Internal Vibrational Modes Research Articles

Raman scattering and phase transition in TlGaS2 under pressure

Raman scattering measurements under pressure were performed in a single crystal of TlGaS2. The analysis of the Raman spectrum suggests that the symmetry of the compound belongs to the monoclinic system. The obtained spectra were decomposed by using the deconvolution method, and the “mode-Grüneisen parameters” of the external and internal vibrational modes were calculated. A first order phase transition at 7.4GPa and at 10GPa for external and internal modes, respectively, was observed.

Collisional cooling in a quadrupole ion trap at sub-ambient temperatures

Quadrupole ion traps have been used successfully as ion storage devices for infrared multiphoton dissociation (IRMPD) experiments. Recently there has been interest in doing low temperature action spectroscopy experiments using ion traps as detectors for IRMPD spectroscopy. Cooling the trapping electrodes has the effect of cooling the trapped ions to the same internal temperature, because quadrupole ion traps operate at He bath gas pressures high enough to produce equilibrium ion internal energy distributions. It has previously been shown that collisions of the ions with the bath gas cool the ions’ internal vibrational modes at a rate that competes with IRMPD excitation at ambient temperatures. To investigate the implications of doing IRMPD in a quadrupole ion trap at lower trapping temperatures, the present study measures the collisional cooling rate constants at sub-ambient temperatures down to 25 K. The change in collisional cooling rate constant with trap temperature is correlated to the increased energy needed to dissociate the ions at these lower trap temperatures. It is found that both the energy needed to effect dissociation and the collisional cooling rate increase exponentially as trap temperature drops.

Relaxation dynamics of a photoinduced di-cobalt-tetraoxolene valence tautomer

The temperature dependence of the relaxation dynamics of a dinuclear cobalt-tetraoxolene complex undergoing photoinduced valence tautomerism is reported and discussed. Two different regimes were detected, one at low (5–20 K) and a second at higher temperatures (20–35 K). The activation energy for the low temperature regime suggests a tunnelling process assisted by lattice phonons. In the thermally activated region the activation energy is far from that expected for the total-symmetric Co–O breathing mode, thus suggesting an important role for other internal vibrational modes.

Theoretical Analysis of the Terahertz Spectrum of the High Explosive PETN

The experimental solid-state terahertz (THz) spectrum (3 to 120 cm(-1)) of the high explosive pentaerythritol tetranitrate (PETN, C(5)H(6)N(4)O(12)) has been modeled using solid-state density functional theory (DFT) calculations. Solid-state DFT, employing the BP density functional, is in best qualitative agreement with the features in the previously reported THz spectrum. The crystal environment of PETN includes numerous intermolecular hydrogen-bonding interactions that contribute to large (up to 80 cm(-1)) calculated shifts in molecular normal-mode positions in the solid state. Comparison of the isolated-molecule and solid-state normal-mode calculations for a series of density functionals reveals the extent to which the inclusion of crystal-packing interactions and the relative motions between molecules are required for correctly reproducing the vibrational structure of solid-state THz spectra. The THz structure below 120 cm(-1) is a combination of both intermolecular (relative rotations and translations) and intramolecular (torsions, large amplitude motions) vibrational motions. Vibrational-mode analyses indicate that the first major feature (67.2 cm(-1)) in the PETN THz spectrum contains all of the optical rotational and translational cell modes and no internal (molecular) vibrational modes.

Coupling between local vibrations and charge transport in discotic materials

Charge transport between molecular units is sensitive to coupling between thermal motion and the electronic structure of these units. The thermal motion of a short column of discotic molecules is simulated by a molecular dynamics simulation in order to provide the correct distribution of distorted molecular units, including the effects of the alkoxy tails. Ab initio calculations are then used to determine the electronic structure of the distorted triphenylene cores and the time dependence of the interaction between these. This goes beyond previous works that have calculated changes in charge transfer by finite displacement of rigid molecular units along translational and rotational coordinates. Two timescales and types of motion are distinguished: slow whole body motions of the disks, and internal vibrational modes of the aromatic cores. The effects of these motions are separated via their different timescales, and are found to be of equal importance in the interaction between the HOMOs of neighbouring molecules. Electron/phonon coupling from these small molecular distortions may be important not only for charge transport, but also for loss of carriers via relaxation of electronically excited states.

Crystal growth, structural and spectroscopic analysis of hypoxanthinium chloride monohydrate

Protonated form of hypoxanthinium chloride monohydrate single crystal has been grown from dilute hydrochloric acid. Single crystal X-ray analysis was carried out and the titled crystal belong to the monoclinic P2 1/ c space group. Hypoxanthine is protonated at N(1) with the hypoxanthine cations, linked to chlorine anion via weak bifurcated N–H⋯Cl hydrogen bonds and interconnected by hydrogen bonding contacts of the type N–H⋯O. Infrared, Raman and UV spectroscopic tools were applied to characterize hypoxanthinium chloride monohydrate. By applying group theoretical methods the internal and external modes of vibrations of the title crystal have been identified and discussed.

A Raman Spectroscopic Study of the Phase Transition of BaZr(PO4)2: Evidence for a Trigonal Structure of the High‐Temperature Polymorph.

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First-principles study of pentaerythritol tetranitrate single crystals under high pressure: Vibrational properties

First-principles theoretical methods were used to investigate the vibrational properties of pentaerythritol tetranitrate (PETN) under hydrostatic compression up to 4 GPa. Bond lengths and bond angles for the PETN molecules and the pressure–volume relation for the crystal under high pressure were calculated and compared with previous calculations and with experimental results. Based on the calculated optimized geometries at ambient conditions and under hydrostatic pressure, the frequencies of the internal vibrational modes of the PETN molecules in the crystal and pressure-induced frequency shifts of these vibrational modes were obtained. The calculated vibrational frequencies are compared with previous single molecule calculations and with experimental data.

Spectroscopic manifestation for the isotopic substitution in potassium dihydrogen phosphate

The normal vibration spectra of potassium dihydrogen phosphate (KDP) and its deuterated analogue K(D x H 1− x )PO 4 (DKDP), which arise mainly from internal vibrations of PO 4 tetrahedrons, were recorded by the micro-Raman spectrophotometer system. The four characteristic internal vibration modes of the (H/D) 2PO 4 anion in (D)KDP are assigned by comparing their polarized Raman spectra. The bands of H-vibrations recorded in the FTIR spectra, which have been interpreted as the O–H/D stretching modes, the in-plane bending, and the out-of-plane bending vibrations, are tentatively assigned as well. The frequency ratio of the O–H/D modes due to the hydrogen or deuterium is 1/1.37, which coincides with the ratio of square root of the reduced mass of O–H and O–D.

FTIR features of lithium-iron phosphates as electrode materials for rechargeable lithium batteries

The essential structural features of lithium-metal phosphates (LMP) have been studied using FTIR spectroscopy which is a sensitive tool to probe the local environment in the solid materials. Various LMP materials where M is iron have been investigated including phospho-olivine LiFePO 4, diphosphate LiFeP 2O 7, Nasicon-type phosphate Li 3Fe 2(PO 4) 3 and dihydrate FePO 4·2H 2O. Vitreous and amorphous materials are also considered. Analysis of internal and external modes of vibration allows to distinguish between the different phases and the type of cationic environment in the framework. Results corroborate the contribution of the main factors which are responsible for the complexity of the spectra, i.e. departure from ideal symmetry, interactions between polyhedra, bridging atoms and lattice distortion.

Calculations of accommodation coefficients for diatomic molecular gases

A theoretical study of energy and momentum accommodation coefficients and reduced force coefficients for molecular gases exchanging energy with surfaces has been carried out. The theoretical model uses classical mechanics for describing translational and rotational motions while internal molecular vibrational modes are treated quantum mechanically. Calculations for diatomic molecular gases are compared with recent measurements using hypersonic beams of N2 incident on SiO2 layers deposited on Kapton substrates. The theory gives good qualitative predictions of the behavior of the various accommodation coefficients as functions of the available experimentally controllable parameters such as incident translational energy, incident beam angle, molecular and surface masses, and surface temperature. Quantitative comparisons with measurements for energy and normal momentum accommodation indicate that these experiments can be used to obtain basic physical information about the molecule-surface interaction such as the physisorption potential well depth and the extent of surface roughness.

Inelastic Neutron Scattering Spectrum of Cs2[B12H12]: Reproduction of Its Solid-State Vibrational Spectrum by Periodic DFT

The inelastic neutron scattering (INS) spectrum of polycrystalline Cs2[B12H12] is assigned through 1200 cm(-1) on the basis of aqueous and solid-state Raman/IR measurements and normal mode analyses from solid-state density functional theory. The Cs+ cations are responsible for frequency shifts of the internal cage vibrational modes and I(h) cage mode splittings due to the crystal T(h) site symmetry. These changes to the [B12H12]2- molecular modes make isolated-molecule calculations inadequate for use in complete assignments. Solid-state calculations reveal that 30/40 cm(-1) shifts of Tg/Hg molecular modes are responsible for structure in the INS spectrum unobserved by optical methods or in aqueous solutions.

Resonant infrared laser-induced desorption of methane condensed on NaCl(100): Isotope mixture experiments

Resonantly enhanced infrared laser-induced desorption of methane condensed on a single-crystal NaCl(100) surface is observed after excitation with the widely tunable infrared laser output of the free-electron laser at the free-electron laser for infrared experiments facility using mass spectroscopic detection and time-of-flight analysis. Desorption of methane is observed only when the exciting light is in resonance with an internal vibrational mode of the molecule. Different intramolecular modes of the three methane isotopologues under study--CH(4), CD(4), and CD(3)H--are excited; the degenerate deformation mode nu(4) is observed for CH(4) and CD(4) at 7.69 and 10.11 microm, respectively, as well as the nu(2) and nu(4) modes of CD(3)H at 7.79, 9.75, and 9.98 microm. The desorption signals for the pure layers of these different methane isotopologues as well as for different mixtures of two of these are investigated as a function of the infrared wavelength and the laser fluence. The desorption behavior for pure and mixed layers is compared and the underlying desorption mechanism is discussed.

Electron Transport through a Molecular Conductor with Center-of-Mass Motion

The linear conductance of a molecular conductor oscillating between two metallic leads is investigated numerically both for Hubbard interacting and noninteracting electrons. The molecule-leads tunneling barriers depend on the molecule displacement from its equilibrium position. The results present an interesting interference which leads to a conductance dip at the electron-hole symmetry point that could be experimentally observable. It is shown that this dip is caused by the destructive interference between the purely electronic and phonon-assisted tunneling channels, which are found to carry opposite phases. When an internal vibrational mode is also active, the electron-hole symmetry is broken but a Fano-like interference is still observed.

Langevin Model of the Temperature and Hydration Dependence of Protein Vibrational Dynamics

The modification of internal vibrational modes in a protein due to intraprotein anharmonicity and solvation effects is determined by performing molecular dynamics (MD) simulations of myoglobin, analyzing them using a Langevin model of the vibrational dynamics and comparing the Langevin results to a harmonic, normal mode model of the protein in vacuum. The diagonal and off-diagonal Langevin friction matrix elements, which model the roughness of the vibrational potential energy surfaces, are determined together with the vibrational potentials of mean force from the MD trajectories at 120 K and 300 K in vacuum and in solution. The frictional properties are found to be describable using simple phenomenological functions of the mode frequency, the accessible surface area, and the intraprotein interaction (the displacement vector overlap of any given mode with the other modes in the protein). The frictional damping of a vibrational mode in vacuum is found to be directly proportional to the intraprotein interaction of the mode, whereas in solution, the friction is proportional to the accessible surface area of the mode. In vacuum, the MD frequencies are lower than those of the normal modes, indicating intramolecular anharmonic broadening of the associated potential energy surfaces. Solvation has the opposite effect, increasing the large-amplitude vibrational frequencies relative to in vacuum and thus vibrationally confining the protein atoms. Frictional damping of the low-frequency modes is highly frequency dependent. In contrast to the damping effect of the solvent, the vibrational frequency increase due to solvation is relatively temperature independent, indicating that it is primarily a structural effect. The MD-derived vibrational dynamic structure factor and density of states are well reproduced by a model in which the Langevin friction and potential of mean force parameters are applied to the harmonic normal modes.

A molecular viewer for the analysis of TLS rigid-body motion in macromolecules

TLS (translation/libration/screw) models describe rigid-body vibrational motions of arbitrary objects. A single-group TLS model can be used to approximate the vibration of an entire protein molecule within a crystal lattice. More complex TLS models are broadly applicable to describing inter-domain and other internal vibrational modes of proteins. Such models can be derived and refined from crystallographic data, but they can also be used to describe the vibrational modes observed through other physical techniques or derived from molecular dynamics. The use of TLS models for protein motion has been relatively limited, partly because the physical meaning of the refined TLS parameters is not intuitive. Here, a molecular viewer, TLSView, is introduced using OpenGL and based on the mmLib library for describing and manipulating macromolecular structural models. This visualization tool allows an intuitive understanding of the physical significance of TLS models derived from crystallographic or other data and may be used as an interactive tool to display and interpret inter-domain or other motions in protein structural models. TLSView may also be used to prepare, analyze and validate TLS models for crystallographic refinement.

Vibrational Study of a Molecular Device Using Molecular Dynamics Simulations

A Potential scenario for the implementation of molecular electronic systems is introduced by applying digital signal processing techniques to results from classical molecular dynamics simulations of a molecular system interconnected by nanosize gold clusters. Under this new scenario, signals can be introduced, processed, and read through interactions with the internal vibrational modes of the small molecular unit. We use modulation operations intrinsically inherent to any molecular system as a concept proof. As an example of this type of analysis, we focus on the individual oscillations between C-H and C-C bonds and cluster-cluster displacements.

Normal mode approach for predicting the mechanical properties of solids from first principles: Application to compressibility and thermal expansion of zeolites

We present a method for analyzing the mechanical properties of solids, based on normal modes and their coupling to lattice strains. This method was used to study elastic compression and thermal expansion of zeolites, with parameters calculated from density functional theory. We find in general that the bulk modulus can be divided into two contributions: a positive term arising from compression without internal relaxation, and a negative term from coupling between compression and internal vibrational modes. For silica polymorphs, the former term varies little among the phases studied, reflecting the intrinsic rigidity of $\mathrm{Si}{\mathrm{O}}_{4}$ tetrahedra. In contrast, the latter term varies strongly from one polymorph to the next, because each polymorph exhibits different symmetry constraints on internal vibrations and their couplings to lattice strains. Typically only a few normal modes contribute to the bulk modulus. To facilitate parametrization of this normal mode model, we constructed a simplified classical spring-tetrahedron model for silica. After fitting to properties of silica sodalite, this model reproduces cell volumes and predicts bulk moduli of $\ensuremath{\alpha}$-cristobalite and silica zeolites CHA, LTA, and MFI. We incorporated anharmonic effects into the theory, allowing the calculation of the thermal expansion coefficient. The resulting expression provides a generalization of classical Gr\"uneisen theory, taking into account additional anharmonicities. This method was used to study thermal expansion of fcc aluminum and an aluminosilica sodalite, yielding good agreement with experiment.

Planar Skyrmions: vibrational modes and dynamics

We study Skyrmion dynamics in a ( 2 + 1 )-dimensional Skyrme model. The system contains a dimensionless parameter α , with α = 0 corresponding to the O(3) sigma-model. If two Skyrmions collide head-on, then they can either coalesce or scatter—this depends on α and on the incident speed v , and is affected by transfer of energy to and from the internal vibrational modes of the Skyrmions. We classify these internal modes and compute their spectrum, for a range of values of α . In particular, we find that there is a fractal-like structure of scattering windows, analogous to those seen for kink–antikink scattering in 1 + 1 dimensions.

The stability and Raman spectra of ikaite, CaCO3{middle dot}6H2O, at high pressure and temperature

Raman analyses of single crystals of ikaite, CaCO3·6H2O, synthesized in a diamond-anvil cell at ambient temperature yield spectra from 0.14 to 4.08 GPa; the most intense peaks are at 228 and 1081 cm-1 corresponding to Eg (external) and A1g (internal) modes of vibrations in CO3 2. ions, respectively. These are in good agreement with Raman spectra previously published for ikaite in powder form at ambient temperature and pressure. Visual observations of a sample consisting initially of a mixture of calcite + water in a hydrothermal diamond-anvil cell yielded a P-T phase diagram up to 2 GPa and 120 °C; the boundary for the reaction ikaite ↔ aragonite + water has a positive slope and is curved convexly toward the aragonite + water field similar to typical melt curves. This curvature can be explained in terms of the Clapeyron equation for a boundary between a solid phase and a more compressible liquid phase or largely liquid phase assemblage.