Fourier series/synthesis/analysis

Fourier series are used in crystal structure analysis in several ways. An electron-density map is a Fourier synthesis with measured values of F hkl) and derived values of phase angles 0 1. A Fourier analysis is the breakdown to component waves, as in the diffraction experiment. Fourier transform theory allows us to travel computationally between real space, p xyz), and reciprocal space, F hkl). 

When a diffraction grating, such as a crystal, interacts with X rays, the electron density that causes this diffraction can be described by a Fourier series, as discussed in Chapter 6. The diffraction experiment effects a Fourier analysis, breaking down the Fourier series (of the electron density) into its components, that is, the diffracted beams with amplitudes, F[hkl). The relative phases a(hkl) are, however, lost in the process in all usual diffraction experiments. This loss of the phase information needed for the computation of an electron-density map is referred to as the phase problem. The aim of X-ray diffraction studies is to reverse this process, that is, to find the true relative phase and hence the true three-dimensional electron density. This is done by a Fourier synthesis of the components, but it is now necessary to know both the actual amplitude F[hkl) and the relative phase, a[hkl), in order to calculate a correct electron-density map (see Figure 8.1). We must be able to reconstruct the electron-density distribution in a systematic way by approximating, as far as possible, a correct [but so far unknown) set of phases In this way the crystallographer, aided by a computer, acts as a lens for X rays. 

Lipson. H., and Beevers, C. A. An improved numerical method of two-dimensional Fourier synthesis for crystals. Proc. Phys. Soc. 48, 772-780 (1936). Patterson, A. L., and Tunell, G. A method for the summation of the Fourier series used in the X-ray analysis of crystal structures. Amer. Mineralogist 27. 655-679 (1942). 

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. 

Time scaling. Because the phase-vocoder (the short-time Fourier transform) gives access to the implicit sinusoidal model parameters, the ideal time-scale operation described by Eq. (7.3) can be implemented in the same framework. Synthesis time-instants / are usually set at a regular interval / +1 - / = R. From the series of synthesis time-instants / analysis time-instants / are calculated according to the desired time warping function tua = T l(t ). The short-time Fourier transform of the time-scaled signal is then ... 

Fourier demonstrated that any periodic function, or wave, in any dimension, could always be reconstructed from an infinite series of simple sine waves consisting of integral multiples of the wave s own frequency, its spectrum. The trick is to know, or be able to find, the amplitude and phase of each of the sine wave components. Conversely, he showed that any periodic function could be decomposed into a spectrum of sine waves, each having a specific amplitude and phase. The former process has come to be known as a Fourier synthesis, and the latter as a Fourier analysis. The methods he proposed for doing this proved so powerful that he was rewarded by his mathematical colleagues with accusations of witchcraft. This reflects attitudes which once prevailed in academia, and often still do. 

This three-dimensional electron-density distribution is represented by a series of parallel sections stacked on top of one another. Each section is a transparent plastic sheet or, more recently, a layer in a computer image) on which the electron-density distribution is represented by contour lines (Figure 3.45), like the contour lines used in geological survey maps to depict altitude (Figure 3.46). The next step) is to interpret the electron-density map. A critical factor is the resolution of the x-ray analysis, which is determined by the number of scattered intensitie.s used in the Fourier synthesis. The fidelity of the image... 

When the application of Eq. (11) to a least squares analysis of x-ray structure factors has been completed, it is usual to calculate a Fourier synthesis of the difference between observed and calculated structure factors. The map is constructed by computation of Eq. (9), but now IFhid I is replaced by Fhki - F/f /, where the phase of the calculated structure factor is assumed in the observed structure factor. In this case the series termination error is virtually too small to be observed. If the experimental errors are small and atomic parameters are accurate, the residual density map is a molecular bond density convoluted onto the motion of the nuclear frame. A molecular bond density is the difference between the true electron density and that of the isolated Hartree-Fock atoms placed at the mean nuclear positions. An extensive study of such residual density maps was reported in 1966.7 From published crystallographic data of that period, the authors showed that peaking of electron density in the aromatic C-C bonds of five organic molecular crystals was systematic. The random error in the electron density maps was reduced by averaging over chemically equivalent bonds. The atomic parameters from the model Eq. (11), however, will refine by least squares to minimize residual densities in the unit cell. 

This expression covers two methods, Fourier analysis and Fourier synthesis. In almost all cases, it is used to mean Fourier analysis, whereby a periodic function is transformed into the sum of a series of sine waves with different frequencies. The result of the transformation consists of intensities and phases of sine waves. Fourier analysis is widely used in nuclear magnetic resonance and infrared spectroscopy to evaluate the intensities and frequencies of the absorbed waves while the sample is irradiated with equal intensities of all frequencies in a specified range. In such applications, the fast Fourier transformation (FFT) algorithm is most commonly used. The frequencies of the sine waves are harmonic and have a base frequency whose period is the measured time of the periodic function. Use of the FFT requires the values of the periodic function at several times in equal intervals. The number of data points has to be a power of two. 

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