Shape simulation

Line shape analysis was performed for the binding of some dihydroxycholate ions to /1-cyclodextrin.205 The dihydroxycholates show different 18-CH3 signals for the complexed and free dihydroxycholate ions. To extract exchange rate constants from the NMR spectra, a complete line-shape simulation was performed. The simulation requires input of the chemical shift difference between the two sites, the line width in the absence of exchange, the residence time in each site (thg and Tg), and the relative population (fHG and fG) of each site (Equation (11)). The values were varied until the simulated and experimental spectra could be superimposed. The dissociation rate... 

The jump rates obtained by the line shape simulations are plotted on the relaxation map in Fig. 22 together with values obtained by other experimental methods. The points of the mechanical and dielectric relaxations correspond to the process of the large-scale side chain motions refered to as the -process and follow the WLF equation very well above Jg,. 11 It should be noted that the present 2FI NMR results are located on the curve obtained by other relaxation experiments. This fact shows that... 

FIGURE 44. Tilt series of 2H NMR spectra from the deuteriomethyl groups Cl 8 (left column) and C20 (right column) of retinal in oriented purple membranes, at seven different sample inclination (a) in the spectrometer field. The line-shape simulations are superimposed over the experimental spectra in order to illustrate the good line fit obtained by the prediction method. Reprinted with permission from Reference 57. Copyright (1994) American Chemical Society... 

FIGURE 45. Orientation and conformation of retinal in bR, constructed from the individual methyl group orientations that have been determined by solid-state 2H NMR. The angles 6 of the C—CD3 bond vectors with respect to the membrane normal (N) were evaluated for Cis (37°), C49 (40°) and C20 (32°) from the zero-tilt spectra shown in Figure 44 and with the aid of line-shape simulation of the tilt series in Figure 42 and 43. Reprinted with permission from Reference 57. Copyright (1994) American Chemical Society... 

Figure 48 shows representative experimental 2H NMR spectra from the labeled retinal in bR in a dark-adapted PM sample. The line shape simulations that were generated in the data analysis are superimposed on the experimental spectra. The powder pattern [Figure 48(a)] serves as a general reference for the tilt series of spectra recorded at various sample inclinations [Figure 48(b)], because it defines the accessible frequency region over which the spectral intensity can occur. The oriented sample was measured at every 22.5° between 0° and 90°, of which three inclinations are represented in Figure 48(b) with a = 0°, 45° and 90°. 

FIGURE 48. Representative 2H NMR spectra (full lines) of dark-adapted bR (90 mg) containing deuteriated retinal, with line shape simulations (dashed lines) superimposed. Both the powder spectrum (a) from randomly oriented PM patches and the tilt series (b) over sample inclinations, a = 0, 45° and 90°, were recorded at — 60 °C (number of scans, 1.7 x 105, for a = 0°). Spectrum (c) was measured at 21 °C with a = 0° (number of scans, 3 x 105). Reprinted with permission from Reference 60. Copyright (1997) American Chemical Society... 

Applications to Biological Samples. - Methods of distance measurements were compared for four doubly spin-labelled derivatives of human carbonic anhydrase.53 The distances between the spin labels were obtained from continuous wave spectra by analysis of the relative intensity of the half-field transition, Fourier deconvolution of the line-shape broadening, and computer simulation of line-shape changes. For variants with interspin distances greater than 18 A, the DEER method also was used. For each variant, at least two methods were applicable and reasonable agreement between distances obtained by different methods was obtained. The useful distance ranges for the techniques employed at X-band with natural isotope abundance spin labels were estimated to be half-field transition (5-10 A), line-shape simulation (up to 15 A), Fourier deconvolution (8 - 20 A), and four-pulse DEER (> 18 A).53... 

CW line-shape simulation. Simulation of the EPR spectrum of di-copper-substituted aminopeptidase from Aeromonas proteolytica found a zero field splitting that corresponded to an interspin distance of about 5 A, which is in good agreement with the X-ray crystallographic value of 4.93 A.55... 

Observations of crystals between crossed polarizers are particularly valuable in the case of some of those twin combinations which in their external shape simulate a single crystal having a symmetry higher than that of one of the individuals. The observation of different extinction directions in different regions demonstrates at once that the crystal is... 

For the investigation of the molecular dynamics in polymers, deuteron solid-state nuclear magnetic resonance (2D-NMR) spectroscopy has been shown to be a powerful method [1]. In the field of viscoelastic polymers, segmental dynamics of poly(urethanes) has been studied intensively by 2D-NMR [78, 79]. In addition to ID NMR spectroscopy, 2D NMR exchange spectroscopy was used to extend the time scale of molecular dynamics up to the order of milliseconds or even seconds. In combination with line-shape simulation, this technique allows one to obtain correlation times and correlation-time distributions of the molecular mobility as well as detailed information about the geometry of the motional process [1]. 

There are many excellent reviews on the standard molecular dynamics method dealing with calculations in the microcanonical ensemble as well as on the Monte Carlo method involving calculations in the canonical, isothermal isobaric, and grand canonical ensemble (< ). In the present article, we shall limit ourselves exclusively to those developments that have taken place since the work of Andersen (4). In the molecular dynamics method, the developments are the constant-pressure, constant-temperature, constant-temperature-constant-pressure, variable shape simulation cell MD, and isostress calculations in the Monte Carlo method, it is the variable shape simulation cell calculation. 

Above 100 K, motional effects on spectrum become pronounced with increasing temperature and, above 230 K, the spectra consist of essentially an isotropic and equally spaced hyperfine triplet, but with different relative intensities. The line shape simulations were carried out by adopting a Brownian rotational diffusion model in order to evaluate the associated (average) rotational correlation time, and its degree of anisotropy, = zpy, /... 

N. Felidj, J. Aubard, and G. Levi, Effects ofvarious halide ions and probe molecules on inelastic Mie scattering from SERS active surfaces Determination of particle size distributions from band shapes simulation, J. Chem. Phys. 24, 9735-9746 (1996). 

K. At temperatures below 20 K, the spectra show features characteristic of the QEC effect. A fair reproduction of the observed spectra was achieved in line shape simulations employing the AB equation with the QEC and stochastic exchange terms as in Eq. (5), augmented with the corresponding quadrupolar terms (see Fig. 4). It was found that the QEC constant A increases slightly with temperature, from the value 19.7 kHz at... 

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