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Normal Modes (normal + mode)
Terms modified by Normal Modes Selected AbstractsDynamics of molecules in crystals from multi-temperature anisotropic displacement parameters.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2000The temperature evolution of atomic anisotropic displacement parameters (ADP's) of perdeuterobenzene and of urea in the temperature range between 12 and 123,K is investigated in terms of the model presented in paper I. For the benzene molecule, the temperature-dependent contributions to the ADP's are well described by three molecular librations and three molecular translations. For the urea molecule, the analysis revealed a low-frequency high-amplitude normal mode (~64,cm,1), which combines out-of-plane deformations of the NH2 groups with molecular libration. The pyramidalization motion allows the hydrogen-bonding pattern to be retained quite well, whereas this pattern is heavily distorted in the higher-frequency molecular librations. The results presented for urea go a step beyond those obtainable in a conventional rigid-body or segmented-rigid-body analysis because they show how correlations of atomic displacements in molecular crystals can be determined from the temperature evolution of ADP's. For both molecules, the analysis reveals temperature-independent contributions to the ADP's accounting for the high-frequency internal vibrations. It is the first time that such contributions have been extracted directly from single-crystal diffraction data for light atoms like hydrogen and deuterium as well as for heavier atoms like carbon, nitrogen and oxygen. These contributions agree well with those calculated from independent spectroscopic information. [source] Trans -splicing in DrosophilaBIOESSAYS, Issue 11 2002Vincenzo Pirrotta Splicing is an efficient and precise mechanism that removes noncoding regions from a single primary RNA transcript. Cutting and rejoining of the segments occurs on nascent RNA. Trans -splicing between small specialized RNAs and a primary transcript has been known in some organisms but recent papers show that trans -splicing between two RNA molecules containing different coding regions is the normal mode in a Drosophila gene.1,3 The mod(mdg4) gene produces 26 different mRNAs encoding as many protein isoforms. The differences lie in alternative 3, exons encoded by different transcriptional units and spliced to the 5, common region by a surprising trans -splicing mechanism. BioEssays 24:988,991, 2002. © 2002 Wiley-Periodicals, Inc. [source] Calculated Raman Optical Activity Signatures of Tryptophan Side ChainsCHEMPHYSCHEM, Issue 15 2008Christoph R. Jacob Dr. Raman optical activity: The different local chirality of an adjacent group can cause a different sign of the ROA intensity of an amino-acid side chain (here tryptophan, see picture centre), even though the normal mode is unchanged. Calculated spectra clearly confirm that ROA spectroscopy can be utilized to determine the absolute conformation of tryptophan side chains in proteins (see figure, left and right). [source] Dynamic performance of twin curved cable-stayed bridgesEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 1 2004C. Gentile Abstract The dynamic behaviour of two curved cable-stayed bridges, recently constructed in northern Italy, has been investigated by full-scale testing and theoretical models. Two different excitation techniques were employed in the dynamic tests: traffic-induced ambient vibrations and free vibrations. Since the modal behaviour identified from the two types of test are very well correlated and a greater number of normal modes was detected during ambient vibration tests, the validity of the ambient vibration survey is assessed in view of future monitoring. For both bridges, 11 vibration modes were identified in the frequency range of 0ndash;10Hz, being a one-to-one correspondence between the observed modes of the two bridges. Successively, the information obtained from the field tests was used to validate and improve 3D finite elements so that the dynamic performance of the two systems were assessed and compared based on both the experimental results and the updated theoretical models. Copyright © 2003 John Wiley & Sons, Ltd. [source] System identification of linear structures based on Hilbert,Huang spectral analysis.EARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 10 2003Part 2: Complex modes Abstract A method, based on the Hilbert,Huang spectral analysis, has been proposed by the authors to identify linear structures in which normal modes exist (i.e., real eigenvalues and eigenvectors). Frequently, all the eigenvalues and eigenvectors of linear structures are complex. In this paper, the method is extended further to identify general linear structures with complex modes using the free vibration response data polluted by noise. Measured response signals are first decomposed into modal responses using the method of Empirical Mode Decomposition with intermittency criteria. Each modal response contains the contribution of a complex conjugate pair of modes with a unique frequency and a damping ratio. Then, each modal response is decomposed in the frequency,time domain to yield instantaneous phase angle and amplitude using the Hilbert transform. Based on a single measurement of the impulse response time history at one appropriate location, the complex eigenvalues of the linear structure can be identified using a simple analysis procedure. When the response time histories are measured at all locations, the proposed methodology is capable of identifying the complex mode shapes as well as the mass, damping and stiffness matrices of the structure. The effectiveness and accuracy of the method presented are illustrated through numerical simulations. It is demonstrated that dynamic characteristics of linear structures with complex modes can be identified effectively using the proposed method. Copyright © 2003 John Wiley & Sons, Ltd. [source] On establishing the accuracy of noise tomography travel-time measurements in a realistic mediumGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 3 2009Victor C. Tsai SUMMARY It has previously been shown that the Green's function between two receivers can be retrieved by cross-correlating time series of noise recorded at the two receivers. This property has been derived assuming that the energy in normal modes is uncorrelated and perfectly equipartitioned, or that the distribution of noise sources is uniform in space and the waves measured satisfy a high frequency approximation. Although a number of authors have successfully extracted travel-time information from seismic surface-wave noise, the reason for this success of noise tomography remains unclear since the assumptions inherent in previous derivations do not hold for dispersive surface waves on the Earth. Here, we present a simple ray-theory derivation that facilitates an understanding of how cross correlations of seismic noise can be used to make direct travel-time measurements, even if the conditions assumed by previous derivations do not hold. Our new framework allows us to verify that cross-correlation measurements of isotropic surface-wave noise give results in accord with ray-theory expectations, but that if noise sources have an anisotropic distribution or if the velocity structure is non-uniform then significant differences can sometimes exist. We quantify the degree to which the sensitivity kernel is different from the geometric ray and find, for example, that the kernel width is period-dependent and that the kernel generally has non-zero sensitivity away from the geometric ray, even within our ray theoretical framework. These differences lead to usually small (but sometimes large) biases in models of seismic-wave speed and we show how our theoretical framework can be used to calculate the appropriate corrections. Even when these corrections are small, calculating the errors within a theoretical framework would alleviate fears traditional seismologists may have regarding the robustness of seismic noise tomography. [source] A thermochemical boundary layer at the base of Earth's outer core and independent estimate of core heat fluxGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 3 2008David Gubbins SUMMARY Recent seismological observations suggest the existence of a ,150-km-thick density-stratified layer with a P -wave velocity gradient that differs slightly from PREM. Such a structure can only be caused by a compositional gradient, effects of a slurry or temperature being too small and probably the wrong sign. We propose a stably stratified, variable concentration layer on the liquidus. Heat is transported by conduction down the liquidus while the light and heavy components migrate through the layer by a process akin to zone refining, similar to the one originally proposed by Braginsky. The layer remains static in a frame of reference moving upwards with the expanding inner core boundary. We determine the gradient using estimates of co, the concentration in the main body of the outer core, and cb, the concentration of the liquid at the inner core boundary. We determine the depression of the melting point and concentrations using ideal solution theory and seismologically determined density jumps at the inner core boundary. We suppose that co determines ,,mod, the jump from normal mode eigenfrequencies that have long resolution lengths straddling the entire layer, and that cb determines ,,bod, the jump determined from body waves, which have fine resolution. A simple calculation then yields the seismic, temperature, and concentration profiles within the layer. Comparison with the distance to the C-cusp of PKP and normal mode eigenfrequencies constrain the model. We explore a wide range of possible input parameters; many fail to predict sensible seismic properties and heat fluxes. A model with ,,mod= 0.8 gm cc,1, ,,bod= 0.6 gm cc,1, and layer thickness 200 km is consistent with the seismic observations and can power the geodynamo with a reasonable inner core heat flux of ,2 TW and nominal inner core age of ,1 Ga. It is quite remarkable and encouraging that a model based on direct seismic observations and simple chemistry can predict heat fluxes that are comparable with those derived from recent core thermal history calculations. The model also provides plausible explanations of the observed seismic layer and accounts for the discrepancy between estimates of the inner core density jumps derived from body waves and normal modes. [source] A solution of the elastodynamic equation in an anelastic earth modelGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 2 2007David Al-Attar SUMMARY A formal solution to the elastodynamic equation in an anelastic earth model is presented. The derivation also incorporates the effects of aspherical structure, rotation, self-gravitation, and pre-stress. It is found that the solution can be expressed as a sum of the normal modes of the earth model along with additional terms accounting for anelastic relaxation processes. However, the derivation does not assume that such an eigenfunction expansion is possible, and so avoids difficulties previously encountered due to the non self-adjointness of the problem. [source] Post-seismic relaxation following the great 2004 Sumatra-Andaman earthquake on a compressible self-gravitating EarthGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 1 2006Fred F. Pollitz SUMMARY The Mw, 9.0 2004 December 26 Sumatra-Andaman and Mw= 8.7 2005 March 28 Nias earthquakes, which collectively ruptured approximately 1800 km of the Andaman and Sunda subduction zones, are expected to be followed by vigorous viscoelastic relaxation involving both the upper and lower mantle. Because of these large spatial dimensions it is desirable to fully account for gravitational coupling effects in the relaxation process. We present a stable method of computing relaxation of a spherically-stratified, compressible and self-gravitating viscoelastic Earth following an impulsive moment release event. The solution is cast in terms of a spherical harmonic expansion of viscoelastic normal modes. For simple layered viscoelastic models, which include a low-viscosity oceanic asthenosphere, we predict substantial post-seismic effects over a region several 100s of km wide surrounding the eastern Indian Ocean. We compare observed GPS time-series from ten regional sites (mostly in Thailand and Indonesia), beginning in 2004 December, with synthetic time-series that include the coseismic and post-seismic effects of the 2004 December 26 and 2005 March 28 earthquakes. A viscosity structure involving a biviscous (Burgers body) rheology in the asthenosphere explains the pattern and amplitude of post-seismic offsets remarkably well. [source] Approximation method for high-degree harmonics in normal mode modellingGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 1 2002R. E. M. Riva Summary For some loading applications, the normal modes approach to the viscoelastic relaxation of a spherical earth requires the use of spherical harmonics up to a high degree. Examples include postseismic deformation (internal loading) and sea level variations due to glacial isostatic adjustment (external loading). In the case of postseismic modelling, the convergence of the solution, given as a spherical harmonic expansion series, is directly dependent on loading depth and requires several thousands of terms for shallow earthquake sources. The particular structure of the analytical fundamental solutions used in normal mode techniques usually does not allow a straightforward calculation, since numerical problems can readily occur due to the stiffness of the matrices used in the propagation routines. Here we show a way of removing this stiffness problem by approximating the fundamental matrix solutions, followed by a rescaling procedure, in this way we can virtually go up to whatever harmonic degree is required. [source] Latitudinal height couplings between single tropopause and 500 and 100 hPa within the Southern HemisphereINTERNATIONAL JOURNAL OF CLIMATOLOGY, Issue 4 2010Adrián E. Yuchechen Abstract In order to provide further insights into the relationships between the tropopause and different mandatory levels, this paper discusses the coupling between standardized tropopause height anomalies (STHAs) and standardized 500-hPa and 100-hPa height anomalies (S5HAs and S1HAs, respectively) within the ,climatic year' for three sets of upper-air stations located approximately along 20°S, 30°S and 45°S. Data used in this research consists in a radiosonde database spanning the period 1973,2007. The mandatory levels are supposed to be included in each radiosonde profile. The tropopause, on the other hand, is calculated from the significant levels available for each sounding using the lapse rate definition. After applying a selection procedure, a basic statistical analysis combined with Fourier analysis is carried out in order to build up the standardized variables. Empirical orthogonal functions (EOFs) in S-mode are used to get the normal modes of oscillation as well as their time evolution, for STHA/S5HA as well as for STHA/S1HA coupling, separately, within the aforementioned latitudes. Overall, there are definite cycles in the time evolution associated with each EOF structure at all three latitudes, the semi-annual wave playing the most important role in most of the cases. Nevertheless, 20°S seems to be the only latitude driven by diabatic heating cycles in the middle atmosphere. Certainly, EOF1 at this latitude has a semi-annual behaviour and seems to be strongly influenced by the tropical convection seasonality. Apparently, the convectively driven release of latent heat in the middle troposphere affects the time evolution of the EOF1 structure. By contrast, the vertical propagation of planetary waves is raised as a possible explanation for the EOF1 and EOF2 behaviour at latitudes beyond 20°S, in view of the close connection existent between the semi-annual oscillation (SAO) and the reversion in the direction of the zonal wind. Copyright © 2009 Royal Meteorological Society [source] Time-dependent and time-independent approaches for the computation of absorption spectra of Uracil derivatives in solutionINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2010Roberto Improta Abstract In this contribution we discuss the most significant benefits and drawbacks of the alternative time-independent (TI) and time-dependent (TD) approaches to the calculation of absorption spectra of molecules in solutions. Eigenstate-free TD methods are in principle the most suitable route to face with the calculation of optical spectra in nonadiabatic systems, most of all in presence of conical intersections easily accessible from the Franck,Condon region. However, here we show that, in selected cases, a combined strategy that adopts TD methods to assess the impact of nonadiabatic couplings on the spectrum and subsequently applies TI methods to include all the degrees of freedom can reveal very convenient. Such a combined TD/TI strategy has been applied to the calculation of the spectrum of Uracil and 5Fluoro-Uracil in acetonitrile. TD studies on reduced dimensionality diabatic models indicate that nonadiabatic effects are moderate and are not the main origin of the diffuse spectral shapes observed in experiments. Subsequent full-coordinate TI calculations allow assigning this feature to intrinsic characteristics of a ,,* excitation of a small molecular ring structure. This latter introduces remarkable deformation in all the ring structure thus inducing a FC activity in many molecular normal modes both due to displacements of the equilibrium structures and to Duschinsky mixings of the normal coordinates. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Coarse-graining of protein structures for the normal mode studiesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2007Kilho Eom Abstract The coarse-grained structural model such as Gaussian network has played a vital role in the normal mode studies for understanding protein dynamics related to biological functions. However, for the large proteins, the Gaussian network model is computationally unfavorable for diagonalization of Hessian (stiffness) matrix for the normal mode studies. In this article, we provide the coarse-graining method, referred to as "dynamic model condensation," which enables the further coarse-graining of protein structures consisting of small number of residues. It is shown that the coarser-grained structures reconstructed by dynamic model condensation exhibit the dynamic characteristics, such as low-frequency normal modes, qualitatively comparable to original structures. This sheds light on that dynamic model condensation and may enable one to study the large protein dynamics for gaining insight into biological functions of proteins. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Ab initio calculations of intramolecular parameters for a class of arylamide polymersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2006Satyavani Vemparala Abstract Using DFT methods, we have determined intramolecular parameters for an important class of arylamide polymers displaying antimicrobial and anticoagulant inhibitory properties. A strong link has been established between these functions and the conformation that the polymers adopt in solution and at lipid bilayer interfaces. Thus, it is imperative for molecular dynamics simulations designed to probe the conformational behavior of these systems to accurately describe the torsional degrees of freedom. Standard force fields were shown to be deficient in this respect. Therefore, we have computed the relevant torsional energy profiles using a series of constrained geometry optimizations. We have also determined electrostatic parameters using our results in combination with standard RESP charge optimization. Force constants for bond and angle potentials were calculated by iteratively matching quantum and classical normal modes via a Monte Carlo scheme. The resulting new set of parameters accurately described the conformation and dynamical behavior of the arylamide polymers. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 693,700, 2006 [source] A molecular mechanics force field for biologically important sterolsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005Zoe Cournia Abstract A parameterization has been performed of the biologically important sterols cholesterol, ergosterol, and lanosterol for the CHARMM27 all-atom molecular mechanics force field. An automated parameterization method was used that involves fitting the potential to vibrational frequencies and eigenvectors derived from quantum-chemical calculations. The partial charges were derived by fitting point charges to quantum-chemically calculated electrostatic potentials. To model the dynamics of the hydroxyl groups of the sterols correctly, the parameter set was refined to reproduce the energy barrier for the rotation of the hydroxyl group around the carbon connected to the hydroxyl of each sterol. The frequency-matching plots show good agreement between the CHARMM and quantum chemical normal modes. The parameters are tested in a molecular dynamics simulation of the cholesterol crystal structure. The experimental geometry and cell dimensions are well reproduced. The force field derived here is also useful for simulating other sterols such as the phytosterols sigmasterol, and campesterol, and a variety of steroids. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1383,1399, 2005 [source] Mechanism and dynamics of organic reactions: 1,2-H shift in methylchlorocarbene,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 8 2002Elfi Kraka Abstract The unified reaction valley approach (URVA) was used to investigate the mechanism of the rearrangement of methylchlorocarbene to chloroethene [reaction(1)] in the gas phase with special emphasis on the role of H tunneling. The reaction valley of (1) was explored using different methods (HF, MP2 and DFT/B3LYP) and different basis sets [6,31G(d), 6,31G(d,p) and cc-pVTZ]. Results were analyzed characterizing normal modes, reaction path vector and curvature vector in terms of generalized adiabatic modes associated with internal parameters that are used to describe the reaction complex. For reaction (1), H tunneling plays a significant role even at room temperature, but does not explain the strongly curved Arrhenius correlations observed experimentally. The probability of H tunneling can be directly related to the curvature of the reaction path and the associated curvature couplings. The reaction is preceeded in the forward and reverse direction by energy-consuming conformational changes that prepare the reactant for the actual 1,2-H shift, which requires only little energy. The effective energy needed for CH bond breaking is just 6,kcal,mol,1 for (1). The gas-phase and the solution-phase mechanisms of (1) differ considerably, which is reflected by the activation enthalpies: 11.4 (gas, calculated) and 4.3,kcal,mol,1 (solution, measured). Stabilizing interactions with solvent molecules take place in the latter case and reduce the importance of H tunneling. The non-linearity of the measured Arrhenius correlations most likely results from bimolecular reactions of the carbene becoming more important at lower temperatures. Copyright © 2002 John Wiley & Sons, Ltd. [source] Spectroscopic investigations and computational study of 2-[acetyl(4-bromophenyl)carbamoyl]-4-chlorophenyl acetateJOURNAL OF RAMAN SPECTROSCOPY, Issue 6 2010C. Yohannan Panicker Abstract The Fourier transform Raman (FT-Raman) and Fourier transform infrared (FT-IR) spectra of 2-[acetyl(4-bromophenyl)carbamoyl]-4-chlorophenyl acetate were studied. The vibrational wavenumbers were examined theoretically using the Gaussian03 set of quantum chemistry codes, and the normal modes were assigned by potential energy distribution (PED) calculations. The simultaneous Raman and infrared (IR) activations of the CO stretching mode in the carbamoyl moiety show a charge transfer interaction through a ,-conjugated path. From the optimized structure, it is clear that the hydrogen bonding decreases the double bond character of the CO bond and increases the double bond character of the CN bonds. The first hyperpolarizability and predicted IR intensities are reported. The calculated first hyperpolarizability is comparable with the reported values of similar structures, which makes this compound an attractive object for future studies of nonlinear optics. Optimized geometrical parameters of the compound are in agreement with similar reported structures. Copyright © 2009 John Wiley & Sons, Ltd. [source] Raman spectra of a pseudo-oxocarbon anion in ionic liquidsJOURNAL OF RAMAN SPECTROSCOPY, Issue 5 2010Humberto C. Garcia Abstract Raman and electronic spectra of the [3,5-bis(dicyanomethylene)cyclopentane-1,2,4-trionate] dianion, the croconate violet (CV), are reported in solutions of ionic liquids based on imidazolium cations. Different normal modes of the CV anion, , (CO), , (CO) + , (CC) + , (CCN), and ,(C,N), were used as probes of solvation characteristics of ionic liquids, and were compared with spectra of CV in common solvents. The spectra of CV in ionic liquids are similar to those in dichloromethane solution, but distinct from those in protic solvents such as ethanol or water. The UV,vis spectra of CV in ionic liquids strongly suggest ,,, interactions between the CV anion and the imidazolium cation. Copyright © 2009 John Wiley & Sons, Ltd. [source] Surface-enhanced Raman scattering and density functional theory studies of bis(4-aminophenyl)sulfone,JOURNAL OF RAMAN SPECTROSCOPY, Issue 2 2010Guillermo Diaz-Fleming Abstract Raman and surface-enhanced Raman scattering (SERS) spectra of dapsone by using colloidal silver nanoparticles have been recorded. Density functional theory was used for the optimization of ground state geometries and simulation of the vibrational spectrum of this molecule. The SERS spectrum with a large silver cluster as a model metallic surface was simulated for the first time. Taking into account the experimental and calculated Raman as well as the SERS normal modes and the corresponding assignments, along with the modeling of the free dapsone and the one in the presence of the colloidal silver nanoparticles, the importance of the sulfone group on the SERS effect in dapsone was inferred. Copyright © 2009 John Wiley & Sons, Ltd. [source] Organic cyclic difluoramino-nitramines: infrared and Raman spectroscopy of 3,3,7,7-tetrakis(difluoramino)octahydro 1,5-dinitro-1,5-diazocine (HNFX)JOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009Philippe F. Weck Abstract We present the first vibrational structure investigation of 3,3,7,7-tetrakis(difluoramino)octahydro-1,5-dinitro- 1,5-diazocine (HNFX),and, more generally, of a member of the new class of gem -bis(difluoramino)-substituted heterocyclic nitramine energetic materials,using combined theoretical and experimental approaches. Optimized molecular structure and vibrational spectra of the Ci, symmetry conformer constituting the HNFX crystal were computed using density functional theory methods. Fourier transform infrared and Raman spectra of HNFX crystalline samples were also collected at ambient temperature and pressure. The average deviation of calculated structural parameters from X-ray diffraction data is ,1% at the B3LYP/6-311 + + G(d,p) level of theory, suggesting the absence of significant molecular distortion induced by the crystal field. Very good agreement was found between simulated and measured spectra, allowing reliable assignment of the fundamental normal modes of vibration of the HNFX crystal. Detailed analysis of the normal modes of the C,(NF2)2 and N,NO2 moieties was performed due to their critical importance in the initial steps of the molecular homolytic fragmentation process. Copyright © 2009 John Wiley & Sons, Ltd. [source] Synthesis and vibrational analysis of N-(2,-Furyl)-ImidazoleJOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009A. E. Ledesma Abstract The N-(2,-furyl)-imidazole (1) has been prepared and characterized using infrared, Raman and multidimensional nuclear magnetic resonance spectroscopies. Theoretical calculations have been carried out by employing the Density Functional Theory (DFT) method, in order to optimize the geometry of their two conformers in the gas phase and to support the assignments of the vibrational bands of 1 to their normal modes. For a complete assignment of the compound, DFT calculations were combined with Scaled Quamtum Mecanic Force Field (SQMFF) methodology in order to fit the theoretical wavenumber values to the experimental one. Furthermore, Natural Bond Orbital (NBO) and topological properties by Atoms In Molecules (AIM) calculations were performed to analyze the nature and magnitude of the intramolecular interactions. The result reveals that two conformers are expected in liquid phase. Copyright © 2009 John Wiley & Sons, Ltd. [source] Vibrational spectra and quantum chemical calculations of uracilyl,pyridinium mesomeric betaineJOURNAL OF RAMAN SPECTROSCOPY, Issue 11 2007A. Schmidt Abstract Modified nucleobases (MNs) are promising molecules with potential application in non-linear optic (NLO) and drug design against a wide number of diseases. In the present paper we report studies on a cross-conjugated mesomeric betaine, which can act as a MN, formed by the covalent union of a 4-dimethylamino pyridinium and a uracilyl groups. The molecule thus formed must be presented by a dipolar canonical formulae in which positive and negative charges are delocalized within separated moieties. Quantum chemistry density functional theory (DFT) calculations, at the B3PW91/6-31G** level, and Fourier transform (FT) infrared and Raman spectra of this molecule and its N -deuterated derivative were performed. The calculated structural properties over the ground state optimized structure evidenced a strong separation between the two conjugated systems. Comparison with previous results obtained for the cationic species indicated that N -protonation clearly affects the degree of conjugation. Assignments of the FT-IR and FT-Raman spectra were supported by the DFT wavenumbers, intensities and normal modes, which also evidenced the separation of the two conjugated systems. Significant deviations were found for the stretching force constants of the inter-ring and the uracilyl skeletal bonds when comparing this molecule with its N -protonated species. Copyright © 2007 John Wiley & Sons, Ltd. [source] Raman and surface-enhanced Raman spectra of flavone and several hydroxy derivativesJOURNAL OF RAMAN SPECTROSCOPY, Issue 7 2007Tatyana Teslova Abstract The Raman and surface-enhanced Raman spectra (SERS) of flavone and three of its hydroxy derivatives, 3-hydroxyflavone (3-HF) and 5-hydroxyflavone (5-HF) and quercetin (3,5,7,3,,4, pentahydroxyflavone) have been obtained. The normal Raman (NR) spectra were taken in the powder form. The SERS spectra were obtained both on Ag colloids and Ag electrode substrates. Assignments of the spectrally observed normal modes were aided by density functional theory (DFT) calculations using the B3LYP functional and the 6-31 + G* basis, a split valence polarized basis set with diffuse functions. Excellent fits were obtained for the observed spectra with little or no scaling. The most intense lines of the NR spectra are those in the CO stretching region (near 1600 cm,1). These lines are often weakened by proximity to the surface, while other lines at lower wavenumbers, due to in-plane ring stretches, tend to be strongly enhanced. The SERS spectrum of flavone is weak both on the colloid and on the electrode, indicating weak attachment to the surface. In contrast, the SERS spectra of the hydroxy derivatives of flavone are intense, indicating the assistance of OH groups in attachment to the surface. The spectra of the various species are compared, and a case study of application to detection of a textile dye (Persian berries), which contains quercetin, is presented. Copyright © 2007 John Wiley & Sons, Ltd. [source] Polarized Raman scattering and phase transition studies of n -diethylenediammonium monohydrogenmonophosphate dihydrateJOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2006S. Elleuch Abstract Polarized Raman scattering studies at room temperature were carried out on N -diethylenediammonium monohydrogenmonophosphate dihydrate single crystal samples, abbreviated N -DDHP. An assignment of the normal modes is proposed based on group theory analysis and correlations with previous data reported for other homologous hydrogen-bonded systems. A careful analysis of the vibrational spectra shows that the assignment of the fundamental vibrational modes can be done based on phosphate, organic and water group vibrations. In addition, differential scanning calorimetry measurement and a Raman spectroscopic study at several temperatures in the range 100,300 K are presented. The occurrence of a low-temperature phase transition near 220 K is well evidenced. From the temperature-dependence behavior of some internal and external modes, this transition is interpreted by an order,disorder transition which involves the structural modifications of both anion and cation groups. Copyright © 2006 John Wiley & Sons, Ltd. [source] Polarized infrared and Raman spectra of KGd(WO4)2 and their interpretation based on normal coordinate analysisJOURNAL OF RAMAN SPECTROSCOPY, Issue 2 2002L. Macalik The direction of the transition dipole moments for the vibrations of the single WOW and double WOOW oxygen bridges in layered scheelite tungstates is derived from the Polarized infrared and Raman spectra of the KGd(WO4)2 single crystal. Their experimental values are compared with those obtained from the calculated atomic Cartesian displacements for the particular normal modes. The assignment of the IR and Raman bands to the respective molecular vibrations was obtained on the basis of the normal coordinate analysis and potential energy distribution. Copyright © 2002 John Wiley & Sons, Ltd. [source] Vibrational analysis of Ni(II)- and Cu(II)-octamethylchlorin by polarized resonance Raman and Fourier transform infrared spectroscopyJOURNAL OF RAMAN SPECTROSCOPY, Issue 6-7 2001Robert J. Lipski We measured the polarized resonance Raman spectra of Cu(II)-2,2,7,8,12,13,17,18-octamethylchlorin in CS2 at various excitation wavenumbers in a spectral region covering the Qy, Qx and Bx optical absorption bands. Additionally, we measured the FTIR-Raman spectrum of the highly overcrowded spectral region between 1300 and 1450 cm,1. The spectral decomposition was carried out by a self-consistent global fit to all spectra obtained. The thus identified Raman and IR lines were assigned by comparison with the resonance Raman spectra of Cu(II)-octaethylporphyrin, by utilizing their depolarization ratio dispersions and by a normal mode analysis. The latter was based on a modified transferable molecular mechanics force field of Ni(II)-octaethylporphyrin [E. Unger, M. Beck, R.J. Lipski, W. Dreybrodt, C.J. Medforth, K.M. Smith and R. Schweitzer-Stenner, J. Phys. Chem. B103, 10229 (1999)]. A comparison of normal mode patterns obtained for Cu(II)-octamethylchlorin and Cu(II)-octaethylporphyrin revealed that some modes are significantly distorted by the reduction of the pyrrole ring, in accordance with results which Boldt et al. reported earlier for Ni(II)-octaethylchlorin [N.J. Boldt, F.J. Donohoe, R.R. Birge and D.F. Bocian, J. Am. Chem. Soc.109, 2284 (1987)]. In contrast to conclusions drawn from this study, however, the results of our vibrational analysis and several further lines of evidence suggest that the normal modes of corresponding chlorines and porphyrins are still comparable, because they display contributions from the same local coordinates. Thus, the classical normal mode classification developed for metalloporphyrins is also applicable to metallochlorins. Finally, we performed a preliminary analysis of the absorption spectrum and the resonance excitation profiles and depolarization ratio dispersions of some Raman lines. The results show that the electronic properties of Cu(II)-octamethylchlorin can still be described in terms of Gouterman's four orbital model [M. Gouterman, J. Chem. Phys.30, 1139 (1959)]. In regions of the Q bands, Raman scattering of A1 modes is determined by interferences between Franck, Condon coupling and interstate Herzberg, Teller coupling between Qx(Qy) and Bx(By) states. The B2 modes are resonance enhanced by Herzberg, Teller coupling between Qx and Qy and between Qx(Qy) and By(Bx). Franck, Condon coupling of A1 modes with large contributions from C,Cm stretching vibrations is comparatively strong for Qx. This is interpreted as reflecting the expansion of the chlorin macrocycle by an electronic transition into this excited state. Copyright © 2001 John Wiley & Sons, Ltd. [source] Experimental and theoretical vibrational spectroscopic study on symmetric and asymmetric halo-bridged complexes of palladium(II) and platinum(II)JOURNAL OF RAMAN SPECTROSCOPY, Issue 4 2001E. Kessenich The symmetric chloro-bridged complexes [(Et3P)2PtCl(µ-Cl)]2, [(Et3P)2Pt(µ-Cl)]22+ and [(C3H5)Pd(µ-Cl)]2 and the asymmetric complexes [(C3H5)Pd(µ-Cl)2Pt(PEt3)2]+ and [(C3H5)Pd(µ-Cl)2Pt(PEt3)Cl] were studied by means of vibrational spectroscopy (infrared, Raman) and computational chemistry. Assignments of all normal modes associated with skeletal stretching are suggested and their displacement vectors are discussed. Copyright © 2001 John Wiley & Sons, Ltd. [source] Experimental evidence of bistability in a semiconductor microcavityPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 4 2004M. Gurioli Abstract Optical bistability in a semiconductor microcavity showing normal mode coupling regime is observed by means of reflectivity and resonant Rayleigh scattering experiments. A third resonance, spectrally lying between the two normal modes, suddenly appears in the optical response when increasing the excitation power. Hysteresis loops are found when monitoring the microcavity optical response at the energy of the third peak. Our experimental findings can not be accounted for simply by exciton bleaching. We conclude that other non-linear mechanisms are relevant in explaining the presence of the third peak and the observed bistable behaviour. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Normal-mode analysis of the structures of perovskites with tilted octahedra.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2002Erratum There is an error in the mode assignment for hettotype 9, [a,b+a,], discussed in the paper by Darlington [Acta Cryst. (2002). A58, 6671], which has been pointed out by Dr Kevin Knight, Rutherford Appleton Laboratory, Didcot, Oxon, England. In this paper, a mode involving displacements of the anions of hettotype 9 was labelled [(½,,0,,½),,M1] rather than [(½,,0,,½),,M2]. Both modes involve plus-like distortion of the octahedra. In the corrected Tables 1,4 shown below, this mode, which is only found in hettotype 9, has been labelled K2 rather than H2. Therefore, there are not seven but eight normal modes of the cubic phase required to describe the displacements found in the nine hettotypes considered. The weights of K2 in all the materials examined in the original paper with the structure of hettotype 9 [labelled W(H1) in the original Table 4] are correct, unaltered by the change in the labelling of the mode. It should be noted that [(½,,0,,½),,M2] is a longitudinal mode , the seven other modes are all transverse. The weights of K2 are not significantly different from zero in the 15 structures examined. [source] Vertical discretizations giving optimal representation of normal modes: Sensitivity to the form of the pressure-gradient termTHE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 621 2006J. Thuburn Abstract The normal-mode dispersion properties and structures of some vertical discretizations of the compressible Euler equations are re-examined. It is shown that the dispersion properties can be sensitive to the form in which the pressure-gradient term is expressed. For a height coordinate and for an isentropic vertical coordinate, discretizations are identified that have optimal dispersion properties and, at the same time, lend themselves to mass conservation by predicting the relevant density variable. Copyright © 2006 Royal Meteorological Society [source] | ||||||||||||||||||||||||||||