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[ccp4bb]: Se-Met and X-ray absorption

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Dear All -

I got flamed for Borhani's message - don't worry I can take it -
and received a few comments that make me wonder whether we use the same
language here in terms of X-ray absorption. X-ray absorption is
a lot less mystical than crystallization, so even at the risk of
appearing redundant/boring/condescending you name it I shall briefly
summarize for the more biologically inclined (admitting that I
simplify as I feel its permissible w/o being flat out wrong;
if something is absolutely stupid or incomprehensible please
tell me; textbook references at the end):

A bound electron can absorb a photon and leave its original
energy level (orbit). The atomic level (quantum number n) it
originates from is used to name the edge - K (1) L (2) M (3) etc.
The lower (tighter bound) the level and the more protons in the
nucleus (heavier the element), the higher the absorption edge energy.

Then the question is what happens to the electron. Assuming a free atom for
now, absorbing at or above the binding energy the electron can take off into
the vacuum and turn into a photoelectron (more about condensed state below),
or at slightly lower energies, it can jump into unoccupied higher levels
of the atom. (If the electron kicks out another electron from a higher
level, we have a secondary Auger electron but due to their low energy  -
for line broadening, the Auger processes are of no relevance for us here).

The superposition of all the discrete possible lower energy resonance
transitions in
the series plus the phototransitions at the series limit create each
absorption edge.
The sum (integration) of the closely spaced and life-time broadened
at the series limit gives a arctangent curve (sigmoid shape) for the basic
edge. The sharp, saw-tooth curve in theoretical absorption cross section
calculations results from assuming sharp photoelectric transitions. The most
prevalent code I know and use to calculate absorption coefficients/edge
energies is Don Cromer's FPRIME.

In case of high transition probabilities (more below), some of the pre-edge
resonance transitions can be rather high, and give rise to stronger
These pre-edge features are also called white lines, because some of the old
dudes (like those who wrote all these nice F-66 ccp4 programs for you) used
film to record absorption: Less x-rays on film due to absorption in the
means less blackening on the negative (i.e, a white line at that energy).
White line resoncances obey dipole selection rules, and their intensity
depends on transition probabilities and initial and empty state density.
K-edges have weaker white lines (s->np transitions) as do L1
edges (n=2,l=0,j=1/2 2s -> nd, n>2) which have 'K- or S-character' due to
compared to l=1 for L2 (n=2,l=1, j=1/2) and L3 (j=3/2) edges.

The L3 edge is at the lowest energy of the L series and twice as high as
due to the transition from the 4 2p3/2 states, at L2 (few keV higher energy)
there is usually also less intensity from the ring (above critcal energy).

It appears that the white line features are what some call 'peak', so
when they talk about 'disappearing peak' they may mean a smaller white line,
not the whole edge disappearing. Btw, that while line region at the low
energy of the edge is called the XANES (Xray Absorption Near Edge

Now to finally sort XAS out, we need to consider condensed matter. A bit
more delicate, but it will become clearer (harharhar). First, on its
way out of the atom, an above-edge energy photoelectron can bounce off
the neighbouring atoms. If there is a distinct near range order - like in a
lets say octahedral environment -  the resonance absorption cross section
oscillates in a decaying way with a period distinct (reciprocal, as you
guessed) to the distances in the coordination shell geometry in the
The amplitude envelope of these periodically extending exafs wiggles tells
you about
the nature of neighbouring atoms - the heavier the more 'wavy' the envelope

So, if you have a rapidly decaying exafs (Extended Xray Absorption Fine
Structure) you know that you have light atoms and/or inhomogenous
around your anomalous atoms - which does not mean much:
Unfortunately, detailed exafs analyis requires much better scans
than we usually do and the difference between a Se atom in solvent and
in the protein environment is not all that big. Well defined metals
in active sites (plastocyanine, cytochrome c oxidase, laccase etc) can
have in fact an interpretable exafs. It naturally also kinda works in
solid matter, but deconvolution is occasionally overdone (30 data points
25 parameters - sounds familar to the low res victims, doesn't it?).

On top of this, if in a chemical environment outer electrons get stripped
(oxidation, delocalization etc) the remaining electrons feel more of
the nuclear charge thus more energy required thus upshift of the edge
features (someone got confused about that apparently). Shifts
range in few to a few 10 eVs, and you nearly always need a reference
spectrum to determine absolute values (think monocromator slew
for example - which is one reason why it is not a bad idea to move
the crystal (energy) from the same side to the peak as you did in your

The condensed state environment also allows due to symmetry violations
Jahn-Teller) additional transitions in the pre-edge region that where
before, plus allows additional band levels to become occupied by
This means that larger white line features often appear. The same holds
for any new bound or localized states, like in oxides, which become now
available compared to the free atom case we described in the beginning.

All of the above to varying degree is the reason why a) the oxidized Se-Met
spectrum is upshifted, b) the white line in the solid Selenate sample shown
in the
structure6:815 paper is so huge, and less high for oxidized Se-Met in

Now let us consider what happens in an inhomogenous environment:

First, each Se that is present will absorb. There is no absorption quenching
or any funky similar stuff. If its there, it will contribute to signal.
Chemically different species will add, and we will obtain a sum of the
partial spectra. This
means that a) the white line features can become less sharp, as will the
edge. But: After the edge, the total signal will be the same - i.e, if your
Se's remain in periodic positions - oxidized or not - up-edge (remote)
anomalous data
can give a decent signal/map (but less white line - or 'peak' contributions
to f" of
perhaps a few tenth to a few e- ). For the f' (inflection wavelength), we
have a
worse scenario: the slope of the edge and/or peak becomes flatter - thus
the derivative (equivalent to the Kramers-Kronig transform) is much smaller
your dispersive gain from sitting on f'max (inflection point) suffers
If the anomalous scatteres are all over the place then signal but of course
no map.
Backsoaking of heavy metals derivatives for anomalous date collection is
thus advisible.

Based on above, I cannot rationally explain how one can have no signal (I
no edge, not only no 'peak',or white line), then oxidize the same material,
and get an absorption scan. Sounds like some trans-substantiation. Most
likely I
did not understand the story right.

For more details on the L-edge and white line superposition stuff you
can glance over the mini-intro (II, III) in that Physical Refuse article :

Details: Agarwal, X-ray spectroscopy, Springer, chapter 7

Another interesting point: If one measures above the edge past the white
vrey good monochromaticity (low bandwidth) actually is not necessary and
a waste of beam. A beam with a bandwidth not exceeding the mosaic spread of
the crystal would allow a really fast (or good signal/noise) data collection
about 100 eV above the edge. The anomalous signal is nothing to sneer about
there and the gain for SAS in data quality could be tremendous. Any thoughts
on that from the SAS gang? I mean going from 1 to 10 eV bandwith does
to spot size (below) but ~10 times the bang should do something for the

Problem to be solved:
The beam fans out to about ~30 mrad at 0.1% bandwidth at 1.0A after the
Mono and needs to be refocussed:
0.1% 12.35eV bandwidth at 12.35 keV (1.000 A)
0.9005 to 1.0005 A
on Si 111 (d 001 = 5.43), d(111)= 3.14 (Pi, funny, isn't it?)
I get delta theta of .923 deg = 1.8 deg 2theta = 30 mrad
which is ugly.

Less excessively, let's say at 0.8 deg or so this might actually
be useful. Lots of partials though.

Any thoughts on feasibility?
Knowledge of the absolute of the fs is actually unimportant here btw.

best regards, BR
Dr. Bernhard Rupp
Macromolecular Crystallography and Structural Genomics
LLNL-BBRP L448                               Phone (925) 423-3273
University of California                     Phax  (925) 424-3130
Livermore, CA 94551                          email    br@llnl.gov
URL                                 http://www-structure.llnl.gov
TB Structural Genomics Consortium  http://www.doe-mbi.ucla.edu/TB
EU Mirror  http://www.dl.ac.uk/CCP/CCP14/ccp/web-mirrors/llnlrupp