Vibrational spectroscopy of the G...C base pair: experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings

The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.     

Molecular potential functions from joint analysis of gas electron diffraction and spectroscopic data

A joint analysis of electron diffraction and spectroscopic data is carried out for BF₃, PBr₃, AsBr₃, SbCl₃, SeO₂ and ClO₂ in terms of the harmonic force fields. The scheme of analysis was extended to include the following spectroscopic observables: vibrational frequencies, rotational, Coriolis coupling and centrifugal distortion constants and, whenever available, those for the isotopic species. For ClO₂ a simplified anharmonic analysis was also performed, the anharmonic spectroscopic observables being involved in this case.

Compelling evidence has been presented that the conventional harmonic approximation for the force field in terms of rectilinear internal coordinates yields the simplest satisfactory representation of diffraction and spectroscopic observations. However, a consistently better fit to experimental data was found when natural curvilinear internal coordinates were used. It is shown here that for the systems considered the joint analysis of data from various sources ensures that reliable and accurate values for equilibrium distances and force field parameters are obtained. The optimized values of spectroscopic constants, structural and force field parameters obtained are presented and compared with those available from the literature.     

Vibrational spectroscopy of protonated imidazole and its complexes with water molecules: ab initio anharmonic calculations and experiments

The results of anharmonic frequency calculations on neutral imidazole (C3N2H4, Im), protonated imidazole (ImH+), and its complexes with water (ImH+)(H2O)n, are presented and compared to gas phase infrared photodissociation spectroscopy (IRPD) data. Anharmonic frequencies are obtained via ab initio vibrational self-consistent field (VSCF) calculations taking into account pairwise interactions between the normal modes. The key results are: (1) Prediction of anharmonic vibrational frequencies on an MP2 ab initio potential energy surface show excellent agreement with experiment and outstanding improvement over the harmonic frequencies. For example, the ab initio calculated anharmonic frequency for (ImH+)(H2O)N2 exhibits an overall average percentage error of 0.6% from experiment. (2) Anharmonic vibrational frequencies calculated on a semiempirical potential energy surface fitted to ab initio harmonic data represents spectroscopy well, particularly for water complexes. As an example, anharmonic frequencies for (ImH+)H2O and (ImH+)(H2O)2 show an overall average deviation of 1.02% and 1.05% from experiment, respectively. This agreement between theory and experiment also supports the validity and use of the pairwise approximation used in the calculations. (3) Anharmonic coupling due to hydration effects is found to significantly reduce the vibrational frequencies for the NH stretch modes. The frequency of the NH stretch is observed to increase with the removal of a water molecule or replacement of water with N2. This result also indicates the ability of the VSCF method to predict accurate frequencies in a matrix environment. The calculation provides insights into the nature of anharmonic effects in the potential surface. Analysis of percentage anharmoncity in neutral Im and ImH+ shows a higher percentage anharmonicity in the NH and CH stretch modes of neutral Im. Also, we observe that anharmonicity in the NH stretch modes of ImH+ have some contribution from coupling effects, while that of neutral Im has no contribution whatsoever from mode-mode coupling. It is concluded that the incorporation of anharmonic effects in the calculation brings theory and experiment into much closer agreement for these systems.     

Anharmonic analysis of the vibrational spectrum of ketene by density functional theory using second-order perturbative approach

The paper reports main results of a comprehensive study of the vibrational spectrum of ketene computed using second-order perturbation theory treatment based on quartic, cubic and semidiagonal quartic force constants. Two different models--a homogeneous model using the same density functionals and basis functions for the harmonic calculations and anharmonic corrections, and a hybrid model in which the two parts of the calculation are conducted using different density functionals and basis sets--have been employed in the present calculations. Different DFT and CCSD methods and DZ and TZ extended basis sets involving diffuse and polarization functions have been used to calculate optimized and vibrationally averaged geometrical parameters, the harmonic and anharmonic vibrational frequencies and the spectroscopic constants such as anharmonicity constants, rotational constants, rotation-vibration coupling constants, Nielsen's centrifugal distortion constants and Coriolis coupling constants. Homogeneous model is found to be superior to the hybrid model in several respects. Difficulties in the hybrid model may arise due to one of the following reasons: (a) the basic requirement that the geometry optimization and frequency calculations must be done at the same level of theory to have valid frequencies is not met in the hybrid model; (b) the molecular structure gets reoptimized at the low level for anharmonic corrections; (c) in addition, the perturbation could also diverge for the above reasons, particularly for the very low, very anharmonic terms where the harmonic approximation is not close enough to make the perturbation work.     

Anharmonic analysis of the vibrational spectra of some cyanides and related molecules of astrophysical importance

A detailed analysis of the vibrational spectra of carbonyl cyanide, diethynyl ketone and acetyl cyanide has been conducted in harmonic and anharmonic approximations. RHF, MP2 and density functional theory (DFT) methods with 6-311++G(2df,2p) basis sets and B3LYP functionals have been employed. Spectroscopic constants such as anharmonicity constants, rotational and centrifugal distortion constants, rotation-vibration coupling constants and Coriolis coupling coefficients have been calculated for each molecule and compared with the experimental data, where available. A close agreement between the calculated and experimental values of the spectroscopic constants has been obtained. Complete assignments have been provided to the fundamental bands, overtones and combination tones of the molecules. Density functional theory based anharmonic frequencies compare well with the experimental frequencies within +/-18 cm(-1) on an average. RHF and MP2 methods, however, give much higher values for the frequencies that need scaling even in the anharmonic approximation.     

Ab initio study of spectroscopic constants and anharmonic force field of 74GeCl2

The equilibrium structure, spectroscopy constants, and anharmonic force field of germanium dichloride have been calculated at MP2, B3LYP, and CCSD(T) levels of theory employing two basis sets, cc-pVDZ and cc-pVTZ, respectively. The computed geometries, rotational constants, and vibration-rotation interaction constants, and quartic centrifugal distortion constants are compared with the available experimental data. The harmonic frequencies, anharmonic constants, and cubic and quartic force constants are predicted. The calculated results show that the MP2 results are in excellent agreement with experiment and represent a substantial improvement over the results obtained from B3LYP. The CCSD(T) method is also an advisable choice to study anharmonic force field of molecules.     

Prediction of vibrational frequencies of UO2(2+) at the CCSD(T) level

Electronic structure calculations at the coupled cluster (CCSD(T)) and density functional theory levels with relativistic effective core potentials and large basis sets were used to predict the isolated uranyl ion frequencies. The effects of anharmonicity and spin-orbit corrections on the harmonic frequencies were calculated. The anharmonic effects are larger than the spin-orbit corrections, but both are small. The anharmonic effects decreased all the frequencies, whereas the spin-orbit corrections increased the stretches and decreased the bend. Overall, these two corrections decreased the harmonic asymmetric stretch frequency by 6 cm-1, the symmetric stretch by 3 cm-1, and the bend by 3 cm-1. The best calculated values for UO22+ for the asymmetric stretch, symmetric stretch, and bend were 1113, 1032, and 174 cm-1, respectively. The separation between the asymmetric and the symmetric stretch band origins was predicted to be 81 cm-1, which is consistent with experimental trends for substituted uranyls in solution and in the solid state. The anharmonic vibrational frequencies of the isoelectronic ThO2 molecule also were calculated and compared to experiment to calibrate the UO22+ results.     

Parametrization of an anharmonic Kirkwood-Keating potential for AlxGa1-xAs alloys

We introduce a simple semiempirical anharmonic Kirkwood-Keating potential to model A(x)B(1-x)C-type semiconductors. The potential consists of the Morse strain energy and Coulomb interaction terms. The optical constants of pure components, AB and BC, were employed to fit the potential parameters such as bond-stretching and -bending force constants, dimensionless anharmonicity parameter, and charges. We applied the potential to finite temperature molecular-dynamics simulations on Al(x)Ga(1-x)As for which there is no lattice mismatch. The results were compared with experimental data and those of harmonic Kirkwood-Keating model and of equation-of-motion molecular-dynamics technique. Since the Morse strain potential effectively describes finite temperature damping, we have been able to numerically reproduce experimentally obtained optical properties such as dielectric functions and reflectance. This potential model can be readily generalized for strained alloys.     

Energy decay mechanisms and anharmonic lattice dynamics: The case of solid nitrogen

The anharmonic frequencies and linewidths of the lattice phonons in -N₂ are calculated on the basis of three different intermolecular potentials which include atom-atom and electrostatic interactions. The distinction between stationary anharmonicity and decay anharmonicity is stressed and the mechanism of energy transfer between the optical lattice phonons and the two-phonon manifold of the crystal is discussed in detail. The temperature dependence of the phonon self-energy is also considered. The results thus obtained for -N₂ are compared with predictions from previous lattice dynamics. SCP and molecular dynamics calculations. The calculated anharmonic effects are substantially independent of the adopted potential: the agreement with experimental data is reasonably good as far as the linewidths are concerned, while the anharmonic deformation of the potential wells (and thus the frequency shifts) is overestimated. We suggest that, while higher orders in the diagram expansion are necessary for a proper account of the stationary anharmonicity, the decay anharmonicity limits its effectiveness to two-phonon processes, thus allowing proper predictions of the phonon lifetimes by using the lowest-order diagrams. Finally, -N₂ is compared to -CO, and the role played by the translation-rotation coupling is discussed.     

The experimental design for computing the harmonic and anharmonic force constant matrices of polyatomic molecules

In the present work we propose a numerical approach to estimate the harmonic and anharmonic force constant matrices, supposing we are able to compute analytically the first order derivative vector of the potential energy surface with respect to the internal coordinates. We use a polynomial least square fit to interpolate this gradient in the stationary point region. The structure of the regression matrix shows that the harmonic force constant matrix may be obtained even for large molecules; the evaluation of the anharmonic contributions request slightly more labor but is possible for 5 to 7 atoms. The present work is applicable even at the CI level and the number of computations remains small. We use the experimental planification to select the geometries to be computed in order to improve the estimation of the regression coefficients i.e. this means to lower their variance.chercheur qualifié du Fonds National Belge de la Recherche Scientifique.     

O-H stretch in phenol and its hydrogen-bonded complexes: band position and relaxation pathways

Anharmonic force fields are a suitable means for identification of vibrational degrees of freedom responsible for the peculiar shape of molecular spectra and the existence of diverse relaxation pathways. In this contribution, we investigated interactions that govern the position of the O-H stretching band in phenol and its dimers with water and ammonia. Dominant couplings are identified, and the nature of relaxation channels is analyzed. The effect of hydrogen bonding on O-H stretching motion and vibrational energy redistribution time through intra- and intermolecular interactions is studied, and possible vibrational predissociation upon O-H stretch excitation is addressed. The results based on computed anharmonic force constants are in accord with the available experimental findings.     

Vibrational spectroscopy at high pressure of the permanganate anion trapped in potassium bromide and potassium perchlorate matrices

The effect of high pressure on the resonance Raman spectra of the permanganate ion isolated in potassium bromide and potassium perchlorate matrices has been investigated at room temperature for pressures up to 50 kbar. The pressure dependences of the anharmonicity constants and harmonic frequencies have been determined from the overtones of the totally symmetric nu1(A1) mode of the permanganate ion. For both matrices, as the pressure increases, the anharmonicity constants decrease slightly, while the harmonic frequencies increase steadily. The effect of the potassium bromide phase transition from a face-centered to a body-centered structure was observed on the permanganate ion Raman spectrum at approximately 24 kbar. The perchlorate matrix does not exhibit any phase transition under the experimental conditions used in this study.     

Anharmonicities of the vO---H…O and vO---D…O vibrations in formic acid crystals

The integrated transition probability, centre of gravity and mean square of the v_O---H…O (IR) band in formic acid crystal are calculated, assuming that the v_O---H…O vibration is ruled by a potential showing several kinds of anharmonicities: it is basically a Morse-type potential whose force constant at the origin and anharmonicity constant depend on a parameter representing the coordinate of a slow vibration. Besides these two anharmonicities (Morse + coupling with a slow vibration) we include in this potential a term representing resonance coupling between two H-bonds (or Fermi resonance with other vibrations of the molecule). We also include in the dipolar moment electrical anharmonicity. By comparison of the calculated results with the corresponding experimental quantities measured for the v_O---H…O and v_O---D…O bands of HCOOH, HCOOD, DCOOH and DCOOD crystals, as described in the preceding article, we can evaluate the orders of magnitude of these different anharmonic contributions, which are found to be all important. A discussion is given of this kind of approach.     

Anharmonic effects in ammonium nitrate and hydroxylammonium nitrate clusters

The covalent and ionic clusters of ammonium nitrate and hydroxyl ammonium nitrate are characterized using density functional theory and second-order vibrational perturbation theory. The most stable structures are covalent acid-base pairs for the monomers and ionic acid-base pairs for the dimers. The hydrogen-bonding distances are greater in the ionic dimers than in the covalent monomers, and the stretching frequencies are significantly different in the covalent and ionic clusters. The anharmonicity of the potential energy surfaces is found to influence the geometries, frequencies, and nuclear magnetic shielding constants for these systems. The inclusion of anharmonic effects significantly decreases many of the calculated vibrational frequencies in these clusters and improves the agreement of the calculated frequencies with the experimental data available for the isolated neutral species. The calculations of nuclear magnetic shielding constants for all nuclei in these clusters illustrate that quantitatively accurate predictions of nuclear magnetic shieldings for comparison to experimental data require the inclusion of anharmonic effects. These calculations of geometries, frequencies, and shielding constants provide insight into the significance of anharmonic effects in ionic materials and provide data that will be useful for the parametrization of molecular mechanical force fields for ionic liquids. Anharmonic effects will be particularly important for the study of proton transfer reactions in ionic materials.     

Update of the anharmonic force field parameters of the ozone molecule

A new set of spectroscopic constants of the ¹⁶O₃ molecule (ω_i, x_ij, y_ijk, γ^DD, _i^X, β_ij^X,…), which determine vibrational dependence of band centres and rotational parameters, is derived from recent accurate analysis of high-resolution experimental ro-vibrational spectra through the theoretical approach based on second-order perturbation expansions in normal coordinates accounting for Darling–Dennison resonance interactions. These values are used to update empirical values of anharmonic coefficients (k_ijl, k_ijlm) of the potential function expansion in normal coordinates. Quadratic f_rr, f_r, f_rr′, f as well as cubic f_rst and quartic f_rstl force constants in internal (bond lengths, bond angle) coordinates are also derived. A detailed discussion is devoted to the accuracy of parameter determination for each of four steps of calculations. It is emphasised that the conventional method based on the inversion of formulae of the perturbation theory gives the largest uncertainties at the last step of calculations: the determination of the anharmonic force field in internal coordinates.     

Anharmonic vibrational probe for N-methylacetamide in different micro-environments

In the present study, anharmonic vibrational properties of the amide modes in N-methylacetamide (NMA), a model molecule for peptide vibrational spectroscopy, are examined by DFT calculations. The 3N-6 normal mode frequencies, diagonal and off-diagonal anharmonicities are evaluated by means of the second order vibrational perturbation theory (VPT2). Good performance of B3LYP/6-31+G** is found for predicting vibrational frequencies in comparison with gas phase experimental data. The amide vibrational modes are assigned through potential energy distribution analysis (PED). The solvation effect on the amide vibrational modes is modeled within the PCM method. From gas phase to polar solvents, red shifts are observed for both harmonic and anharmonic vibrational frequency of amide I mode while the CO bond length increases upon the solvent polarity. Cubic and quartic force constants are further calculated to evaluate the origin of the anharmonicity for the amide I mode of NMA in different micro-environments.     

Vibrational dynamics of the hydrogen bond in H(2)S-HF: Fourier-transform-infrared spectra and ab initio theory

The rotationally resolved infrared spectrum of the hydrogen bonded complex H(2)S-HF and of its isotopomer D(2)S-DF in the HF/DF stretching range have been observed in a supersonic jet Fourier-transform infrared (FTIR) experiment and indicate a predissociation lifetime of 130 ps for H(2)S-HF. Complementary spectra taken at a temperature of 190 K in a cell without resolved rotational structure indicate the presence of strong anharmonic couplings between low frequency intermolecular modes and the HF donor stretch mode previously observed in other complexes with heavier acceptor molecules without rotational fine structure. The anharmonic analysis of the hot band progressions and of the rotational data confirm the coupling mechanism. The coupling constants and the absolute frequency of the hydrogen bonded stretch mode are in excellent agreement with theoretical predictions based on adiabatic variational calculations on potential surfaces computed at MP2 and CCSD(T) level. Complementary calculations with a perturbational approach further confirm the coupling model.     

Vibrational anharmonicity effects in electronic tunneling through molecular bridges

Effects of anharmonic bridge vibrations on electronic tunneling in donor-bridge-acceptor complexes are studied using a model of anharmonic bridge vibration coupled nonlinearly to an electronic degree of freedom. An anharmonicity parameter is introduced, enabling to reproduce the standard harmonic model with linear coupling as a limiting case. The frequency of electronic tunneling oscillations between the donor and acceptor sites is shown to be sensitive to the nuclear anharmonicity, where stretching and compression modes have an opposite effect on the electronic frequency. This phenomenon, that cannot be accounted for within the harmonic approximation, is analyzed and explained.     

Low-lying electronic states of the Ti2 dimer: electronic absorption spectroscopy in rare gas matrices in concert with quantum chemical calculations

Absorption spectra were measured for Ti2 in Ne and Ar matrices. The spectra give evidence for several electronic transitions in the region between 4000 and 10 000 cm(-1) and provide important information about some excited electronic states of Ti2 in proximity to the ground state. The vibrational fine structure measured for these transitions allowed to calculate the force constants and the anharmonicity of the potential energy curves of the excited states, and to estimate changes in the internuclear Ti-Ti distances relative to the electronic ground state. The quantum chemical studies confirm the previously suggested (3)Delta(g) state as the ground state of Ti2. The equilibrium bond distance is calculated to be 195.4 pm. The calculated harmonic frequency of 432 cm(-1) is in good agreement with the experimental value of 407.0 cm(-1). With the aid of the calculations it was possible to assign the experimentally observed transitions in the region between 4000 and 10 000 cm(-1) to the 1 (3)Pi(u)<--(3)Delta(g), 1 (3)Phi(u)<--(3)Delta(g), 2 (3)Pi(u)<--(3)Delta(g), 2 (3)Phi(u)<--(3)Delta(g), and (3)Delta(u)<--(3)Delta(g) excitations (in the order of increasing energy). The calculated relative energies and harmonic frequencies are in pleasing agreement with the experimentally obtained values, with deviations of less than 5% and 2%, respectively. The bond distances estimated on the basis of the experimental spectra tally satisfactorily with the predictions of our calculations.     

Vibrational spectroscopy of (SO4(2-)).(H2O)n clusters, n=1-5: harmonic and anharmonic calculations and experiment

The vibrational spectroscopy of (SO4(2-)).(H2O)n is studied by theoretical calculations for n=1-5, and the results are compared with experiments for n=3-5. The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception (H2O bending mode), the anharmonicity of the observed transitions, all in the experimental window of 540-1850 cm(-1), is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the n=1 and n=2 clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for (SO4(2-)).(H2O)(5): The global minimum of the potential energy corresponds to a C(s) structure, but with incorporation of ZPE the lowest energy structure is C2v, in accordance with experiment. (6) No stable structures were found for (OH-).(HSO4-).(H2O)n, for n相似文献