Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes

Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen banded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel tripler, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41-O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees, helical twist of the average structure from this simulation had a value of 36 degrees, while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel tripler, it was energetically comparable to the parallel tripler. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel tripler by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically Together these results indicate that the parallel C.G*G tripler with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.

A simple computational model for predicting .pi.-facial selectivity in reductions of sterically unbiased ketones. Relative importance of electrostatic and orbital interactions

Various factore controlling the preferred facial selectivity in the reductions of a number of sterically unbiased ketones have been evaluated using a semiempirical MO procedure. MNDO optimized geometries do not reveal any significant ground-state distortions which can be correlated with the observed face selectivities. Electrostatic effecta due to an approaching reagent were modeled by placing a test negative charge at a fixed distance from the carbonyl carbon on each of the two faces. A second series of calculations was carried out using the hydride ion as a test nucleophile. The latter calculations effectively include orbital interactions involving the u and u* orbitals of the newly formed bond in the reaction. The computed energy differences with the charge model are generally much larger compared to those with the hydride ion. However, both models lead to predictions which are qualitatively consistent with the experimentally determined facial preferences for most of the systems. Thus, electrostatic interactions between the nucleophile and the substrate seem to effectively determine the face selectivities in these molecules. However, there are a few exceptions in which orbital interactions are found to contribute significantly and occasionally reverse the preference dictated by electrostatic effecta. The remarkable succew of the hydride model calculations, in spite of retaining the unperturbed geometries of the substrates, points to the unimportance of torsional effeds and orbital distortions associated with the pyramidalized carbonyl unit in the transition state in most of the substrates considered. Additional experimental results are reported which provide useful calibration for the present computational approach.

Electronic excitations and alternation of conjugated polymers

The electronic excitations and fluorescence of conjugated polymers are related to large or small alternation ? of the transfer integrals t(1 ± ?) along the backbone. The fluorescence of polysilanes (PSs) and poly (para-phenylenevinylene (PPV) is linked to large ?, which places the one-photon gap Eg below the lowest two-photon gap Ea and reduces distortions due to electron-phonon (e-p) coupling. In contrast to small ? not, vert, similar 0.1 in ?-conjugated polymers, such as polyacetylene (PA), para-conjugated phenyls lead to an extended ?-system with increased alternation, to states localized on each ring and to charge-transfer excitations between them. Surprisingly good agreement is found between semiempirical parametric method 3 (PM3) bond lengths and exact Pariser-Parr-Pople (PPP) ?-bond orders for trans-stilbene, where the PPV bipolarons are confined to two phenyls. Stilbene spectra are consistent with increased alternation and small e-p distortions.

Is tetramethyleneethane a ground state triplet?

We have examined a number of possible ways by which tetramethyleneethane (TME) can be a ground state triplet, as claimed by experimental studies, in violation of Ovchinnikov’s theorem for alternant hydrocarbons of equal bond lengths. Model exact π calculations of the low-lying states of TME, 3,4-dimethylenefuran and 3,4-dimethylenepyrrole were carried out using a diagrammatic valence bond approach. The calculations failed to yield a triplet ground state even after (a) tuning of electron correlation, (b) breaking alternancy symmetry, and (c) allowing for geometric distortions. In contrast to earlier studies of fine structure constants in other conjugated systems, the computedD andE values of all the low-lying triplet states of TME for various geometries are at least an order of magnitude different from the experimentally reported values. Incorporation of σ-π mixing by means of UHF MNDO calculations is found to favour a singlet ground state even further. A reinterpretation of the experimental results of TME is therefore suggested to resolve the conflict.

Banded spatiotemporal chaos in sheared nematogenic fluids

We present the results of a numerical study of a model of the hydrodynamics of a sheared nematogenic fluid, taking into account the effects of order-parameter stresses on the velocity profile but allowing spatial variations only in the gradient direction. When parameter values are such that the stress from orientational distortions is comparable to the bare viscous stress, the system exhibits steady states with the characteristics of shear banding. In addition, nonlinearity in the coupling of extensional flow to orientation leads to the appearance of a new steady state in which the features of both spatiotemporal chaos and shear banding are present.

An electron diffraction study of quasicrystals in Ti-37 at% Mn and Ti-24 at% Mn-13 at% Fe alloys

Electron diffraction studies were carried out to establish the icosahedral phase formation in rapidly quenched Ti-37 at% Mn and Ti-24 at% Mn-13 at% Fe alloys. Distortions in the diffraction spots and diffuse intensities in the diffraction patterns were investigated. The existence of a rational approximant structure and a decagonal like phase are also reported.

Lopsidedness in WHISP galaxies I. Rotation curves and kinematic lopsidedness

The frequently observed lopsidedness of the distribution of stars and gas in disc galaxies is still considered as a major problem in galaxy dynamics. It is even discussed as an imprint of the formation history of discs and the evolution of baryons in dark matter haloes. Here, we analyse a selected sample of 70 galaxies from the Westerbork Hi Survey of Spiral and Irregular Galaxies. The Hi data allow us to follow the morphology and the kinematics out to very large radii. In the present paper, we present the rotation curves and study the kinematic asymmetry. We extract the rotation curves of the receding and approaching sides separately and show that the kinematic behaviour of disc galaxies can be classified into five different types: symmetric velocity fields where the rotation curves of the receding and approaching sides are almost identical; global distortions where the rotation velocities of the receding and approaching sides have an offset that is constant with radius; local distortions leading to large deviations in the inner and negligible deviations in the outer parts (and vice versa); and distortions that divide the galaxies into two kinematic systems that are visible in terms of the different behaviour of the rotation curves of the receding and approaching sides, which leads to a crossing and a change in side. The kinematic lopsidedness is measured from the maximum rotation velocities, averaged over the plateau of the rotation curves. This gives a good estimate of the global lopsidedness in the outer parts of the sample galaxies. We find that the mean value of the perturbation parameter denoting the lopsided potential as obtained from the kinematic data is 0.056. Altogether, 36% of the sample galaxies are globally lopsided, which can be interpreted as the disc responding to a halo that was distorted by a tidal encounter. In Paper II, we study the morphological lopsidedness of the same sample of galaxies.

Theoretical analysis of x-ray-absorption near-edge fine structure at the O and metal K edges of LaFeO3 and LaCoO3

We present experimental x-ray-absorption spectra at the oxygen and 3d transition-metal K edges of LaFeO3 and LaCoO3. We interpret the experimental results in terms of detailed theoretical calculations based on multiple-scattering theory. Along with providing an understanding of the origin of various experimental features, we investigate the effects of structural distortions and the core-hole potential in determining the experimental spectral shape. The results indicate that the core-hole potential as well as many-body effects within the valence electrons do not have any strong effect on the spectra suggesting that the spectral features can be directly interpreted in terms of the electronic structure of such compounds.

Structure-reactivity correlations of excited states of perfluorinated compounds: A time resolved Raman study

This paper reports the TR3 spectral studies on perfluorinated organic systems with the objective to understand the influence of perfluorination on the excited states. We have recorded the TR3 spectra and Raman excitation profiles of the triplet excited states of decafluorobenzophenone and fluoranil. It is found that the influence of perfluorination is more pronounced in the triplet excited state than the ground state and thus leads to enhanced reactivity for perfluorinated compounds through larger structural distortions.

Encapsulation of cobalt phthalocyanine in zeolite-Y: Evidence for nonplanar geometry

Cobalt (11) phthalocyanine (CoPc) molecules have been encapsulated within the supercage of zeolite-Y. The square-planar complex, being larger than the almost spherical cage, is forced to adopt a distorted geometry on encapsulation. A comparative spectroscopic and magnetic investigation of CoPc encapsulated in zeolite-Y and in the unencapsulated state is reported. These results supported by molecular modeling have been used to understand the nature and extent of the loss of planarity of CoPc on encapsulation. The encapsulated molecule is shown to be the trans-diprotonated species in which the center of inversion is lost due to distortions required to accommodate the square complex within the zeolite. Encapsulation also leads to an enhancement of the magnetic moment of the CoPc. This is shown to be a consequence of the nonplanar geometry of the encapsulated molecule resulting in an excited high-spin state being thermally accessible.

Transmission of correlated sources over fading multiple access channel

In this paper we address the problem of transmission of correlated sources over a fading multiple access channel (MAC). We provide sufficient conditions for transmission with given distortions. Next these conditions are specialized to a Gaussian MAC (GMAC). Transmission schemes for discrete and Gaussian sources over a fading GMAC are considered. Various power allocation strategies are also compared. Keywords: Fading MAC, Power allocation, Random TDMA, Amplify and Forward, Correlated sources.

Direct mdct domain psychoacoustic modeling

We extend the recently proposed spectral integration based psychoacoustic model for sinusoidal distortions to the MDCT domain. The estimated masking threshold additionally depends on the sub-band spectral flatness measure of the signal which accounts for the non- sinusoidal distortion introduced by masking. The expressions for masking threshold are derived and the validity of the proposed model is established through perceptual transparency test of audio clips. Test results indicate that we do achieve transparent quality reconstruction with the new model. Performance of the model is compared with MPEG psychoacoustic models with respect to the estimated perceptual entropy (PE). The results show that the proposed model predicts a lower PE than other models.

Correlations between structure and thermodynamic properties of spinels and their applications in technology

Measurements a/the Gibbs' energy enthalpy and entrupy vffarmation oj chromites, vanadites and alumlnat.:s 0/ F", Ni. Co'. Mn, Zn Mg and Cd, using solid oxide galvanic cells over a ternperature range extending approximately lOOO°C, have shown that the '~'Ilir"!,,, J'JrIl/iJ~ tion 0/ cubic 2-3 oxide spinel phases (MX!O,), from component oxide (MO) with rock-salt and X.Os whir c(1f'l/!ldwn st!'llt'lw,·. call b,' represented by a semi-empirical correlalion, ~S~ = --LiS + L'i,SM +~S~:"d(±O.3) cal.deg-1 mol-1 where /',.SM Is the entropy 0/calian mixing oillhe tetrahedral alld octahedral sites o/the spinel and Sr:~ is tlie enfropy associaf,'d Wifh Ih,' randomization a/the lahn-Telier distortions. A review a/the methods/or evaluating the cation distriblltion lfl spille!s suggeJ{j' l/r,l! Ihe most promising scheme is based Oil octahedral site preference energies from the crystal field theory for the Iral1silioll IIIl'f"! IlIIL';. For I/""-Irallsifioll melal cal ions site preference energies are derived relative /0 thol'lt fLI, [ransilion metal ions from measured high tClllP('ftJi ure Cal iUlI disll iiJuriol1 in spine! phases thar contail! one IransilioJl metal and another non-transition metal carion. For 2-3 srinds compulatiorrs b,IS"J Oil i.!c[J;' Temkin mixing on each catioll subialtice predici JistributionJ that are In fair agreement with X-ray and 1I1'IIIrOll ditTraction, /IIdg""!ic dll.! electrical propcrries, and spectroscopic measurements. In 2-4 spineis mixing vI ions do not foliow strictly ideal slllIistli:al Jaws, Th,' OIl/up) associated with the randomizalion 0/the Jllhn-Teller dislOriioll" appear to be significant, only ill spinels witll 3d'. 3d', 3d' (ifld~UI' iOtls in tetrahedral and 3d' and 3d9 ions in octahedral positions. Application 0/this structural model for predicting the thermodynamic proputies ofspinel solid .,olutiofl5 or,' illustrated. F,lr complex systems additional contributions arising from strain fields, redox equilibria and off-center ions have to be qllalllififti. The entropy correlation for spinels provides a method for evaluating structure tran:.jormafiofl entropies in silllple o.\id.-s, ["founlllion on the relative stabilities ofoxides in different crystallCtructures is USe/III for computer ea/culaliof! a/phase dfugrullls ofIlIrer,',,1 III (N.lll1ie5 by method, similar to thost: used by Kaufman and Bernstein for refractory alloy systems. Examples oftechnoiogical appliCation tnclude the predictioll ofdeoxidation equilibria in Fe-Mn-AI-O s),slelll at 1600°C duj ,'Ulllpltfalion 0/phase relutions in Fe-Ni-Cr-S system,

Suppressed rf dissipation in 107Ag17+ ion irradiated Bi2Sr2CaCu2O8 single crystals by enhanced flux line tilt modulus

We have studied the isothermal, magnetic field (H‖c) dependent rf power P(H) dissipation (Hrf‖a) in the superconducting state of Bi2Sr2CaCu2O8 single crystals prior to and after irradiation with 250 MeV 107Ag17+ ions. In the pristine state, P(H) shows an initial decrease with increase in field, reaches a minimum at HM(T) and increases monotonically for H>HM(T). This behavior arises when the electromagnetic coupling between the pancake vortices in adjacent CuO layers becomes dominant on increasing the field and minimizes the distortions of the flux lines by confining the 2D vortices. In the post irradiated state, such an initial decrease and the minimum in P(H) is not observed but only a much reduced rf dissipation that monotonically increases with field from H = 0 onwards is seen. We attribute this difference to the strong enhancement of the tilt modulus C44 of the flux lines on irradiation when the pancake vortices in adjacent CuO bilayers are pinned along the track forming a well-stacked flux line in the field direction (‖c). We have also observed that the rf dissipation disappears at a certain temperature Tsf, at which the normal core of the flux line becomes commensurate with the columnar track diameter.

Wavelet transform analysis of truncated fringe patterns in 3-D surface profilometry

Wavelet transform analysis of projected fringe pattern for phase recovery in 3-D shape measurement of objects is investigated. The present communication specifically outlines and evaluates the errors that creep in to the reconstructed profiles when fringe images do not satisfy periodicity. Three specific cases that give raise to non-periodicity of fringe image are simulated and leakage effects caused by each one of them are analyzed with continuous complex Morlet wavelet transform. Same images are analyzed with FFT method to make a comparison of the reconstructed profiles with both methods. Simulation results revealed a significant advantage of wavelet transform profilometry (WTP), that the distortions that arise due to leakage are confined to the locations of discontinuity and do not spread out over the entire projection as in the case of Fourier transform profilometry (FTP).