Chemistry Reference
In-Depth Information
Interesting applications of low temperature single crystal diffraction have been
presented in the field of metal organic frameworks (MOF) [
57
], porous materials
based on metal
connectors
and organic
linkers
. Some large pore MOFs are able to
host and exchange molecules like N
2
,CO
2
, noble gases, etc. The main problem is
locating sites where the gas might be trapped, given the very weak interaction
between the guest and the host framework. Therefore, diffraction on cooled species
could reveal sites available to N
2
and Ar in channels of MOF-5, a structure with
cubic array of Zn
4
O(CO
2
)
6
units connected by phenylene linkers [
58
].
Sometimes low temperature is claimed to be important to locate H atoms. This
could be true in the case of organic species, where a reduced thermal motion of Hs
may enhance electron density peaks in Fourier maps. These peaks compete against
lone pair peaks of some atoms (especially O or N) and against peaks inside
chemical bonds. At low temperature and using only low resolution data, the
residuals due to lone pairs are smaller than residuals due to H atoms, yet missing
in the structural model. In the case of organometallic molecules, expectations
should instead be much lower, because the main source of residual peaks in a
Fourier map are uncorrected absorption effects, which might overlap with potential
sites for H atoms, especially those in the vicinity of a metal (like an agostic
hydrogen, a hydride, etc.) [
59
].
3
Therefore, reducing the thermal motion of H
may not be sufficient if careful absorption correction is not applied.
A problem affecting X-ray diffraction pattern of real crystals very close to
ideality is
extinction
that is the manifest breakdown of the kinematic approxima-
tion. Within the mosaic crystals theory [
60
] we recognize a
primary extinction
(attenuation of the incident beam within a given crystal domain) and a
secondary
extinction
(power loss due to the diffraction in the blocks traversed by the incident
beam before it reaches the particular block under consideration).
Primary extinction
depends on the size of the domain and on the amplitude of the structure factors. The
“critical thickness,” beyond which extinction is negligible, inversely depends on l.
Secondary extinction
depends on the degree of perfection of the crystal, hence on
the misalignment of the domains (or mosaicity). The critical
mosaic spread
, above
which the effect is negligible, depends on l. Extinction may be severely aniso-
tropic, especially if the crystal is under stress, which increases the mosaicity. As a
matter of fact, an empirical way to decrease extinction is to stress the crystal by
cooling and warming it, though the crystal may break during this procedure. For
example, the mosaic spread of a crystal of KHC
2
O
4
[
61
] studied at low temperature
with three consecutive experiments was initially 3.3
00
(first experiment with MoK
a
3
In [
59
] the authors reported the structure of a tri-osmium complex containing a hydride and
clearly stated that a low temperature X-ray diffraction experiment would not be useful to locate the
hydride if an accurate absorption correction is not carried out. Curiously, a few years before they
had contacted Prof. A. Sironi and myself at the University of Milan proposing a low temperature
data collection on that compound, with the purpose of locating the not so clearly visible hydride.
As evident from [
59
], we were able to convince them on the real problems connected with the
location of hydrogens close to heavy metals.
