Heavy atom method/technique

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. 

As discussed in section 2.3, the electron diffraction intensities need to be corrected before being employed for structure analysis. An empirical method has been set up to correct simultaneously all kinds of distortions in the diffraction data by referring to the heavy atom method and the Wilson statistic technique in X-ray crystallography. After correction, the intensity of each diffraction beam can approximately lead to the modulus of the corresponding structure factor [26]. 

The most demanding element of macromolecular crystallography (except, perhaps, for dealing with macromolecules that resist crystallization) is the so-called phase problem, that of determining the phase angle ahkl for each reflection. In the remainder of this chapter, I will discuss some of the common methods for overcoming this obstacle. These include the heavy-atom method (also called isomorphous replacement), anomalous scattering (also called anomalous dispersion), and molecular replacement. Each of these techniques yield only estimates of phases, which must be improved before an interpretable electron-density map can be obtained. In addition, these techniques usually yield estimates for a limited number of the phases, so phase determination must be extended to include as many reflections as possible. In Chapter 7,1 will discuss methods of phase improvement and phase extension, which ultimately result in accurate phases and an interpretable electron-density map. 

The application of the Patterson technique to locate strongly scattering atoms is often called the heavy atom method (which comes from the fact that heavy atoms scatter x-rays better and the Patterson technique is most often applied to analyze x-ray diffraction data). This allows constructing of a partial structure model ( heavy atoms only), which for the most part define phase angles of all reflections (see Eq. 2.107). The heavy atoms-only model can be relatively easily completed using sequential Fourier syntheses (either or both standard, Eq. 2.133, and difference, Eq. 2.135), sometimes enhanced by a least squares refinement of all found atoms. 

The heavy atom method for structure determination, though not useful for macromolecular crystals, is an easily understandable approach and it is illustrative of the ideas and devices that are incorporated into the other, more applicable techniques. The heavy atom method only works, it should be said at the outset, when the molecule under study contains at least... 

In order to exploit the heavy atom method with crystals of conventional molecules, or to utilize the isomorphous replacement method or anomalous dispersion technique for macro-molecular structure determination, it is necessary to identify the positions, the x, y, z coordinates of the heavy atoms, or anomalously scattering substituents in the crystallographic unit cell. Only in this way can their contribution to the diffraction pattern of the crystal be calculated and employed to generate phase information. Heavy atom coordinates cannot be obtained by biochemical or physical means, but they can be deduced by a rather enigmatic procedure from the observed structure amplitudes, from differences between native and derivative structure amplitudes, or in the case of anomalous scattering, from differences between Friedel mates. 

To resolve the ambiguities in interpretation of the single-stranded regions in the electron density map, we used a variation of a technique which is very common in small molecule crystallography. Phases are calculated from model coordinates of a fragment of the structure which has been seen by the heavy atom method or the direct... 

Secondary isotope effects are small. In fact, most of the secondary deuterium KIEs that have been reported are less than 20% and many of them are only a few per cent. In spite of the small size, the same techniques that are used for other kinetic measurements are usually satisfactory for measuring these KIEs. Both competitive methods where both isotopic compounds are present in the same reaction mixture (Westaway and Ali, 1979) and absolute rate measurements, i.e. the separate determination of the rate constant for the single isotopic species (Fang and Westaway, 1991), are employed (Parkin, 1991). Most competitive methods (Melander and Saunders, 1980e) utilize isotope ratio measurements based on mass spectrometry (Shine et al., 1984) or radioactivity measurements by liquid scintillation (Ando et al., 1984 Axelsson et al., 1991). However, some special methods, which are particularly useful for the accurate determination of secondary KIEs, have been developed. These newer methods, which are based on polarimetry, nmr spectroscopy, chromatographic isotopic separation and liquid scintillation, respectively, are described in this section. The accurate measurement of small heavy-atom KIEs is discussed in a recent review by Paneth (1992). 

Often the products of nuclear reactions have very short half-lives. This is especially true for the heaviest elements obtained by bombardment of heavy targets with heavy ions. To identify and characterize such short-lived nuclides, fast separations are required solvent extraction techniques are well suited to provide the required fast separations. For example, the SISAK method [68] has been successfully used in conjunction with in-line gas jet separators at heavy ion accelerators to identify short half-life actinide isotopes produced by collision of heavy atoms. The Sisak method involves use of centrifugal contactors, with phase residence times as low as tenths of a second, in conjunction with in-line radiometric detection equipment. 

By far, the most common procedure for the determination of heavy-atom positions is the difference Patterson method it is often used in combination with the difference Fourier technique to locate sites in second and third derivatives. 

A feature of these acidic antibiotics is that their chemical constitutions were established by crystal structure analysis, having defied classical organic chemistry, even aided by spectroscopic techniques. The reason for this is apparent from the formulae, (X)—(XII), examples chosen because the heavy atom salts are isomorphous with those of alkali metals. The formulae show the correct absolute configurations as determined by X-ray methods. 

The advantages of the difference Laue technique is that wavelength and position dependent corrections are not needed except in the case of significant change in the mass absorbtion coefficient during the course of the experiment (eg. the binding of heavy atoms). A modified difference Laue method was exploited by Faber et al. (1987) in the determination of the positions of the heavy atom binding sites in crystals of xylose isomerase. 

In order to understand the interactions between these bis-intercalating drugs and IMA more fully, we have crystallized several complexes of them and undertaken the structure determination by x-ray diffraction technique. One of the crystal forms diffracts to 1.6 A resolution with a space group of F222. The crystal structure was determined by the multiple isomorphous replacement method using three different heavy atom derivatives. The structure was refined to an R-factor of 19% and there were moderate number of solvent molecules clearly visible. The crystal... 

Variational one-center restoration. In the variational technique of one-center restoration (VOCR) [79, 80], the proper behavior of the four-component molecular spinors in the core regions of heavy atoms can be restored as an expansion in spherical harmonics inside the sphere with a restoration radius, Rvoa, that should not be smaller than the matching radius, Rc, used at the RECP generation. The outer parts of spinors are treated as frozen after the RECP calculation of a considered molecule. This method enables one to combine the advantages of two well-developed approaches, molecular RECP calculation in a gaussian basis set and atomic-type one-center calculation in numerical basis functions, in the most optimal way. This technique is considered theoretically in [80] and some results concerning the efficiency of the one-center reexpansion of orbitals on another atom can be found in [75]. 

While it is very easy, when one knows the structure of the crystal and the wavelength of the rays, to predict the diffraction pattern, it is quite another matter to deduce the crystal structure in all Its details from the observed pattern and the known wavelength. The first step is lo determine the spacing of the atomic planes from the Bragg equation, and hence the dimensions of the unit cell. Any special symmetry of the space group of the structure will be apparent from space group extinction. A Irial analysis may (hen solve the structure, or it may be necessary to measure the structure factors and try to find the phases or a Fourier synthesis. Various techniques can be used, such as the F2 series, the heavy atom, the isomorphous series, anomalous atomic scattering, expansion of the crystal and other methods. 

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