[Ifeffit] RE: Ifeffit Digest, Vol 17, Issue 18: RE: Solution flow cells

Fri Jul 23 03:45:40 CDT 2004

Dear Scott,

We have done some time-resolved XAFS measurements on aqueous solution of
Ru(II)(bpy)3 complex using free-flowing jet. It forms a liquid sheet of
approx. 100 microns thickness and thus you can avoid windows etc.
However you might run into some trouble when using in vacuum. In
principle you can find many manufacturers who provide these kinds of
jets equipped with sapphire nozzles for dye lasers. I know that some of
these jets are also used for cutting and polishing jewelry...if you need
any more details you could look up our paper about the setup: M. Saes et
al., Rev. Sci. Instrum., 75(2004), 24-30.
I hope it helps,

Wojciech Gawelda

*********************************************************************
Wojciech Gawelda

Laboratoire de Spectroscopie Ultrarapide (LSU)

Institut des Sciences et Ingénierie Chimiques (ISIC),

Faculté des Sciences de Base (SB-BSP)

Ecole Polytechnique Fédérale de Lausanne (EPFL)

CH-1015 Lausanne-Dorigny, Switzerland

Tel.:  +41 (21) 693 0452

Fax.: +41 (21) 693 0422 

E-mail: wojciech.gawelda at epfl.ch

WWW: http://lsu.epfl.ch

*********************************************************************

-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
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Sent: vendredi, 23. juillet 2004 08:47
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 17, Issue 18

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Today's Topics:

   1. Solution flow cells (Scott Calvin)
   2. RE: Solution flow cells (Kelly, Shelly D.)
   3. Re: Solution flow cells (Tsu-Chien Weng)
   4. RE: Solution flow cells (Matt Newville)
   5. RE: Solution flow cells (Jensen, Mark P.)
   6. RE: Solution flow cells (SCHLEGEL Michel 177447)

----------------------------------------------------------------------

Message: 1
Date: Thu, 22 Jul 2004 15:34:00 -0400
From: Scott Calvin <scalvin at slc.edu>
Subject: [Ifeffit] Solution flow cells
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <3.0.1.32.20040722153400.00b14170 at mail.slc.edu>
Content-Type: text/plain; charset="us-ascii"

Hi all,

I've been doing a literature search for an article I'm writing up, and I
can't seem to find any examples of an XAS flow cell desgined for
liquids.
Sealed cells for liquids, yes; flow cells for passing gases over solids,
yes; but no solution-chemistry flow cell. I feel like someone must have
published work in that area before, but I can't seem to find it.

So, does anyone know of any work done using a liquid-phase XAS flow
cell?

--Scott Calvin
Sarah Lawrence College

------------------------------

Message: 2
Date: Thu, 22 Jul 2004 14:55:29 -0500
From: "Kelly, Shelly D." <SKelly at anl.gov>
Subject: RE: [Ifeffit] Solution flow cells
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <1C1577844A0BDF448E14E8CCB2F74424015A267F at ANLMAIL.anl.gov>
Content-Type: text/plain;	charset="us-ascii"

Hi Scott,

See below: 
> Hi all,
> 
> I've been doing a literature search for an article I'm 
> writing up, and I can't seem to find any examples of an XAS 
> flow cell desgined for liquids. Sealed cells for liquids, 
> yes; flow cells for passing gases over solids, yes; but no 
> solution-chemistry flow cell. I feel like someone must have 
> published work in that area before, but I can't seem to find it.
> 
> So, does anyone know of any work done using a liquid-phase 
> XAS flow cell?

Simon Bare uses a flow cell for passing liquids/gasses over a sample.
This one is a glass container with kapton windows with ports for input
and output.  Also I have seen something like that at PNC cat.  I think
that Ed Stern et. al. was using it.  The one at PNC cat circulated the
liquid through a boron carbide section that is x-ray transparent.

Shelly

------------------------------

Message: 3
Date: Thu, 22 Jul 2004 16:44:40 -0400
From: Tsu-Chien Weng <tsuchien at umich.edu>
Subject: Re: [Ifeffit] Solution flow cells
To: Scott Calvin <scalvin at slc.edu>,	XAFS Analysis using Ifeffit
	<ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <F452155A-DC1F-11D8-8255-000A959EB970 at umich.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi Scott,

> I've been doing a literature search for an article I'm writing up, and

> I
> can't seem to find any examples of an XAS flow cell desgined for 
> liquids.
> Sealed cells for liquids, yes; flow cells for passing gases over 
> solids,
> yes; but no solution-chemistry flow cell. I feel like someone must
have
> published work in that area before, but I can't seem to find it.
>
> So, does anyone know of any work done using a liquid-phase XAS flow 
> cell?

We (Penner-Hahn group) have done solution EXAFS measurement and 
time-resolved XAS at Bio-CAT at the APS.  A Kapton tube is used for 
x-ray window and connected to PE tubes using epoxy glue.

Tsu-Chien
<Chien>001000</Chien>

------------------------------

Message: 4
Date: Thu, 22 Jul 2004 15:55:07 -0500 (CDT)
From: Matt Newville <newville at cars.uchicago.edu>
Subject: RE: [Ifeffit] Solution flow cells
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:

<Pine.LNX.4.44.0407221538340.2941-100000 at millenia.cars.aps.anl.gov>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Just to follow up on and add to Shelly's and Tsu-Chien's
responses:  

There's a paper by M.  Hoffmann, et al (J. Fulton, and others 
from PNNL) on a flow-cell, especially for high pressure fluids.  
I believe it's in J Phys Chem (1999), but don't have the exact 
citation.  This might be the one Shelly saw at PNC CAT.

Mark Antonio has a nice electrochemical cell in which he can
change both potential, but can't remember if he can flow in a
changed solution... is that "flow"?

I believe the catalyst people who run at ESRF (esp. the DXAFS
line) have some nice flow cells too, but don't know if or 
where it's published.

--Matt

------------------------------

Message: 5
Date: Thu, 22 Jul 2004 16:06:41 -0500
From: "Jensen, Mark P." <mjensen at anl.gov>
Subject: RE: [Ifeffit] Solution flow cells
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
	<0D4E53E4DC6CA449B9F71E5282984F8C2F0DE3 at anchim2.chm.anl.gov>
Content-Type: text/plain;	charset="us-ascii"

And just to add to Matt, Shelly, and Tsu-Chien's responses.

Matt mentioned Mark Antonio's electrochemical cell. It is not a flow
cell, though we did design a closely related, but unpublished, cell
design for in the beam titrations.

------------------------------
Mark P. Jensen
Chemistry Division
Argonne National Laboratory
9700 South Cass Avenue
Argonne, Illinois  60439-4831
USA
630-252-3670
630-252-7501 FAX
mjensen at anl.gov

> -----Original Message-----
> From: Newville, Matthew G. 
> Sent: Thursday, July 22, 2004 2:55 PM
> To: XAFS Analysis using Ifeffit
> Subject: RE: [Ifeffit] Solution flow cells
> 
> Just to follow up on and add to Shelly's and Tsu-Chien's
> responses:  
> 
> There's a paper by M.  Hoffmann, et al (J. Fulton, and others 
> from PNNL) on a flow-cell, especially for high pressure fluids.  
> I believe it's in J Phys Chem (1999), but don't have the 
> exact citation.  This might be the one Shelly saw at PNC CAT.
> 
> Mark Antonio has a nice electrochemical cell in which he can 
> change both potential, but can't remember if he can flow in a 
> changed solution... is that "flow"?
> 
> I believe the catalyst people who run at ESRF (esp. the DXAFS
> line) have some nice flow cells too, but don't know if or 
> where it's published.
> 
> --Matt
> 
> 
> 
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> 

------------------------------

Message: 6
Date: Fri, 23 Jul 2004 08:45:10 +0200
From: SCHLEGEL Michel 177447 <schlegel at azurite.cea.fr>
Subject: RE: [Ifeffit] Solution flow cells
To: "'XAFS Analysis using Ifeffit'"
	<ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
	<3808A7D2DCEAD6118B63009027287265078A27 at azurite.saclay.cea.fr>
Content-Type: text/plain; charset="iso-8859-1"

Scott, 

> I've been doing a literature search for an article I'm 
> writing up, and I can't seem to find any examples of an 
> XAS flow cell desgined for liquids.
> Sealed cells for liquids, yes; flow cells for passing gases 
> over solids, yes; but no solution-chemistry flow cell. I 
> feel like someone must have published work in that area before,
> but I can't seem to find it.

Maybe not exactly a flow cell, but a rapid biblio research on 
"Web of Science" using the"stopped-flow" and "EXAFS or XAS or XANES"
keywords has unearthed some 23 references over the last ten years,
many of them probably utterly irrelevant. Nevertheless, I copied 
them in the attached text file.

Best regards,

Michel Schlegel

-------------- next part --------------
Record 1 of 23
Author(s): Matsui, J; Park, H; Otsuka, K; Oyama, M
Title: Kinetics and mechanisms of the reactions of 9-substituted
anthracene cation radicals with water or methanol in acetonitrile
Source: JOURNAL OF ELECTROANALYTICAL CHEMISTRY, 558: 49-57 OCT 30 2003
Abstract: The reactions of 9-substituted anthracene cation radicals (XA
(+) (.) s) with water and methanol in acetonitrile were analyzed using
an electron transfer stopped-flow (ETSF) method. By adopting the
tris(2,4-dibromophenyl)amine cation radical (TDBPA (+ .)) as a reaction
initiator, five XA (+ .) s, i.e. phenyl, bromo, acetyl, benzyl, and
methyl derivatives, could be generated quantitatively by mixing XA with
TDBPA (+ .) and the chemical reaction processes of XA (+ .) s with water
or methanol (ROH) could then be followed by observing dynamic
transformation processes of the absorption spectra. Consequently, the
reaction orders of XA (+ .) and ROH as well as the reaction rates could
be determined. The order of the reactivity was anthracene (+ .) >
9-methylanthracene (+ .) > 9-benzylanthracene (+ .) > 9-acetylanthracene
(+ .), 9-bromoanthracene (+ .) > 9-phenylanthracene (+ .), and diverse
changes in the reaction orders of both XA (+ .) and ROH were observed
indicating s!
ome mechanistic changes. The order of the reactivity was difficult to
explain only on the basis of the character of XAs or XA (+ .)s. However,
as a hypothesis, it can be assumed that when the electron transfer
between XA (+ .) and XA(ROH) (+ .) is favorable to formation of
XA(ROH)(2+), the reaction order of [XA (+ .)] is second, and the
reaction rates become faster. (C) 2003 Elsevier B.V. All rights
reserved.

Record 2 of 23
Author(s): Headspith, J; Salvini, G; Thomas, SL; Derbyshire, G; Dent, A;
Rayment, T; Evans, J; Farrow, R; Anderson, C; Cliche, J; Dobson, BR
Title: XSTRIP - a silicon micro strip-based X-ray detector for
ultra-fast X-ray spectroscopy studies
Source: NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION
A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT, 512
(1-2): 239-244 OCT 11 2003
Abstract: For a number of years, an exciting and important area of
synchrotron radiation science has been X-ray absorption spectroscopy
fine structure studies of dynamically changing samples on the sub-second
time-scales. By utilizing this technique, precise measurement of
detailed structural changes can be investigated during a chemical or
phase change reaction without the need for repeated experiments or
expensive stopped flow techniques. Until recently, instrumentation to
facilitate these studies has been based on commercially available
detectors developed predominantly for other applications. Whilst these
systems have yielded quality science, they have been subject to a number
of fundamental limitations, particularly their speed, linearity and
dynamic range. We have developed a new detector, XSTRIP, to overcome
some of these. This new instrument marries dedicated silicon microstrip
technology with specialist low noise, custom developed, fast readout
integrated circuits, !
to yield an instrument that will unlock whole new areas of science to
researchers. This paper will discuss some of the drawbacks of historical
systems, give details of the XSTRIP system and also present the
operating parameters of the system. In addition, some of the initial
scientific experimental results will also be presented. (C) 2003
Published by Elsevier B.V.

Record 3 of 23
Author(s): Rahman, MBA; Evans, J; Dent, AJ
Title: Time-resolved energy dispersive EXAFS measurement of
oligomerisation reaction catalysed by nickel homogeneous catalyst on
addition of triphenylphosphine and AlEt2(OEt) as Co-catalyst
Source: ASIAN JOURNAL OF CHEMISTRY, 15 (2): 1097-1102 APR-JUN 2003
Abstract: Energy dispersive EXAFS (EDE) data have been analysed for the
nickel (3-diketonate catalysts, Ni(dpM)(2), using curved wave theory
with ab initio phase shift's. The derived parameters for metal compounds
were in good agreement, within experimental error of 0.02-0.05 Angstrom
for the bond distances. Time-resolved EDE studies on Ni(dpm)(2) : PPh3 :
AlEt2(OEt): 1-hexene of I : 2 : 4 : 20 were acquired within 0.24 s for
each spectrum. The growth of a pre-edge feature and change at the top of
the edge can be clearly seen to show that the reaction reached
completion in less than 6 s. A stopped flow system was used for in situ
time-resolved EDE studies on the nickel systems at room temperature. EDE
measurements using a new rectangular Si(III) monochromator and Hamamatsu
S4874 photodiode array at Station 9.3, Daresbury Laboratory have yielded
consecutive spectral data taken at 1-1000 accumulations with 2-30 ms
integration time to follow the changes during initiation of the!
 catalytic reaction.

Record 4 of 23
Author(s): Rahman, MBBA; Bolton, PR; Evans, J; Dent, AJ; Harvey, I;
Diaz-Moreno, S
Title: Application of stopped flow techniques and energy dispersive
EXAFS for investigation of the reactions of transition metal complexes
in solution: Activation of nickel beta-diketonates to form homogeneous
catalysts, electron transfer reactions involving iron(III) and oxidative
addition to iridium(I)
Source: FARADAY DISCUSSIONS, 122: 211-222 2003
Abstract: Stopped-flow techniques of rapid mixing have been combined
with energy dispersive X-ray absorption spectroscopy to monitor the
reaction of Ni(dpm)(2) {dpm = (BuC)-C-t(O)CHC(O)Bu-t} by aluminium
alkyls (AlEt2X, X = OEt and Et) to form the active species for the
catalytic di- and tri-merisation of hex-1-ene. Acquisition times down to
ca. 30 ms were achieved on Station 9.3 of the SRS using a photodiode
array detector. The EXAFS features of the resulting solution complexes
are of the form [Ni(O-O)(R) (alkene)]. In the presence of PPh3,
[Ni(O-O)(R)(PPh3)] appears to be the predominant type of species. The
reduction of aqueous Fe(III) by hydroquinone was investigated on ID24 at
the ESRF by Fe K-edge energy dispersive EXAFS with a CCD camera as
detector; spectra were obtained in 1 ms or longer. No intermediate inner
sphere complex was detected prior to the formation of aqueous Fe(II).
Finally the oxidative addition of CH3SO3CF3 to [IrI2(CO)(2)](-) was
monitored on Station!
 9.3 with a silicon microstrip detector. A single acquisition of 400 mus
was feasible, with spectra recorded in multiples of 1.2 ms. In that
time, the first stage of the reaction had been completed, with a slower
stage thereafter. The results are consistent with the two-stage ionic
oxidative addition mechanism.

Record 5 of 23
Author(s): Rao, LF; Zhang, ZC; Friese, JI; Ritherdon, B; Clark, SB;
Hess, NJ; Rai, D
Title: Oligomerization of chromium(III) and its impact on the oxidation
of chromium(III) by hydrogen peroxide in alkaline solutions
Source: JOURNAL OF THE CHEMICAL SOCIETY-DALTON TRANSACTIONS, (2):
267-274 2002
Abstract: Monomeric, dimeric and trimeric chromium(III) species in
solution were separated by ion exchange and characterized with UV/Vis
absorption and Extended X-ray Absorption Fine Structure Spectroscopy
(EXAFS). The kinetics of the oxidation of the separated species by
hydrogen peroxide in alkaline solutions were studied by conventional and
stopped-flow UV/Vis absorption spectroscopy. Results indicate that the
intensity of Cr-Cr scattering in the EXAFS spectra (d(Cr-Cr) similar
to2.99 Angstrom), a measure of the degree of oligomerization, increases
as the solution alkalinity is increased. As the oligomerization
proceeds, the rate of oxidation by hydrogen peroxide in alkaline
solutions decreases in the order: monomer > dimer > trimer >
aged/unseparated alkaline chromium(III) solution where higher oligomers
dominate. The dominant redox pathway has an inverse order with respect
to C-NaOH. The data suggest that the rate-determining step involves the
weakening of the bridging !
bonds in the oligomer and a concomitant release of one hydroxyl group
from the chromium(III) moiety upon the attack by hydrogen peroxide.

Record 6 of 23
Author(s): de Seny, D; Heinz, U; Wommer, S; Kiefer, M; Meyer-Klaucke, W;
Galleni, M; Frere, JM; Bauer, R; Adolph, HW
Title: Metal ion binding and coordination geometry for wild type and
mutants of metallo-beta-lactamase from Bacillus cereus 569/H/9 (BcII) -
A combined thermodynamic, kinetic, and spectroscopic approach
Source: JOURNAL OF BIOLOGICAL CHEMISTRY, 276 (48): 45065-45078 NOV 30
2001
Abstract: One high affinity (nm) and one low affinity (IM) macroscopic
dissociation constant for the binding of metal ions were found for the
wild-type metallo-beta -lactamase from Bacillus cereus as well as six
single-site mutants in which all ligands in the two metal binding sites
were altered. Surprisingly, the mutations did not cause a specific
alteration of the affinity of metal ions for the sole modified binding
site as determined by extended x-ray absorption fine structure (EXAFS)
and perturbed angular correlation of gamma -rays spectroscopy,
respectively. Also UV-visible absorption spectra for the mono-cobalt
enzymes clearly contain contributions from both metal sites. The
observations of the very similar microscopic dissociation constants of
both binding sites in contrast to the significantly differing
macroscopic dissociation constants inevitably led to the conclusion that
binding to the two metal sites exhibits negative cooperativity. The slow
association rates fo!
r forming the binuclear enzyme determined by stopped-flow fluorescence
measurements suggested that fast metal exchange between the two sites
for the mononuclear enzyme hinders the binding of a second metal ion.
EXAFS spectroscopy of the mono- and di-zinc wild type enzymes and two
di-zinc mutants provide a definition of the metal ion environments,
which is compared with the available x-ray crystallographic data.

Record 7 of 23
Author(s): Inamo, M; Kamiya, N; Inada, Y; Nomura, M; Funahashi, S
Title: Structural characterization and formation kinetics of
sitting-atop (SAT) complexes of some porphyrins with copper(II) ion in
aqueous acetonitrile relevant to porphyrin metalation mechanism.
Structures of aquacopper(II) and Cu(II)-SAT complexes as determined by
XAFS spectroscopy
Source: INORGANIC CHEMISTRY, 40 (22): 5636-5644 OCT 22 2001
Abstract: The formation of the sitting-atop (SAT) complexes of
5,10,15,20-tetraphenylporphyrin (H(2)tpp),
5,10,15,20-tetrakis(4-chlorophenyl)porphyrin (H(2)t(4-Clp)p),
5,10,15,20-tetramesitylporphyrin (H(2)tmp), and
2,3,7,8,12,13,17,18-octaethylporphyrin (H(2)oep) with the Cu(H) ion was
spectrophotometrically confirmed in aqueous acetonitrile (AN), and the
formation rates were determined as a function of the water concentration
(Cw). The decrease in the conditional first-order rate constants with
the increasing Cw was reproduced by taking into consideration the
contribution of [Cu(H2O)(an)(5)](2+) in addition to [Cu(an)(6)](2+) to
form the Cu(II)-SAT complexes. The second-order rate constants for the
reaction of [Cu(an)(6)](2+) and [Cu(H2O)(an)(5)](2+) at 298 K were
respectively determined as follows: (4.1 +/- 0.2) x 10(5) and (3.6 +/-
0.2) x 10(4) M-1 s(-1) for H(2)tpp, (1.15 +/- 0.06) x 10(5) M-1 s(-1)
and negligible for H(2)t(4-Clp)p, and (4.8 +/- 0.3) x 10(3) and (1.3 +/!
- 0.3) x 10(2) M-1 s(-1) for H(2)tmp. Since the reaction of H(2)oep was
too fast to observe the reaction trace due to the dead time of 2 ms for
the present stopped-flow technique, the rate constant was estimated to
be greater than 1.5 x 10(6) M-1 s(-1). According to the structure of the
Cu(II)-SAT complexes determined by the fluorescent XAFS measurements,
two pyrrolenine nitrogens of the meso-substituted porphyrins (H(2)tpp
and H(2)tmp) bind to the Cu(Il) ion with a Cu-N(pyr) distance of ca.
2.04 Angstrom, while those of the beta -pyrrole-substituted porphyrin
(H(2)oep) coordinate with the corresponding bond distance of 1.97
Angstrom. The shorter distance of H(2)oep is ascribed to the flexibility
of the porphyrin ring, and the much greater rate for the formation of
the Cu(H)-SAT complex of H(2)oep than those for the meso-substituted
porphyrins is interpreted as due to a small energetic loss at the
porphyrin deformation step during the formation of the Cu(H)SAT complex.
The o!
verall formation constants, beta (n), of [Cu(H2O)(n)(an)(6-n)](2+) for
the water addition in aqueous AN were spectrophotometrically determined
at 298 K as follows: log(beta (1)/M-1) = 1.19 +/- 0.18, log(beta
(2)/M-2) = 1.86 +/- 0.35, and log(beta (3)/M-3) = 2.12 +/- 0.57. The
structure parameters around the Cu(II) ion in [Cu(H2O)(n)(an)(6-n)](2+)
were determined using XAFS spectroscopy.

Record 8 of 23
Author(s): Funahashi, S; Inada, Y; Inamo, M
Title: Dynamic study of metal-ion incorporation into porphyrins based on
the dynamic characterization of metal ions and on sitting-atop complex
formation
Source: ANALYTICAL SCIENCES, 17 (8): 917-927 AUG 2001
Abstract: We succeeded in the detection of the sitting-atop (SAT)
copper(II) complex of TPP (5,10,15,20-tetraphenylporphyrin) in
acetonitrile (AN) as a solvent with a very low Bronsted basicity, where
two pyrrolenine nitrogens in the Cu(II)-SAT complex coordinate to the
metal ion and two protons still remain on the pyrrole nitrogens. The
structure parameters around the copper(II) ion in the Cu(II)-SAT
complex, as determined by a fluorescent EXAFS method, suggest an axially
elongated and equatorially distorted six-coordinate geometry. We
measured the rates of the formation reaction of the SAT complexes for a
series of transition metal(II) ions in AN using the stopped-flow
technique. We propose the mechanism where there is a rapid deformation
equilibrium of the porphyrin ring prior to the rate-determining step of
the bond rupture of a coordinated solvent molecule on the metal(II) ion.
Furthermore, we measured the rates of the deprotonation reaction of the
Cu(II)-SAT complex by!
 some Bronsted bases and indicated that the rate -determining step is
the attack of the base on the proton of the pyrrole nitrogen in the SAT
complex. Finally, a unified mechanism relevant to the porphyrin
metalation mechanism has been proposed.

Record 9 of 23
Author(s): Matocha, CJ; Sparks, DL; Amonette, JE; Kukkadapu, RK
Title: Kinetics and mechanism of birnessite reduction by catechol
Source: SOIL SCIENCE SOCIETY OF AMERICA JOURNAL, 65 (1): 58-66 JAN-FEB
2001
Abstract: The complex interactions of oxidizable organic ligands with
soil Mn(III,IV) (hydr)oxide minerals have received little study by in
situ spectroscopic techniques. We used a combination of an in situ
electron paramagnetic resonance stopped-flow (EPR-SF) spectroscopic
technique and stirred-batch studies to measure the reductive dissolution
kinetics of birnessite (delta -MnO2), a common Mn mineral in soils, by
catechol (1,2-dihydroxybenzene). The reaction was rapid, independent of
pH, and essentially complete within seconds under conditions of
excess-catechol at pH 4 to 6. The overall empirical second-order rate
equation describing the reductive dissolution rate was d[Mn(II)]/ dt =
k[CAT](1.0)[SA](1.0) where k = 4 (+/-0.5) (10(-3) L m(-2) s(-1) and
[CAT] and [SA] are the initial concentrations in molarity and meters
square per liter. In the process, catechol was oxidized to the
two-electron o-quinone product. The energy of activation (E.) for the
reaction was 59 (+/-7) !
kJ mol(-1) and the activation entropy (SI) was -78 +/- 225 mol(-1) K-1,
suggesting that the reaction was surface-chemical controlled and occurs
by an associative mechanism. Rates of catechol disappearance from
solution with simultaneous Mn(II) and o-quinone production were
comparable. These data strongly suggest that precursor surface-complex
formation is rate-limiting and that electron transfer is rapid, The
rapid reductive dissolution of birnessite by catechol has significant
implications for C and Mn cycling in soils and the availability of Mn to
plants.

Record 10 of 23
Author(s): Inada, Y
Title: Local structure analysis of short-lived reaction intermediates by
means of a time-resolved stopped-flow extended X-ray absorption
fine-structure technique
Source: BUNSEKI KAGAKU, 49 (8): 563-573 AUG 2000
Abstract: Three types of time-resolved stopped-flow extended X-ray
absorption fine-structure (EXAFS) instruments have been developed by
combining an EXAFS spectrometer equipped with the original time-resolved
detection system and a stopped-flow unit to analyze the local structure
around the metal center in short-lived reaction intermediates. The whole
X-ray energy region used to obtain an EXAFS spectrum could be measured
simultaneously for the instrument in the dispersive mode, and a.
time-resolution on the order of ms has been acheived in the case of die
instrument using synchrotron radiation as an X-ray source. By using
these time-resolved stopped-flow EXAFS instruments, we have analyzed the
local structure around the metal center in some short-lived reaction
intermediates, such as a peroxochromium intermediate formed in a
reduction reaction of chromate ion by hydrogen peroxide in an acidic
aqueous solution; a Cu(II)/Hg(II) heterodinuclear porphyrin intermediate
formed in !
the Cu(II) ion incorporation process into 5,10,15,20-tetrakis
(4-sulfonatophenyl) porphyrin in the presence of the Hg(II) ion in
water, and a chloride-bridged precursor intermediate formed in the
inner-sphere reduction of CoCl(NH3)(5)(2+) by Fe2+ in
N,N-dimethylformamide. According to the obtained local structure of the
reaction intermediate, the reaction mechanisms and the structural
characteristics of the reaction intermediates have been microscopically
clarified.

Record 11 of 23
Author(s): Ozutsumi, K; Ohtaki, H
Title: Structure analysis of reaction intermediates in metal
substitution reactions in solution by the stopped-flow EXAFS method
Source: BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN, 72 (9): 1947-1956 SEP
1999
Abstract: Improvements of XAFS (X-Ray Absorption Fine Structure)
measurements in the time domain are summarized and several examples of
structure determination of reaction intermediates by the EXAFS (Extended
X-Ray Absorption Fine Structure) method are given. The local structure
around the copper(II) or cobalt(II) ion is described in the reaction
intermediate in the metal substitution reaction of the homodinuclear
mercury(II) porphyrinato
(5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin; H(6)tpps) complex in
an acetate buffer determined by the stopped-flow EXAFS (SF-EXAFS)
method, which was developed by us. Comparison of the bond lengths in the
intermediates with those in the reactants and the products of the metal
substitution reaction, the structure of which has been determined by the
same method, revealed the cause of the instability of the reaction
intermediates.

Record 12 of 23
Author(s): Cheung, KC; Strange, R; Harvey, I; Dobson, B; Derbyshire, G;
Kay, J; Binsted, N; Linford, R; Hasnain, S
Title: Conversion of the oldest XAFS station at the first dedicated SR
source to a state-of-the-art XAFS facility
Source: JOURNAL OF SYNCHROTRON RADIATION, 6: 161-163 Part 3 MAY 1 1999
Abstract: Station 7.1 was the first XAFS station to operate at the
Synchrotron Radiation Source (SRS) starting in 1981. A major upgrade of
7.1 has been taking place aimed towards a multidimensional XAFS and
single crystal facility for 3d elements (Ca to Zn). The optical upgrade
included a collimating mirror and QuEXAFS monochromator, also a highly
compact and rapid count-rate multi-element solid state detector has been
designed, built and recently commissioned. A stopped-flow system is
commissioned and a diffractometer stage is planned. The necessary
analytical tools for 3D XAFS refinement using crystallographic data as
the starting 3D model have been developed for solution XAFS.

Record 13 of 23
Author(s): Dent, A; Evans, J; Newton, M; Corker, J; Russell, A; Abdul
Rahman, MB; Fiddy, S; Mathew, R; Farrow, R; Salvini, G; Atkinson, P
Title: High-quality energy-dispersive XAFS on the 1 s timescale applied
to electrochemical and catalyst systems
Source: JOURNAL OF SYNCHROTRON RADIATION, 6: 381-383 Part 3 MAY 1 1999
Abstract: A long program involving the development of a fast linear and
stable detector, and the recent upgrade of the bent monochromator to a
4-point one at station 9.3 Daresbury Laboratory is showing exciting
results such that it has now become possible to obtain analysable XAFS
data on 50mM solutions in time scales of a second or less. Three
examples of such data are shown: a homogeneous Ni catalyst reaction
using a stopped flow system, a heterogeneous catalyst reduction showing
time dependent data collected in a microreactor, and an electrochemical
system showing the oxidation of small Pt particles as the potential is
changed. The improvements have come from two major developments - the
monochromator and the detector.

Record 14 of 23
Author(s): Ohtaki, H
Title: Development of modern solution chemistry: a search of new fields
Source: COORDINATION CHEMISTRY REVIEWS, 186: 735-759 MAY 1999
Abstract: In order to investigate new fields and how one can approach a
new field of chemistry, studies carried out by Nobel laureates are
surveyed from the historical point of view and are classified into five
categories. A brief discussion shows how they created new fields of
chemistry and how one can open a gate to a new world. A short history of
the development of solution chemistry is reviewed in connection with a
view for the development of theories and methodologies used for
investigations in solution chemistry. New fields and new methodologies
have often been discovered by extension and combination of existing
theories and methodologies with anew vision recognising existing
chemistry from another side of the traditional face of chemistry.
A:recently developed method to determine the structure of short-lived
reaction intermediates in Solution, which has not been determinable by
traditional analytical methods, is shown as an example. This is a method
combining a stoppe!
d-flow technique and the EXAFS method. Some results obtained for metal
substitution reactions of porphyrin complexes are given, and emphasis is
placed on an effective combination of different methodologies to create
a new method of investigation. (C) 1999 Elsevier Science S.A. All rights
reserved.

Record 15 of 23
Author(s): Nishimoto, J; Tabata, M; Eguchi, T; Takauchi, J
Title: Kinetics and mechanism of the acid-base reaction of the diacid
salts of porphyrin with pyridine in chloroform
Source: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2, (7):
1539-1543 JUL 1998
Abstract: The acid-base reaction of the diacid salts of
5,10,15,20-tetraphenylporphyrin [(H(4)tpp)(2+)(X-)(2); X- = Cl- and Br-]
with pyridine is so slow in chloroform that the reaction has been
followed using a conventional stopped-flow apparatus. The reaction rate
is first-order with respect to the concentrations of porphyrin and
pyridine, The reaction rate is enhanced by water and suppressed by
1,4-dioxane. The rate equation is given by the following equation:
-d[(H(4)tpp)(2+)(X-)(2)]/dt = k(1)'[(H(4)tpp)(2+)(X-)(2)][H2O][py] +
k(2)'[(H(4)tpp)(2+)(X-)(2)][H2O](2)[py] =
k(1)[(H(4)tpp)(2+)(X-)(2)(H2O)] [py] + k(2)[(H(4)tpp)(2+)
(X-)(2)(H2O)(2)][py]
The values of k(1)' and k(2)' are (4.5 +/- 0.2) x 10(4) dm(6)
mol(-2)s(-1) and (4.3 +/- 0.3) x 10(5) dm(9) mol(-3)s(-1) for Br-, and
(1.95 +/- 0.07) x 10(4) dm(6) mol(-2)s(-1) and(1.11 +/- 0.14) x 10(5)
dm(9) mol(-3)s(-1) for Cl- at 25 degrees C, respectively. The reaction
mechanism is discussed from the viewpoint of hydration of the diacid
porphyrin, pyridine and 1,4-dioxane.

Record 16 of 23
Author(s): Ozutsumi, K; Ohnishi, S; Ohtaki, H; Tabata, M
Title: Structure of the short-lived intermediate formed during the metal
substitution reaction of the Mercury(II) porphyrin complex with
cobalt(II) ion in aqueous solution determined by the stopped-flow EXAFS
method
Source: ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL
SCIENCES, 53 (4): 469-475 APR 1998
Abstract: The local structure around the cobalt(II) ion in the reaction
intermediate formed during the metal substitution reaction of the
homodinuclear mercury(II) porphyrin
(5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin; H(2)tpps(4-)) complex
with a cobalt(II) ion in an acetate buffer has been determined by the
stopped-flow EXAFS method. The structure of the reactant and the product
of the above reaction has also been determined by the same method. The
coordination geometry around the cobalt(II) ion in the heterodinuclear
intermediate, [Hg(tpps)Co-II](2-) is six-coordinate octahedral with four
additional water and/or acetate oxygen atoms. The Co-II- N and Co-II-O
bond lengths in the intermediate are 212(2) and 221(1) pm, respectively.
The product, [Co-II(tpps)](4-), has a six-coordinate octahedral
structure, the Co-II-N and Co-II-O bond lengths being 203(1) and 215(1)
pm, respectively. The Co-II-N bond length in the intermediate is ca. 9
pm longer than that in the product!
... The Co-II-O bond length in the intermediate is also ca. 9 pm longer
than that of 212(1) pm in the reactant, the cobalt(II) acetato complex,
and ca. 6 pm longer than that in the product. The longer Co-II-O bond in
the intermediate as compared to those in the reactant and in the product
appears to be responsible for the instability of the intermediate. The
oxidized product, [Co-III(tpps)](3-), has a six-coordinate structure
with two additional Co-III-O bonds. The Co-III-N and Co-III-O bond
lengths are 189(1) and 197(2) pm, respectively, and are much shorter
than those in [Co-II(tpps)](4-).

Record 17 of 23
Author(s): Klabunde, T; Krebs, B
Title: The dimetal center in purple acid phosphatases
Source: METAL SITES IN PROTEINS AND MODELS, 89: 177-198 1997
Book series title: STRUCTURE AND BONDING
Abstract: Purple acid phosphatases (PAPs) contain a dinuclear metal
center in their active site and hydrolyze phosphoric acid esters at low
pH. Characteristic of this group of acid phosphatases is their
resistance to inhibition by tartrate and their purple color, due to the
presence of a tyrosine residue ligated to a ferric iron. The mammalian
enzymes all contain a mixed-valent di-iron unit in their catalytic
active form, first identified in the bovine spleen and porcine uterus
enzymes, while a heterodinuclear Fe(III)Zn(II) unit has been
characterized for the most studied plant enzyme from kidney bean. The
enzymes from porcine uterus and bovine spleen can be converted into
active FeZn forms and the plant enzyme can be transformed into an active
FeFe form. In recent years the dimetal center of PAPs has been studied
using numerous spectroscopic methods such as Mossbauer spectroscopy,
EPR, NMR, EXAFS, magnetic, electrochemical and resonance Raman studies
characterizing most of !
the metal coordinating residues, the metal-metal separation and
providing evidence of the similarity between enzymes from different
sources. Analysis of the products of hydrolysis of a substrate
containing a chiral phosphorus by P-31 NMR, stopped-flow measurements
and kinetic studies all support a reaction path involving nucleophilic
attack of a Fe(III)-bound hydroxide ligand on the phosphate ester. The
recently solved crystal structure of the plant enzyme provides the
structural basis for the understanding of the two-metal ion mechanism of
this class of enzymes.

Record 18 of 23
Author(s): Inada, Y; Funahashi, S
Title: Laboratory stopped-flow XAFS apparatus. Structure determination
of the short-lived peroxochromium intermediate formed during reduction
process of chromate(VI) ion by hydrogen peroxide
Source: ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL
SCIENCES, 52 (6): 711-718 JUN 1997
Abstract: In order to determine the structure parameters of the reaction
intermediate formed during the reduction process of chromate(VI) ion by
hydrogen peroxide, a laboratory stopped-flow X-ray absorption fine
structure (XAFS) apparatus, which was constructed by a rotating anode
X-ray generator, an energy scanning spectrometer, a stopped-flow
assembly, and X-ray detectors, was newly developed. Using the apparatus,
the Cr K-edge XAFS spectrum of the reaction intermediate was measured.
One oxo group, two peroxo groups, and one water molecule are coordinated
to the Cr(VI) center in the intermediate, CrO(O-2)(2)(H2O), with Cr-O
bond lengths of 157, 168, and 193 pm, respectively. The geometry around
the Cr(VI) center is probably 6-coordinate pentagonal pyramidal.

Record 19 of 23
Author(s): YOSHIDA, N; NAGAMURA, T
Title: STOPPED-FLOW TIME-RESOLVED EXTENDED X-RAY-ABSORPTION
FINE-STRUCTURE TECHNIQUE FOR STUDYING REACTION DYNAMICS IN SOLUTION
Source: REVIEW OF SCIENTIFIC INSTRUMENTS, 66 (1): 52-54 Part 1 JAN 1995

Record 20 of 23
Author(s): ROWLETT, RS; CHANCE, MR; WIRT, MD; SIDELINGER, DE; ROYAL, JR;
WOODROFFE, M; WANG, YFA; SAHA, RP; LAM, MG
Title: KINETIC AND STRUCTURAL CHARACTERIZATION OF SPINACH
CARBONIC-ANHYDRASE
Source: BIOCHEMISTRY, 33 (47): 13967-13976 NOV 29 1994
Abstract: We have carried out kinetics studies of spinach carbonic
anhydrase (CA) using stopped-flow spectrophotometry at steady state and
C-13-NMR exchange at chemical equilibrium. We found that the rate of CO2
reversible arrow HCO3- exchange catalyzed by spinach CA at pH 7.0 to be
3-5 times faster than the maximal k(cat) for either CO2 hydration or
HCO3- dehydration at steady state, suggesting a rate-determining H+
transfer step in the catalytic mechanism. Correspondingly, we measured a
pH-independent solvent deuterium isotope effect on k(cat) of
approximately 2.0, and found that the rate of catalysis was
significantly decreased at external buffer concentrations below 5 mM.
Our results are consistent with a zinc-hydroxide mechanism of action
with for spinach CA, similar to that of animal carbonic anhydrases. We
have also collected X-ray absorption spectra of spinach CA. Analysis of
the extended fine structure (EXAFS) suggests that the coordination
sphere of Zn in spinach C!
A must have one or more sulfur ligands, in contrast to animal CAs which
have only nitrogen and oxygen ligands. The models which best fit the
data have average Zn-N(O) distances of 1.99-2.06 Angstrom, average Zn-S
distances of 2.31-2.32 Angstrom, and a total coordination number of 4-6.
We conclude that animal and spinach CAs are convergently evolved enzymes
which are structurally quite different, but functionally equivalent.

Record 21 of 23
Author(s): OHTAKI, H; INADA, Y; FUNAHASHI, S; TABATA, M; OZUTSUMI, K;
NAKAJIMA, K
Title: DIRECT STRUCTURAL DETERMINATION OF THE SHORT-LIVED INTERMEDIATE
FORMED IN THE DYNAMIC INCORPORATION OF A COPPER(II) ION INTO A
MERCURY(II) PORPHYRIN BY THE STOPPED-FLOW EXAFS METHOD
Source: JOURNAL OF THE CHEMICAL SOCIETY-CHEMICAL COMMUNICATIONS, (8):
1023-1025 APR 21 1994
Abstract: Structure parameters around the Cull ion in a reaction
intermediate formed in the course of Cu-II ion incorporation into an
Hg-II porphyrin were directly determined using a new stopped-flow EXAFS
apparatus, and elongation of the Cu-N bond in the unstable
heterodinuclear porphyrin intermediate was observed

Record 22 of 23
Author(s): OHTAKI, H
Title: A RAPID DIRECT ANALYSIS OF THE STRUCTURE OF REACTION
INTERMEDIATES BY THE EXAFS METHOD COMBINED WITH A STOPPED-FLOW TECHNIQUE
Source: PURE AND APPLIED CHEMISTRY, 65 (12): 2589-2592 DEC 1993
Abstract: A partial structure of the copper(II) ion of a reaction
intermediate at the formation of a copper(II) porphyrin complex in the
metal substitution reaction of the mercury(II) porphyrin complex with
the copper(II) ion in an aqueous acetate buffer solution has been
determined by using a newly developed rapid EXAFS apparatus, which is
constructed by combining a stopped-flow and a laboratory-scale EXAFS
equipments. The porphyrin used is
5,10,15,20-tetrakis(4-sulfonatophenyl)porphine. Two Cu-N bonds in the
reaction intermediate have been found to be 204 pm, which are longer
than the Cu-N bonds (200 pm) in the final product of the copper(II)
porphyrin complex, and it has been estimated that the copper(II) ion in
the intermediate is about 40 pm out from the center of the porphine
ring, and thus the mercury(II) and copper(II) ions are almost in contact
in the heterodinuclear complex. Since we did not clearly see the Hg...Cu
nonbonding interaction in the EXAFS spectrum, the !
position of the atoms may be significantly fluctuating due to the
repulsion between the atoms.

Record 23 of 23
Author(s): INADA, Y; FUNAHASHI, S
Title: IN-LABORATORY STOPPED-FLOW EXTENDED X-RAY-ABSORPTION
FINE-STRUCTURE APPARATUS IN THE DISPERSIVE MODE FOR DETERMINATION OF THE
STRUCTURE OF SHORT-LIVED INTERMEDIATES
Source: REVIEW OF SCIENTIFIC INSTRUMENTS, 65 (1): 18-24 JAN 1994
Abstract: We have constructed an in-laboratory stopped-flow extended
x-ray absorption fine structure (EXAFS) apparatus by combining
laboratory EXAFS equipment in the dispersive mode and a stopped-flow
unit with two 150-mum-thick boron nitride windows. The rotating anode
x-ray generator with a Mo target was used as an x-ray source. The
self-scanning photodiode array was adopted as a position
sensitive-linear x-ray detector. In order to obtain a suitable x-ray
flux intensity, the accumulation of weak intensities during a short gate
time was carried out by repeating the measurements. We have confirmed
the performance of our apparatus by repeatedly measuring a number of
static EXAFS spectra of 0.20 mol dm-3 aqueous solution of copper(II)
sulfate. By use of our newly developed apparatus, we have succeeded in
the direct determination of the structure of the reaction intermediate,
the heterodinuclear copper(II)/mercury(II) complex, formed in the
copper(II) ion incorporation into th!
e homodinuclear mercury(II) complex of
5,10,15,20-tetrakis(4-sulfonatophenyl)porphine.

------------------------------

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