I am in a little confusion whether the change in relative intensities at an identified 2 Theta angles from initial to stability (like a change from 100% to 60%) means change in the polymorphic form? Is this applicable always?
The 2theta positions of reflections are determined by lattice parameters are space group symmetry on the basis of the Bragg law. The intensities depend on the crystal structure, i.e., atomic positions, temperature factors, site occupancies. Below is a couple of useful textbooks dealing with these issues:
Structure Determination from Powder Diffraction Data
Eds. W.I.F. Dawid, K. Shankland, L.B. McCusker, Ch. Baerlocher
The 2theta positions of reflections are determined by lattice parameters are space group symmetry on the basis of the Bragg law. The intensities depend on the crystal structure, i.e., atomic positions, temperature factors, site occupancies. Below is a couple of useful textbooks dealing with these issues:
Structure Determination from Powder Diffraction Data
Eds. W.I.F. Dawid, K. Shankland, L.B. McCusker, Ch. Baerlocher
Dear Shivakumar, this is a very tricky question, so, it is not easy to answer. This is even more difficult to answer, because according to your question, I don't know, how much you are experienced with the powder diffraction technique and theory. For reading more about the powder diffraction, look at this link: http://pd.chem.ucl.ac.uk/pdnn/pdindex.htm#qual1.
Anyway, every maximum at a given 2Theta value corresponds to some hkl reflection. 2Theta positions of reflections defines unit cell parameters. Intensities of reflections define atomic positions in the unit cell. So, it is the very simple answer to "what is a relationship between 2Theta values and intensities?".
When some compounds change its structure to another polymorph, at least atomic positions in the unit cell have to change. So, you will at least see changes in intensities of reflections in the powder pattern. Usually, when some compound change its crystal structure, it changes also the unit cell parameters, so, you can see the complete change of the powder diffraction pattern. This is because unit cell change (it means that 2Theta positions of reflection change) together with atomic positions (it means that also intensities will change).
During the polymorphic change, usually both will change - unit cell together with atomic positions. But, also, only the change of atomic position is exceptionally possible. In this case, you will only see change of relative intensities. But the effect of changing only relative intensities can be caused by e.g. preference orientation, absorption and also by instrumental settings (e.g. by measuring with or without automatic divergence slit). So in the case that you see only change of intensities, you have to eliminate all these effects before you can claim, that your compound is undergoing the polymorphic change.
May you show the diffraction patterns and the nominal name of the compound? That will facilitate the interpretation. In my opinion, the change in the intensity is too high to be considered coming from experimental setup only. There are close crystallographic spatial groups that can show (bias a reordering of the atoms in the same geometry) only a difference in the intensities with the same lattice parameters.