, while final-state orbitals of Rydberg character make only minor contributions. The lowest C 1s-->1pi* excitation energy is found to agree in the (experimental and theoretical) spectra of all molecules except for 1,3-cyclohexadiene (C6H8) where an energy smaller by about 0.6 eV is obtained. The theoretical analysis can explain this result by different binding properties of this molecule compared to the others.     

Vibrational spectra and potential energy distributions for 4,5-dichloro-3-hydroxypyridazine by density functional theory and normal coordinate calculations

The solid phase FT-IR and FT-Raman spectra of 4,5-dichloro-3-hydroxypyridazine have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The spectra were interpreted with the aid of normal coordinate analysis following a full structure optimization and force field calculations based on the density functional theory (DFT) using the standard B3LYP/6-31G* and B3LYP/6-311+G** method and basis set combinations. The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. The IR and Raman spectra were predicted theoretically and compared with the experimental spectra.     

Structural assignment of disialylated biantennary N-glycan isomers derivatized with 2-aminopyridine using negative-ion multistage tandem mass spectral matching

To investigate the possibility of structural assignment based on negative-ion multistage tandem mass (MS(n)) spectral matching, four isomers of disialylated biantennary N-glycans (alpha2-6 and/or alpha2-3 linked sialic acid on alpha1-6 and alpha1-3 antennae) derivatized with 2-aminopyridine (PA) were analyzed by employing high-performance liquid chromatography/electrospray ionization linear ion trap time-of-flight mass spectrometry (HPLC/ESI-LIT-TOFMS), which uses helium gas for ion trapping and collision-induced dissociation (CID). It is shown that the MS(2) spectra derived from each precursor ion [M-2H](2-) are reproducible and useful for distinguishing the four isomers. Thus, they can be assigned by negative-ion MS(2) spectral matching based on correlation coefficients. In addition, MS(3) spectra derived from D-type fragment ions clearly differentiate the alpha2-3- or alpha2-6-linked sialic acid on the alpha1-6 antenna due to their characteristic spectral patterns. The C(4)-type fragment ions, which are produced from both the alpha1-6 and alpha1-3 antennae, show the characteristic MS(3) spectra reflecting alpha2-3- or alpha2-6- linkage type or a mixture of both types. Thus, the differentiation and assignment of these disialylated biantennary N-glycan isomers can also be supported with the MS(3) spectra of C(4)- and D-type ions.     

Molecular structure and vibrational spectra of 3-chloro-4-fluoro benzonitrile by ab initio HF and density functional method

In this work, the experimental and theoretical spectra of 3-chloro-4-fluoro benzonitrile (3C4FBN) were studied. The Fourier transform infrared and Fourier transform Raman spectra of 3C4FBN were recorded in the solid phase. The optimized geometry was calculated by HF and B3LYP methods with 6-311++G(d,p) basis set. The harmonic-vibrational frequencies, infrared intensities and Raman scattering activities of the title compound were performed at and HF/B3LYP/6-311++G(d,p) level of theories. The scaled theoretical wave number showed very good agreement with the experimental values. The thermodynamic functions of the title compound was also performed at HF/6-31G(d,p) and B3LYP/6-311++G(d,p) level of theories. A detailed interpretation of the infrared and Raman spectra of 3C4FBN was reported. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.     

Vibrational spectra and ab initio analysis of tert-butyl,trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene III. 3,3-Dimethyl-1-(trimethylsilyl)cyclopropene

The experimental Raman and IR vibrational spectra of 3,3-dimethyl-1-(trimethylsilyl)cyclopropene in the liquid phase were recorded. Total geometry optimisation was carried out at the HF/6-31G* level and the HF/6-31G*//HF/6-31G* force field was computed. This force field was corrected by scale factors determined previously (using Pulay's method) for correction of the HF/6-31G*//HF/6-31G* force fields of 3,3-dimethylbutene-1, 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The theoretical vibrational frequencies calculated from the scaled quantum mechanical force field and the theoretical intensities obtained from the quantum mechanical calculation were used to construct predicted spectra and to perform the vibrational analysis of the experimental spectra.     

Comparison of experimental and ab initio HF and DFT vibrational spectra of benzimidazole

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of benzimidazole. The laser Raman and Fourier transform infrared spectra of benzimidazole were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities, Raman scattering activities, depolarization ratios and reduced masses were calculated by HF and density functional B3LYP method with the 6-311G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-31G(d,p)/6-311G(d,p) and B3LYP/6-31G(d,p)/6-311G(d,p) levels of theory. A detailed interpretations of the infrared and Raman spectra of benzimidazole is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.     

Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 2-amino-5-methylphenol

The laser Raman and Fourier transform infrared spectra of 2-amino-5-methylphenol were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities, Raman scattering activities, depolarization ratios and reduced masses were calculated by HF and density functional B3LYP methods by using 6-311+G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-31G(d,p)/6-311+G(d,p) and B3LYP/6-31G(d,p)/6-311+G(d,p) levels of theory. A detailed interpretations of the infrared and Raman spectra of 2-amino-5-methylphenol is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.