Home About us Contact
|
Home About us Contact | ||
|
|
||
Vibrational Motion (vibrational + motion)
Selected AbstractsThe Breakdown of the Minimum Polarizability Principle in Vibrational Motions as an Indicator of the Most Aromatic CenterCHEMISTRY - A EUROPEAN JOURNAL, Issue 20 2005Miquel Torrent-Sucarrat Dr. Abstract The vibrational motions that disobey the minimum polarizability principle (MPP) in ,-conjugated molecules are distortions of the equilibrium geometry that produce a reduction in the polarizability due to the localization of , electrons. For aromatic species, this electronic localization is responsible for the subsequent reduction in the aromaticity of the system. In the present work, we diagonalize the Hessian matrix of the polarizability with respect to the vibrational nontotally symmetric normal coordinates, to calculate the nontotally symmetric distortions that produce the maximum breakdown of the MPP in a series of twenty polycyclic aromatic hydrocarbons. It is shown that the nuclear displacements that break the MPP have larger components in those rings that possess the highest local aromaticity. Thus, these vibrational motions can be used as an indicator of local aromaticity. [source] Optimal modal reduction of vibrating substructuresINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 3 2003Paul E. Barbone Abstract A structure which consists of a main part and a number of attached substructures is considered. A ,model reduction' scheme is developed and applied to each of the discrete substructures. Linear undamped transient vibrational motion of the structure is assumed, with general external forcing and initial conditions. The goal is to replace each discrete substructure by another substructure with a much smaller number of degrees of freedom, while minimizing the effect this reduction has on the dynamic behaviour of the main structure. The approach taken here involves Ritz reduction and the Dirichlet-to-Neumann map as analysis tools. The resulting scheme is based on a special form of modal reduction, and is shown to be optimal in a certain sense, for long simulation times. The performance of the scheme is demonstrated via numerical examples, and is compared to that of standard modal reduction. Copyright © 2003 John Wiley & Sons, Ltd. [source] Theoretical study of NMR chemical shift induced by H/D isotope effectINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2010Kimikazu Sugimori Abstract The isotope effect induced by deuterium substituted species is observed in molecular properties, such as geometry, kinetics, and electronic state, of the molecules through nuclear-electron interaction. Theoretical considerations and experimental alignments have been studied by ab initio molecular orbital, density functional theory, and other empirical strategies. The Born-Oppenheimer approximation with nuclear vibrational wavefunction can treat isotope effect because nuclear mass effect account for the average distance of vibrational motion. In this study, we introduce Morse anharmonic oscillator model to calculate average internuclear distance of diatomic molecules having X-H bonding and X-D bonding. Morse parameters are determined by fitting to potential energy surface of molecular orbital and/or density functional calculations, and then the average distance are obtained as the expectation value of the analytical Morse vibrational wavefunction. Nuclear magnetic resonance shielding constants of the H/D isotopomer are calculated again on the average distance by using GIAO with B3LYP and CCSD calculation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Wavelet transform analysis of ab initio molecular dynamics simulation: Application to core-excitation dynamics of BF3JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2007Takao Otsuka Abstract We propose a novel analysis method of ab initio molecular dynamics (AIMD) simulation using a continuous wavelet transform (c-WT) technique. The c-WT technique, one of the time-frequency signal analysis methods, provides a clear view of the dynamical information in time developments. Combined with the auto-correlation function of velocity by AIMD simulation, c-WT analysis enables us to well understand dynamical distribution, such as the vibrational properties following a change of electronic structure in a molecular system. As a practical application, AIMD simulation of core-excited BF3 (B1s , 2a) is illustrated. AIMD simulation leads to the change of vibrational motion as well as structural deformation by core-excitation. The c-WT analysis clarifies the relationship between structural deformation and the related significant vibrational modes in core-excitation within 50 fs. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Diffuse scattering from large-angle, thermally induced, orientational disorder in molecular crystalsACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2007John Reid Large-angle rotational motion (libration) characteristic of molecular solids has not been properly included in many scattering calculations because of the need to develop scattering theory through small-angle approximations. A simple but effective approach to calculating the influence of large-angle librations on the thermal disorder scattering given by molecular solids is to treat the molecules as independent librators, each in a harmonic potential well, using the mathematics appropriate for large-angle rotations. The resulting probability distribution for angular misorientations is Gaussian and this distribution can be used to smear the molecular form factor, enabling the librational influence on the scattering to be calculated. It is shown how to apply this direct approach quite generally and by way of examples the technique is used with the molecular solids sulfur hexafluoride (SF6), adamantane (C10H16) and buckminsterfullerene (C60). For these materials, the molecular Fourier transform (i.e. the molecular form factor) have been calculated in selected planes in reciprocal space, followed by the separate effects of librational and translational smearing. It is found that the librational smearing produces a large effect on the form factor, particularly at larger scattering vectors, that is not sensitive to approximations in the argument. Additionally, the Debye,Waller effect of vibrational motion is included in the calculations, showing quantitatively the decreasing influence of vibrations on the scattering with increasing scattering vector. Both effects illustrate with pedagogic clarity how different processes modify the basic molecular scattering. [source] Resonance Raman spectra and excited state structural dynamics of ethylene trithiocarbonate in the A - and B -band absorptionsJOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2009Huigang Wang Abstract A - and B -band resonance Raman spectra were acquired for ethylene trithiocarbonate in cyclohexane solution. The results indicate that the S3 state structural dynamics is mostly along vibrational motions of the CS stretch ,11, while the S4 state one has motions mainly via the SCS symmetric stretch ,18, CS stretch ,11, and the HCH rock + SCS antisymmetric stretch ,14 reaction coordinates. The very different excited state structural dynamics were briefly discussed in terms of vibronic couplings using local symmetry point group. Copyright © 2009 John Wiley & Sons, Ltd. [source] A molecular viewer for the analysis of TLS rigid-body motion in macromoleculesACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2005Jay Painter TLS (translation/libration/screw) models describe rigid-body vibrational motions of arbitrary objects. A single-group TLS model can be used to approximate the vibration of an entire protein molecule within a crystal lattice. More complex TLS models are broadly applicable to describing inter-domain and other internal vibrational modes of proteins. Such models can be derived and refined from crystallographic data, but they can also be used to describe the vibrational modes observed through other physical techniques or derived from molecular dynamics. The use of TLS models for protein motion has been relatively limited, partly because the physical meaning of the refined TLS parameters is not intuitive. Here, a molecular viewer, TLSView, is introduced using OpenGL and based on the mmLib library for describing and manipulating macromolecular structural models. This visualization tool allows an intuitive understanding of the physical significance of TLS models derived from crystallographic or other data and may be used as an interactive tool to display and interpret inter-domain or other motions in protein structural models. TLSView may also be used to prepare, analyze and validate TLS models for crystallographic refinement. [source] The Breakdown of the Minimum Polarizability Principle in Vibrational Motions as an Indicator of the Most Aromatic CenterCHEMISTRY - A EUROPEAN JOURNAL, Issue 20 2005Miquel Torrent-Sucarrat Dr. Abstract The vibrational motions that disobey the minimum polarizability principle (MPP) in ,-conjugated molecules are distortions of the equilibrium geometry that produce a reduction in the polarizability due to the localization of , electrons. For aromatic species, this electronic localization is responsible for the subsequent reduction in the aromaticity of the system. In the present work, we diagonalize the Hessian matrix of the polarizability with respect to the vibrational nontotally symmetric normal coordinates, to calculate the nontotally symmetric distortions that produce the maximum breakdown of the MPP in a series of twenty polycyclic aromatic hydrocarbons. It is shown that the nuclear displacements that break the MPP have larger components in those rings that possess the highest local aromaticity. Thus, these vibrational motions can be used as an indicator of local aromaticity. [source] The Jahn,Teller Effect of the TiIII Ion in Aqueous Solution: Extended Ab Initio QM/MM Molecular Dynamics Simulations,CHEMPHYSCHEM, Issue 10 2004Chinapong Kritayakornupong Dr. Abstract Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIIIin aqueous solution. The hydration structure of TiIIIis discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIIIO vibrations, were evaluated. A fast dynamical Jahn,Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn,Teller effect. [source] | ||||||||||