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Internal Motions (internal + motion)
Selected AbstractsComparative analysis of ArnCl2 (2 , n , 30) clusters taking into account molecular relaxation effectsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2006G. G. Ferreira Abstract Cluster structures are discussed in a nonrigid analysis, using a modified minima search method based on stochastic processes and classical dynamics simulations. The relaxation process is taken into account considering the internal motion of the Cl2 molecule. Cluster structures are compared with previous works in which the Cl2 molecule is assumed to be rigid. The interactions are modeled using pair potentials: the Aziz and Lennard,Jones potentials for the ArAr interaction, a Morse potential for the ClCl interaction, and a fully spherical/anisotropic Morse,Spline,van der Waals (MSV) potential for the ArCl interaction. As expected, all calculated energies are lower than those obtained in a rigid approximation; one reason may be attributed to the nonrigid contributions of the internal motion of the Cl2 molecule. Finally, the growing processes in molecular clusters are discussed, and it is pointed out that the growing mechanism can be affected due to the nonrigid initial conditions of smaller clusters such as ArnCl2 (n , 4 or 5), which are seeds for higher-order clusters. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Variable-temperature studies of the 4-isopropylphenol crystal structure from X-ray diffraction.ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2002Comparison of thermal expansion, molecular dynamics with spectroscopic results Crystalline 4-isopropylphenol, C9H12O, an optically non-linear material, was studied by X-ray diffraction in order to determine its structure at several temperatures in the 95,300,K range. The thermal expansion coefficients have been calculated from the lattice parameters' dependence on temperature. The rigid-body analysis of the anisotropic displacement parameters including the correlation with the internal motion of large amplitude provided the values of the molecular translation and libration tensors at the temperatures studied and was used to characterize the torsional motion of the isopropyl group. The calculated normal modes and internal torsion frequency were compared with the wave numbers at the maximum of bands in the low-frequency Raman scattering, FTIR and inelastic neutron scattering spectra. [source] 1H NMR study of internal motions and quantum rotational tunneling in (CH3)4NGeCl3MAGNETIC RESONANCE IN CHEMISTRY, Issue 2 2008K. J. Mallikarjunaiah Abstract (CH3)4NGeCl3 is prepared, characterized and studied using 1H NMR spin lattice relaxation time and second moment to understand the internal motions and quantum rotational tunneling. Proton second moment is measured at 7 MHz as function of temperature in the range 300,77 K and spin lattice relaxation time (T1) is measured at two Larmor frequencies, as a function of temperature in the range 270,17 K employing a homemade wide-line/pulsed NMR spectrometers. T1 data are analyzed in two temperature regions using relevant theoretical models. The relaxation in the higher temperatures (270,115 K) is attributed to the hindered reorientations of symmetric groups (CH3 and (CH3)4N). Broad asymmetric T1 minima observed below 115 K down to 17 K are attributed to quantum rotational tunneling of the inequivalent methyl groups. Copyright © 2007 John Wiley & Sons, Ltd. [source] Spatial distribution of galaxies in the Puppis regionMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2004Pierre Chamaraux ABSTRACT We determine the spatial distribution of the galaxies located behind the part of the zone of avoidance of the Milky Way defined by 220° < l < 260°, |b| < 20°, ,, 0°, up to a distance of 8000 km s,1. We use a sample of 369 galaxies with measured redshifts, of which 97 have been detected with the Nançay radio telescope. We show that our sample can be considered to be complete in apparent diameter down to 1.9 arcmin, a property that allows us to correct the density of galaxies for the loss of objects with distance. We then search for groups of galaxies using a companionship method and find 12 groups with at least five members, of which five are new. The members of one group are H i deficient by a factor of 1.6 on average. The method is then used to search for large structures and allows us to characterize the Puppis wall at 1400 < V0 < 2600 km s,1; it is 30 Mpc long, with the main axis being parallel to the sky plane, and it connects the Antlia cluster to the Fornax cluster through the zone of avoidance. The density of galaxies in the wall is approximately 20 times the general density of galaxies, i.e. half that observed in the densest part of the Pisces,Perseus supercluster. No internal motions are found along the line of sight, indicating that the Puppis wall has not yet collapsed. [source] The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinasePROTEIN SCIENCE, Issue 4 2004Anthony Mittermaier Abstract We have used 15N- and 2H-NMR spin relaxation experiments to study the response of backbone and side-chain dynamics when a leucine or valine is substituted for a completely buried phenylalanine residue in the SH3 domain from the Fyn tyrosine kinase. Several residues show differences in the time scales and temperature dependences of internal motions when data for the three proteins are compared. Changes were also observed in the magnitude of dynamics, with the valine, and to a lesser extent leucine mutant, showing enhanced flexibility compared to the wild-type (WT) protein. The motions of many of the same amide and methyl groups are affected by both mutations, identifying a set of loci where dynamics are sensitive to interactions involving the targeted side chain. These results show that contacts within the hydrophobic core affect many aspects of internal mobility throughout the Fyn SH3 domain. [source] Weak alignment offers new NMR opportunities to study protein structure and dynamicsPROTEIN SCIENCE, Issue 1 2003Ad Bax Protein solution nuclear magnetic resonance (NMR) can be conducted in a slightly anisotropic environment, where the orientational distribution of the proteins is no longer random. In such an environment, the large one-bond internuclear dipolar interactions no longer average to zero and report on the average orientation of the corresponding vectors relative to the magnetic field. The desired very weak ordering, on the order of 10,3, can be induced conveniently by the use of aqueous nematic liquid crystalline suspensions or by anisotropically compressed hydrogels. The resulting residual dipolar interactions are scaled down by three orders of magnitude relative to their static values, but nevertheless can be measured at high accuracy. They are very precise reporters on the average orientation of bonds relative to the molecular alignment frame, and they can be used in a variety of ways to enrich our understanding of protein structure and function. Applications to date have focused primarily on validation of structures, determined by NMR, X-ray crystallography, or homology modeling, and on refinement of structures determined by conventional NMR approaches. Although de novo structure determination on the basis of dipolar couplings suffers from a severe multiple minimum problem, related to the degeneracy of dipolar coupling relative to inversion of the internuclear vector, a number of approaches can address this problem and potentially can accelerate the NMR structure determination process considerably. In favorable cases, where large numbers of dipolar couplings can be measured, inconsistency between measured values can report on internal motions. [source] Dynamical characterization of residual and non-native structures in a partially folded protein by 15N NMR relaxation using a model based on a distribution of correlation timesPROTEIN SCIENCE, Issue 4 2002Françoise Ochsenbein Abstract A spectral density model based on a truncated lorentzian distribution of correlation times is used to analyze the nanosecond time-scale dynamics of the partially unfolded domain 2 of annexin I from its 15N NMR relaxation parameters measured at three magnetic field strengths. The use of a distribution of correlation times enables the characterization of the dynamical features of the NH bonds of the protein in terms of heterogeneity of dynamical states in the nanosecond range. The variation along the sequence of the two dynamical parameters introduced, namely the center and the width of the distribution, points out the different types of residual secondary structures present in the D2 domain. Moreover, it allows a physically sensible interpretation of the dynamical behavior of the different residual helices and of the non-native structures. Also, a striking correspondence is found between the parameters obtained using an extended Lipari and Szabo model and the parameters obtained using the distribution of correlation times. This result led us to propose a specific interpretation of the model-free order parameter for internal motions in the nanosecond range in the case of unfolded states. [source] Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopyPROTEIN SCIENCE, Issue 12 2001Wei Li Abstract Translation initiation factor 1A (aIF-1A) from the archaeon Methanococcus jannaschii was expressed in Escherichia coli, purified, and characterized in terms of its structure and dynamics using multidimensional NMR methods. The protein was found to be a member of the OB-fold family of RNA-associated proteins, containing a barrel of five beta-strands, a feature that is shared with the homologous eukaryotic translation initiation factor 1A (eIF-1A), as well as the prokaryotic translation initiation factor IF1. External to the , barrel, aIF-1A contains an ,-helix at its C-terminal and a flexible loop at its N-terminal, features that are qualitatively similar to those found in eIF-1A, but not present in prokaryotic IF1. The structural model of aIF-1A, when used in combination with primary sequence information for aIF-1A in divergent species, permitted the most-conserved residues on the protein surface to be identified, including the most likely candidates for direct interaction with the 16S ribosomal RNA and other components of the translational apparatus. Several of the conserved surface residues appear to be unique to the archaea. Nitrogen-15 relaxation and amide exchange rate data were used to characterize the internal motions within aIF-1A, providing evidence that the protein surfaces that are most likely to participate in intermolecular interactions are relatively flexible. A model is proposed, suggesting some specific interactions that may occur between aIF-1A and the small subunit of the archaeal ribosome. [source] | ||||||||||