Isomorphic replacement

This plays a critical role in the method of isomorphous replacement, which we discuss below. 

A teclmique that employs principles similar to those of isomorphous replacement is multiple-wavelength anomalous diffraction (MAD) [27]. The expression for the atomic scattering factor in equation (B1.8.2h) is strictly accurate only if the x-ray wavelength is well away from any characteristic absorption edge of the element, in which case the atomic scattering factor is real and Filiki) = Fthkl V- Since the diffracted... 

Occurrence. Niobium and tantalum usually occur together. Niobium never occurs as the metal, ie, ia the free state. Sometimes it occurs as a hydroxide, siUcate, or borate most often it is combiaed with oxygen and another metal, forming a niobate or tantalate ia which the niobium and tantalum isomorphously replace one another with Htde change ia physical properties except density. Ore concentrations of niobium usually occur as carbonatites and are associated with tantalum ia pegmatites and alluvial deposits. Principal niobium-beariag minerals can be divided iato two groups, the titano- and tantalo-niobates. 

In small-molecule crystallography the phase problem was solved by so-called direct methods (recognized by the award of a Nobel Prize in chemistry to Jerome Karle, US Naval Research Laboratory, Washington, DC, and Herbert Hauptman, the Medical Foundation, Buffalo). For larger molecules, protein aystallographers have stayed at the laboratory bench using a method pioneered by Max Perutz and John Kendrew and their co-workers to circumvent the phase problem. This method, called multiple isomorphous replacement... 

MIR), requires the introduction of new x-ray scatterers into the unit cell of the crystal. These additions should be heavy atoms (so that they make a significant contribution to the diffraction pattern) there should not be too many of them (so that their positions can be located) and they should not change the structure of the molecule or of the crystal cell—in other words, the crystals should be isomorphous. In practice, isomorphous replacement is usually done by diffusing different heavy-metal complexes into the channels of preformed protein crystals. With luck the protein molecules expose side chains in these solvent channels, such as SH groups, that are able to bind heavy metals. It is also possible to replace endogenous light metals in metal-loproteins with heavier ones, e.g., zinc by mercury or calcium by samarium. 

The intensity differences obtained in the diffraction pattern by illuminating such a crystal by x-rays of different wavelengths can be used in a way similar to the method of multiple isomorphous replacement to obtain the phases of the diffracted beams. This method of phase determination which is called Multiwavelength Anomalous Diffraction, MAD, and which was pioneered by Wayne Hendrickson at Columbia University, US, is now increasingly used by protein cystallographers. 

The variation that exists in the 0 F ratio of MMe6Oi5F-type compounds enables isomorphic replacement of alkali metal cations by other cations with appropriate radii. For instance, a copper-containing compound, Cuo.6Nb6Oi4 6F( 4, which crystallizes in a LiNbeOisF type structure, was obtained [255]. 

The P —alumina structures are remarkable not only for their ionic conductivities but also for the versatility in isomorphous replacement. There is little of the structure of (Na2S)l+Jt 11A1203 which cannot be substituted, at least in part, by an alternative ion. MgO and Li20 are preferred additives to P —alumina in order to obtain good ionic conduction with no electronic contribution. 

Bixbyite, found only in Utah, about 35 miles southwest of Simpson, is described by Penfield and Foote2) as forming shiny black cubic crystals with a trace of octahedral cleavage. The composition assigned it by them was Fe++Mn+40A, with a little isomorphous replacement of Fe++ by Mg++ and Mn++ and of Mn+i by Ti+i. It was shown by Zachariasen that the X-ray data exclude this formulation, and indicate instead that the mineral is a solid solution of Mn20A and Fe20A. We shall reach a similar conclusion. 

Bearing in mind that the relative sizes of the ions permit isomorphous replacement of OH by F but not by Cl, we write with considerable confidence the formula (Si, Al, Fe, P)18O20(OH, F)laCl, which agrees well with analyses 1, 2, and 3. Inasmuch as aluminium (as well as phosphorus) may replace silicon with coordination number 4, it is evident that there are at least five silicon atoms in the unit, corresponding to the chemical formula... 

A very simple treatment can be carried out by assuming that the liquid phase is a series of ideal solutions of lead and thallium, and that in the solid phase isomorphous replacement of thallium atoms in the PbTl3 structure by lead atoms occurs in the way corresponding to the formation of an ideal solution. For the liquid phase the free energy would then be represented by the expression... 

There seem to be many binary metallic systems in which there are phases of this sort. In the sodium-lead system there are two such phases. One of them, based on the ideal structure Na3Pb, extends from 27 to 30 atomic percent lead, with its maximum at about 28 atomic percent lead and the other, corresponding to the ideal composition NaPb3, extends from 68 to 72 atomic percent lead, with maximum at about 70 atomic percent. The intensities of X-ray reflection have verified that in the second of these phases sodium atoms occupy the positions 0, 0, 0, and the other three positions in the unit cell are occupied by lead atoms isomorphously replaced to some extent by sodium atoms (Zintl Harder, 1931). These two phases are interesting in that the ranges of stability do not include the pure compounds Na8Pb and NaPb3. 

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. 

The structure was solved by the multiple isomorphous replacement technique using four heavy atom derivatives uranyl acetate, plati-nous chloride, tetramethyllead acetate, and p-chloromercury benzoate. All four derivatives gave interpretable heavy atom Patterson syntheses. The heavy atom sites could be correlated between the de-... 

Isomorphous replacement is where the phases from a previous sample are used directly for a protein that has crystallized in exactly the same space group as before. This is usually applicable to determining the structure of many protein-ligand complexes or protein mutants. 

Multiple isomorphous replacement allows the ab initio determination of the phases for a new protein structure. Diffraction data are collected for crystals soaked with different heavy atoms. The scattering from these atoms dominates the diffraction pattern, and a direct calculation of the relative position of the heavy atoms is possible by a direct method known as the Patterson synthesis. If a number of heavy atom derivatives are available, and... 

Sheet silicates (Q ) with significant isomorphic replacement of Si by AF+ or Fe +. These were decomposed by poly(acrylic add) to silica gel. The chlorite, thuringite, formed a strong cement but was much affected by water. 

In the elucidation of the X-ray structure of hCP by the method of isomorphous replacement, gold and mercury heavy atom derivatives were utilized. In the case of the mercury derivative, p-chloromercury-benzoate, the heavy atom bound to the free sulphydryl residue, C221, but for the gold cyanide derivative the gold atom was found to bind in the vicinity of the trinuclear copper cluster. A realistic explanation of this... 

The isomorphous replacement method requires attachment of heavy atoms to protein molecules in the crystal. In this method, atoms of high atomic number are... 

Once a suitable crystal is obtained and the X-ray diffraction data are collected, the calculation of the electron density map from the data has to overcome a hurdle inherent to X-ray analysis. The X-rays scattered by the electrons in the protein crystal are defined by their amplitudes and phases, but only the amplitude can be calculated from the intensity of the diffraction spot. Different methods have been developed in order to obtain the phase information. Two approaches, commonly applied in protein crystallography, should be mentioned here. In case the structure of a homologous protein or of a major component in a protein complex is already known, the phases can be obtained by molecular replacement. The other possibility requires further experimentation, since crystals and diffraction data of heavy atom derivatives of the native crystals are also needed. Heavy atoms may be introduced by covalent attachment to cystein residues of the protein prior to crystallization, by soaking of heavy metal salts into the crystal, or by incorporation of heavy atoms in amino acids (e.g., Se-methionine) prior to bacterial synthesis of the recombinant protein. Determination of the phases corresponding to the strongly scattering heavy atoms allows successive determination of all phases. This method is called isomorphous replacement. 

Complete 100% isomorphism, complete isomorphous replacement of atoms-components ... 

But many computations of phase-formation based on the application of pseudo-potential, quantum-mechanical techniques, statistic-thermodynamic theories are carried out now only for comparatively small number of systems, for instance [1-3], A lot of papers dedicated to the phenomenon of isomorphic replacement, arrangement of an adequate model of solids, energy theories of solid solutions, for instance [4-7], But for the majority of actual systems many problems of theoretical and prognostic assessment of phase-formation, solubility and stable phase formation are still unsolved. 

Spatial-energy principles of isomorphic replacement were found ... 

Complete (100%) isomorphic replacement at approximate equality of P-parameters of valence orbitals of interchangeable atoms PE PE... 

Surface charge at the phase boundary may be caused by lattice imperfections at the solid surface and by isomorphous replacements within the lattice. For example, if in any array of solid Si02 tetrahedra an Si atom is replaced by an Al atom (Al has one electron less than Si), a negatively charged framework is established ... 

Similarly, isomorphous replacement of the A1 atom by Mg atoms in networks of aluminum oxide octahedra leads to a negatively charged lattice. Clays are representative examples where such atomic substitution causes the charge at the phase boundary. Sparingly soluble salts also carry a surface charge because of lattice imperfections. 

The solids occurring in nature are seldom pure solid phases. Isomorphous replacement by a foreign constituent in the crystalline lattice is an important factor by which the activity of the solid phase may be decreased. If the solids are homogeneous, that is, contain no concentration gradient, one speaks of homogeneous solid solutions. The thermodynamics of solid solution formation has been discussed by Vaslow and Boyd (1952) for solid solutions formed by AgCI(s) and AgBr(s). 

The crystal structure of the MoeB-MoaD complex (Figure 3.4) was determined by multiple isomorphous replacement in its apo-state at 1.7-A resolution, with bound ATP at 2.9-A resolution and after formation of the covalent MoaD-adenylate at 2.1-A resolution [38]. The latter two structures were obtained by soaking either ATP or Mg-ATP into crystals of the apo-complex. 

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