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Structure Determination and Supramolecular Network of Organic Compouns


Method : X-ray Crystallography 2 widely applied analytical technique:

X-ray powder Diffraction (XRD) X-ray Fluorescent (XRF)

In this research, XRD will be used. Objectives: crystal packing and hydrogen interaction of the organic compound

Max von Laue discover the diffraction of X-ray by crystals. After the Laues discovery of diffraction of X-ray, Braggs Law was developed by William Lawrence Bragg. Until now, crystallography still plays the important role in determining the molecular structure of metal and compound, though there are several can be used to do so. For example: Nuclear Magnetic Resonance(NMR)

X-rays have the proper wavelength (in the ngstrm range, ~10-10m) to be scattered by the electron cloud of an atom of comparable size. This is the reason why X-ray had been used for diffraction in atomic scale spacing.

X-ray was first discovered by Wilhelm Rntgen. It can be generated from cathode ray tube.

X-rays are generated by heating a filament to produce electrons, accelerating the electrons toward a target by applying a voltage, and bombarding the target material with electrons.


When electrons have sufficient energy to dislodge inner shell electrons of the target material, upper shell electrons move down to vacancies, characteristic X-ray spectra are produced.

The common target for single crystal diffraction is Copper. Cu K radiation = 1.5418

There are 2 way to form X-ray:

Bremstrahlung Characteristic

In X-ray crystallography, we only interested in characteristic X-rays.


Filtering, by foils or crystal monochrometers, is required to produce monochromatic X-rays needed for diffraction. These X-rays are collimated and passed through the crystal mounted on a pin on a goniometer head.


The head is mounted to a goniometer which allows to position the crystal in different orientations in the beam.


The sample rotates in the path of the collimated Xray beam at an angle while the X-ray detector is mounted on an arm to collect the diffracted X-rays and rotates at an angle of 2. The diffracted X-rays are recorded using image plates or counter.

solid that have periodic arrangement of constituent atom to infinite range. A perfect crystal maintains this periodicity in both the x and y directions from - to +. The idea can be expressed by saying that a crystal possesses a translational symmetry. The crystal appears exactly the same as it did before the translation. In other words the crystal remains invariant under any such translation.

is made up of a lattice and a basis. lattice : hypothetical regular and periodic arrangement of points in space. basis : collection of atoms in particular fixed arrangement in space.

The small component which combine together with pure translation repetitive will form a crystal. A primitive unit cell is the unit cell with the smallest area which produces this coverage. The choice of the unit cell is not unique. The unit cell can be primitive and non-primitive (or conventional).


The unit cell parameters are the three coordinate lengths (a, b, c) determined by placing the origin of the coordinate system at a lattice point, and the three angles (,,) subtended by the lattice cell axes.



Bravais lattice : all lattice points are equivalent and hence by necessity all atoms in the crystal are of the same kind. Non-Bravais lattice: some of the lattice points are non-equivalent and not same kind of atom.

Plane that passing through lattice points are called lattice planes. The orientation of planes or faces in a crystal can be described in terms of their intercepts on the three axes. This set of three numbers is known as Miller Indices of the concerned plane.


Procedure for finding Miller Indices :

Find where the plane cuts the axes ( at A, B, C,) Express the intercepts as a, b, c Reduce the reciprocals to the simplest set of integers h, k, l The plane is then the (hkl) plane. Conventionally, choose h, k, and l with common factors removed.

note if intercept is at innity, corresponding index is 0. note convention: round brackets note convention: if plane pass through origin, the plane can be moved side way for easier interpretation. note convention: negative values are quoted with a bar over. This is called the `Miller Indices of the plane in the form (h k l).

Crystal lattices are classified according to their symmetry properties, such as inversion, reflection and rotation. Inversion center. A cell has an inversion center if there is a point at which the cell remains invariant under transformation r -> -r. Reflection plane. A cell has a reflection plane if it remains invariant when a mirror reflection in this plane is performed. Rotation axis. This is an axis such that, if the cell rotated around the axis trough some angle, the cell remains invariant. The axis is called n-fold if the angle of rotation is .Only 2-, 3-, 4-, and 6-fold axes are possible.


is the lattice in which the Fourier transform of the spatial wavefunction of the original lattice is represented. It is important to learn reciprocal lattice because the diffraction pattern from the experiment give information in reciprocal lattice.