Re: [Ifeffit] P K-edge EXAFS

[Mangold, Stefan (IPS)]

some additional comments:

- it is a bit tricky to operate ionisation chambers at this low energies (low 
pressure)
- some Beamlines have issues with higher harmonics (high angles of mirrors to 
get low cut off energies)
- preparation of good sample is tricky


best regards

Stefan Mangold

Am 14.09.2023 um 06:09 schrieb Mike Massey 
mailto:mmas...@gmail.com>>:

The other difficulty I have experienced with P EXAFS is that a lot of the 
second-shell backscatterers are fairly weak, so picking that signal out is 
pretty difficult.

I have some spectra of minerals and that's where I've wanted to start with P 
EXAFS (since the structures are well-constrained). But as has been mentioned, 
low-frequency oscillations and background subtraction have massive impacts on 
the P K-edge EXAFS function (tested this by taking spectra of the same sample 
during different runs and getting different EXAFS due to slightly different 
background).

I don't think it's necessarily impossible, I just personally put it in the 
not-right-now basket.





On Sep 14, 2023, at 07:42, Mike Massey 
mailto:mmas...@gmail.com>> wrote:


In my experience the main difficulties with EXAFS on P (phosphate) come from 
two factors (not signal to noise, it's not hard to get a nice smooth line, but):

1) You've got 4 O atoms, guaranteed, so any other signal will be small and on 
top of that very strong signal generated from the first-neighbor O

Unfortunately,

2) You have very limited data range, either due to instrumental limitations, or 
due to interference from sulfur

Don't get me wrong I still have some data sitting around and I'd love to try P 
EXAFS analysis on it just to try and grasp that brass ring but...It's not the 
easiest task ever.

If you want good data quality "scan longer" is always an option. Some might 
think it's crazy but I do think I have some P XAS data where I took 30 or 60 
scans, maybe overnight or something. The scans are so short that repeats are 
easy.


Hope this commentary is helpful.



Mike




On Sep 14, 2023, at 07:04, Marcelo Eduardo Alves 
mailto:meal...@gmail.com>> wrote:


Hi there,
I begin by examining phosphorus adsorption by goethite, hematite, and gibbsite.
Why is it difficult, if not impossible, to obtain EXAFS spectra at the P-K edge 
that can be properly used, i.e., spectra with a high signal-to-noise ratio, 
especially for dilute samples?
Would it be possible to use arsenic as a phosphorus proxy to get conclusions 
from As K-edge EXAFS data that could be extended to P?
Thank you.

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Re: [Ifeffit] P K-edge EXAFS

[Mike Massey]

The other difficulty I have experienced with P EXAFS is that a lot of the 
second-shell backscatterers are fairly weak, so picking that signal out is 
pretty difficult.

I have some spectra of minerals and that's where I've wanted to start with P 
EXAFS (since the structures are well-constrained). But as has been mentioned, 
low-frequency oscillations and background subtraction have massive impacts on 
the P K-edge EXAFS function (tested this by taking spectra of the same sample 
during different runs and getting different EXAFS due to slightly different 
background).

I don't think it's necessarily impossible, I just personally put it in the 
not-right-now basket.





> On Sep 14, 2023, at 07:42, Mike Massey  wrote:
> 
> 
> In my experience the main difficulties with EXAFS on P (phosphate) come from 
> two factors (not signal to noise, it's not hard to get a nice smooth line, 
> but):
> 
> 1) You've got 4 O atoms, guaranteed, so any other signal will be small and on 
> top of that very strong signal generated from the first-neighbor O
> 
> Unfortunately,
> 
> 2) You have very limited data range, either due to instrumental limitations, 
> or due to interference from sulfur
> 
> Don't get me wrong I still have some data sitting around and I'd love to try 
> P EXAFS analysis on it just to try and grasp that brass ring but...It's not 
> the easiest task ever.
> 
> If you want good data quality "scan longer" is always an option. Some might 
> think it's crazy but I do think I have some P XAS data where I took 30 or 60 
> scans, maybe overnight or something. The scans are so short that repeats are 
> easy.
> 
> 
> Hope this commentary is helpful.
> 
> 
> 
> Mike
> 
> 
> 
> 
>>> On Sep 14, 2023, at 07:04, Marcelo Eduardo Alves  wrote:
>>> 
>> 
>> Hi there,
>> 
>> I begin by examining phosphorus adsorption by goethite, hematite, and 
>> gibbsite.
>> 
>> Why is it difficult, if not impossible, to obtain EXAFS spectra at the P-K 
>> edge that can be properly used, i.e., spectra with a high signal-to-noise 
>> ratio, especially for dilute samples?
>> 
>> Would it be possible to use arsenic as a phosphorus proxy to get conclusions 
>> from As K-edge EXAFS data that could be extended to P?
>> 
>> Thank you.
>> 
>> 
>> 
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Re: [Ifeffit] P K-edge EXAFS

[Robert Gordon]

Hi,
You could try X-ray emission rather than EXAFS. It has shown some 
success in showing changes

in phosphate environment with bonding environment.

e.g. https://pubs.rsc.org/en/content/articlelanding/2021/sc/d1sc01266e

cheers,
-R.


On 2023-09-13 12:47 p.m., matthew marcus wrote:
Good points.  At these low energies, an EXAFS range is a large 
fraction of the total energy range, so there tends to be a lot of 
curvature of baselines and post-edges.  True about the 4O 1NN shell 
that dominates, but the same happens with As.  All the interesting 
stuff is in the higher shells.  Most data I've seen has been XANES.

mam

On 9/13/2023 12:42 PM, Mike Massey wrote:
In my experience the main difficulties with EXAFS on P (phosphate) 
come from two factors (not signal to noise, it's not hard to get a 
nice smooth line, but):


1) You've got 4 O atoms, guaranteed, so any other signal will be 
small and on top of that very strong signal generated from the 
first-neighbor O


Unfortunately,

2) You have very limited data range, either due to instrumental 
limitations, or due to interference from sulfur


Don't get me wrong I still have some data sitting around and I'd love 
to try P EXAFS analysis on it just to try and grasp that brass ring 
but...It's not the easiest task ever.


If you want good data quality "scan longer" is always an option. Some 
might think it's crazy but I do think I have some P XAS data where I 
took 30 or 60 scans, maybe overnight or something. The scans are so 
short that repeats are easy.



Hope this commentary is helpful.



Mike




On Sep 14, 2023, at 07:04, Marcelo Eduardo Alves  
wrote:




Hi there,

I begin by examining phosphorus adsorption by goethite, hematite, 
and gibbsite.


Why is it difficult, if not impossible, to obtain EXAFS spectra at 
the P-K edge that can be properly used, i.e., spectra with a high 
signal-to-noise ratio, especially for dilute samples?


Would it be possible to use arsenic as a phosphorus proxy to get 
conclusions from As K-edge EXAFS data that could be extended to P?


Thank you.


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Re: [Ifeffit] P K-edge EXAFS

[matthew marcus]

Good points.  At these low energies, an EXAFS range is a large fraction 
of the total energy range, so there tends to be a lot of curvature of 
baselines and post-edges.  True about the 4O 1NN shell that dominates, 
but the same happens with As.  All the interesting stuff is in the 
higher shells.  Most data I've seen has been XANES.

mam

On 9/13/2023 12:42 PM, Mike Massey wrote:
In my experience the main difficulties with EXAFS on P (phosphate) come 
from two factors (not signal to noise, it's not hard to get a nice 
smooth line, but):


1) You've got 4 O atoms, guaranteed, so any other signal will be small 
and on top of that very strong signal generated from the first-neighbor O


Unfortunately,

2) You have very limited data range, either due to instrumental 
limitations, or due to interference from sulfur


Don't get me wrong I still have some data sitting around and I'd love to 
try P EXAFS analysis on it just to try and grasp that brass ring 
but...It's not the easiest task ever.


If you want good data quality "scan longer" is always an option. Some 
might think it's crazy but I do think I have some P XAS data where I 
took 30 or 60 scans, maybe overnight or something. The scans are so 
short that repeats are easy.



Hope this commentary is helpful.



Mike




On Sep 14, 2023, at 07:04, Marcelo Eduardo Alves  
wrote:




Hi there,

I begin by examining phosphorus adsorption by goethite, hematite, and 
gibbsite.


Why is it difficult, if not impossible, to obtain EXAFS spectra at the 
P-K edge that can be properly used, i.e., spectra with a high 
signal-to-noise ratio, especially for dilute samples?


Would it be possible to use arsenic as a phosphorus proxy to get 
conclusions from As K-edge EXAFS data that could be extended to P?


Thank you.


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Re: [Ifeffit] P K-edge EXAFS

[Mike Massey]

In my experience the main difficulties with EXAFS on P (phosphate) come from 
two factors (not signal to noise, it's not hard to get a nice smooth line, but):

1) You've got 4 O atoms, guaranteed, so any other signal will be small and on 
top of that very strong signal generated from the first-neighbor O

Unfortunately,

2) You have very limited data range, either due to instrumental limitations, or 
due to interference from sulfur

Don't get me wrong I still have some data sitting around and I'd love to try P 
EXAFS analysis on it just to try and grasp that brass ring but...It's not the 
easiest task ever.

If you want good data quality "scan longer" is always an option. Some might 
think it's crazy but I do think I have some P XAS data where I took 30 or 60 
scans, maybe overnight or something. The scans are so short that repeats are 
easy.


Hope this commentary is helpful.



Mike




> On Sep 14, 2023, at 07:04, Marcelo Eduardo Alves  wrote:
> 
> 
> Hi there,
> 
> I begin by examining phosphorus adsorption by goethite, hematite, and 
> gibbsite.
> 
> Why is it difficult, if not impossible, to obtain EXAFS spectra at the P-K 
> edge that can be properly used, i.e., spectra with a high signal-to-noise 
> ratio, especially for dilute samples?
> 
> Would it be possible to use arsenic as a phosphorus proxy to get conclusions 
> from As K-edge EXAFS data that could be extended to P?
> 
> Thank you.
> 
> 
> 
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Re: [Ifeffit] P K-edge EXAFS

[matthew marcus]

It's not impossible, but difficult for a couple of reasons:
1.	Not too many beamlines can do it.  It's hard for soft X-ray beamlines 
and soft for hard X-ray beamlines.  Air absorption is significant.  If a 
Si DCM is used, the Bragg angle has to be higher than many 
monochromators can reach.


2.	The spectrum typically features a tall white line, which is very 
subject to overabsorption in concentrated samples.  The small absorption 
depths make it hard to do transmission without running into 
thickness/hole effects.  Harmonic contamination can be an issue.


3.	If you work in fluorescence, you have the low fluorescence yield to 
contend with, as well as absorption in a detector window of typical 
thickness.  The energy resolution of a typical SDD is insufficient to 
cleanly separate the fluorescence from elastic.


That's not to say that it can't be done.  It has.  It's just a bit more 
difficult than, for instance, Fe.


As to substituting As for P, that seems dangerous.  For one thing, the 
atoms are different sizes.  You may recall that sometime back there was 
a flap over some bacteria that supposedly had been transitioned from 
using P to using As for life functions.  This turned out to be bogus.  I 
gather that ATAs doesn't work the same as ATP, for instance.  It's not 
an isomorphous replacement.

mam

On 9/13/2023 12:03 PM, Marcelo Eduardo Alves wrote:

Hi there,

I begin by examining phosphorus adsorption by goethite, hematite, and 
gibbsite.


Why is it difficult, if not impossible, to obtain EXAFS spectra at the 
P-K edge that can be properly used, i.e., spectra with a high 
signal-to-noise ratio, especially for dilute samples?


Would it be possible to use arsenic as a phosphorus proxy to get 
conclusions from As K-edge EXAFS data that could be extended to P?


Thank you.



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[Ifeffit] P K-edge EXAFS

[Marcelo Eduardo Alves]

Hi there,

I begin by examining phosphorus adsorption by goethite, hematite, and
gibbsite.

Why is it difficult, if not impossible, to obtain EXAFS spectra at the P-K
edge that can be properly used, i.e., spectra with a high signal-to-noise
ratio, especially for dilute samples?

Would it be possible to use arsenic as a phosphorus proxy to get
conclusions from As K-edge EXAFS data that could be extended to P?

Thank you.
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