Modes Of Molecular Motion Research Articles

On selection rules in two-dimensional terahertz-infrared-visible spectroscopy.

Two-dimensional terahertz-infrared-visible (2D TIRV) spectroscopy directly measures the coupling between quantum high-frequency vibrations and classical low-frequency modes of molecular motion. In addition to coupling strength, the signal intensity in 2D TIRV spectroscopy can also depend on the selection rules of the excited transitions. Here, we explore the selection rules in 2D TIRV spectroscopy by studying the coupling between the high-frequency CH3 stretching and low-frequency vibrations of liquid dimethyl sulfoxide (DMSO). Different excitation pathways are addressed using variations in laser pulse timing and different polarizations of exciting pulses and detected signals. The DMSO signals generated via different excitation pathways can be readily distinguished in the spectrum. The intensities of different excitation pathways vary unequally with changes in polarization. We explain how this difference stems from the intensities of polarized and depolarized Raman and hyper-Raman spectra of high-frequency modes. These results apply to various systems and will help design and interpret new 2D TIRV spectroscopy experiments.

Shock-wave structure in non-polar diatomic and polyatomic dense gases under rotation and vibration

This study investigates the effect of rotation and vibration on the structure of shock waves in moderately dense diatomic and polyatomic non-polar gases using the one-temperature Navier–Stokes–Fourier approach. The modified Enskog equation of state of the gas is taken to include the denseness and shielding effects. The specific heat at constant volume has been taken to be temperature-dependent. The shear viscosity, the bulk viscosity, and the thermal conductivity have been assumed to follow the temperature-dependent power-law model. Nitrogen and oxygen gas have been taken as the test cases for diatomic gases while carbon dioxide was taken for the polyatomic gases. The implicit system of equations is derived and solved numerically for density and temperature. The inclusion of denseness, rotational, and vibrational modes of molecular motion have a significant effect on the density and temperature profiles, the inverse shock thickness, the bulk to shear viscosity ratio, and the molar specific heat at constant pressure. The gas having a low characteristic vibrational temperature has been found to have a high value of inverse shock thickness. The inverse shock thickness, the bulk to shear viscosity ratio, and the molar specific heat at constant pressure for nitrogen and carbon dioxide are found to be in good agreement with the experimental values.

Effect of Vibrational Nonequilibrium on Isolator Shock Structure

Analyses of dual-model scramjet engines often rely on the assumption of thermally perfect gas, for which the internal modes of molecular motion are assumed to be in thermal equilibrium. With an increase in enthalpy and in the presence of shocks and expansion waves, the equilibrium assumption does not hold within a scramjet inlet-isolator section. For the flight Mach numbers considered here, the molecular vibrational modes are affected, leading to not only a change in the gas properties but a redistribution of the total energy. In this work, a multitemperature model is used to describe thermal nonequilibrium of flow through a square duct with an inlet Mach number of 1.9. The highly resolved simulations show that the pseudoshock structure is altered due to nonequilibrium, with the leading edge of the shock structure moving upstream. Moreover, the length of the pseudoshock is considerably increased. Both of these effects are shown to be caused by slow relaxation of the molecules. Furthermore, even at the isolator’s exit, equilibrium is not established, which is manifested as a pressure defect. If and when the fluid reaches thermal equilibrium, inside the downstream combustor, there is a potential for a sudden surge in local pressure that could endanger scramjet operation.

Dielectric properties of liquid-crystal azomethine polymer with a side alkyl-substituted chain, doped with fullerene C60

We studied the actual and imaginary components of the dielectric constant of liquid-crystal azomethine polymer with a side chain, doped with 0.5 wt % of fullerene C60, over a wide range of temperatures and frequencies; measurements were made by means of dielectric spectroscopy. By analyzing the frequency dependence of the dielectric constant, we detected the relaxation processes (α, β1, and β2) in the nanocomposite, corresponding to certain modes of molecular motion and described them by the Arrhenius equations (β1- and β2-processes) and the Vogel–Fulcher–Tamman equation (α-process). An antiplasticization effect is discovered after doping the polymer with fullerene C60, which manifests itself in increasing the glass transition temperature of the nanocomposite compared to this parameter typical of pure polymer.

Damping mechanism and different modes of molecular motion through the glass transition of chlorinated butyl rubber and petroleum resin blends

AbstractTo further investigate the effect of petroleum resin on damping mechanism and different modes of motion of chlorinated butyl rubber (CIIR), two kinds of petroleum resins with different molecular structures, aliphatic C5 resin and aromatic C9 resin, were incorporated into CIIR. The experimental results showed that the aliphatic C5 resin exhibited a better miscibility with CIIR, compared with aromatic C9 resin. With increase in the content of the C5 resin, the α process and the α′ process of CIIR moved to the higher temperature but to different extents, and the effective damping temperature range was broadened remarkably. The CIIR/C9 resin blends showed two loss peaks, which corresponded to the CIIR matrix and the C9 resin dispersed phase, respectively. The C9 resin neither moved different relaxation modes of CIIR to room temperature nor enhanced the value of the loss damping peak. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40464.

Fixman compensating potential for general branched molecules.

The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

The proper glass transition temperature of amorphous polymers on dynamic mechanical spectra

Glass transition is crucial to the thermal and dynamical properties of polymers. Thus, it is important to detect glass transition temperature (T g) with a sensitive and proper method. Dynamic mechanical analysis (DMA) is one of the most frequently used methods to determine T g due to its advantage of high sensibility. However, there is controversy in the past literatures to determine the proper glass transition temperature among three transition temperatures, i.e., T g1, T g2 and T g3 in the dynamic mechanical spectra, which correspond to the temperature abscissa of intersect value of two tangent lines on storage modulus (E′), the peak of the loss modulus (E″) and the peak of the loss tangent (tan δ). In this work, these three transition temperatures were compared with the glass transition temperature determined by DSC (T gDSC). Based on the discussion of different modes of molecular motion around the glass transition region, it is demonstrated that T g1 and T g2 have the same molecular mechanism as T gDSC, i.e., local segmental motion which is enthalpic in nature and determines the proper glass transition temperature, while T g3 is assigned to the transition temperature of entropic Rouse modes, thus cannot be used as the proper glass transition temperature.

Thermodynamical Quantities of Chalcogenide Dimers (O2, S2, Se2, and Te2) from Spectroscopic Data

Attempts have been made to calculate the thermodynamical quantities of diatomic molecules such as O2, S2, Se2, and Te2from spectroscopic data with the help of partition function theory. The results have been calculated in the temperature range 100–3000°C. In order to increase accuracy of the calculated quantities, we have incorporated nonrigidity, anharmonicity, and stretching effects of molecules. The variation of these quantities with temperature have been studied and explained in terms of various modes of molecular motions.

Molecular dynamics in chlorinated butyl rubber containing organophilic montmorillonite nanoparticles

The dynamic mechanical loss tangent (tanδ) of chlorinated butyl rubber (CIIR) shows an asymmetrical double-peak structure with a shoulder on the low-temperature side and a maximum on the high-temperature side, which are attributed to local segmental motion and Rouse modes, respectively. To study the effect of nanoparticles on these two different modes of molecular motion, organophilic montmorillonite nanoparticles (OMMT) were incorporated into CIIR. With the increase of OMMT weight fraction, a filler network is formed and becomes more and more compact in the CIIR matrix, which exerts significant effect on the molecular dynamics of CIIR. The maximum and the shoulder of the tanδ peak are both suppressed by the filler network, but the maximum is suppressed to a higher extent and finally even becomes lower than the shoulder at high filler loading. The temperature position of the maximum is also shifted toward lower temperature with the formation of the filler network, while that of the shoulder remains nearly constant. These phenomena can be interpreted in terms of the different restriction extents of the filler network on the different modes of molecular motion.

Research on Dynamic Mechanical Properties of Poly(m-Phenyleneisophthalamide) Paper

The dynamic mechanical properties of PMIA-Pulp applied paper were investigated. At the same time, the dynamic mechanical properties of DuPont T410 paper were compared. Measurements of the dynamic mechanical properties were carried out on samples of low crystallinity and low orientation over a temperature range from 20°C to +500°C, at a frequency of 110 Hz, at a heating rate of 3°C/min. As the temperature from low to high, three different mechanical states with glassy state, rubber state and fluid state were appeared on DMA temperature curve, it responded the different mode of molecular motion. Storage modulus and glass transition peak of DuPont T410 paper were higher than the self-made applied paper. It means DuPont T410 Paper had a high resistance to external forces and deformation, as well as a good rigidity. Molecular chain freedom movement was difficult and the energy required to move relatively larger.

Using Two-Dimensional Correlation Dynamic Mechanical Spectroscopy to Detect Different Modes of Molecular Motions in the Glass−Rubber Transition Region in Polyisobutylene

In this Article, we report the first study of the molecular dynamics in the glass-rubber transition region in polyisobutylene by 2D correlation dynamic mechanical spectroscopy (2DC-DMS). With the help of the high resolution and high sensitivity of the technique, the sub-Rouse modes are independently separated from the Rouse modes and local segmental motion (LSM). According to the positions and widths of autopeaks of three modes of molecular motions, the loss tangent peak is resolved into three peaks by nonlinear fitting method. Moreover, the glass-rubber transition region is divided into three regions. 2DC-DMS has been demonstrated to be a powerful tool for studying the molecular motions with different time/length scales.

Detecting different modes of molecular motion in polyisobutylene and chlorinated butyl rubber by using dielectric probes

To explore the complex molecular dynamics of glass-forming substances in the softening dispersion region from the glassy state to the rubbery state, polyisobutylene (PIB) and chlorinated butyl rubber (CIIR), representives of an amorphous polymer with effective chain packing and low intermolecular cooperativity, were doped with low molecular weight brominated para-tert-octyl phenolic resin (PR) and then tested using dielectric spectroscopy. The results show that the PR molecules, having little effect on the overall molecular dynamics of PIB and CIIR, can be used as the dielectric probes to successfully monitor local segmental motion, sub-Rouse modes and Rouse modes in the dielectric spectra simultaneously. The relaxation times of the local segmental motion and the Rouse modes can be directly obtained from the dielectric spectra. It is found that the Rouse modes have weaker temperature-dependence than the local segmental motion, indicating the thermorheological complexity of PIB and CIIR. Consequently, the local segmental motion superposes the Rouse modes at a temperature near Tg. This study suggests that the dielectric probes have the capability to detect and study different modes of molecular motion around the softening dispersion region.

Photophysical Probes of the Amorphous Solid State of Proteins

The properties of amorphous solid proteins influence the texture and stability of low-moisture foods, the shelf-life of pharmaceuticals, and the viability of seeds and spores. We have investigated the relationship between molecular mobility and oxygen permeability in dry food protein films—bovine α-lactalbumin (α-La), bovine β-lactoblobulin (β-Lg), bovine serum albumin (BSA), soy 11S globulin, and porcine gelatin—using phosphorescence from the triplet probe erythrosin B. Measurements of the phosphorescence decay in the absence (nitrogen) and presence (air) of oxygen versus temperature provide estimates of the non-radiative decay rate for matrix-induced quenching (k TS0) and oxygen quenching (k Q[O2]) of the triplet state. Since the oxygen quenching constant is the product of the oxygen solubility ([O2]) and a term (k Q) proportional to the oxygen diffusion coefficient, it is a measure of the oxygen permeability through the films. For all proteins except gelatin, Arrhenius plots of k TS0 reveal a gradual increase of apparent activation energy across a broad temperature range starting at ∼50 °C; this suggests that there is a steady increase in the available modes of molecular motion with increasing temperature within the protein matrix. Arrhenius plots for k Q[O2] were linear for all proteins with activation energies ranging from 24 to 29 kJ/mol. The magnitude of the oxygen quenching constants varied in the different proteins; the rates were approximately 10-fold higher in α-La, β-Lg, and BSA than in 11S glycinin and gelatin. Although the rate of oxygen permeability was not directly affected by the increased mobility of the protein matrix, plots of k Q[O2] versus k TS0 were linear over nearly three orders of magnitude in the protein films, suggesting that the matrix mobility plays a specific role in modulating oxygen permeability. This effect may reflect differences in matrix-free volume that directly influence both mobility and oxygen solubility.

ChemInform Abstract: High-Resolution Solid-State NMR Studies of Synthetic and Biological Macromolecules

Publisher Summary This chapter reviews the high-resolution solid-state nuclear magnetic resonance (NMR) studies of synthetic polymers and naturally occurring biological macromolecules with emphasis placed on revealing their conformations. A survey of high-resolution solid-state NMR studies of both types of macromolecular system has the advantage of being able to cover the topics of conformation and dynamics of polymers in general. A proportion of the studies reviewed have been devoted to the analysis of secondary structures in biological macromolecules, such as peptides, proteins, and polysaccharides, while the majority of the studies reviewed have been performed for the analysis of phase structure, the various modes of molecular motions, and their influence on the mechanical properties of synthetic polymers. The scope of this chapter is restricted mainly to studies of 13C nuclei, although some studies using other rare spin 1/2 nuclei, such as 31Po r 15N are reviewed where appropriate. This is because the use of 13C NMR is most suitable for organic macromolecules and the majority of studies on these subjects have been caried out by the means of 13C NMR spectroscopy.

Overcoming Misconceptions about Configurational Entropy in Condensed Phases

Configurational and thermal entropy yield identical numerical values for ΔS only when the system's "dimensionless" energy gaps (Δε /kT ) between the accessible quantized energy levels are minimized by temperature to nearly infinitesimal values so that the spreading of energy among the system's microstates becomes effectively classical and equiprobable. The molecular partition function provides the numerical value for the effective number of both accessible states and spatial configurations per molecule, for which this condition is valid at a given temperature. Considering the phenomenon of mixing and standard molar entropy values leads to the conclusion that configurational entropy calculations are significant and thermodynamically valid because of their fundamental connection to the process of random energy re-distributions in a system, via the available modes of molecular motion.

Thermodynamic Properties of Platinum Diatomics

Thermodynamic properties of diatomic molecules containing platinum (PtH, PtC, PtN and PtO) have been calculated using spectroscopic data and partition function theory. Values of the Gibbs energy (G), enthalpy (H), entropy (S) and specific heat capacity at constant pressure (C P) are presented for each species in the temperature range from 100 K to 3000 K. To obtain the most accurate data, anharmonicity, nonrigidity and stretching effects have been incorporated in the calculations. The variation of these properties with temperature is also discussed in terms of different modes of molecular motion.

Phosphorescence Probes of Molecular Mobility, Oxygen Permeability, and Dynamic Site Heterogeneity in Amorphous Soybean Glycinin

The physical properties of amorphous biomolecules are important to the stability of low-moisture foods and pharmaceuticals. In the amorphous solid state, slow molecular motions are suitable for study by phosphorescent techniques. We use phosphorescence of erythrosin B dispersed in soy glycinin films to characterize the molecular mobility, oxygen permeability, and dynamic heterogeneity of the protein matrix. Films are spread from concentrated solutions of probe/protein at mole ratios of 0.045/1. Measurements as a function of temperature are made of phosphorescence intensity decays, emission spectra, and time-resolved emission spectra. Decays are fit with a stretched exponential function and both lifetimes and stretching exponents decrease with temperature. Arrhenius analysis of non-radiative quenching constants suggests that the protein matrix undergoes a broad softening transition between 70 and 120C during which additional modes of molecular motion are activated. The stretching exponent, a measure of the breadth of distribution of lifetimes and hence probe site heterogeneity, decreases gradually with temperature up to 70C and more steeply at higher temperatures, providing evidence of the onset of softening at 70C. Oxygen quenching rates, calculated from a comparison between emission lifetimes in the presence and absence of oxygen, vary roughly linearly with collisional quenching rates, which suggests that the local molecular mobility responsible for collisional quenching also modulates oxygen permeability. Delayed emission spectra are fit to a double lognormal function that provides peak emission energy and bandwidth. Bandwidth increases dramatically above 70C, which reflects an increase in the width of the distribution of energetically distinct matrix environments and provides further evidence of softening. The emission spectra blue shift with increasing delay time providing strong evidence that probes reside in distinct sites that vary in molecular mobility. Research supported by CSREES.

The nature of crystal disorder in milled pharmaceutical materials

The purpose of this study was to study the nature of disorder in milled crystalline materials. Specifically to elucidate if the induced disorder represents crystal defects or amorphous regions. Felodipine and griseofulvin were chosen as model drugs and subjected to milling. Cryomilling was chosen in order to mitigate the influence of heat generated by the process. Amorphous drug samples were produced by quenching the melt. Crystalline, amorphous and cryomilled drug samples were characterized by powder X-ray diffraction (PXRD), thermal analysis (DSC), thermal polarization (thermally stimulated polarization current), and surface energy (inverse gas chromatography). The PXRD analysis shows that cryomilling reduces the crystallinity of the two drugs, while maintaining the same crystal form. Heat capacity measurements (DSC) show that milled material for either drug does not exhibit a glass transition but shows instead an exothermic (crystallization like) event. The thermal polarization profiles revealed that none of the modes of molecular motion (polarization peaks) characteristic of the amorphous form were observed in either the unmilled crystalline or milled forms for either drug. For each drug, the polarization spectra of milled forms were similar, but not identical, to those of the corresponding unmilled crystalline materials. Inverse gas chromatography (IGC) measurements showed that the surface energy of cryomilled samples was higher than those of the unmilled and amorphous forms for both drugs. The polarization and heat capacity measurements show that the disorder induced by milling either griseofulvin or folodipine consists of crystal defects rather than amorphous regions. The exothermic event in the milled samples is attributed to the crystallization of defects in the crystal. These results when combined with the IGC measurements indicate that the milled material retains its crystalline character, making it more stable (at the core) than the amorphous form. However, the milled material has also the most active surface, making it the more interactive with other surfaces as an activated powder.

Study of Molecular Dynamics and the Solid State Phase Transition Mechanism for Unsymmetrical Thiopyrophosphate Using X-ray Diffraction, DFT Calculations and NMR Spectroscopy

Differential scanning calorimetry (DSC) and low-temperature X-ray diffraction studies showed that 2-thio-(5,5-dimethyl-1,3,2-dioxaphosphorinanyl)2'-oxo-dineopentyl-thiophosphate (compound 1) undergoes reversible phase transition at 203 K related to the change of symmetry of the crystallographic unit. Solid state NMR spectroscopy was used to establish the dynamic processes of aliphatic groups and the phosphorus skeleton. 13C and 31P variable temperature NMR studies as well as T1 and T1rho measurements of relaxation times revealed the different mode of molecular motion for each neopentyl residue directly bonded to phosphorus. It is concluded that molecular dynamics of aliphatic groups causes different van der Waals interactions in the crystal lattice and is the driving force of phase transition for compound 1. Finally, we showed that very sharp phase transition temperature makes compound 1 an excellent candidate as a low-temperature NMR thermometer in the solid phase.

Modes of Molecular Motion in Low Molecular Weight Polystyrene

The variations with temperature of the viscosity, η, and the relaxation times for various low molecular weight, unentangled polystyrenes (PS) are analyzed. We find that the temperature dependence of η does not directly reflect the behavior of the global chain modes. Depending on molecular weight and temperature, η can exhibit a stronger temperature dependence than even the local segmental modes. However, this is only a consequence of the strong temperature dependence of the recoverable compliance Js. The Rouse relaxation time, τ1, deduced from the product of the viscosity and the recoverable compliance, has the expected behavior. For example, this Rouse time for a PS of molecular weight equal to 2 kg/mol has the same temperature dependence as that for self-diffusion; hence, there is no enhancement of translational diffusion in the polymer. The same conclusion was reached by Urakawa et al. [Urakawa, O.; Swallen, S. F.; Ediger, M. D.; von Meerwall, E. D. Macromolecules 2004, 37, 1558], although the analysis...