2.5 Structure factor

Structure factors are crucial in crystallography, describing how atoms scatter radiation in crystals. They link atomic positions to diffracted beam intensity, enabling scientists to decode crystal structures from diffraction patterns.

Mathematically, structure factors are complex numbers representing amplitude and phase of scattered waves. They're calculated using atomic positions and form factors, determining diffraction peak intensities and positions in experiments.

Definition of structure factor

• Fundamental concept in crystallography that describes the amplitude and phase of a wave diffracted from a crystal lattice
• Mathematical function that relates the atomic positions within a unit cell to the intensity of the diffracted beam
• Provides a quantitative measure of how atoms in a crystal scatter incident radiation (X-rays, neutrons, or electrons)

Mathematical representation

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• Expressed as a complex number, with both amplitude and phase components
• Represented by the symbol $F_{hkl}$, where $h$, $k$, and $l$ are the Miller indices of the corresponding lattice planes
• Mathematical formula: $F_{hkl} = \sum_{j=1}^{N} f_j \exp[2\pi i(hx_j + ky_j + lz_j)]$
  • $f_j$ is the atomic form factor of the $j$-th atom
  • $x_j$, $y_j$, and $z_j$ are the fractional coordinates of the $j$-th atom in the unit cell
  • $N$ is the total number of atoms in the unit cell

Physical interpretation

• Represents the resultant wave scattered by all atoms in the unit cell in a particular direction
• Magnitude of the structure factor determines the intensity of the diffracted beam
• Phase of the structure factor contains information about the relative positions of atoms in the unit cell
• Provides a link between the atomic arrangement and the observed diffraction pattern

Role in diffraction

• Structure factor plays a crucial role in understanding and interpreting diffraction patterns obtained from crystalline materials
• Determines the intensity and position of diffraction peaks in X-ray, neutron, or electron diffraction experiments
• Enables the extraction of structural information from diffraction data

Relationship to atomic positions

• Structure factor is sensitive to the positions of atoms within the unit cell
• Changes in atomic positions lead to changes in the structure factor and, consequently, the diffracted intensity
• Allows for the determination of atomic coordinates and the overall crystal structure

Influence on diffracted intensity

• Intensity of a diffracted beam is proportional to the square of the absolute value of the structure factor: $I_{hkl} \propto |F_{hkl}|^2$
• Stronger diffraction peaks correspond to larger structure factor values
• Systematic absences (zero intensity) occur when the structure factor is zero due to destructive interference

Derivation for crystals

• Structure factor can be derived by considering the periodic arrangement of atoms in a crystal lattice
• Assumes that the crystal is composed of identical unit cells that repeat in three dimensions
• Treats the diffraction process as a Fourier transform of the atomic positions

Periodic arrangement of atoms

• Crystals are characterized by a regular, repeating arrangement of atoms or molecules
• Unit cell is the smallest repeating unit that represents the entire crystal structure
• Translational symmetry allows the crystal to be described by the contents of a single unit cell

Fourier transform of atomic positions

• Diffraction pattern can be considered as a Fourier transform of the electron density distribution in the crystal
• Structure factor is the Fourier transform of the atomic positions within the unit cell
• Fourier transform relationship: $F_{hkl} = \int_V \rho(\mathbf{r}) \exp[2\pi i(\mathbf{h} \cdot \mathbf{r})] d\mathbf{r}$
  • $\rho(\mathbf{r})$ is the electron density at position $\mathbf{r}$
  • $\mathbf{h}$ is the reciprocal lattice vector $(h, k, l)$
  • $V$ is the volume of the unit cell

Calculation methods

• Structure factor can be calculated using different approaches depending on the complexity of the crystal structure and the available computational resources
• Two common methods are direct summation and Fourier transform approach

Direct summation

• Involves summing the contributions from each atom in the unit cell using the structure factor formula
• Straightforward approach suitable for small unit cells with a limited number of atoms
• Computationally intensive for large and complex structures

Fourier transform approach

• Utilizes the Fourier transform relationship between the electron density and the structure factor
• Electron density is first calculated from the atomic positions and form factors
• Structure factor is then obtained by applying a Fourier transform to the electron density
• More efficient for larger structures and can be accelerated using fast Fourier transform (FFT) algorithms

Dependence on atomic form factors

• Atomic form factor is a measure of the scattering power of an individual atom
• Depends on the type of atom and the scattering angle
• Plays a crucial role in determining the structure factor and the overall diffraction pattern

Definition of atomic form factor

• Represents the Fourier transform of the electron density distribution of an isolated atom
• Describes the scattering amplitude of an atom as a function of the scattering angle
• Denoted by $f_j$ for the $j$-th atom in the unit cell

Relationship to electron density

• Atomic form factor is related to the electron density distribution of an atom
• Higher electron density regions (core electrons) contribute more to the form factor than valence electrons
• Form factor decreases with increasing scattering angle due to the finite size of the electron distribution

Systematic absences

• Systematic absences refer to the regular occurrence of zero intensity reflections in a diffraction pattern
• Arise from destructive interference caused by the specific arrangement of atoms in the unit cell
• Provide valuable information about the symmetry and space group of the crystal

Conditions for zero intensity

• Structure factor becomes zero when certain conditions are met, leading to systematic absences
• Conditions depend on the symmetry elements present in the crystal, such as screw axes or glide planes
• Examples: $F_{hkl} = 0$ for $h + k = 2n + 1$ in a body-centered lattice, or $F_{0k0} = 0$ for $k = 2n + 1$ in a primitive monoclinic lattice with a $b$-glide plane

Connection to crystal symmetry

• Systematic absences are a direct consequence of the symmetry operations in the crystal
• Different space groups have characteristic systematic absence conditions
• Analysis of systematic absences helps in determining the space group and the presence of certain symmetry elements

Applications in crystallography

• Structure factor is a fundamental tool in crystallography, enabling the determination and refinement of crystal structures
• Plays a central role in various stages of the structure solution process

Structure determination

• Structure factors are used to calculate the electron density distribution in the unit cell
• Fourier synthesis techniques (Patterson or direct methods) utilize structure factor amplitudes to determine the approximate atomic positions
• Iterative process of structure solution and refinement relies on the comparison of calculated and observed structure factors

Refinement of atomic positions

• Refinement is the process of adjusting the atomic positions and other structural parameters to minimize the difference between calculated and observed structure factors
• Least-squares refinement methods optimize the agreement between the model and the experimental data
• Refined structure factors are used to generate more accurate electron density maps and improve the overall structure model

Temperature effects

• Thermal motion of atoms in a crystal affects the structure factor and the resulting diffraction pattern
• Increasing temperature leads to a reduction in the intensity of diffraction peaks
• Temperature effects are accounted for by introducing the Debye-Waller factor in the structure factor calculation

Debye-Waller factor

• Also known as the temperature factor or atomic displacement parameter (ADP)
• Describes the average displacement of an atom from its equilibrium position due to thermal vibrations
• Represented by the parameter $B$ or $U$, related to the mean-square displacement of the atom
• Incorporated into the structure factor formula as an exponential term: $f_j \exp(-B_j \sin^2 \theta / \lambda^2)$

Influence on peak intensity

• Debye-Waller factor leads to a reduction in the peak intensity with increasing scattering angle
• Higher temperature results in larger atomic displacements and a more pronounced decrease in intensity
• Correction for temperature effects is essential for accurate structure determination and refinement

Experimental measurement

• Structure factors are experimentally determined through diffraction techniques
• X-ray and neutron diffraction are the most common methods for measuring structure factors

X-ray diffraction techniques

• X-rays interact with the electron density distribution in the crystal
• Single-crystal X-ray diffraction provides a three-dimensional dataset of structure factor amplitudes
• Powder X-ray diffraction gives a one-dimensional pattern with overlapping peaks, requiring additional analysis to extract structure factors

Neutron diffraction techniques

• Neutrons interact with the atomic nuclei and are sensitive to the distribution of nuclear scattering lengths
• Complementary to X-ray diffraction, as neutrons can distinguish between elements with similar electron densities (isotopes)
• Particularly useful for studying light elements (hydrogen) and magnetic structures

Interpretation of structure factor

• Structure factors contain valuable information about the atomic arrangement and electron density distribution in the crystal
• Interpretation of structure factors involves extracting phase information and generating electron density maps

Phase information

• Structure factors are complex quantities, but only their amplitudes are directly measured in diffraction experiments
• Phase information is lost during the measurement process, leading to the "phase problem" in crystallography
• Various methods (Patterson, direct methods, molecular replacement) are used to estimate or determine the phases

Electron density maps

• Once the structure factors (amplitudes and phases) are known, an electron density map can be calculated using Fourier synthesis
• Electron density map represents the three-dimensional distribution of electrons in the unit cell
• Atomic positions and other structural features can be directly visualized and interpreted from the electron density map
• Iterative refinement of the structure model against the electron density map leads to a more accurate and complete understanding of the crystal structure