Intramolecular hydrogen bond: Can it be part of the basis set of valence internal coordinates in normal mode analysis?

It has been shown earlier1] that the relaxed force constants (RFCs) could be used as a measure of bond strength only when the bonds form a part of the complete valence internal coordinates (VIC) basis. However, if the bond is not a part of the complete VIC basis, its RFC is not necessarily a measure of bond strength. Sometimes, it is possible to have a complete VIC basis that does not contain the intramolecular hydrogen bond (IMHB) as part of the basis. This means the RFC of IMHB is not necessarily a measure of bond strength. However, we know that IMHB is a weak bond and hence its RFC has to be a measure of bond strength. We resolve this problem of IMHB not being part of the complete basis by postulating `equivalent' basis sets where IMHB is part of the basis at least in one of the equivalent sets of VIC. As long as a given IMHB appears in one of the equivalent complete VIC basis sets, its RFC could be used as a measure of bond strength parameter.

Normal-mode sound propagation in an ocean with sinusoidal surface waves

The normal-mode solution to the problem of acoustic wave propagation in an isovelocity ocean with a wavy surface is considered. The surface wave amplitude is assumed to be small compared to the acoustic wavelength, and the method of multiple scales is employed to study the interaction between normal-mode acoustic waves and the surface waves. A nonresonant interaction causes small fluctuations of the amplitude and phase of the acoustic wave at a rate dependent on the frequency of the surface wave. Backscatter occurs if the wavenumber of the surface wave is larger than that of the acoustic wave. The interaction becomes resonant if appropriate phase-matching conditions are satisfied. In this case, two acoustic normal modes get coupled, resulting in a large-scale periodic exchange of energy from one mode to another.

Conformational Analysis and Electronic Structure of Monothiodiacetamide: Normal Coordinate Analysis and Molecular Orbital Study

The infrared spectra of monothiodiacetamide (MTDA, CHaCONHCSCH3) and its N-deuterated compound in solution, solid state and at low temperature are measured. Normal coordinate analysis for the planar vibrations of MTDAd o and -dl have been performed for the two most probable cis-trans-CONHCSor -CSNHCO-conformers using a simple Urey-Bradley force function. The conformation of MTDA derived from the vibrational spectra is supported by the all valence CNDO/2 molecular orbital method. The vibrational assignments and the electronic structure of MTDA are also given.

Selenoacetamide: Vibrational assignments and normal coordinate analysis

The i.r. spectra of selenoacetamide and its N-deuterated species have been recorded The fundamental frequencies of these compounds have been assigned. Force constants derived for thioacetamide and acetamide were transferred to the present compound and a good agreement with the observed frequencies were achieved. The results are discussed in relation to acetamide and thioacetamide.

Vibrational Spectra and Normal Coordinate Analysis of N-Methyl Thiourea

The infrared spectra of N-methylthiourea (NMTU) and its N-deuterated and S-methylated species were measured. Assignment of the infrared and Raman spectra of NMTU has been accomplished by correlation with thiourea and by use of infrared band shifts on N-deuteration as well as S-methylation. Normal coordinate analysis was performed for all the fundamentals of NMTU and NMTU-d3, the assignments obtained from the force field calculations being discussed in relation to those in other related thioureas and thioamides. The potential barriers to the internal rotations for the �NH2, �CH3, and �CN groups were estimated from the force constants.

Two forms of Pf1 Inovirus: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the asymmetric unit

Inovirus is a helical array of alpha-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

Two forms of PF1 INOVIRUS: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the assymetric unit

Inovirus is a helical array of agr-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

Normal mode sound propagation in an ocean with random narrow-band surface waves

Normal mode sound propagation in an isovelocity ocean with random narrow-band surface waves is considered, assuming the root-mean-square wave height to be small compared to the acoustic wavelength. Nonresonant interaction among the normal modes is studied straightforward perturbation technique. The more interesting case of resonant interaction is investigated using the method of multiple scales to obtain a pair of stochastic coupled amplitude equations which are solved using the Peano-Baker expansion technique. Equations for the spatial evolution of the first and second moments of the mode amplitudes are also derived and solved. It is shown that, irrespective of the initial conditions, the mean values of the mode amplitudes tend to zero asymptotically with increasing range, the mean-square amplitudes tend towards a state of equipartition of energy, and the total energy of the modes is conserved.

Mixed Mode Analysis of Obliquely Oriented Edge Cracked Semicircular Disk Under Compression

A new mixed-mode compression fracture specimen, obliquely oriented edge cracked semicircular disk (OECSD) is analyzed by extending pure opening mode configuration of edge cracked semicircular disk (ECSD) under Hertzian compression. Photoelastic experiments are conducted on two different specimens of OECSD of same size and different crack lengths and inclinations. Finite element method (FEM) is used to solve a number of cases of the problem varying crack length and crack inclination. FE results show a good match with experiments. Inclination of edge crack in OECSD can be so made as to obtain any mode-mixity ratio between zero and one and beyond for any crack length. The new specimen can be used for fracture testing under compression more conveniently than the existing ones in several ways.

Resonant mode analysis in toroidal cavities with elliptic cross-sections

Resonant cavity modes in a torus with elliptical cross section are studied by means of a direct variational method. The nonlinear effects of toroidicity and ellipticity on the frequency of the basic mode are analyzed simply and systematically without the restriction of linear theory. It is shown that the toroidicity effect on the m = 0 transverse magnetic mode is less-than-or-equal-to 11%. The frequency of the mode shifts approximately 11-29% when the elongation of the cross section changes from 1 to 2. The effects of toroidicity and ellipticity differ for each resonant mode.

Crystal structure and phase transition studies in perovskite-type oxides using powder-diffraction techniques and symmetry-mode analysis : SrLnMRuO6 (Ln=La,Pr,Nd; M=Zn,Co,Mg,Ni,Fe) and ALn2CuTi2O9 (A=Ca,Ba; Ln=La,Pr,Nd,Sm)

La tesis se ha centrado en la síntesis y caracterización estructural de materiales tipo perovskita: SrLnMRuO6 (Ln=La,Pr,Nd; M=Zn,Co,Mg,Ni,Fe) y ALn2CuTi2O9 (A=Ca,Ba; Ln=La,Pr,Nd,Sm). El estudio de las estructuras de los materiales se ha realizado mediante el análisis de los patrones de difracción en polvo de rayos-X, sincrotrón y/o neutrones. En el refinamiento por el método de Rietveld de las estructuras se han sustituido las coordenadas atómicas (el método más común), por coordenadas colectivas: las amplitudes de los modos que describen la distorsión de la fase prototipo. Los resultados generales para la serie SrLnMRuO6 (Ln=La,Pr,Nd; M=Zn,Co,Mg,Ni) a temperatura ambiente se ha recogido en un diagrama en el que se han indicado las amplitudes de los modos que transforman de acuerdo a las irreps en función del factor de tolerancia, ya que todos ellos cristalizan en la misma fase monoclínica (P21/n); y a temperaturas altas se ha construido un diagrama de fase. Los materiales SrLnFeRuO6 ( Ln=La,Pr,Nd) y CaLn2CuTi2O9 cristalizan en la fase ortorrómbica Pbnm a temperatura ambiente; mientras que BaLn2CuTi2O9 tienen una estructura más simétrica, I4/mcm. A altas temperaturas se han identificado las transiciones de fase inducidas por el cambio de temperatura.A temperaturas bajas se han analizado las estructuras magnéticas de algunos de los compuestos mediante difracción de neutrones.

Study of crystal structure and phase transition studies in perovskite-type oxides using powder-diffraction techniques and symmetry-mode analysis.

251 p.