Ab initio calculation of vibrational frequencies and Raman spectra of barium peroxide glass including comparison of tetrahedral BaO4 with GeO4 and SiO4

We have calculated the vibrational frequencies of clusters of atoms from the first principles by using the density-functional theory in the local density approximation (LDA). We are also able to calculate the electronic binding energy for all of the clusters of atoms from the optimized structure. We have made clusters of BanOm (n, m=1-6) and have determined the bond lengths, vibrational frequencies as well as intensities in each case. We find that the peroxide cluster BaO2 occurs with the O-O vibrational frequency of 836.3 cm(-1). We also find that a glass network occurs in the material which explains the vibrational frequency of 67 cm(-1). The calculated values agree with those measured from the Raman spectra of barium peroxide and Ba-B-oxide glass. We have calculated the vibrational frequencies of BaO4, GeO4 and SiO4 each in tetrahedral configuration and find that the vibrational frequencies in these systems depend on the inverse square root of the atomic mass.     

Mono,di, tri and tetraethylene glycol: Spectroscopic characterization using density functional method and experiment

We report infrared and electronic absorption spectra of mono, di, tri and tetra ethylene glycol (EG) in gas phase, their cation and anion and in water solvent using density functional theory calculations at B3LYP/TZVP level. Structural paramaters, rotational and centrifugal distortional constants and dipole moments are also reported. A siginificant shifts in vibrational frequencies and peaks in electronic absorption spectra have been observed upon ionization of mono, di, tri and tetra ethylene glycols. We have also obtained experimental vibrational spectrum of monoethylene glycol. Vibrational frequencies of mono ethylene glycol from theory and experiment are compared. We have used integral equation formalism polarizable continuum model (IEFPCM) model to study the influence of water solvent on vibrational frequencies of neutral mono, di, tri and tetra ethylene glycol. Electronic absorption spectra for these molecules have been obtained using Time dependent density functional theory (TDDFT).     

DFT calculation of the chromyl nitrate, CrO2(NO3)2 The molecular force field

We have carried out a structural and vibrational theoretical study for chromyl nitrate. The density functional theory has been used to study its structure and vibrational properties. The geometries were fully optimised at the B3LYP/Lanl2DZ, B3LYP/6-31G* and B3LYP/6-311++G levels of theory and the harmonic vibrational frequencies were evaluated at the same levels. The calculated harmonic vibrational frequencies for chromyl nitrate are consistent with the experimental IR and Raman spectra in the solid and liquid phases. These calculations gave us a precise knowledge of the normal modes of vibration taking into account the type of coordination adopted by nitrate groups of this compound as monodentate and bidentate. We have also made the assignment of all the observed bands in the vibrational spectra for chromyl nitrate. The nature of the Cr-O and Cr<--O bonds in the compound were quantitatively investigated by means of Natural Bond Order (NBO) analysis. The topological properties of electronic charge density are analysed employing Bader's Atoms in Molecules theory (AIM).     

Determination of molecular vibrational state energies using the ab initio semiclassical initial value representation: application to formaldehyde

We have demonstrated the use of ab initio molecular dynamics (AIMD) trajectories to compute the vibrational energy levels of molecular systems in the context of the semiclassical initial value representation (SC-IVR). A relatively low level of electronic structure theory (HF/3-21G) was used in this proof-of-principle study. Formaldehyde was used as a test case for the determination of accurate excited vibrational states. The AIMD-SC-IVR vibrational energies have been compared to those from curvilinear and rectilinear vibrational self-consistent field/vibrational configuration interaction with perturbation selected interactions-second-order perturbation theory (VSCF/VCIPSI-PT2) and correlation-corrected vibrational self-consistent field (cc-VSCF) methods. The survival amplitudes were obtained from selecting different reference wavefunctions using only a single set of molecular dynamics trajectories. We conclude that our approach is a further step in making the SC-IVR method a practical tool for first-principles quantum dynamics simulations.     

Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

Two-dimensional infrared spectroscopy is capable of following the transfer of vibrational energy between modes in real time. We develop a method to include vibrational relaxation in simulations of two-dimensional infrared spectra at finite temperature. The method takes into account the correlated fluctuations that occur in the frequencies of the vibrational states and in the coupling between them as a result of interaction with the environment. The fluctuations influence the two-dimensional infrared line shape and cause vibrational relaxation during the waiting time, which is included using second-order perturbation theory. The method is demonstrated by applying it to the amide-I and amide-II modes in N-methylacetamide in heavy water. Stochastic information on the fluctuations is obtained from a molecular dynamics trajectory, which is converted to time dependent frequencies and couplings with a map from a density functional calculation. Solvent dynamics with the same frequency as the energy gap between the two amide modes lead to efficient relaxation between amide-I and amide-II on a 560 fs time scale. We show that the cross peak intensity in the two-dimensional infrared spectrum provides a good measure for the vibrational relaxation.     

Vibrational and thermal effects on the dipole polarizability of methane and carbon tetrachloride from vibrational structure calculations

We present a theoretical study of vibrational and thermal effects on the dipole polarizability of methane and carbon tetrachloride. Using a fourth order Taylor expansion in rectilinear normal coordinates of the potential and property surfaces we solve the vibrational problem using vibrational structure theory, e.g., through vibrational self-consistent-field or vibrational configuration-interaction theory. For each vibrational state we calculate in addition the vibrational state average polarizability. Constructing the vibrational partition function by "brute force" allows for prediction of thermal effects on the dipole polarizability. The method is not restricted in any way to polarizabilities nor to the specific representation of the potential and property surfaces employed in this work. Any molecular property with a suitable normal coordinate representation may be considered. We discuss the performance of vibrational self-consistent field as compared to vibrational configuration interaction and study in detail the convergence of the former method with respect to the number of vibrational states included in the thermal averaging. Based on calculations including up to 170,000 vibrational self-consistent-field states we present thermal effects on the dipole polarizability of methane and carbon tetrachloride in the temperature ranges 0-1100 and 0-500 K, respectively. The predicted thermal effect on the dipole polarizability of methane is found to be approximately 0.8% which compare well with previous experimental measurements.     

Calculation of vibrational transition frequencies and intensities in water dimer: comparison of different vibrational approaches

We have calculated frequencies and intensities of fundamental and overtone vibrational transitions in water and water dimer with use of different vibrational methods. We have compared results obtained with correlation-corrected vibrational self-consistent-field theory and vibrational second-order perturbation theory both using normal modes and finally with a harmonically coupled anharmonic oscillator local mode model including OH-stretching and HOH-bending local modes. The coupled cluster with singles, doubles, and perturbative triples ab initio method with augmented correlation-consistent triple-zeta Dunning and atomic natural orbital basis sets has been used to obtain the necessary potential energy and dipole moment surfaces. We identify the strengths and weaknesses of these different vibrational approaches and compare our results to the available experimental results.     

Sum-frequency vibrational spectroscopy of chiral liquids off and close to electronic resonance and the antisymmetric Raman tensor

The strength of the chiral vibrational peaks in infrared-visible sum-frequency (SF) vibrational spectra from isotropic chiral liquids is proportional to the square of the corresponding antisymmetric Raman element. Under the Born-Oppenheimer adiabatic approximation with nonadiabatic corrections, the antisymmetric Raman tensor is much weaker than the symmetric counterpart, but becomes significantly stronger as the input frequency (or the sum-frequency in SF generation) approaches electronic resonance. We verify the theory with experimental results obtained from infrared-visible doubly resonant sum-frequency generation from an isotropic solution of chiral molecules.     

Anharmonic Vibrational Signatures of DNA Bases and Watson-Crick Base Pairs

Changes of molecular structure and associated charge distributions, and changes of anharmonic vibrational parameters from DNA base monomers to the Watson-Crick base pairs, have been investigated at the density functional theory level. Through examination of the NH2, N H, and C=O stretching vibrational modes that are involved in the multiple H-bonds in the base pairs, sensitivity of their diagonal and off-diagonal anharmonicities, as well as anharmonic vibrational couplings, to the structure change are predicted. Our results reveal the intrinsic connection between the anharmonic vibrational potentials, H-bonding, and electrostatic interactions in DNA bases.     

Identification of the atomic scale structures of the gold-thiol interfaces of molecular nanowires by inelastic tunneling spectroscopy

We examine theoretically the effects of the bonding geometries at the gold-thiol interfaces on the inelastic tunneling spectra of propanedithiolate (PDT) molecules bridging gold electrodes and show that inelastic tunneling spectroscopy combined with theory can be used to determine these bonding geometries experimentally. With the help of density functional theory, we calculate the relaxed geometries and vibrational modes of extended molecules each consisting of one or two PDT molecules connecting two gold nanoclusters. We formulate a perturbative theory of inelastic tunneling through molecules bridging metal contacts in terms of elastic transmission amplitudes, and use this theory to calculate the inelastic tunneling spectra of the gold-PDT-gold extended molecules. We consider PDT molecules with both trans and gauche conformations bound to the gold clusters at top, bridge, and hollow bonding sites. Comparing our results with the experimental data of Hihath et al. [Nano Lett. 8, 1673 (2008)], we identify the most frequently realized conformation in the experiment as that of trans molecules top-site bonded to both electrodes. We find the switching from the 42 meV vibrational mode to the 46 meV mode observed in the experiment to be due to the transition of trans molecules from mixed top-bridge to pure top-site bonding geometries. Our results also indicate that gauche molecular conformations and hollow site bonding did not contribute significantly to the experimental inelastic tunneling spectra. For pairs of PDT molecules connecting the gold electrodes in parallel we find total elastic conductances close to twice those of single molecules bridging the contacts with similar bonding conformations and small splittings of the vibrational mode energies for the modes that are the most sensitive to the molecule-electrode bonding geometries.     

Prediction of vibrational frequencies of possible intermediates and side products of the methanol synthesis on ZnO(0001) by ab initio calculations

We used ab initio density functional theory in combination with an embedded cluster approach to calculate vibrational spectra and formation enthalpies of possible intermediates and side products (spectator species) in the synthesis of methanol out of syngas on the ZnO(0001) surface. Our investigations are based upon our previous work on possible reaction pathways and activation barriers for this reaction at oxygen vacancies on ZnO(0001). We present and discuss calculated vibrational frequencies of short-living formyl, hydroxymethylene, formaldehyde, acetale, and hydroxymethyl intermediates and compare the calculated frequencies of formate and methoxy species as well as CO and CO(2) species, at the defect free surface and at oxygen vacancies, with recent experimental findings. All investigated species show characteristic features in their spectra. Therefore, the analysis of their vibrational frequencies is a suitable mean to distinguish them and gain new insights in this reaction which is of recent experimental interest. We are able to identify the structure and characteristics of different surface species, such as monodentate and polydentate carbonate and formate species, in agreement with experimental results.     

Calculating molecular vibrational spectra beyond the harmonic approximation

We present a new approach for calculating anharmonic corrections to vibrational frequency calculations. The vibrational wavefunction is modelled using translated Hermite functions thus allowing anharmonic effects to be incorporated directly into the wavefunction whilst still retaining the simplicity of the Hermite basis. We combine this new method with an optimised finite-difference grid for computing the necessary third and fourth nuclear derivatives of the energy. We compare our combined approach to existing anharmonic models—vibrational self-consistent field theory (VSCF), vibrational perturbation theory (VPT), and vibrational configuration interaction theory (VCI)—and find that it is more cost effective than these alternatives. This makes our method well-suited to computing anharmonic corrections for frequencies in medium-sized molecules. Contribution of the Mark S. Gordon 65th Birthday Festschrift Issue.     

Theory of time-resolved sum-frequency generation and its applications to vibrational dynamics of water

A molecular theory of time-resolved sum-frequency generation (SFG) has been developed. The theoretical framework is constructed using the coupled-oscillator model in the adiabatic approximation. This theory can treat not only the vibrational spectroscopy but also vibrational dynamics. An application of this theory is also provided for estimation of the time constants of the intermolecular vibrational energy transfer between water molecules. This approach can be used for molecular analysis of the experimental results of Shen at al. on the SFG studies of vibrational dynamics of water.     

Coupled cluster and density functional theory studies of the vibrational contribution to the optical rotation of (S)-propylene oxide

In a previous study (Chemical Physics Letters 2005, 401 , 385) we computed the optical rotatory dispersion of (S)-propylene oxide in gas phase and solution using the hierarchy of coupled cluster models CCS, CC2, CCSD, and CC3. Even for the highly correlated CC3 model combined with a flexible basis set, the theoretical gas-phase specific rotation at 355 nm was found to be negative in contrast to the experimental result. We argued that vibrational contributions could be crucial for obtaining a complete understanding of the experimental result. Here, we show that this indeed is the case by using coupled cluster models and density functional theory methods to calculate the vibrational contributions to the gas-phase specific rotation at 355, 589.3, and 633 nm. While density functional theory (B3LYP and SAOP functionals) overestimates the specific rotation at 355 nm by approximately 1 order of magnitude and yields an incorrect sign at 589.3 and 633 nm, the coupled cluster results are in excellent agreement with the experimentally measured optical rotations. We find that all vibrational modes contribute significantly to the optical rotation and that temperature effects must be taken into account.     

A mode-coupling theory of vibrational line broadening in near-critical fluids

We present a fully microscopic mode-coupling theory of near-critical line broadening. All the structural and dynamical input required by the theory is calculated directly from intermolecular potentials. We compute vibrational frequency time-correlation functions and line shapes as the critical point is approached along both the critical isochore and the liquid-gas coexistence curve. Theory is shown to be in good agreement with simulation.     

Adsorption and diffusion on a stepped surface: atomic hydrogen on Pt(211)

We present density functional theory calculations for atomic hydrogen interacting with a stepped surface, the Pt(211) surface. The calculations have been performed at the generalized gradient approximation level, using a slab representation of the surface. This is the state-of-the-art method for calculating the interaction of atoms or molecules with metal surfaces, nevertheless only few studies have used it to study atoms or molecules interacting with stepped surfaces, and none, to the best of our knowledge, have considered hydrogen interacting with stepped platinum surfaces. Our goal has been to initiate a systematic study of this topic. We have calculated the full three-dimensional potential energy surface (PES) for the H/Pt(211) system together with the vibrational band structure and vibrational eigenfunctions of H. A deep global minimum of the PES is found for bridge-bonded hydrogen on the step edge, in agreement with experimental results for the similar H/Pt(533) system. All the local vibrational excitations at the global minimum have been identified, and this will serve as a helpful guide to the interpretation of future experiments on this (or similar) system(s). Furthermore, from the calculated PES and vibrational band structure, we identify a number of consequences for the interpretation or modelling of diffusion experiments studying the coverage and directional dependence of atomic hydrogen diffusion on stepped platinum surfaces.     

The vibrational auto-adjusting perturbation theory

In this work a new method to calculate anharmonic vibrational ground and excited state energies is proposed. The method relies on the auto-adjusting perturbation theory (APT) which has been successfully used to diagonalize square matrices. We use as zeroth order correction the self-consistent vibrational energies, and with the APT approach we calculate the vibrational anharmonic correlation correction to any desired order. In this paper we present the methodology and apply it to a model system and formaldehyde. Vibrational APT approach shows a robust convergent behavior even for the states where the standard (Rayleigh-Schrödinger) vibrational Møller-Plesset perturbation theory is clearly divergent.     

Fluctuating energy level Landau-Teller theory: application to the vibrational energy relaxation of liquid methanol

State-to-state vibrational energy relaxation (VER) rates of the OH-stretch fundamental to select vibrational modes of liquid methanol are presented. The rates are calculated via a modified, fluctuating Landau-Teller (FLT) theory approach, which allow for dynamical vibrational energy level shifts. These rates are then compared to previously published results from Gulmen and Sibert [J. Phys. Chem. A 2004, 108, 2389] for the traditional Landau-Teller (LT) method as well as results calculated through time-dependent perturbation theory (TD), which naturally allow for the fluctuation. For the first time, this method is applied to a polyatomic molecular system, and the FLT theory greatly reduces the discrepancy between the LT and TD results or, at a minimum, is comparable to the LT approach with very little additional computational cost.     

A multimode analysis of the gas-phase photoelectron spectra in oligoacenes

We present a multimode vibrational analysis of the gas-phase ultraviolet photoelectron spectra of the first ionization in anthracene, tetracene, and pentacene, using electron-vibration constants computed at the density functional theory level. The first ionization of each molecule exhibits a high-frequency vibronic structure; it is shown that this regularly spaced feature is actually the consequence of the collective action of several vibrational modes rather than the result of the interaction with a single mode. We interpret this feature in terms of the missing mode effect. We also discuss the vibronic coupling constants and relaxation energies obtained from the fit of the photoelectron spectra with the linear vibronic model.     

Dielectric effect on thermodynamic properties in vinblastine by DFT/Onsager modelling

We know that vinblastine, as one of the vinca alkaloids, has played a major role in cancer chemotherapy by inhibiting the polymerisation of tubulin into microtubules. We present an in-depth investigation of the structural, infrared (IR) spectra of vinblastine. The structure of vinblastine is theoretically investigated using the density functional theory and Hartree–Fock levels of theory with the standard 6-31g* and 6-31g** basis sets. The vibrational spectral data obtained from IR spectra are assigned modes based on the results of the theoretical calculations as intensity and frequency curves. The fundamental vibrational modes were characterised depending on the stability of vinblastine in different dielectric constants. Thermodynamic analysis of data demonstrates good correlation of vinblastine at various media by SCRF–Onsager model with linear coefficient (R ²). Thus, the goal of this article is to evaluate and quantify the molecular basis for vinblastine structure in variant positions.