Is it a limitation on Instrument or the inherent nature of the atoms?
It is electron density that we measure by X-ray diffraction. The heavier an atom is and the more electrons it has, the stronger is its effect on the diffraction pattern. This also means that, especially in the presence of
heavy atoms, light atoms are somewhat more difficult to localize. The lightest atom of all is hydrogen: it has only one electron, localized away from the nucleus. Therefore, hydrogen atoms are notoriously difficult to
detect with X-ray diffraction methods.
More useful information can be found in below file.
https://www.google.com/url?sa=t&source=web&rct=j&url=https://ocw.mit.edu/courses/chemistry/5-067-crystal-structure-refinement-fall-2009/lecture-notes/MIT5_067F09_lec3.pdf&ved=2ahUKEwj4yeSis5DZAhXFmLQKHTDlDoEQFjAAegQIDRAB&usg=AOvVaw1RkdNYXMbt__ZojHGTiRgO
If this answer help you, try to recommend it.
It is electron density that we measure by X-ray diffraction. The heavier an atom is and the more electrons it has, the stronger is its effect on the diffraction pattern. This also means that, especially in the presence of
heavy atoms, light atoms are somewhat more difficult to localize. The lightest atom of all is hydrogen: it has only one electron, localized away from the nucleus. Therefore, hydrogen atoms are notoriously difficult to
detect with X-ray diffraction methods.
More useful information can be found in below file.
https://www.google.com/url?sa=t&source=web&rct=j&url=https://ocw.mit.edu/courses/chemistry/5-067-crystal-structure-refinement-fall-2009/lecture-notes/MIT5_067F09_lec3.pdf&ved=2ahUKEwj4yeSis5DZAhXFmLQKHTDlDoEQFjAAegQIDRAB&usg=AOvVaw1RkdNYXMbt__ZojHGTiRgO
If this answer help you, try to recommend it.
The difference electron contrast between a single electron and vacuum is tiny. Think about the size of a hydrogen atom... about 74 pm. Could you measure this with a ruler? Sometimes you can infer (but not measure) the position of a H-atom in a crystal structure but this involves other knowledge about the location of atoms. In the old days one could introduce a heavy atom to provide more scattering and allow structures to be elucidated.
Hydrogen atom is very difficult to detect with the X-ray diffraction method. Because it is a lighter chimical element with only one electron et this method is related with electron density.
In oder to verify the effect I would recommend to download a program for the calculation of diffraction patterns, such as e.g. PowderCell (a download link is here: http://www.ccp14.ac.uk/ccp/web-mirrors/powdcell/a_v/v_1/powder/e_cell.html) there you can create an arbitrary structure e.g. fcc, and exchange say an aluminium or copper atom against a hydrogen atom in the unit cell. You will directly see the resulting difference in the diffractogram! Just try it - Dirk
The question implies to me that the problem concerns single-crystal diffraction (to "observe" atoms), and then that kind of task should not be performed by people who do not know the essentials, it is far too complicated.
On the other hand, if you are dealing with powder diffraction, the question whether you have introduced hydrogen or not in your structure is solved by comparison with the pristine state, but you should not expect any intensity differences (because of the extremely low scattering power of hydrogen) but always some change in the pattern, at least a change of cell dimensions, but in the case of higher concentrations hydrogen atom ordering can occur and introduce even a change of structure.
As for the choice of neutron diffraction, as suggested, one should not use normal hydrogen (H) because of very high absorption but use deuterium (D) instead. For neutrons, the scattering power is not related to the number of electrons, and it can differ immensely between isotopes of the same element! For neutrons, light atoms can scatter equally well as heavy ones, which means that the intensities of the same compound as recorded by XRD will be quite different (but the lattice remains the same, of course).
Hi Siva,
In X-ray crystallography, atomic positions are refined based on the X-ray scattering factors of each atom type (element). More the number of electrons in an atom, more will be its power to scatter X ray and therefore a higher scattering factor. In case of Hydrogen atom the problem is twofold: (1) it has only one electron and therefore very low scattering factor (2) the electron density distribution (from this 1 electron) around Hydrogen atom are usually displaced or pulled towards the bonding region (H-X bond). For this reason, the H-X bond lengths determined using X-ray diffraction are much shorter than the actual bond lengths. The most widely accepted experimental method is neutron diffraction where the scattering power of an atom is not decided by the electron density but the neutron scattering cross section of the atomic nuclei. So if you need to know the accurate Hydrogen positions, use neutron diffraction (however this requires extremely sophisticated experimental facility , and is not an easy method ).
However, there is a good news. A newly developed quantum crystallography technique known as Hirshfied atom refinement (HAR)by Jayatilaka can accurately determine Hydrogen atom positions even from a X-ray data. While the conventional X-ray structure determination protocols use spherical electron density-based scattering factors, HAR uses aspherical and therefore more realistic scatter factors derived from quantum mechanical wavefunctions for the refinement. The H atom positions thus determined show very good agreement with corresponding neutron diffraction values.
See the following papers:
Hydrogen atoms can be located accurately and precisely by x-ray crystallography- Grabowsky, Jayatilaka et al. http://advances.sciencemag.org/content/2/5/e1600192
Hirshfied atom refinement (HAR)- Jayatilaka, https://www.ncbi.nlm.nih.gov/pubmed/25295177
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