Calculation of vibrational spectra of linear tetrapyrroles. 3. Hydrogen-bonded hexamethylpyrromethene dimers

The structure and vibrational spectra of hexamethylpyrromethene (HMPM) have been investigated by X-ray crystallography, IR and Raman spectroscopies, and density functional theory calculations. HMPM crystallizes in the form of dimers, which are held together by bifurcated N-H(...N)(2) hydrogen bonds, involving one intramolecular and one intermolecular N-H...N interaction. The monomers are essentially planar, and the mean planes of the monomers lie approximately perpendicular to one another, so that the four N atoms in the dimer form a distorted tetrahedron. The structure of the HMPM dimer is well-reproduced by B3LYP/6-31G calculations. A comparison of the calculated geometry of the dimer with that of the monomer reveals only small changes in the N-H...N entity and the methine bridge angles upon dimerization. These are a result of weakening of the intramolecular N-H...N hydrogen bond and the formation of a more linear N-H...N intermolecular hydrogen bond. Using an empirical relation between the shift of the N-H stretching frequency of pyrrole and the enthalpy of adduct formation with bases [Nozari, M. S.; Drago, R. S. J. Am. Chem. Soc. 1970, 92, 7086-7090], estimates of the strength of the intra- and intermolecular hydrogen bonds are obtained. IR and Raman spectroscopies of HMPM and its isotopomers deuterated at the pyrrolic nitrogen atom and at the methine bridge reveal that the molecule is monomeric in nonpolar organic solvents but dimeric in a solid Ar matrix and in KBr pellets. The matrix IR spectra show a splitting of vibrational modes for the dimer, particularly those involving the N-H coordinates. Due to intrinsic deficiencies of the B3LYP/6-31G approximation, a satisfactory reproduction of these modes of the monomeric and dimeric HMPM requires specific adjustments of the NH scaling factors for the calculated force constants and, in the case of the NH out-of-plane modes of HMPM dimers, also of intra- and intermolecular coupling constants. This parametrization does not significantly affect the other calculated modes, which in general reveal a very good agreement with the experimental data.     

Density functional theory study of vibrational spectra and assignment of fundamental vibrational modes of 1-methyl-4-piperidone

The FT-IR and FT-Raman spectra of 1-methyl-4-piperidone was recorded and the observed bands were interpreted with the aid of normal coordinate analysis following a full structure optimization and force field calculation based on the density functional theory (DFT) using the standard B3LYP/6-311G** method and basis set combinations. A very good agreement obtained between the simulated and experimental spectra was established and unambiguous vibrational assignments of various modes were proposed based on the results of potential energy distribution (PED) calculations.     

Density functional theory study of vibrational spectra, and assignment of fundamental vibrational modes of 1-bromo 4-fluoronaphthalene

The FTIR and FT-Raman spectra of 1-bromo 4-fluoronaphthalene have been recorded in the regions 4000-100cm(-1) and 3500-100cm(-1), respectively. The spectra were interpreted with the aid of normal coordinate analysis based on DFT (density functional theory) using standard B3LYP/6-311+G** basis set combination for the most optimized geometry. Normal coordinate calculations performed with the DFT force field and subsequently corrected by a recommended set of scale factors, yielded fairly good agreement between observed and calculated frequencies. On the basis of the comparison between calculated and experimental results, assignments of fundamental modes were examined.     

A new way of analyzing vibrational spectra. I. Derivation of adiabatic internal modes

A new way of analyzing measured or calculated vibrational spectra in terms of internal vibrational modes associated with the internal parameters used to describe geometry and conformation of a molecule is described. The internal modes are determined by solving the Euler–Lagrange equations for molecular fragments ϕ_n described by internal parameters ζ_n. An internal mode is localized in a molecular fragment by describing the rest of the molecule as a collection of massless points that just define molecular geometry. Alternatively, one can consider the new fragment motions as motions that are obtained after relaxing all parts of the vibrating molecule but the fragment under consideration. Because of this property, the internal modes are called adiabatic internal modes, and the associated force constants k_a, adiabatic force constants. Minimization of the kinetic energy of the vibrating fragment ϕ_n yields the adiabatic mass m_a (corresponding to 1/G_nn of Wilson's G matrix) and, by this, adiabatic frequencies ω_a. Adiabatic modes are perfectly suited to analyze and understand the vibrational spectra of a molecule in terms of internal parameter modes in the same way as one understands molecular geometry in terms of internal coordinates. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67 : 1–9, 1998     

Determining the vibrational pattern via overtone cold spectra: C-H methyl stretches of propyne

Vibrationally mediated photodissociation and photoacoustic (PA) spectroscopy were employed for studying the intramolecular dynamics of propyne initially excited to the first through fourth overtone of methyl C-H stretching modes. Room-temperature PA and jet-cooled action spectra, monitoring the absorption of the parent and the yield of the ensuing H photofragments, respectively, were obtained. The PA spectra exhibit mainly broad features, while the action spectra, due to inhomogeneous structure reduction, expose multiple peaks of recognizable shapes in the differing overtone manifolds. Symmetric rotor simulations of the band contours of the action spectra allowed retrieving of band origins and linewidths. The linewidths of the bands in each manifold enabled estimates for energy redistribution times out of the corresponding states to the bath states, the times ranging from 18+/-6 ps for two quanta of C-H excitation to subpicosecond for five quanta. The data were also analyzed in terms of a normal-mode model and a joint local-/normal-mode model. These models enabled determination of harmonic frequencies, anharmonicities, and interaction parameters reproducing the observed data in all monitored regions and provided spectral assignments. The measured Doppler profiles were well fitted by Gaussians with widths suggesting low average translational energies for the released H photofragments. These low energies and their similarities to those for dissociation of propyne isotopomers preexcited to acetylenic C-H stretches were ascribed to an indirect dissociation process occurring after internal conversion to the ground electronic state and isomerization to allene.     

Density functional theory study of vibrational spectra, and assignment of fundamental vibrational modes of succinimide and N-bromosuccinimide

This work deals with the vibrational spectroscopy of succinimide and N-bromosuccinimide. The mid and far FTIR and FT-Raman spectra were measured in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) using standard B3LYP/6-31G(*) and B3LYP/6-311+G(**) methods and 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. Unambiguous vibrational assignment of all the fundamentals were made using the total energy distribution (TED).     

Crystal structure and vibrational spectra of AlVO4. A DFT study

We present periodic density functional calculations within the generalized gradient approximation (Perdew-Wang 91) on structure and vibrational properties of bulk AlVO(4). The optimized structure agrees well with crystallographic data obtained by Rietveld refinement (the mean absolute deviation of bond distances is 0.032 A), but the deviations are larger for the lighter oxygen atoms than for the heavier Al and V atoms. All observed bands in the Raman and IR spectrum have been assigned to calculated harmonic frequencies. Bands in the 1020-900 cm(-1) region have been assigned to V-O((2)) stretches in V-O((2))-Al bonds. The individual bands do not arise from vibrations of only one bond, not even from vibrations of several bonds of one VO(4) tetrahedron. The results confirm that vibrations around 940 cm(-1) observed for vanadia particles supported on thin alumina film are V-O-Al interface modes with 2-fold coordinated oxygen atoms in the V-O((2))-Al interface bonds.     

Calculation and analysis of the structure and vibrational spectra of uracil tautomers

The structure and vibrational spectra of twelve tautomers are calculated in the B3LYP/6-311+G(d,p) approximation and analyzed. Spectral manifestations of isomeric uracil transformations into one out of the twelve tautomeric forms and cis— trans- isomeric transformations of the tautomers themselves are considered. All tautomeric transformations are shown to be characterized by the presence of at least one vibration, whose frequency is different by ~ 100-200 cm^-1 from a similar vibrational frequency of the precursor and also by a pronounced change in the intensity of bending vibrations of OH hydroxyl groups and stretching vibrations of CO bonds.     

Calculation of polymer blend compositions from vibrational spectra: A simple method

In this work, the application of a new approach for quantitative analysis, originally developed for Raman spectroscopy, is extended to IR spectroscopy. The attractive features of this methodology are its simplicity and ease of use in comparison with traditional approaches. Unlike other methods, rich spectral information containing several overlapped peaks can be used in the calculations. A robust and well‐conditioned calculation scheme renders precise results, which are independent of the operator's decisions. The method was applied to study the chemical compositions of homogeneous polymer blends made of polystyrene and poly(vinyl methyl ether). Raman and IR blend spectra were acquired with confocal Raman microspectroscopy and attenuated total reflection/Fourier transform infrared, respectively. The blend compositions were calculated from the corresponding vibrational spectra with the proposed strategy, and excellent agreement between those values and the true ones was found for both techniques. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1144–1151, 2005     

α-Azidopolynitroalkanes. Synthesis and vibrational spectra

Methods for the preparation of α-azidopolynitroalkanes by reactions of polynitroalkanes or α-(difluoroamino)polynitroalkanes with NaN₃ were developed. In the case of tetranitromethane, one or two nitro groups can be substituted, depending on the reaction conditions. The reaction of 1,1,1-trinitroethane with NaN₃ affords nitro-1,2,3-triazole, together with 1-azido-1,1-dinitroethane. The IR spectra of α-azidopolynitroalkanes were studied. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 338–341, February, 1997.     

Density functional theory study of vibrational spectra. 8. Assignment of fundamental vibrational modes of 9,10-anthraquinone and 9,10-anthraquinone-d8

Density functional theory (using Becke's exchange and Lee-Yang-Parr's correlation functionals (BLYP)) and ab initio Hartree-Fock calculations were carried out in order to investigate the molecular structure and vibrational spectra of 9,10-anthraquinone and its perdeuterated analog. The calculated structural and spectral features are in good agreement with the available experimental results. Most of the BLYP/6-31G* non-CH(D) stretching frequencies are slightly lower than reliable experimental assignments; the mean absolute deviation is about 14 cm⁻¹. On the basis of agreement between calculated and experimental results, assignments of the fundamental vibrational modes were examined and some reassignments were proposed. The calculated results can serve as a guide for a future experimental search for the missing fundamentals of the target molecules.     

Prediction of vibrational spectra from microwave spectra

Explicit and simple relations are derived for the Kivelson-Wilson parameters which can directly generate the vibrational spectrum of XY₂ bent type molecules. These relations are also shown to generate the above parameters for the different isotopes of a parent molecule. These predictions are verified in the case of some molecules of the above symmetry for which experimental microwave studies have been made.     

Basis set dependence of the vibrational wavenumbers of the out-of-plane modes of conjugated π-electron ring systems

Basis set dependence of the vibrational wavenumbers of out-of-plane modes calculated at the MP2 level of ab initio molecular orbital theory is examined for benzene, p-benzoquinodimethane, p-benzoquinone, furan, and thiophene. Various polarization functions up to (3df,p) are used in combination with the 6-31G and 6-311G basis sets. It is shown that, especially in the case of normal modes with alternate out-of-plane motions of the carbon atoms (such as the ν₄ (b_2g) mode of benzene), the calculated wavenumbers depend strongly on the exponents (_d) of the d functions on the carbon atoms. It is therefore necessary to include d functions with an optimum exponent (_d0.4) on the carbon atoms to obtain reasonable out-of-plane vibrational force fields. In a few cases (such as the ν₁₆ (a₂) mode of furan), inclusion of a set of f functions on the carbon atoms has some effects on the calculated wavenumbers of out-of-plane modes. However, unless the basis set contains an optimum set of d functions, inclusion of a set of f functions does not improve the agreement between the observed and calculated vibrational wavenumbers. As a case with an exaggerated effect of basis set, it is shown that the wavenumber of the ν₄₁ (b_2g) mode of the planar optimized structure of p-benzoquinodimethane is calculated to be imaginary by using the 6-311G(d,p) or 6-311G(df,p) basis set at the MP2 level. For all the molecules treated in the present study, reasonable out-of-plane vibrational force fields are obtained by using the 6-31G(2df,p) and 6-311G(2df,p) basis sets.     

Raman spectra of vibrational and librational modes in methane clathrate hydrates using density functional theory

The sI type methane clathrate hydrate lattice is formed during the process of nucleation where methane gas molecules are encapsulated in the form of dodecahedron (5(12)CH(4)) and tetrakaidecahedron (5(12)6(2)CH(4)) water cages. The characterization of change in the vibrational modes which occur on the encapsulation of CH(4) in these cages plays a key role in understanding the formation of these cages and subsequent growth to form the hydrate lattice. In this present work, we have chosen the density functional theory (DFT) using the dispersion corrected B97-D functional to characterize the Raman frequency vibrational modes of CH(4) and surrounding water molecules in these cages. The symmetric and asymmetric C-H stretch in the 5(12)CH(4) cage is found to shift to higher frequency due to dispersion interaction of the encapsulated CH(4) molecule with the water molecules of the cages. However, the symmetric and asymmetric O-H stretch of water molecules in 5(12)CH(4) and 5(12)6(2)CH(4) cages are shifted towards lower frequency due to hydrogen bonding, and interactions with the encapsulated CH(4) molecules. The CH(4) bending modes in the 5(12)CH(4) and 5(12)6(2)CH(4) cages are blueshifted, though the magnitude of the shifts is lower compared to modes in the high frequency region which suggests bending modes are less affected on encapsulation of CH(4). The low frequency librational modes which are collective motion of the water molecules and CH(4) in these cages show a broad range of frequencies which suggests that these modes largely contribute to the formation of the hydrate lattice.     

Reassignment of fundamental vibrational modes of cyclic S4N3 cation

MP2/6 31G* calculations were carried out to investigate the vibrational spectrum of cyclic S4N3+. The results indicate that previous assignments of several fundamental vibrational modes are in error. On the basis of the calculated results, reassignments of these modes are proposed.     

Calculation of intensities of torsional transitions in vibrational spectra of molecules with internal rotation

Institute of Physiologically Active Substances. Translated from Zhurnal Strukturnoi Khimii, Vol. 31, No. 6, pp. 36–41, November–December, 1990.