Experimental and Theoretical Investigations of Terahertz Spectra of the Structural Isomers: Mannose and Galactose

The high-resolution terahertz spectra of the two structural isomers, mannose and galactose, have been measured by terahertz time-domain spectroscopy (THz-TDS) in the range of 0.5–4.0 THz at room temperature. Significant differences between these similar molecules have been found in their THz characteristic spectra, implying that THz-TDS is a powerful tool for identifying isomers. Structural analyses and normal mode calculations of the two systems were performed using solid-state density functional theory (DFT) with the PBE and PW91 density functionals as well as using gas-state DFT with B3LYP hybrid functional. Among these calculations, the solid-state simulated results obtained from the PBE method exhibit a good agreement with the experimentally measured spectra. According to the calculated results of PBE, the observed spectral features were assigned as primarily external lattice translations, deformations, and rotations with lesser contributions due to intramolecular motion of pyranose ring, CH2OH group, and hydroxyl groups.

Molecular Level Interpretation of Vibrational Spectra of Ordered Ice Phases

<div> <div> <div> <p>We build on results from our previous investigation into ice Ih using a combination of classical many-body molecular dynamics (MB-MD) and normal mode (NM) calculations to obtain molecular level information on the spectroscopic signatures in the OH stretching region for all seven of the known ordered crystalline ice phases. The classical MB-MD spectra are shown to capture the important spectral features by comparing with experimental Raman spectra. This motivates the use of the classical simulations in understanding the spectral features of the various ordered ice phases in molecular terms. This is achieved through NM analysis to first demonstrate that the MB-MD spectra can be well recovered through the transition dipole moments and polarizability tensors calculated from each NM. From the normal mode calculations, measures of the amount of symmetric and antisymmetric stretching are calculated for each ice, as well as an approximation of how localized each mode is. These metrics aid in viewing the ice phases on a continuous spectrum determined by their density. As in ice Ih, it is found that most of the other ordered ice phases have highly delocalized modes and their spectral features cannot, in general, be described in terms of molecular normal modes. The lone exception is ice VIII, the densest crystalline ice phase. Despite being found only at high pressure, the symmetry index shows a clear separation of symmetric and antisymmetric stretching modes giving rise to two distinct features. </p> </div> </div> </div>

Molecular Level Interpretation of Vibrational Spectra of Ordered Ice Phases

<div> <div> <div> <p>We build on results from our previous investigation into ice Ih using a combination of classical many-body molecular dynamics (MB-MD) and normal mode (NM) calculations to obtain molecular level information on the spectroscopic signatures in the OH stretching region for all seven of the known ordered crystalline ice phases. The classical MB-MD spectra are shown to capture the important spectral features by comparing with experimental Raman spectra. This motivates the use of the classical simulations in understanding the spectral features of the various ordered ice phases in molecular terms. This is achieved through NM analysis to first demonstrate that the MB-MD spectra can be well recovered through the transition dipole moments and polarizability tensors calculated from each NM. From the normal mode calculations, measures of the amount of symmetric and antisymmetric stretching are calculated for each ice, as well as an approximation of how localized each mode is. These metrics aid in viewing the ice phases on a continuous spectrum determined by their density. As in ice Ih, it is found that most of the other ordered ice phases have highly delocalized modes and their spectral features cannot, in general, be described in terms of molecular normal modes. The lone exception is ice VIII, the densest crystalline ice phase. Despite being found only at high pressure, the symmetry index shows a clear separation of symmetric and antisymmetric stretching modes giving rise to two distinct features. </p> </div> </div> </div>

Apparent contradiction between calculated kinetic and potential energy fractions of phonons in molecular solids with implications on condensed-phase chemistry

ABSTRACTMany computational and experimental analyses of molecular excitation rely on relative atomic velocities to identify the excitation of chemical bonds. These are often interpreted through the aid of normal mode calculations. We address two potential gaps in this approach: 1. Relative velocities may not reflect the total potential energy absorbed by the bond. 2. Normal mode calculations omit interactions between neighboring molecules, effectively assuming a similarity between condensed- and gas-phase chemistry. Phonon calculations implicitly include interactions between neighboring molecules and allow analyses of both relative velocities and potential energies in solids.In the present work, we compare kinetic and potential energy fractions of the phonon modes of the molecular solids nitromethane and β-HMX. We show that velocity-based methods are likely sufficient to analyze nitromethane. However, they cannot detect the majority of excitation ofthe N-N bonds in β-HMX, the scission of which appears to begin major decomposition pathways in the molecules.In the broader context of condensed-phase chemistry, this implies that important interactions may not all be identifiable through analyses that rely solely on relative atomic velocities.

Negative cooperativity in the nitrogenase Fe protein electron delivery cycle

Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to two ammonia (NH3) molecules through the participation of its two protein components, the MoFe and Fe proteins. Electron transfer (ET) from the Fe protein to the catalytic MoFe protein involves a series of synchronized events requiring the transient association of one Fe protein with each αβ half of the α2β2 MoFe protein. This process is referred to as the Fe protein cycle and includes binding of two ATP to an Fe protein, association of an Fe protein with the MoFe protein, ET from the Fe protein to the MoFe protein, hydrolysis of the two ATP to two ADP and two Pi for each ET, Pi release, and dissociation of oxidized Fe protein-(ADP)2 from the MoFe protein. Because the MoFe protein tetramer has two separate αβ active units, it participates in two distinct Fe protein cycles. Quantitative kinetic measurements of ET, ATP hydrolysis, and Pi release during the presteady-state phase of electron delivery demonstrate that the two halves of the ternary complex between the MoFe protein and two reduced Fe protein-(ATP)2 do not undergo the Fe protein cycle independently. Instead, the data are globally fit with a two-branch negative-cooperativity kinetic model in which ET in one-half of the complex partially suppresses this process in the other. A possible mechanism for communication between the two halves of the nitrogenase complex is suggested by normal-mode calculations showing correlated and anticorrelated motions between the two halves.

A study of the conformational profile and the vibrational spectra of the plant hormone indole-3-acetic acid

The structural stability of indole-3-acetic acid was investigated by DFT-B3LYP calculations with the 6-311G** basis set. From the calculations the gauche–gauche (gg) structure was predicted to be the second lowest energy minimum for the acid. It is energetically only 0.57 kcal/mol above the lowest conformer which is the trans–cis (tc) structure. A further stable conformer, however, highest in energy, is the trans–trans (tt) one, which is by 2.68 kcal/mol higher in energy than tc. The tc conformer upon full optimization turned a little bit away from real tc to a near tc (ntc) structure (defining torsional angles only changed by a few decigrades). However, the X-ray data indicate a structure in the solid, which is most similar to gg, stabilized by intermolecular eight ring hydrogen bonds. In the present DFT calculations such stabilizations cannot be accounted for, because the calculations treat only isolated molecules. To take such interactions into account at least dimers would have to be optimized. Therefore the vibrational frequencies of the gg conformer were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of normal coordinate analysis, normal mode calculations and experimental infrared and Raman data. However, some of the observed lines are obviously due to a small amount of the tc conformer present.

Failure of Flawed Utility Poles in Wind Gusts

The purpose of this study is to account for failures of wood utility poles in wind storms based on dynamic analysis and pole imperfections. The utility pole supporting multiple overhead transmission lines is modeled as a uniform Bernoulli–Euler cantilevered beam fixed at the base and subjected to three types of suddenly applied transverse loads that simulate a wind gust: a uniform pole pressure, a point load at the tip accounting for line and transformer drag, and another point load near midlength, accounting for drag on lines strung from that location. The dynamic pole moments are based on normal mode calculations rather than static calculations with a dynamic impact factor, and the critical flexural stresses include stress concentrations arising from pole imperfections such as holes, knots, and surface gouges. A case study illustrates the results for one of about 400 failed wood poles downed in a single New Jersey storm in 2003 with 107 km/h (67 m/h) wind gusts. Here, the critical pole stress based on the dynamic model and a hole imperfection exceeded the proportional limit stress of the wood. The predicted dynamic stresses are higher than those based on the National Electrical Safety Code.

VIBRATIONAL MODES IN SMALL Agn, Aun CLUSTERS: A FIRST PRINCIPLE CALCULATION

Although the stable structures and other physical properties of small Ag n and Au n, were investigated in the literature, phonon calculations are not done yet. In this work, we present plane-wave pseudopotential calculations based on density-functional formalism. The effect of using the generalized gradient approximation (GGA) and local density approximation (LDA) to determine the geometric and electronic structure and normal mode calculations of Ag n and Au n, is studied up to eight atoms. Pure Au n and Ag n clusters favor planar configurations. We calculated binding energy per atom. We have also calculated the normal mode calculations and also scanning tunneling microscope (STM) images for small clusters for the first time.