The normal co-ordinate analysis, vibrational spectra and theoretical infrared intensities of some thiocarbonyl halide molecules /

TITLE: The normal co-ordinate analysis, vibrational spectra and theoretical infrared intensities of some thiocarbonyl halides. AUTHOR: J. L. Brema SUPERVISOR: Dr. D. C. Moule NUMBER OF PAGES: 89 ABSTRACT: The vibrational assignment of the five-in-plane fundamental modes of CSClBr has been made on the basis of infrared gas phase and liquid Raman spectral analyses to supplement our earlier vibrational studies. Even though the one out-of-plane fundamental was not observed spectroscopically an attempt has been made to predict its frequency. The vibrational spectra contained impurity bands and the CSClBr assignment was made only after a thorough analysis of the impurities themselves. A normal co-ordinate analysis calculation was performed assuming a Urey-Bradley force field. This calculation yielded the fundamental frequencies in good agreement with those observed after refinement of the originally transferred force constants. The theoretical frequencies are the eigenvalues of the secular equation and the calculation also gave the corresponding eigenvectors in the form of the very important LLj matrix. The [l] matrix is the transfoirmation between internal co-ordinates and normal co-ordinates and it is essential for Franck-Condon calculations on electronically excited molecules and for infrared Integrated band intensity studies. Using a self-consistent molecular orbital calculation termed "complete neglect of differential overlap" (CNDO/2) , theoretical values of equilibrium bond lengths and angleswere calcuted for a series of carbonyl and thlocarbonyl molecules. From these calculations valence force field force constants were also determined but with limited success. With the CNIX)/2 method theoretical dipole moment derivatives with respect to symmetrized internal co-ordinates were calculated and the results should be useful in a correlation with experimentally determined values.

Infrared intensities of furan, pyrrole and thiophene: beyond the double harmonic approximation

Infrared intensities of the fundamental, overtone and combination transitions in furan, pyrrole and thiophene have been calculated using the variational normal coordinate code MULTIMODE. We use pure vibrational wavefunctions, and quartic force fields and cubic dipole moment vector surfaces, generated by density functional theory. The results are compared graphically with second-order perturbation calculations and with relative intensities from experiment for furan and pyrrole.

The infrared fundamental intensities of some cyanopolyynes

Some cyanopolyynes, HCnN (n = 1, 3, ... , 17), are investigated by means of calculations at the MP2/cc-pVTZ and CCSD/cc-pVDZ levels. Although the MP2/cc-pVTZ results for geometries and molecular dipole moments are encouraging, the CCSD/cc-pVDZ level was superior for the study of infrared fundamental intensities. The main bands are also analyzed with a charge-charge flux-dipole flux (CCFDF) partition model based on quantities given by the Quantum Theory of Atoms in Molecules (QTAIM). The intensity of vibrations corresponding to the stretching of CH bonds (3471-3473 cm(-1)) increases in line with the number of carbon atoms (from 61 to 146 km mol(-1) between HCN and HC13N). This increase is due to the charge flux contribution while the other contributions remain roughly unaltered except for HCN. Moreover, the hydrogen atom loses an almost constant amount of electronic charge during the CH bond enlargement and a small fraction of this charge spreads to atoms farther and farther away from hydrogen as the molecule size increases. The band associated with the doubly degenerate CH bending vibrations (643-732 cm(-1)) presents approximately the same intensity in all the studied cyanopolyynes (from 67 to 76 km mol(-1)). The CCFDF/QTAIM contributions are also nearly the same for these bending modes in HC5N and larger systems. The intensity of the mode mostly identified as CN stretching (around 2378-2399 cm(-1) except for HCN) increases from HCN up to HC7N (from 0.3 to 83 km mol(-1)) and nearly stabilizes around 80-90 km mol(-1) for larger systems. The CCFDF/QTAIM contributions for this mode also change significantly up to HC7N and remain almost constant in larger systems. We also observed the appearing of a very relevant band between 2283 and 2342 cm(-1). This mode is mainly associated with the symmetric stretching of CC triple bonds near the molecule center and exhibits large charge fluxes while the other contributions are almost negligible in the largest cyanopolyynes. The two vibrational bands associated with the smallest frequencies are also studied and extrapolation equations are suggested to predict their positions in larger cyanopolyynes. (C) 2012 Elsevier B.V. All rights reserved.

Vibrational analysis of boldine hydrochloride using QM/MM approach

A complete vibrational analysis was performed on the molecular structure of boldine hydrochloride using QM/MM method. The equilibrium geometry, harmonic vibrational frequencies and infrared intensities were calculated by QM/MM method with B3LYP/6-31G(d) and universal force field (UFF) combination using ONIOM code. We found the geometry obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. A detailed interpretation of the infrared spectra of boldine hydrochloride is reported. The scaled theoretical wave numbers are in perfect agreement with the experimental values. The FT-IR spectra of boldine hydrochloride in the region 4000-500 cm(-1) were recorded in CsI (solid phase) and in chloroform with concentration 5 and 10 mg/ml.

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.

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.

Intermolecular charge transfer and vibrational analysis of hydrogen bonding in acetazolamide

In the present work the structural and spectral characteristics of acetazolamide 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) employing B3LYP with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. Based on these results, we have discussed the correlation between the vibrational modes and the structure of the dimers of acetazolamide. The calculated vibrational spectra of three dimers of acetazolamide have been compared with observed spectra, and the assignment of observed bands was carried out using potential energy distribution. The observed spectra agree well with the values computed from the OFT. A comparison of observed and calculated vibrational spectra clearly shows the effect of hydrogen bonding. The frequency shifts observed for the different dimers are in accord with the hydrogen bonding in acetazolamide. Natural bond orbital (NBO) analyses reflect the charge transfer interaction in the individual hydrogen bond units and the stability of different dimers of acetazolamide. (C) 2012 Elsevier B.V. All rights reserved.

Theoretical investigation of LaC3n+ (n = 0, 1, 2) clusters by density functional theory

LaC3n+ (n = 0, 1, 2) clusters have been studied using B3LYP (Becke 3-parameter-Lee-Yang-Parr) density functional method. The basis set is Dunning/ Huzinaga valence double zeta for carbon and [2s2p2d] for lanthanum, denoted LANL1DZ. Four isomers are presented for each cluster; two of them are edge binding isomers with C-2 upsilon symmetry, the other two are Linear chains with C-infinity upsilon symmetry. Meanwhile, two spin states for each isomer, that is, singlet and triplet for LaC3+, doublet and quartet for LaC3 and LaC32+, respectively, are also considered. Geometries, vibrational frequencies, infrared intensities, and other quantities are reported and discussed. The results indicate that at some spin states; the C-2 upsilon symmetry isomers are the dominant structures, while for the other spin states, linear isomers are energetically favored. (C) 1998 John Wiley & Sons, Inc.

Vibrational spectroscopic studies and computational study of quinoline-2-carbaldehyde benzoyl hydrazone

FT-IR spectrum of quinoline-2-carbaldehyde benzoyl hydrazone (HQb H2O) was recorded and analyzed. The synthesis and crystal structure data are also described. The vibrational wavenumbers were examined theoretically using the Gaussian03 package of programs using HF/6-31G(d) and B3LYP/6-31G(d) levels of theory. The data obtained from vibrational wavenumber calculations are used to assign vibrational bands obtained in infrared spectroscopy of the studied molecule. The first hyperpolarizability, infrared intensities and Raman activities are reported. The calculated first hyperpolarizability is comparable with the reported values of similar derivatives and is an attractive object for future studies of non-linear optics. The geometrical parameters of the title compound obtained from XRD studies are in agreement with the calculated values. The changes in the CAN bond lengths suggest an extended p-electron delocalization over quinoline and hydrazone moieties which is responsible for the non-linearity of the molecule

Assessment of the consistency of near-infrared water vapor line intensities using high-spectral-resolution ground-based Fourier transform measurements of solar radiation

Calculations of the absorption of solar radiation by atmospheric gases, and water vapor in particular, are dependent on the quality of databases of spectral line parameters. There has been increasing scrutiny of databases such as HITRAN in recent years, but this has mostly been performed on a band-by-band basis. We report nine high-spectral-resolution (0.03 cm(-1)) measurements of the solar radiation reaching the surface in southern England over the wave number range 2000 to 12,500 cm(-1) (0.8 to 5 mm) that allow a unique assessment of the consistency of the spectral line databases over this entire spectral region. The data are assessed in terms of the modeled water vapor column that is required to bring calculations and observations into agreement; for an entirely consistent database, this water vapor column should be constant with frequency. For the HITRAN01 database, the spread in water vapor column is about 11%, with distinct shifts between different spectral regions. The HITRAN04 database is in significantly better agreement (about 5% spread) in the completely updated 3000 to 8000 cm(-1) spectral region, but inconsistencies between individual spectral regions remain: for example, in the 8000 to 9500 cm(-1) spectral region, the results indicate an 18% (+/- 1%) underestimate in line intensities with respect to the 3000 to 8000 cm(-1) region. These measurements also indicate the impact of isotopic fractionation of water vapor in the 2500 to 2900 cm(-1) range, where HDO lines dominate over the lines of the most abundant isotope of H2O.

Intensities in infrared bands V: Bond polar properties in dimethylacetylene

The absolute intensities of all except one of the infra-red fundamental vibration bands of dimethyl acetylene have been determined, and the results have been used to compute polar properties of the C—H and C—C bonds. It has been found that if the very probable assumption is made that the acetylenic carbon atoms carry a residual negative charge, the hydrogen atoms in the C—H bonds must carry a residual positive charge. The probable value of the C—H dipole is about 04 Debye, and that of the C—C bond about 1 Debye. Comparisons have been made with the results of similar work with related molecules.

Assessment of the consistency of H2O line intensities over the near-infrared using sun-pointing ground-based Fourier transform spectroscopy

We report on the consistency of water vapour line intensities in selected spectral regions between 800–12,000 cm−1 under atmospheric conditions using sun-pointing Fourier transform infrared spectroscopy. Measurements were made across a number of days at both a low and high altitude field site, sampling a relatively moist and relatively dry atmosphere. Our data suggests that across most of the 800–12,000 cm−1 spectral region water vapour line intensities in recent spectral line databases are generally consistent with what was observed. However, we find that HITRAN-2008 water vapour line intensities are systematically lower by up to 20% in the 8000–9200 cm−1 spectral interval relative to other spectral regions. This discrepancy is essentially removed when two new linelists (UCL08, a compilation of linelists and ab-initio calculations, and one based on recent laboratory measurements by Oudot et al. (2010) [10] in the 8000–9200 cm−1 spectral region) are used. This strongly suggests that the H2O line strengths in the HITRAN-2008 database are indeed underestimated in this spectral region and in need of revision. The calculated global-mean clear-sky absorption of solar radiation is increased by about 0.3 W m−2 when using either the UCL08 or Oudot line parameters in the 8000–9200 cm−1 region, instead of HITRAN-2008. We also found that the effect of isotopic fractionation of HDO is evident in the 2500–2900 cm−1 region in the observations.

Reliability of near-infrared spectroscopy for measuring biceps brachii oxygenation during sustained and repeated isometric contractions

We examine the test-retest reliability of biceps brachii tissue oxygenation index (TOI) parameters measured by near-infrared spectroscopy during a 10-s sustained and a 30-repeated (1-s contraction, 1-s relaxation) isometric contraction task at 30% of maximal voluntary contraction (30% MVC) and maximal (100% MVC) intensities. Eight healthy men (23 to 33 yr) were tested on three sessions separated by 3 h and 24 h, and the within-subject reliability of torque and each TOI parameter were determined by Bland-Altman+/-2 SD limits of agreement plots and coefficient of variation (CV). No significant (P>0.05) differences between the three sessions were found for mean values of torque and TOI parameters during the sustained and repeated tasks at both contraction intensities. All TOI parameters were within+/-2 SD limits of agreement. The CVs for torque integral were similar between the sustained and repeated task at both intensities (4 to 7%); however, the CVs for TOI parameters during the sustained and repeated task were lower for 100% MVC (7 to 11%) than for 30% MVC (22 to 36%). It is concluded that the reliability of the biceps brachii NIRS parameters during both sustained and repeated isometric contraction tasks is acceptable.

Cerebral cortex activation mapping upon electrical muscle stimulation by 32-channel time-domain functional near-infrared spectroscopy

The application of different EMS current thresholds on muscle activates not only the muscle but also peripheral sensory axons that send proprioceptive and pain signals to the cerebral cortex. A 32-channel time-domain fNIRS instrument was employed to map regional cortical activities under varied EMS current intensities applied on the right wrist extensor muscle. Eight healthy volunteers underwent four EMS at different current thresholds based on their individual maximal tolerated intensity (MTI), i.e., 10 % < 50 % < 100 % < over 100 % MTI. Time courses of the absolute oxygenated and deoxygenated hemoglobin concentrations primarily over the bilateral sensorimotor cortical (SMC) regions were extrapolated, and cortical activation maps were determined by general linear model using the NIRS-SPM software. The stimulation-induced wrist extension paradigm significantly increased activation of the contralateral SMC region according to the EMS intensities, while the ipsilateral SMC region showed no significant changes. This could be due in part to a nociceptive response to the higher EMS current intensities and result also from increased sensorimotor integration in these cortical regions.