From: Francis E Reyes
Date: 13 September 2011 20:01
Hi all
Suppose you have a high resolution xtal structure (from usual x-ray diffraction) and you wanted to verify the location of a ligand. You can purchase a heavy atom isotope version of the ligand.
[1] Is it possible to do a neutron diffraction difference map (where you simply calculated Fobs(heavy) - Fobs(light) to verify the location of the ligand?
[1b] Suppose you couldn't measure the diffraction of the light version of the ligand. Can the x-ray data be combined with the neutron diffraction of the heavy atom isotope to unambiguously assign the ligand site?
[2] What would be the minimum resolution required from the neutron diffraction? (This is particularly important as you may be unable to grow high diffracting crystals or large crystals)
Note that you don't necessarily want to solve the structure of the structure from neutron diffraction from scratch, but rather you want to use it as a tool to verify the location of a ligand binding site.
Thanks!
F
---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
----------
From: Sean Seaver
Dear Francis,
It is possible, but would recommend exhausting all possibilities with X-ray crystallography. The reason is that neutron crystallography as you mentioned has its own challenges/considerations such as possibly having to determine a new crystallization condition, crystal size, unit cell volume, symmetry, level of deuteration, data collection and processing (this table may serve as a good reference: http://1.usa.gov/qc5JoA ). Of course, these can be overcome, but in the case of determining whether a ligand is present would stick with X-rays. As a side note, I assume you've checked your possible isotope scatters neutrons well.
~2.2 Angstroms - this paper ( http://bit.ly/qgwHvI ) maybe handy see Table 3 on pg. 384, it compares the resolution of X-ray and neutron data collections.
Take Care,
Sean Seaver
P212121
http://store.p212121.com/
----------
From: Tim Gruene
Dear Francis,
ad [1]: if you are going for neutron diffraction, you probably want the
ligand to have its hydrogens replaced with deuteria, rather than a
'heavy atom derivative' of your ligand. The scattering power for
neutrons does not correlate with the weight of the nucleus und deuterium
scatters as strongly as O,C, ... (see ITCr, Vol. C, Chapter 4.4) In that
case you also do not need a difference map against the X-ray data
because the scattering of X-rays by hydrogens can be neglected.
ad [1b]: see [1]; remark: since we are doing science as opposed to math
or philosophy, there is no 'unambiguity'. There is only a model for the
experimental data which - depending on your means of validation - fits
the data more or less well.
ad [2]: That probably depends on whether your ligand site is fully
occupied and whether the ligand is disordered or not.
Cheers,
Tim
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
Date: 13 September 2011 20:01
Hi all
Suppose you have a high resolution xtal structure (from usual x-ray diffraction) and you wanted to verify the location of a ligand. You can purchase a heavy atom isotope version of the ligand.
[1] Is it possible to do a neutron diffraction difference map (where you simply calculated Fobs(heavy) - Fobs(light) to verify the location of the ligand?
[1b] Suppose you couldn't measure the diffraction of the light version of the ligand. Can the x-ray data be combined with the neutron diffraction of the heavy atom isotope to unambiguously assign the ligand site?
[2] What would be the minimum resolution required from the neutron diffraction? (This is particularly important as you may be unable to grow high diffracting crystals or large crystals)
Note that you don't necessarily want to solve the structure of the structure from neutron diffraction from scratch, but rather you want to use it as a tool to verify the location of a ligand binding site.
Thanks!
F
---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
----------
From: Sean Seaver
Dear Francis,
It is possible, but would recommend exhausting all possibilities with X-ray crystallography. The reason is that neutron crystallography as you mentioned has its own challenges/considerations such as possibly having to determine a new crystallization condition, crystal size, unit cell volume, symmetry, level of deuteration, data collection and processing (this table may serve as a good reference: http://1.usa.gov/qc5JoA ). Of course, these can be overcome, but in the case of determining whether a ligand is present would stick with X-rays. As a side note, I assume you've checked your possible isotope scatters neutrons well.
~2.2 Angstroms - this paper ( http://bit.ly/qgwHvI ) maybe handy see Table 3 on pg. 384, it compares the resolution of X-ray and neutron data collections.
Take Care,
Sean Seaver
P212121
http://store.p212121.com/
----------
From: Tim Gruene
Dear Francis,
ad [1]: if you are going for neutron diffraction, you probably want the
ligand to have its hydrogens replaced with deuteria, rather than a
'heavy atom derivative' of your ligand. The scattering power for
neutrons does not correlate with the weight of the nucleus und deuterium
scatters as strongly as O,C, ... (see ITCr, Vol. C, Chapter 4.4) In that
case you also do not need a difference map against the X-ray data
because the scattering of X-rays by hydrogens can be neglected.
ad [1b]: see [1]; remark: since we are doing science as opposed to math
or philosophy, there is no 'unambiguity'. There is only a model for the
experimental data which - depending on your means of validation - fits
the data more or less well.
ad [2]: That probably depends on whether your ligand site is fully
occupied and whether the ligand is disordered or not.
Cheers,
Tim
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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