Ion density map

SIMS was the first mass spectrometry technique used to generate two-dimensional ion density maps or images from a variety of solid materials and thin sections of biological tissues.108 SIMS involves the bombardment of a sample... 

Fig. 1.4. Imaging IM-MS for mapping the spatial coordinates of analytes based on structure and molecular weight, (a) Optical Image of a thin coronal rat brain tissue section adjacent the section analyzed by IMS. (b) Lipid imaging of the analytes indicated at an Ion mobility arrival time of 480-484 gs and m/z 700-840 is illustrated in (c)-(e). Extracted ion density maps for two phospholipids at m/z 771-776 and 819-823, respectively. (Reprinted with permission from ref. (59),)...

In our study of the hydrogen molecule-ion in Chapter 3, we considered the electron density map shown in Figure 18.8. It is obvious by inspection that the... 

X-Ray diffraction from single crystals is the most direct and powerful experimental tool available to determine molecular structures and intermolecular interactions at atomic resolution. Monochromatic CuKa radiation of wavelength (X) 1.5418 A is commonly used to collect the X-ray intensities diffracted by the electrons in the crystal. The structure amplitudes, whose squares are the intensities of the reflections, coupled with their appropriate phases, are the basic ingredients to locate atomic positions. Because phases cannot be experimentally recorded, the phase problem has to be resolved by one of the well-known techniques the heavy-atom method, the direct method, anomalous dispersion, and isomorphous replacement.1 Once approximate phases of some strong reflections are obtained, the electron-density maps computed by Fourier summation, which requires both amplitudes and phases, lead to a partial solution of the crystal structure. Phases based on this initial structure can be used to include previously omitted reflections so that in a couple of trials, the entire structure is traced at a high resolution. Difference Fourier maps at this stage are helpful to locate ions and solvent molecules. Subsequent refinement of the crystal structure by well-known least-squares methods ensures reliable atomic coordinates and thermal parameters. 

Second, the spin density maps must cover the atoms which are involved in the contacts. On the one hand, the localized d spins of the transition metal ions must paradoxically be sufficiently delocalized toward the ligand atoms. On the other hand, the n carriers of the donor set have to extend toward the peripheral atoms. In fact the electrons belonging to the two networks must meet at the intermolecular contact, otherwise the networks would ignore each other. 

Figure 8. Calculated spin polarization density map in a Co/Cr—O—Li plane in LiCri/gCoy/gOz from DFT calculations."pj-ie positions of the Cr, Co, Li, and O ions are indicated. Li(l) has a Cr ion as its second cation coordination shell, while Li(2) has a Cr + ion in its first cation coordination shell. The Li spectra of LiCr/ioi-/32 x= 0.05 and 0.1) are shown along with the assignments of resonances corresponding to Li(l) and Li(2) local environments.

The volume properties of crystalline mixtures must be related to the crystal chemical properties of the various cations that occupy the nonequivalent lattice sites in variable proportions. This is particularly true for olivines, in which the relatively rigid [Si04] groups are isolated by Ml and M2 sites with distorted octahedral symmetry. To link the various interionic distances to the properties of cations, the concept of ionic radius is insufficient it is preferable to adopt the concept of crystal radius (Tosi, 1964 see section 1.9). This concept, as we have already noted, is associated with the radial extension of the ion in conjunction with its neighboring atoms. Experimental electron density maps for olivines (Fujino et al., 1981) delineate well-defined minima (cf figure 1.7) marking the maximum radial extension (rn, ,x) of the neighboring ions ... 

In crystal structure analyses of proteins, the presence of Ca ions is usually determined indirectly. Ions, being larger and more electron dense, are differentiated from water molecules based on their peak heights in electron density maps, and their high occupancies and low thermal motion parameters during least-squares refinement of the... 

It is also possible to determine accurate electron density maps for the ionic crystal structures using X-ray crystallography. Such a map is shown for NaCl and LiF in Figure 1.45. The electron density contours fall to a minimum—although not to zero—in between the nuclei and it is suggested that this minimum position should be taken as the radius position for each ion. These experimentally determined ionic radii are often called crystal radii the values are somewhat different from the older sets and tend to make the anions smaller and the cations bigger than previously. The most comprehensive set of radii has been compiled by... 

Fig. 16.13. Pore structure of the acetylcholine receptor, based on electron microscopy studies. a) Electron density map of the acetylcholine receptor of the postsynaptic membrane of the electric organ of the ray Torpedo californicus, based on electron microscopy studies. The receptor has a long funnel-like structure in the extracellular region, which narrows at the center of the pore. A smaller funnel structure is observed in the cytoplasmic region of the receptor. Another protein is situated on the cytoplasmic side. The long arrow indicates the direction of ion passage and the small arrow shows the postulated binding site for acetylcholine, b) Schematic representation of the acetylcholine receptor with the M2 hehx as the central block in the ion channel. According to Unwin, (1993).

Fig. 16.14. Configuration of the M2 helices of the acetylcholine receptor in the closed and open states. The schematic representation is based on a comparison of the electron density map of the acetylcholine receptor in closed and open states. Only three of the five M2 helices are shown, a) Closed state the M2 helices are bent at the middle. The leucine residues point into the interior of the pore and prevent passage of ions, b) Open state the M2 helices are turned outwards at a tangent and the bulky leucine residues are removed from the center of the pore. Reorientation of the M2 helices causes a reorientation of polar amino adds that coat the interior of the pore. The polar amino acids (Ser and Thr residues) are oriented closer to the center of the pore and create a hydrophilic coating of the pore inner wall, which facilitates ion passage. According to Unwin,...

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