Hydrogen-bonding between pyrimidine and water: a vibrational spectroscopic analysis

We present an experimental and a theoretical study on hydrogen-bonding between pyrimidine and water as the H-donor. The degree of hydrogen-bonding in this binary system varies with mixture composition. This was monitored experimentally by polarization-resolved linear Raman spectroscopy with the pyrimidine ring breathing mode nu1 as a marker band. A subsequent quantitative line shape analysis of the isotropic Raman intensity for 24 pyrimidine/water mixtures clearly revealed a splitting into three spectral components upon dilution with water. The two additional peaks have been assigned to distinct groups of hydrogen-bonded species that differ in the number of pyrimidine nitrogen atoms (N) involved in hydrogen-bonding to water hydrogen atoms (H). From the integrated Raman intensities for "free" and "hydrogen-bonded" pyrimidine, a concentration profile for these species was established. Our assignments and interpretations are supported by quantum mechanical calculations of structures and by vibrational spectra for pyrimidine and 10 pyrimidine/water complexes with increasing water content. Also, accurate structure-spectra correlations for different cluster subgroups have been determined; within each particular cluster subgroup the water content varies, and a perfect negative correlation between NH hydrogen-bond distances and nu1 wavenumbers was observed.     

Conformational analysis and vibrational spectroscopic investigation of 3-phenylpropylamine

The possible stable forms of 3-phenylpropylamine (3-PPA) molecule were experimentally and theoretically studied by infrared and Raman spectroscopy. FT-IR and Raman spectra of 3-PPA were recorded in the regions of 4000–400 cm⁻¹ and 3700–60 cm⁻¹, respectively. The potential energy surface corresponding to the internal rotations of the molecule was investigated by semi-empirical quantum mechanical methods, and appropriate conformers defined with B3LYP hybrid density functional theory method along with the basis sets of different size and type. Results from experimental and theoretical data showed the trans–trans–gauche (TTG) to be the most stable form of a 3-PPA molecule.     

Theoretical vibrational analysis of monohalogenated phenols

Harmonic vibrational frequencies of a representative series of X-phenols (X = F, Cl, Br) in ortho, meta and para positions are determined using density functional theory (B3LYP) in conjunction with 6-311 + + G(d,p), 6-311 + + G(2d,2p), and 6-311 + + G(2df,2p) basis sets. Their complete and clear-cut vibrational assignment based on the concept of the potential energy distribution is carried out. Such assignment allows to resolve a number of uncertainties appeared in the previous studies and to propose a new explanation of frequency alterations of particular vibrational modes in this series.     

Evaluation of CO coordination energies from spectroscopic data: on the use of vibrational isotopic effects

For molecules containing a linearly coordinated carbonyl group, relationships linking 13C and 18O isotopic effects on the CO stretching vibration to the force constant of the M-C coordination bond are proposed. These relationships are rationalized by simple considerations involving the mechanical coupling of the CO and M-C oscillators, tested on model triatomic molecules, and generalized to larger systems. Previous theoretical considerations and several examples presented here show that the long-accepted relation between the shift in the stretching frequency of the coordinated CO with respect to that of isolated CO and the coordination strength has no general predictive power. In contrast, the force constant of the coordination bond can be correlated with the coordination binding energy, and a method for empirically estimating this important parameter from spectroscopic observations of the strongly absorbing CO stretching vibrations of molecular systems or adsorbates is proposed.     

Theoretical investigation of the structure and vibrational spectrum of the Li2CO2 molecule

The special features of the potential-energy surface (PES) and the paths for the intramolecular rearrangements of the Li₂CO₂ molecule have been investigated by the SCF method in the double-zeta Huzinaga—Dunning basis supplemented by d-type polarization functions in the carbon and oxygen atoms (DZ + P). It has been shown that there are two minima, which correspond to C_s and C₂ structures, on the PES of the molcule. All the remaining structures of the molecule considered either correspond to saddle points or do not represent special points on the PES at all. The force constants, vibrational frequencies, and intensities of the vibrational transitions in the IR spectra have been calculated for both isomers in the DZ basis. The theoretical values of the vibrational frequencies and the isotope shifts are in good agreement with the experimental data obtained with matrix isolation: the mean deviation of the scaled theoretical frequencies for the C_s isomer amounts to 13 cm^–1 or 1.6%. An analysis of the Mulliken populations, as well as a comparison of the geometric parameters and force constants of the isomers of Li₂CO₂ with the corresponding parameters of the Li₂O and CO molecules and of the CO₂ ^2– ion, have shown that the chemical bonds in both isomers may be represented by the scheme (Li⁺)₂CO₂ ^2–. The similarity between the PES's of the Li₂CO₂ and Li₂CO₃ molecules has been demonstrated and explained in the framework of the Gillespie—Nyholm model.Ivanovo Chemical-Engineering Institute. Translated from Zhurnal Strukturnoi Khimii, Vol. 32, No. 2, pp. 30–38, March–April, 1991.     

Theoretical calculation and vibrational spectral analysis of L-arginine trifluoroacetate

Fourier transform infrared and Raman spectra of the nonlinear optical crystal, L-arginine trifluoroacetate (L-arginine.CF3COOH, abbreviated as LATF) have been calculated by the first-principles calculation and investigated in experiment. The calculated results are slightly different from those experimental values because of the distinction resulted from the intermolecular hydrogen bonds. The role of this type of intermolecular interaction on the crystal vibrational spectra and nonlinear optical properties has been discussed. The absorption-edge on the IR side has been estimated by the theoretical approach on basis of the calculated infrared spectrum, which will be meaningful for further research on NLO crystal.     

Structures and vibrational spectroscopic parameters of selenoxopropanedinitrile and selenoxosilanedicarbonitrile: Theoretical study based on density functional theory method

The molecular structures and vibrational spectra in harmonic and anharmonic approximations have been studied for selenoxopropanedinitrile and selenoxosilanedicarbonitrile in the gas phase. Density functional theory method with B3LYP functional and cc‐pVTZ basis set has been employed. Optimized structural parameters and spectroscopic constants, namely, anharmonic, rotational and centrifugal distortion, rotation–vibration coupling, and Coriolis coupling parameters, are reported. Infrared vibrational and Raman frequencies are provided with complete assignments to the fundamental bands, overtones, and combination tones of the molecules. This study shows that silicon for carbon substitution affects mainly those properties that are dependent on the CSe bond. The literature for these molecules is not available and therefore the data from this work would be suitable for their characterizations as and when they are synthesized. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:208–217, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20535     

Water in toluene revisited: vibrational patterns in the stretching region

The symmetric (v1) and antisymmetric (v3) stretching bands of water monomers in toluene are revisited using two approaches: (i) calculation of dipole autocorrelation functions (ii) the solvatochromic behaviour of both vibration frequency shifts. The time constants extracted from the autocorrelations account for meaningful differences between the couplings established by the antisymmetric and symmetric vibrations with the solvent. The dipole autocorrelation function for the symmetric stretching band fits well a Lorentzian spectral density and shows a higher contribution to hindered rotation relatively to the one obtained from the antisymmetric stretching. The spectral shifts of stretching frequencies in toluene and in other relevant solvents were interpreted as arising from the electronic and orientational polarisations. Characteristic donor/acceptor interactions also contribute to the red shift and were tested by using empirical solvent basicity scales such as Kamlet-Taft beta and the recently proposed SB. The deviations detected in toluene as regards the continuum dielectric predictions are quantitatively treated and account for the specific interaction between the water and the molecular pi electron system referred to in the literature.     

Picosecond IR-UV pump-probe spectroscopic study on the intramolecular vibrational energy redistribution of NH2 and CH stretching vibrations of jet-cooled aniline

Intramolecular vibrational energy redistribution (IVR) of the NH2 symmetric and asymmetric stretching vibrations of jet-cooled aniline has been investigated by picosecond time-resolved IR-UV pump-probe spectroscopy. A picosecond IR laser pulse excited the NH2 symmetric or asymmetric stretching vibration of aniline in the electronic ground state and the subsequent time evolutions of the excited level as well as redistributed levels were observed by a picosecond UV pulse. The IVR lifetimes for symmetric and asymmetric stretches were obtained to be 18 and 34 ps, respectively. In addition, we obtained the direct evidence that IVR proceeds via two-step bath states; that is, the NH2 stretch energy first flows into the doorway state and the energy is further dissipated into dense bath states. The rate constants of the second step were estimated to be comparable to or slower than those of the first step IVR. The relaxation behavior was compared with that of IVR of the OH stretching vibration of phenol [Y. Yamada, T. Ebata, M. Kayano, and M. Mikami J. Chem. Phys. 120, 7400 (2004)]. We found that the second step IVR process of aniline is much slower than that of phenol, suggesting a large difference of the "doorway state increasing the dense bath states" anharmonic coupling strength between the two molecules. We also observed IVR of the CH stretching vibrations, which showed much faster IVR behavior than that of the NH2 stretches. The fast relaxation is described by the interference effect, which is caused by the coherent excitation of the quasistationary states.     

Gold cluster carbonyls: vibrational spectroscopy of the anions and the effects of cluster size, charge, and coverage on the CO stretching frequency

We report the vibrational spectra of the carbonyl complexes of anionic gold clusters in the range of the CO stretching frequency as measured in the gas phase using IR multiple photon dissociation spectroscopy. The investigated complexes contain between 3 and 14 Au atoms and up to 7 CO ligands. Special attention is given to the complexes that exhibit saturation CO coverage as well as to the monocarbonyl species. In conjunction with data from the corresponding cationic complexes we quantify how the CO stretching frequency varies with the charge state of the gold cluster. Our results provide a size- and charge-dependent basis to interpret values of the CO stretching frequency measured for CO on deposited gold clusters in terms of the charge states of the clusters.     

Coriolis interaction and intramolecular vibrational redistribution: A high-resolution spectroscopic probe of the rotational contribution to vibrational

We present here high-resolution fluorescence excitation spectra of the 12₀² band of pyrimidine in a molecular beam, which provide compelling ev     

Picosecond IR-UV pump-probe spectroscopic study of the dynamics of the vibrational relaxation of jet-cooled phenol. II. Intracluster vibrational energy redistribution of the OH stretching vibration of hydrogen-bonded clusters

A picosecond time-resolved IR-UV pump-probe spectroscopic study has been carried out for investigating the intracluster vibrational energy redistribution (IVR) and subsequent dissociation of hydrogen-bonded clusters of phenol (C6H5OH) and partially deuterated phenol (C6D5OH, phenol-d5) with various solvent molecules. The H-bonded OH stretching vibration was pumped by a picosecond IR pulse, and the transient S1-S0 UV spectra from the pumped level as well as the redistributed levels were observed with a picosecond UV laser. Two types of hydrogen-bonded clusters were investigated with respect to the effect of the H-bonding strength on the energy flow process: the first is of a strong "sigma-type H-bond" such as phenol-(dimethyl ether)(n=1) and phenol dimer, and the second is phenol-(ethylene)(n=1) having a weak "pi-type H-bond." It was found that the population of the IR-pumped OH level exhibits a single-exponential decay, whose rate increases with the H-bond strength. On the other hand, the transient UV spectrum due to the redistributed levels showed a different time evolutions at different monitoring UV frequency. From an analysis of the time profiles of the transient UV spectra, the following three-step scheme has been proposed for describing the energy flow starting from the IVR of the initially excited H-bonded OH stretching level to the dissociation of the H bond. (1) The intramolecular vibrational energy redistribution takes place within the phenolic site, preparing a hot phenol. (2) The energy flows from the hot phenol to the intermolecular vibrational modes of the cluster. (3) Finally, the hydrogen bond dissociates. Among the three steps, the rate constant of the first step was strongly dependent on the H-bond strength, while the rate constants of the other two steps were almost independent of the H-bond strength. For the dissociation of the hydrogen bond, the observed rate constants were compared with those calculated by the Rice, Ramsperger, Kassel, and Marcus model. The result suggests that dissociation of the hydrogen bond takes place much faster than complete energy randomization within the clusters.     

Picosecond IR-UV pump-probe spectroscopic study of the dynamics of the vibrational relaxation of jet-cooled phenol. I. Intramolecular vibrational energy redistribution of the OH and CH stretching vibrations of bare phenol

The intramolecular vibrational energy redistribution (IVR) of the OH stretching vibration of jet-cooled phenol-h6 (C6H8OH) and phenol-d8 (C6D8OH) in the electronic ground state has been investigated by picosecond time-resolved IR-UV pump-probe spectroscopy. The OH stretching vibration of phenol was excited with a picosecond IR laser pulse, and the subsequent temporal evolutions of the initially excited level and the redistributed ones due to the IVR were observed by multiphoton ionization detection with a picosecond UV pulse. The IVR lifetime for the OH stretch vibration of phenol-h6 was determined to be 14 ps, while that of the OH stretch for phenol-d8 was found to be 80 ps. This remarkable change of the IVR rate constant upon the dueteration of the CH groups strongly suggests that the "doorway states" for the IVR from the OH level would be the vibrational states involving the CH stretching modes. We also investigated the IVR rate of the CH stretching vibration for phenol-h6. It was found that the IVR lifetime of the CH stretch is less than 5 ps. The fast IVR is described by the strong anharmonic resonance of the CH stretch with many other combinations or overtone bands.     

Vibrational relaxation study of CO stretching mode of liquid N,N-dimethylformamide: Comparative study with theoretical calculation

The study reports to the bandshape analysis of CO stretching band of liquid N,N-dimethylformamide using various polar and non-polar solvents. The changes in bandwidths and anisotropy shift have been explained for neat liquid as well as binary mixtures using different solvents. The vibrational relaxation rates were correlated with different solvent concentrations to understand interacting nature of molecules. Ab initio calculation is carried out to give a complete picture of the molecule and vibrational spectra. The calculated characteristics of DMF are in good agreement with experimental values, allowing them to be used in spectral and structural analysis.     

Theoretical prediction of vibrational spectra: the harmonic force field and the vibrational spectrum of 4-methylpyridine

The geometry, complete harmonic force field and dipole moment derivatives have been computed for 4-methylpyridine at the Hartree-Fock level using a 4-21 basis set of Gaussian orbitals. A set of eleven scale factors, six of which were previously derived from benzene and the other five for the vibrational motions of the methyl group from toluene by fitting their computed force fields to their observed vibrational spectra, was used to scale the computed harmonic force constants of 4-methylpyridine. The vibrational frequencies and the associated infrared absorption intensities of 4-methyl -pyridine were then predicted from this scaled force field without any fitting to the experimental data of 4-methylpyridine. Comparison with experimental spectra permitted a few corrections to be made in previous experimental or semiempirical assignments. The mean-deviations between experimental and predicted frequencies was only 5.6 cm^-1 for the non-CH stretching frequencies or 8.3 cm^-1 overall. Computed intensities are qualitatively m agreement with experiment. The optimization of scale factors for the five methyl vibrational motions produced a trivial improvement in the fit.     

Raman spectroscopic investigations of the structure and phase transitions of liquid crystalline lead(II) alkanoates

Lead(II) alkanoates with even chain lengths from octanoate to octadecanoate have been investigated by Raman spectroscopy. In the low frequency region, transverse and longitudinal acoustical modes (TAM, LAM) have been assigned. It was shown that LAM-1 is the vibration of the double chain with the node of the vibration in the Pb²⁺ layer. A fully extended conformation of the chains in the low temperature phase was confirmed. The frequencies and intensities of the LAMs as compared with those of the alkanes and the fatty acids led to an estimate of the force constant and polarizability of the Pb²⁺ -COO^- bond relative to the C-C bond. The defects at the chain ends were investigated in the ρ(CH₃) and v(CC) region. For the intermediate (CM) phase, both the Pb²⁺ layer distance reduction and the chain length independent enthalpy contributions can be attributed mainly to defects at the chain ends.     

Ultrafast infrared spectroscopy of riboflavin: dynamics, electronic structure, and vibrational mode analysis

Femtosecond time-resolved infrared spectroscopy was used to study the vibrational response of riboflavin in DMSO to photoexcitation at 387 nm. Vibrational cooling in the excited electronic state is observed and characterized by a time constant of 4.0 +/- 0.1 ps. Its characteristic pattern of negative and positive IR difference signals allows the identification and determination of excited-state vibrational frequencies of riboflavin in the spectral region between 1100 and 1740 cm (-1). Density functional theory (B3LYP), Hartree-Fock (HF) and configuration interaction singles (CIS) methods were employed to calculate the vibrational spectra of the electronic ground state and the first singlet excited pipi* state as well as respective electronic energies, structural parameters, electronic dipole moments and intrinsic force constants. The harmonic frequencies of the S 1 excited state calculated by the CIS method are in satisfactory agreement with the observed band positions. There is a clear correspondence between computed ground- and excited-state vibrations. Major changes upon photoexcitation include the loss of the double bond between the C4a and N5 atoms, reflected in a downshift of related vibrations in the spectral region from 1450 to 1720 cm (-1). Furthermore, the vibrational analysis reveals intra- and intermolecular hydrogen bonding of the riboflavin chromophore.     

Toward spectroscopic accuracy of ab initio calculations of vibrational frequencies and related quantities: a case study of the HF molecule

Calculations at various coupled-cluster (CC) levels with and without the inclusion of linear r _{i j} -dependent terms are performed for the HF molecule in its ground state with a systematic variation of basis sets. The main emphasis is on spectroscopic properties such as the equilibrium distance r _e and the harmonic vibration frequency ω_e. Especially with the R12 methods (including linear r _{i j} -dependent terms), convergence to the basis set limit is reached. However, the results (at the basis set limit) are rather sensitive to the level of the treatment of electron correlation. The best results are found for the CCSDT1-R12 and CCSD[T]-R12 methods (CCSD[T] was previously called CCSD+T(CCSD)), while CCSD(T) overestimates ω_e by ≈6 cm⁻¹. The good agreement of conventional CCSD(T) with experiment for basis sets far from saturation (e.g. truncated at g-functions) is probably the result of a compensation of errors. The contribution of core-correlation is non-negligible and must be included (effect on ω_e≈5 cm⁻¹). Relativistic effects are also important (23 cm⁻¹), while adiabatic effects are much smaller (<1cm⁻¹) and non-adiabatic effects on ω_e can be simulated in replacing nuclear by atomic masses; for rotation nuclear masses appear to be the better choice, at least for hydrides. From a potential curve based on calculations with the CCSDT1-R12 method with relativistic corrections, the IR spectrum is computed quantum-mechanically. Both the band heads and the rotational structures of the observed spectra are reproduced with a relative error of ≈10⁻⁴ for the three isotopomers HF, DF, and TF. Received: 3 July 1998 / Accepted: 4 August 1998 / Published online: 28 October 1998