Local Mode Parameters Research Articles

Automatic Generation of Local Vibrational Mode Parameters: From Small to Large Molecules and QM/MM Systems.

LModeAGen, a new protocol for the automatic determination of a nonredundant, complete set of local vibrational modes is reported, which is based on chemical graph concepts. Whereas local mode properties can be calculated for a selection of parameters targeting specific local modes of interest, a complete set of nonredundant local mode parameters is requested for the adiabatic connection scheme (ACS), relating each local vibrational mode with a normal mode counterpart, and for the decomposition of normal modes (CNM) in terms of local mode contributions, a unique way to analyze vibrational spectra. So far, nonredundant parameter sets have been generated manually following chemical intuition or from a set of redundant parameters in a trial-and-error fashion, which has hampered the study of larger systems with hundreds of parameters. LModeAGen was successfully applied for a test set of 11 systems, ranging from small molecules to the large QM (>100 atoms) subsystem of carbomonoxy-neuroglobin protein, described with a hybrid QM/MM method. The ωB97X-D/aug-cc-pVDZ, M06L/def2-TZVP, and QM/MM ωB97X-D/6-31G(d,p)/AMBER model chemistries were adopted for the description of the molecules in the test set. Our new protocol is an important step forward for a routine ACS and CNM analysis of the vibrational spectra of complex and large systems with hundreds of atoms, providing new access to important encoded electronic structure information.

The weak fundamental NH-stretching transition in amines

Absolute intensities of NH-stretching fundamental and overtone transitions of gas phase aniline, methylamine, ethylamine, cyclopropylamine, methylethylamine, diethylamine and pyrrolidine have been measured with long path length conventional absorption spectroscopy. To support the assignments of NH-stretching transitions, transition frequencies and intensities were calculated with the local mode model using ab initio calculated local mode parameters and dipole moment functions obtained at the CCSD(T)-F12a/VDZ-F12 level of theory. For aniline, the absolute intensities of the NH-stretching transitions show the typical decrease of approximately an order of magnitude for each successive vibrational excitation. For methylamine, ethylamine, cyclopropylamine, methylethylamine, diethylamine and pyrrolidine, the observed absolute intensities of the fundamental NH-stretching transition is weak and of similar strength or even weaker than the corresponding first overtone transition. Characteristic for the amines with a normal fundamental intensity is a conjugated double bond next to the amine group.

Absolute Intensities of NH-Stretching Transitions in Dimethylamine and Pyrrole

Vibrational spectra of vapor-phase dimethylamine (DMA) and pyrrole have been recorded in the 1000 to 13000 cm(-1) region using long path conventional spectroscopy techniques. We have focused on the absolute intensities of the NH-stretching fundamental and overtone transitions; Δν(NH) = 1-4 regions for DMA and the Δν(NH) = 1-3 regions for pyrrole. In the Δν(NH) = 1-3 regions for DMA, evidence of tunneling splitting associated with the NH-wagging mode is observed. For DMA, the fundamental NH-stretching transition intensity is weaker than the first NH-stretching overtone. Also, the fundamental NH-stretching transition in DMA is much weaker than the fundamental transition in pyrrole. We have used an anharmonic oscillator local mode model with ab initio calculated local mode parameters and dipole moment functions at the CCSD(T)/aug-cc-pVTZ level to calculate the NH-stretching intensities and explain this intensity anomaly in DMA.

Vibrational overtone spectra and interactions of C 2H 4 and H 2CCHCH 3 in liquid Kr

Vibrational overtone spectra of ethene and propene dissolved in liquid krypton at 120 K have been recorded between 5000 and 16500 cm −1. Spectral regions for the first four overtones were measured using a Fourier transform spectrophotometer. The fifth overtone (Δ υ = 6) spectra in liquid Kr were recorded with a double beam (pump-probe) thermal lens technique. Local-mode parameters were calculated for C–H oscillators in solution and compared with gas phase local mode parameters. The bandwidth (Δ ω 1/2) of the absorption bands of ethene correlate with the magnitude of the collision frequency with the solvent atoms. For propene, the shapes of the absorption bands in gas phase and in liquid krypton are similar. Density functional theory calculations of the structural parameters and C–H vibrational frequencies of propene in gas phase and in solution are reported. Frequency shifts (Δ ω) with respect to gas phase results are attributed to changes in harmonic frequency and anharmonicity of the particular C–H bond of the sample dissolved in liquid krypton.

Vibrational C–H overtone spectroscopy and bond distances of butenes dissolved in liquid Xe

Vibrational overtone spectra of isobutene, cis-2-butene, and trans-2-butene dissolved in liquid xenon at 163 K, have been recorded between 5000 and 16500 cm −1. Spectral regions for the first four overtones were measured using a Fourier transform spectrophotometer. The fifth overtone (Δ υ = 6) spectra were recorded with a double beam (pump–probe) thermal lens technique. Band deconvolution allowed isolation of individual transitions. Local-mode parameters were calculated for C–H oscillators in solution and compared with gas phase local-mode parameters. Density functional theory calculations were done to obtain C–H bond lengths and vibrational frequencies for the three butene isomers. Frequency shifts (Δ ω) with respect to gas phase results are attributed to changes in harmonic frequency and anharmonicity of the particular C–H bond of the sample dissolved in the inert liquid solvent.

Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides

A molecular mechanics (MM) force field-based empirical electrostatic potential map (MM map) for amide-I vibrations is developed with the aim of seeking a quick and reasonable approach to computing local mode parameters and their distributions in solution phase. Using N-methylacetamide (NMA) as a model compound, the instantaneous amide-I normal-mode parameters (transition frequency and dipole) obtained at the level of MM force fields are converted to solution phase values by a four-site potential scheme, but without the need for quantum mechanical frequency computations of solute-solvent clusters as are required in constructing ab initio-based electrostatic potential or field maps. The linear IR line shape of the amide-I mode in NMA obtained from the frequency-time correlation function on the basis of the MM map are found to be comparable to those from the ab initio-based maps. Our results show that the amide-I local mode parameters are largely determined by the solvated peptide structure rather than by explicit solvent molecules, suggesting an inherent local structure sensitivity of the amide-I mode in solvated peptides. Applications to alanine di- and tripeptides are satisfactorily demonstrated, showing its usefulness as an alternative approach in providing vibrational parameters for the simulation of linear IR and 2D IR spectra of the amide-I modes in polypeptides.

Vibrational Overtone Spectroscopy of Saturated Hydrocarbons Dissolved in Liquefied Ar, Kr, Xe, and N2

This article presents a collection of vibrational overtone spectra of hydrocarbons in cryogenic solutions. Vibrational overtone spectra of ethane and propane dissolved in liquid argon and n-butane and isobutane dissolved in liquid krypton were recorded between 5000 and 14,000 cm(-1). Spectral regions for the first four overtones were measured using a Fourier transform spectrophotometer. The fifth overtone (Deltaupsilon = 6) spectra were recorded with a double beam (pump-probe) thermal lens technique using concentrations as low as 10-3 mole fraction. We obtained the C-H (Deltaupsilon = 6) spectra of (a) liquid ethane at 100 K and ethane in solutions in liquid Ar at 92 K and liquid N2 at 85 K, (b) liquid propane at 148 K and propane in liquid Ar at 93 K, (c) n-butane in liquid Kr at 129 K, (d) n-pentane in liquid Xe at 160 K, and (e) isobutane liquid at 135 K and isobutane in liquid Kr at 130 K. Local-mode parameters were calculated for primary, secondary, and tertiary C-H oscillators in solution and compared with gas-phase local-mode parameters. The peak frequency shift (Deltaomega) from gas phase to solution is explained by the change in harmonic frequency and anharmonicity in solution with respect to the gas-phase values. The bandwidth (Deltaomega1/2) of the (Deltaupsilon = 6) C-H absorption bands of ethane in solution can be explained in terms of collisions with the solvent molecules.

Weak Intramolecular Interactions in Ethylene Glycol Identified by Vapor Phase OH−Stretching Overtone Spectroscopy

Vapor phase OH-stretching overtone spectra of ethylene glycol were recorded to investigate weak intramolecular hydrogen bonding. The spectra were recorded with conventional absorption spectroscopy and laser photoacoustic spectroscopy in the first to fourth OH-stretching overtone regions. The room-temperature spectra are dominated by two conformers that show weak intramolecular hydrogen bonding. A less abundant third conformer, with no sign of hydrogen bonding, is also observed. Vapor phase spectra of the ethylene-d(4) glycol isotopomer were also recorded and used to identify an interfering resonance between CH-stretching and OH-stretching states in the fourth overtone. Anharmonic oscillator local mode calculations of the OH-stretching transitions have provided an accurate simulation of the observed spectra. The local mode parameters were calculated with coupled cluster ab initio methods. The calculations facilitate assignment of the different conformers in the spectra and illustrate the effect of the intramolecular hydrogen bonding.

Site−Site Potentials in Neopentane and Tetramethylsilane

Neopentane and TMS are used as model M(CH(3))(4) systems to investigate intramolecular interactions. The nonbonded site-site potential between two proximal hydrogen atoms on different methyl groups, V(nb)(d(HH)), is not Lennard-Jones- or Morse-like but is found to be pseudolinear in hydrogen-hydrogen internuclear separation, d(HH), for both neopentane and TMS. The Morse potential is found to be a poor basis in which to expand V(nb)(d(HH)). The nonbonded site-site potential is conformation-dependent and not transferable between molecules. The individual contributions to V(nb)(d(HH)) are presented. The local mode parameters for neopentane and TMS are calculated ab initio for a variety of molecular conformations. The ab initio values of the local mode frequency and local mode anharmonicity are increasingly blue-shifted with increasing steric hindrance. Electron correlation is found to be increasingly important with decreasing internuclear separations, d(HH).

The OH-stretching and OOH-bending overtone spectrum of HOONO

We have simulated the HOONO vibrational overtone spectrum with use of a local mode Hamiltonian that includes the OH-stretching, OOH-bending, and NOOH-torsional modes and coupling between all three modes. The local mode parameters and the dipole moment function are calculated with coupled-cluster ab initio theory and an augmented Dunning-type triple-zeta basis set. We investigate the accuracy of the local mode parameters obtained from two different potential-energy fitting routines, as well as the sensitivity of these parameters to the basis set employed. We compare our simulated spectra to previously published action spectra in the first and second OH-stretching overtone regions. In addition we have recorded the spectrum in the OH-stretch and OOH-bend combination region around 7700 cm-1 and we also compare to this. Our simulated spectrum is in qualitative agreement with experiment in the first and second OH-stretching overtone and in the stretch-bend regions.

CH Stretching Vibrational Overtone Spectra of tert-Butylbenzene, tert-Butyl Chloride, and tert-Butyl Iodide

The vapor phase CH stretching vibrational overtone spectra of tert-butylbenzene and tert-butyl chloride are measured in the Delta upsilon(CH) = 2-7 region, while the spectrum of tert-butyl iodide is recorded in the Delta upsilon(CH) = 2-6 region. The overtone spectrum of tert-butylbenzene is too complex to make detailed spectral assignments. Local mode frequencies, omega, and anharmonicities, omegax, are obtained for tert-butyl chloride and tert-butyl iodide. The torsional dependencies of the local mode frequency, delta(omega), and anharmonicity, delta(omega)(x), are calculated for the tert-butyl halides. Nonbonded, through-space intramolecular interactions are observed in the blue-shifting of sterically hindered CH oscillators. Scaling factors are presented for relating ab initio calculated local mode parameters to experimental values for alkyl CH oscillators. Fermi resonances are observed between local mode states and local mode/normal mode combination states in tert-butyl chloride and tert-butyl iodide. Vibrational overtone transition intensities are calculated in the range Delta upsilon(CH) = 3-9 using the harmonically coupled anharmonic oscillator (HCAO) model and ab initio dipole moment functions. The resultant HCAO intensities are compared to experimental intensities at Delta upsilon(CH) = 3.

Absolute Intensities of CH Stretching Overtones in Alkenes

We have measured the CH stretching vibrational spectrum of ethene gas in the regions corresponding to 1-5 quanta in the CH stretching vibration with Fourier transform infrared and conventional absorption spectroscopy and have determined the corresponding oscillator strengths. We have calculated the CH stretching vibrational oscillator strengths for a series of alkenes: ethene, propene, 1,3-butadiene, cis-2-butene, and trans-2-butene. The CH stretching intensities are calculated with a simple Morse oscillator local mode model for CH groups and with the harmonically coupled anharmonic oscillator local mode model for CH2 and CH3 groups. The local mode parameters, frequencies, and anharmonicities are obtained from experiments. The harmonic coupling coefficients and the dipole moment functions are calculated with a range of ab initio methods. These include self-consistent-field Hartree-Fock, density functional, correlated, and multireference theories, combined with basis sets ranging from double- to quadruple-zeta quality augmented with polarization and diffuse functions. Variation in calculated oscillator strengths with the choice of ab initio method is systematically studied and compared with observed intensities. From this comparison between the calculated and observed values, we can quantitatively understand the relative usefulness of various ab initio dipole moment functions in calculations of vibrational oscillator strength for alkenes.

Calculated OH-Stretching Vibrational Transitions in the Water−Nitrogen and Water−Oxygen Complexes

We have calculated the fundamental and overtone OH-stretching vibrational band intensities of the water−nitrogen (H2O·N2) and water−oxygen (H2O·O2) complexes. The calculations use the harmonically coupled anharmonic oscillator local mode model with local mode parameters obtained from scaled ab initio calculations and ab initio calculated dipole moment functions. The H2O·N2 and H2O·O2 complexes are weakly bound and the individual molecular units are only slightly perturbed by complexation, unlike what is found for the water dimer (H2O·H2O) and the water−nitric acid complex (H2O·HNO3). The fundamental OH-stretching intensity in H2O·N2 is enhanced and the first overtone intensity weakened compared to H2O as an effect of the hydrogen bonding. In H2O·O2 the OH-stretching intensities are comparable to those of H2O. On a per water unit basis, the calculated OH-stretching intensities of the higher overtones of H2O·N2 and H2O·O2 are similar to those of H2O·H2O. The possible effect of H2O·N2 and H2O·O2 on the atmos...

Calculated OH-Stretching Vibrational Transitions of the Water−Nitric Acid Complex

We have calculated fundamental and overtone OH-stretching vibrational band frequencies and intensities of the water−nitric acid complex. The calculations use the simple harmonically coupled anharmonic oscillator (HCAO) local-mode model with local-mode parameters obtained from scaled ab initio calculations and ab initio-calculated dipole moment functions. The ab initio calculations were performed at the HF, B3LYP, and QCISD levels of theory predominantly with the 6-311++G(2d,2p) basis set. We have compared our results for the water−nitric acid complex with results for the water dimer and the nitric acid and water molecules. The results show that the water−nitric acid complex is more strongly bound, and the changes in spectroscopic properties compared to the individual molecules are more significant than those for the water dimer. The total OH-stretching intensity of the water−nitric acid complex is significantly higher than the sum of the intensities for the individual molecules in the fundamental and higher overtone regions. The transitions associated with the hydrogen-bonded OH bond show a very large red shift compared to the OH-stretching transitions of the nitric acid molecule. These red-shifted bands provide likely spectral regions for the detection of the water−nitric acid complex in the near-infrared. The effect of the water−nitric acid complex on atmospheric OH radial productions and absorption of solar radiation is discussed.

Refined local mode analysis of the stretching vibrational levels of C2D2

Dideuteroacetylene, C2D2, is a remarkable species for which the stretch-bend separability of the vibrational states is such that all the experimentally known stretching levels can be reproduced with an rms of 1.1 cm−1 by using a simple stretching coordinate Hamiltonian model. The only two levels which deviate significantly from the calculations point out the effect of the 1/244 stretch-bend resonance previously identified. The local mode parameters retrieved from the fit of the experimental levels allow for a very satisfactory prediction of the available energy levels of the 12C13CD2 species. A comparison between the local mode and normal mode approaches is presented.

Calculated CH-Stretching Overtone Spectra of Naphthalene, Anthracene and Their Cations

We have calculated fundamental and overtone CH-stretching vibrational band frequencies and intensities of neutral and cationic naphthalene and anthracene, the smallest of the polycyclic aromatic hydrocarbons. The calculations use a simple anharmonic oscillator local mode model with local mode parameters obtained from scaled ab initio calculations and ab initio calculated dipole moment functions. The ab initio calculations were performed at the self-consistent-field Hartree−Fock and the B3LYP hybrid density functional levels of theory with the 6-31G(d) and 6-311+G(d,p) basis sets. The vapor phase overtone spectra of anthracene and both cations have not yet been observed. We find that the cation frequencies are blue shifted and the overtone transitions are of comparable intensities to those in the neutral molecules, contrary to the fundamental transitions which are significantly weaker in the cations. The method presented here can provide an accurate estimate of CH-stretching overtone spectra of neutral and cationic polycyclic aromatic hydrocarbons.

Calculation of OH-stretching band intensities of the water dimer and trimer

We have calculated fundamental and overtone OH-stretching vibrational band intensities of the water dimer and trimer. The intensities were determined with a simple harmonically coupled anharmonic oscillator (HCAO) local mode model and ab initio dipole moment functions. The dipole moment functions were calculated at the self-consistent-field Hartree–Fock and quadratic configuration interaction including single and double excitations levels of theory with the 6–31G(d), 6–311+G(d,p), and 6–311++G(2d,2p) basis sets. The overtone spectra of the dimer and trimer have not been observed and a method of obtaining local mode parameters from scaled ab initio calculations has been suggested. We find that the falloff in absolute intensity with increasing overtone of the dimer and trimer is similar to the falloff observed for the monomer. Our calculations show that the total overtone intensity of the dimer and trimer, although distributed differently, is close to two and three times the total intensity of the monomer for a given region. One significant difference between the monomer and the dimer and trimer is the appearance of the red shifted hydrogen bonded OH-stretching band in the dimer and trimer spectra. We suggest that these red shifted bands are ideal for attempts to observe the water dimer in the atmosphere. The method presented can provide an accurate estimate of the OH-stretching intensities for molecules for which vibrational spectra have not been observed. Such calculations are of importance in atmospheric solar energy absorption models.

The H2S Spectrum around 0.7 μm

The overtone spectrum of H2S has been recorded by intracavity laser spectroscopy in the 14100–14400 cm−1spectral region. The rovibrational analysis was performed allowing one to assign not only lines involving the pair of interacting states {(402), (303)} ({(60+, 0), (60−, 0)} in local mode notation), but also lines involving the interacting states {(322), (223)} ({50+, 2), (50−, 2)} in local mode notation). Indeed, apart from the strong H22interactions that link the rotational levels of the states (60±, 0) on the one hand, and the rotational levels of the states (50+, 2) on the other hand, we observe that the rotational levels of the two pairs of states interact strongly through anharmonic and Coriolis-type resonances. These resonances transfer intensity to lines involving the (50+, 2) pair of states. Altogether 80 rotational upper-state levels have been observed and reproduced satisfactorily using an Hamiltonian matrix that takes explicitly into account the various interactions and assumes the same vibrational energy and rotational constants for the two components of the local mode pairs. The following band centers have been obtained: ν0(60+, 0) = 14291.122 cm−1and ν0(50±, 2) = 14284.705 cm−1. Finally a local mode-type behavior is evidenced by the values of the Hamiltonian constants, and refined vibrational local mode parameters are obtained.

Vibrationally excited states in C3v molecules: CH and CD stretchings in CH3CD3

Abstract The infrared spectrum of gaseous CH3CH3 has been recorded in the range of 3000–15 000 cm−1. Overtone and combination bands up to five quanta of excitation in CH and CD stretchings have been assigned. A total of 71 vibrational states for CH3, involving stretchings and bendings, has been analyzed on the basis of a normal mode model. The relations between the normal and local mode parameters associated with CH stretchings were imposed and three Fermi resonance interactions were included. Twelve parameters reproduce the experimental data related to CH3 with an r.m.s. error of 2.16. Less satisfactory results have been obtained by treating 36 vibrational states involving stretchings and bendings of the CD3 group with the same model.

High resolution spectra of GeH4 v=6 and 7 stretch overtones. The perturbed local mode vibrational states

Here we report the preliminary analysis of the high resolution spectra of 70GeH4 (6000) and (7000) stretch overtone bands obtained by intracavity laser absorption spectroscopy (ICLAS). The observed P(J+1), Q(J), and R(J−1) transitions agree well with the combination difference relations, indicating that the Coriolis coupling in the degenerate states is negligible. This is an important feature for a spherical top molecule near the local mode limit. The vibration–rotational energy levels of upper states as well as those of some perturber states are obtained. The improved local mode parameters of GeH4 are also derived.