Ab initio studies of the structure and vibrational spectra of methyl isocyanide-borane and acetonitrile-borane

The SCF/DZP and MP2/DZP methods of ab initio quantum chemistry have been utilized to study the structure, vibrational spectra, binding energy, and barrier to internal rotation of methyl isocyanide-borane and acetonitrile-borane adducts. The eclipsed conformation of the complexes was predicted to be a minimum, and the staggered form is a transition state with a barrier height of about 10 cal/mol. The vibrational analyses of CH3NC-BH3 and CH3CN-BH3 and several of their isotopomers have been carried out by the GF matrix method. Computations have also been carried out for free CH3NC and CH3CN in order to investigate the changes in CH3NC and CH3CN as a result of their complex formation with BH3. To obtain an acceptable set of force constants, a recently proposed procedure ''RECOVES'' has been utilized. The increase in the N=C/C=N stretching force constant of CH3NC/CH3CN on adduct formation is interpreted with the help of Parr and Borkman's model. The binding energies for the two adducts have been determined taking basis set superposition error (BSSE) into consideration. The effect of the BSSE on structure, dipole moment, and vibrational frequencies of CH3CN and CH3NC is also evaluated. The predicted infrared band intensities for the two complexes are in good agreement with the experimentally observed features, and they have been utilized in the assignment of vibrational frequencies.

An investigation of the first-order spin-state transition in Fe(Phen)(2)(NCS)(2) EXAFS and infrared spectroscopy

The structure of Fe(Phen)(2)(NCS)(2) has been examined across the first-order spin-state transition by EXAFS with full multiple scattering analysis. The EXAFS data at 298 K can be satisfactorily assigned to the high-spin state, but the analysis of the low-temperature data at 90 K is not entirely unequivocal, although consistent with the predominant presence of the low-spin state. That some proportion of the high-spin state remains at low temperatures, well below the first-order transition, is clearly evidenced in the infrared spectra, suggesting possible sublattice ordering.

SCF and electron correlation studies on structure, force constants and vibrational spectra of borane monoammoniate complex

Effects of basis set and electron correlation on the equilibrium geometry, force constants and vibrational spectra of BH3NH3 have been studied. A series of basis sets ranging from double zeta to triple zeta including polarization and diffuse functions have been utilized. All the SCF based calculations overestimate the dative B-N bond distance and considerable improvement occurs when the treatment for electron correlation is introduced. Detailed vibrational analysis for BH3NH3 has been carried out. The mean absolute percentage deviation of the ab initio predicted vibration frequencies of (BH3NH3)-B-11 from the experiment is about 10% for the SCF based calculations and the MP2 method shows better agreement, the overall deviation being 5-6%. The ground state effective force constants of BH3NH3 were obtained using RECOVES procedure. The RECOVES sets of force constants are found to be highly satisfactory for the prediction of the vibrational frequencies of different isotopomers of BH3NH3. The mean absolute percentage deviation of the calculated frequencies of different isotopomers from the experiment is much less than 1%. The RECOVES-MP2/augDZP set of force constants was found to be the best set among the different sets for this molecule. Theoretical infrared intensities are in fair agreement with the observed spectral features.

Ab initio studies of solvent effect on conformational equilibria and vibrational spectra of dipropionamide

Systematic ab initio molecular orbital studies of the conformational equilibria and vibrational spectra of dipropionamide using the basis sets 6-31g(d) and 6-31++G(d,p) have been carried out. The vibrational spectra of dipropionamide have been satisfactorily interpreted taking into account the agreement between the calculated frequencies, infrared and Raman band intensities and the shifts in the spectra of deuterated molecules with those observed. The previous assignments of most of the vibrational bands are well confirmed, a few bands need reassignment, however. The solvent effects were investigated by self-consistent reaction field theory using dipole and self-consistent isodensity polarized continuum model methods. The introduction of a dielectric medium has only a marginal effect on the conformational equilibria and vibrational spectra. However, the calculated changes in geometry and vibrational spectra on going from the gas phase to the solution phase are in accord with the increasing weight of the dipolar resonance structure in polar solvents. (C) 2002 Elsevier Science B.V. All rights reserved.

An infrared spectroscopic study of the low-spin to intermediate-spin state (1A1–3T1) transition in rare earth cobaltates, LnCoO3 (Ln=La, Pr and Nd)

Low-spin (LS) to intermediate-spin (IS) state transitions in crystals of LnCoO3 (Ln=La, Pr and Nd) have been investigated by variable temperature infrared spectroscopy. The spectra reveal the occurrence of the transition around 120, 220 and 275 K, respectively, in LaCoO3,PrCoO3 and NdCoO3, at which temperatures the intensities of the stretching and the bending modes associated with the LS state decrease, accompanied by an increase in the intensities of the bands due to IS state. The characteristic frequencies of both the spin states decrease with increase in temperature, showing anomalies around the transition.

An infrared spectroscopic study of the low-spin to intermediate-spin state ((1)A(1)-T-3(1)) transition in rare earth cobaltates, LnCoO(3) (Ln = La, Pr and Nd)

Low-spin (LS) to intermediate-spin (IS) state transitions in crystals of LnCoO(3) (Ln = La, Pr and Nd) have been investigated by variable temperature infrared spectroscopy. The spectra reveal the occurrence of the transition around 120, 220 and 275 K, respectively, in LaCoO3,PrCoo(3) and NdCoO3, at which temperatures the intensities of the stretching and the bending modes associated with the LS state decrease, accompanied by an increase in the intensities of the bands due to IS state. The characteristic frequencies of both the spin states decrease with increase in temperature, showing anomalies around the transition. (C) 2001 Published by Elsevier Science B.V.

Infrared studies of the phase transitions of alkylammonium halides, RNH3X, and bis-(alkylammonium) tetrahalogenometallates(II), (RNH3)2MX4, (R = alkyl, M = metal, X = Cl or Br)

Internal vibration modes of bis-(alkylammonium) tetrachlorometallates(II) and the corresponding alkylammonium chlorides have been studied through their phase transitions using infrared spectroscopy. The studies show that the vibrational states of alkylammonium ions change markedly through the phase transitions. Spectra of the analogous tetrabromometallates and alkylammonium bromides also confirm this behaviour. There is appreciable motion of the alkylammonium ions in the high-temperature phases; thus, CH3NH+3 ions are essentially undistorted in these phases. The low-temperature, ordered phases show evidence of stronger hydrogen bonding of the cations and for the presence of C—N torsional modes.

Combined Raman and infrared investigation of the insulator-to-metal transition in NiS(2-x)Se(x) compounds

Ambient-condition Raman spectra were collected in the strongly correlated NiS(1-x)Se(x) pyrite (0 <= x <= 1.2). Two samples (x = 0 and x = 0.55) were studied as a function of pressure up to 10 GPa, and for the x = 0.55 sample the pressure dependence of the infrared reflectivity was also measured (0-10 GPa). This gave a complete picture of the optical response of that system on approaching the metallic state both by application of pressure and/or by Se alloying, which corresponds to a volume expansion. A peculiar nonmonotonic (V-shaped) volume dependence was found for the quasiparticle spectral weight of both pure and Se-doped compounds. In the x = 0.55 sample the vibrational frequencies of the chalcogen dimer show an anomalous volume dependence on entering the metallic phase. The abrupt softening observed, particularly significant for the Se-Se pair, indicates the relevant role of the softness of the Se-Se bond as previously suggested by theoretical calculations.

Study on the structure and vibrational spectra of efavirenz conformers using DFT: Comparison to experimental data

Efavirenz, (S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3 ,1-benzoxazin-2-one, is an anti HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. A systematic quantum chemical study of the possible conformations, their relative stabilities and vibrational spectra of efavirenz has been reported. Structural and spectral characteristics of efavirenz have been studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for potential energy curve, optimized geometries and vibrational spectra have been carried out using 6-311++G(d,p) basis sets and B3LYP functionals. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of efavirenz. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The infrared and the Raman spectra of the molecule based on OFT calculations show reasonable agreement with the experimental results. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. (C) 2011 Elsevier B.V. All rights reserved.

Isomeric identification of methylated naphthalenes using gas phase infrared spectroscopy

We report gas phase mid-infrared spectra of 1- and 2- methyl naphthalenes at 0.2 cm(-1) resolution. Assignment of observed bands have been made using scaled quantum mechanical (SQM) calculations where the force fields rather the frequencies are scaled to find a close fit between observed and calculated bands. The structure of the molecules has been optimized using B3LYP level of theory in conjunction with standard 6-311G** basis set to obtain the harmonic frequencies. Using the force constants in Cartesian coordinates from the Gaussian output, scaled force field calculations are carried out using a modified version of the UMAT program in the QCPE package. Potential energy distributions of the normal modes obtained from such calculations helped us assign the observed bands and identify the unique features of the spectra of 1- and 2-MNs which are important for their isomeric identification.

Study of molecular structure and vibrational spectra of poly (beta,-1-malic acid) PMLA] using DFT approach

Poly (beta-L-malic acid) (PMLA) is a biodegradable polymer and it has various important applications in the biomedical field. In the present work the structural and spectral characteristics of PMLA have been studied by methods of infrared. Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) using oligomeric approach employing B3LYP with complete relaxation in the potential energy surface using 6-311++G (d, p) basis set. Based on results, we have discussed the correlation between the vibrational modes and the structure of the PMLA. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The calculated infrared and the Raman spectra of the polymer based on DFT calculations show reasonable agreement with the experimental results. (c) 2012 Elsevier Ltd. All rights reserved.

Identification of Early Biomarkers during Acetaminophen-Induced Hepatotoxicity by Fourier Transform Infrared Microspectroscopy

Acetaminophen is a widely prescribed drug used to relieve pain and fever; however, it is a leading cause of drug-induced liver injury and a burden on public healthcare. In this study, hepatotoxicity in mice post oral dosing of acetaminophen was investigated using liver and sera samples with Fourier Transform Infrared microspectroscopy. The infrared spectra of acetaminophen treated livers in BALB/ mice show decrease in glycogen, increase in amounts of cholesteryl esters and DNA respectively. Rescue experiments using L-methionine demonstrate that depletion in glycogen and increase in DNA are abrogated with pre-treatment, but not post-treatment, with L-methionine. This indicates that changes in glycogen and DNA are more sensitive to the rapid depletion of glutathione. Importantly, analysis of sera identified lowering of glycogen and increase in DNA and chlolesteryl esters earlier than increase in alanine aminotransferase, which is routinely used to diagnose liver damage. In addition, these changes are also observed in C57BL/6 and Nos2(-/-) mice. There is no difference in the kinetics of expression of these three molecules in both strains of mice, the extent of damage is similar and corroborated with ALT and histological analysis. Quantification of cytokines in sera showed increase upon APAP treatment. Although the levels of Tnf alpha and Ifn gamma in sera are not significantly affected, Nos2(-/-) mice display lower Il6 but higher Il10 levels during this acute model of hepatotoxicity. Overall, this study reinforces the growing potential of Fourier Transform Infrared microspectroscopy as a fast, highly sensitive and label-free technique for non-invasive diagnosis of liver damage. The combination of Fourier Transform Infrared microspectroscopy and cytokine analysis is a powerful tool to identify multiple biomarkers, understand differential host responses and evaluate therapeutic regimens during liver damage and, possibly, other diseases.

Microwave, infrared-microwave double resonance, and theoretical studies of C2H4 center dot center dot center dot H2S complex

In this manuscript, rotational spectra of four new isotopologues of the S-H center dot center dot center dot pi bonded C2H4 center dot center dot center dot H2S complex, i.e., C2D4 center dot center dot center dot H2S, C2D4 center dot center dot center dot D2S, C2D4 center dot center dot center dot HDS, and (CCH4)-C-13 center dot center dot center dot H2S have been reported and analyzed. All isotopologues except C2D4 center dot center dot center dot HDS show a four line pattern whereas a doubling of the transition frequencies was observed for C2D4 center dot center dot center dot HDS. These results together with our previous report on the title complex M. Goswami, P. K. Mandal, D. J. Ramdass, and E. Arunan, Chem. Phys. Lett. 393(1-3), 22-27 (2004)] confirm that both subunits (C2H4 and H2S) are involved in large amplitude motions leading to a splitting of each rotational transition to a quartet. Further, the results also confirm that the motions which are responsible for the observed splittings involve both monomers. Molecular symmetry group analysis, considering the interchange of equivalent H atoms in H2S and C2H4 could explain the observed four line pattern and their intensities in the microwave spectrum. In addition, hydride stretching fundamentals of the complex were measured using coherence-converted population transfer Fourier Transform Microwave-infrared (IR-MW double resonance) experiments in the S-H and C-H stretch regions. Changes in the tunneling splittings upon vibrational excitation are consistent with the isotopic dependence of pure rotational transitions. A complexation shift of 2.7-6.5 cm(-1) has been observed in the two fundamental S-H stretching modes of the H2S monomer in the complex. Vibrational pre-dissociation in the bound S-H stretch has been detected whereas the instrument-limited line-shapes in other S-H and C-H stretches indicate slower pre-dissociation rate. Some local perturbations in the vibrational spectra have been observed. Two combination bands have been observed corresponding to both the S-H stretching fundamentals and what appears to be the intermolecular stretching mode at 55 cm(-1). The tunneling splitting involved in the rotation of C2H4 unit has been deduced to be 1.5 GHz from the IR-MW results. In addition, ab initio barrier heights derived for different motions of the monomers support the experimental results and provide further insight into the motions causing the splitting. (C) 2013 AIP Publishing LLC.

Layerwise decomposition of water dynamics in reverse micelles: A simulation study of two-dimensional infrared spectrum

We present computer simulation study of two-dimensional infrared spectroscopy (2D-IR) of water confined in reverse micelles (RMs) of various sizes. The present study is motivated by the need to understand the altered dynamics of confined water by performing layerwise decomposition of water, with an aim to quantify the relative contributions of different layers water molecules to the calculated 2D-IR spectrum. The 0-1 transition spectra clearly show substantial elongation, due to in-homogeneous broadening and incomplete spectral diffusion, along the diagonal in the surface water layer of different sized RMs. Fitting of the frequency fluctuation correlation functions reveal that the motion of the surface water molecules is sub-diffusive and indicate the constrained nature of their dynamics. This is further supported by two peak nature of the angular analogue of van Hove correlation function. With increasing system size, the water molecules become more diffusive in nature and spectral diffusion almost completes in the central layer of the larger size RMs. Comparisons between experiments and simulations establish the correspondence between the spectral decomposition available in experiments with the spatial decomposition available in simulations. Simulations also allow a quantitative exploration of the relative role of water, sodium ions, and sulfonate head groups in vibrational dephasing. Interestingly, the negative cross correlation between force on oxygen and hydrogen of O-H bond in bulk water significantly decreases in the surface layer of each RM. This negative cross correlation gradually increases in the central water pool with increasing RMs size and this is found to be partly responsible for the faster relaxation rate of water in the central pool. (C) 2013 AIP Publishing LLC.

Vibrational spectra of fluorene, 1-methylfluorene and 1,8-dimethylfluorene

In this paper, we report the gas phase infrared spectra of fluorene and its methylated derivatives using a heated multipass cell and argon as a carrier gas. The observed spectra in the 4000-400 cm(-1) range have been fitted using the modified scaled quantum mechanical force field (SQMFF) calculation with the 6-311G** basis. The advantage of using the modified SQMFF method is that it scales the force constants to find the best fit to the observed spectral lines by minimizing the fitting error. In this way we are able to assign all the observed fundamental bands in the spectra. With consecutive methyl substitutions two sets of bands are found to shift in a systematic way. The set of four aromatic C-H stretching vibrations around 3000 cm(-1) shifts toward lower frequencies while the single most intense aromatic C-H out-of-plane bending mode around 750 cm(-1) shifts toward higher frequencies. The reason for shifting of aromatic C-H stretching frequency toward lower wave numbers with gradual methyl substitution has been attributed to the lengthening of the C-H bonds due to the +I effect of the methyl groups to the ring current as revealed from the calculations. While the unexpected shifting of the aromatic C-H out-of-plane bend toward higher wave numbers with increasing methyl substitution is ascribed to the lowering of the number of adjacent aromatic C-H bonds on the plane of the benzene ring with gradual methyl substitutions. (C) 2013 Elsevier B.V. All rights reserved.