AIP Con e ence P oceedings 963, 621 (2007); h ps://doi.o g/10.1063/1.2827049 963, 621
© 2007 Ame ican Ins i u e o Physics.
Coupling MD Simula ions and X- ay
Abso p ion Spec oscopy o S udy Ions in
Solu ion
Ci e as: AIP Con e ence P oceedings 963, 621 (2007); h ps://doi.o g/10.1063/1.2827049
Published Online: 03 Decembe 2007
E. Sánchez Ma cos, E. C. Be e , J. M. Ma ínez, R. R. Pappala do, R. Ayala, and A. Muñoz-Páez
Coupling MD Simula ions and X- ay Abso p ion
Spec oscopy o S udy Ions in Solu ion
E. Sanchez Ma cos*, E.G. Be e *, J.M. Ma inez *, R.R. Pappala do *, R. Ayala^ and
A. Munoz-Paez.'''
* Uni e si y
o Se ille. Dep . o Physical Chemis y.
"^ Uni e si y
o Se ille. CSIC-ICMSE. Dep . o Ino ganic Chemis y.
Abs ac . The s uc u e o ionic solu ions is a key-poin in unde s anding physicochemical p ope ies o elec oly e solu ions.
Among he educed numbe o expe imen al echniques which can supply di ec in o ma ion on he ion en i onmen , X-
ay Abso p ion echniques (XAS) ha e gained impo ance du ing he las decades al hough hey a e no ee o di icul ies
associa ed o he da a analysis leading o p o ide eliable s uc u es. Compu e simula ions o ions in solu ion is a heo e ical
al e na i e o p o ide in o ma ion on he sol a ion s uc u e. Thus, he use o compu a ional chemis y can inc ease he
imde s anding o hese sys ems al hough an accu a e desc ip ion o ionic sol a ion phenomena ep esen s nowadays a
signi ican challenge o heo e ical chemis y. We p esen : (a) he assignmen o ea u es in he XANES spec um o well
de ined s uc u al mo i in he ion en i onmen , (b) MD-based e alua ion o EXAFS pa ame e s used in he i ing p ocedu e
o make easie he s uc u al esolu ion, and (c) he use o he ag eemen be ween expe imen al and simula ed XANES spec a
o help in he choice o a gi en in e molecula po en ial o Compu e Simula ions. Chemical p oblems examined a e: (a)
he iden i ica ion o he second hyd a ion shell in dilu e aqueous solu ions o highly-cha ged ca ions, such as C +, Rli +,
I ^+,
(b) he in isibili y by XAS o ce ain s uc u es cha ac e ized by Compu e Simula ions bu exhibi ing high dynamical
beha io and (c) he sol a ion o B ^ in ace oni ile.
Keywo ds: Aqueous solu ion; Ionic hyd a ion; Molecula
Dynamics,
EXAFS, XANES, spec a simula ion.
PACS:
61.20.Gy, 61.20.Qg, 61.20.Ja, 78.70Dm
INTRODUCTION.
The main expe imen al echniques o s uc u al s udies o ionic solu ions a e X- ay di ac ion (XRD), neu on
di ac ion (ND) and X- ay abso p ion spec oscopy (XAS). Al hough XRD and ND can yield s uc u al in o ma ion
abou diso de ed sys ems like mos liquids, hei accu acy dec eases s ongly in he case o muhicomponen sys ems
(XRD) o equi es conside able syn he ic e o s o pe o m he iso opic subs i u ions (ND). These ac s along wi h
he need o ela i ely high concen a ions p eclude o ce ain ex en hei use. Because XAS is elemen -speci ic, he
local s uc u e a ound one ype o a om can be sol ed, addi ionally, i can be applied o a wide ange o concen a ions,
anging ypically om a ew millimola o se e al mola . Then, XAS ep esen s he mos sui able echnique o supply
di ec s uc u al in o ma ion on highly dilu e elec oly e solu ions.
The X- ay Abso p ion spec um has been adi ionally di ided in o wo ene gy egions. The low ene gy pa o he
spec um, ex ending up o '-^ 50 - 100 eV abo e he abso bing edge, called X- ay Abso p ion Nea Edge S uc u e
(XANES) egion and he high ene gy pa o he spec um (o e 100 eV abo e he h eshold up o app oxima ely 1000
eV) called Ex ended X- ay Abso p ion Fine S uc u e (EXAFS). Since he 1980s, one o he XAS echniques, ex ended
X- ay abso p ion ine s uc u e (EXAFS), has been applied o de e mine he pseudo pa ial pai co ela ion unc ions
o a oms in bo h c ys alline and amo phous sys ems. The main limi a ion o he echnique is he high co ela ion
among ac o s a ec ing he ampli ude and he la ge numbe o mul iple sca e ing pa hs which may con ibu e o he
ampli ude. The XANES egion has been shown o be dependen on many pa ame e s o he sys em unde s udy: he
oxida ion s a e o
he
abso be a om, bond angles, coo dina ion geome y, dis ances o he abso bing a om o he i s ,
and highe coo dina ion shells, e c. Con e sely o he EXAFS egion, he e is no simple o mula ion ha encompasses
all hese pa ame e s. This ac has usually led o he use o XANES in o ma ion on a mo e quali a i e le el ha
en isages he spec um as a " inge p in " o he sys em unde s udy. In he las yea s, implemen a ion o models o
he abso p ion phenomena ha e allowed he de elopmen o codes which accu a ely simula e he XANES egion hus
app oaching he si ua ion o he EXAFS egion. This way he heo e ical simula ion o XANES o ionic solu ions is
an eme ging b anch.
CP963,
Vol. 1, Compu a ional Me hods in
Science
and Enginee ing,
Theo y
and
Compu a ion:
Old P oblems andNew
Challenges,
edi ed by G. Ma oulis and T. Simos
© 2007 Ame ican Ins i u e o Physics 978-0-7354-0477-9/07/$23.00
621
A s a egy o educe he deg ee o unce ain y in he analysis o he XAS spec a has been he inclusion o
independen in o ma ion de i ed om compu e simula ions o bo h EXAFS and XANES spec a[l, 2, 3, 4]. Once
eliable s uc u al and dynamic in o ma ion is ob ained om compu e simula ions, he mic oscopic desc ip ion o
he close en i onmen o he abso be a om allows he independen compu a ion o some o he pa ame e s in ol ed
in he spec oscopic da a analysis and he assignmen o ce ain ea u es o a gi en spec um o pa icula s uc u al
a angemen s a ound i .
The aim o his wo k is o p esen a se ies o s uc u al esul s de i ed om expe imen al and heo e ical me hods o
a se ies o single ions. Pa icula a en ion is de o ed o he expe imen al de e mina ion o he second hyd a ion shell o
C (III),
Rh(III), I (III) and Pd(II) aquaions. The case o
he
squa e-plana Pd(II) aquaion in oduces he peculia i y o
he possible de e mina ion o wa e molecules in he axial egion, called meso-sheU[5,6]. Finally, he syne gy achie ed
by combining bo h spec oscopic and heo e ical esul s imp o es he analysis p ocess in wo ways: (i) by e ining he
XAS da a analysis and (ii) by suppo ing he in e molecula po en ial de eloped as well as he mic oscopic ision o
he hyd a ion de i ed om compu e simula ions. These wo poin s will be illus a ed by he s udy o he sol a ion
s uc u e o B ^ in ace oni ile, aking he ep oduc ion o he expe imen al B K-edge XANES o his sys em[7] as
he e e ence o elucida e he mos app op ia e b omide-ace oni ile in e molecula po en ial.
METHODOLOGY
Classical Molecula Dynamics (MD) simula ions co esponding o ansi ion me al ions p esen ed in his wo k a e
based on he use o he Hyd a ed Ion (HI) concep o model he ca ion-wa e in e ac ions
[8].
The high pe u ba ion
exe ed by he me al ion on he wa e molecules di ec ly in e ac ing wi h i , allows he conside a ion o hem om
he es o he sol en . Then, he aquaion [M(H20)„]'"+ is adop ed as he ep esen a i e en i y in solu ion and he
desc ip ion o he in e ac ions in ol ing he ca ion is pe o med h ough he de ini ion o wo in e ac ion po en ials:
one o he hyd a ed ion-wa e (HIW) o ces and one o he in e nal dynamics o he aquaion, i.e. ion- i s shell
wa e (IWl) o ces[9]. De ails o he de elopmen o in e molecula po en ials o he di e en ca ions employed in
his wo k can be ound elsewhe e (C (III),[10, 9] Rh(III),[ll] I (III)[4] and Pd(II)[5]). In he case o Pd(II) in wa e ,
Ca -Pa inello ab ini io MD simula ions we e also ca ied ou o a sys em o med by one Pd(II) ca ion and 70 wa e
molecules[12].
The B -ace oni ile (ACN) in e ac ion po en ials es ed o desc ibe he sol a ion o b omide in ace oni ile a e buil
on he basis o he ace oni ile model p oposed by G abuleda e al.[13] combined wi h he b omide pa ame iza ion
pe o med by McCammon e al.[14] (he ea e caUed Po . A). A second se o po en ials is a modi ica ion o he
p e ious one, based on he hyd a ed ion concep . The quan um-mechanical op imized s uc u e o he [B (ACN)9]^
clus e was used as a e e ence o modi y he an de Waals pa ame e c gj-H ^^ ^^^^ ^ ^^y
^^'^^
^^^ po en ials leads
o a simila op imized s uc u e han he quan um-mechanical, (Po . B). The hi d se o po en ials consis in he
modi ica ion o he CB -H pa ame e which was educed om 3.6 A o Po . A, o 3.2 A o Po . B and o a alue o
2.9 A (Po . C). This ange allows an insigh in o he ela ionships be ween XANES spec um and s uc u e. De ails o
hese in e molecula po en ials and simula ion condi ions can be ound elsewhe e[15].
MD simula ions p o ided snapshos s e enly spaced in ime o he analysis o he EXAFS and XANES pa . The
FEFF8.10 code de eloped by Reh and
col.
[16]
was used o calcula e he co esponding indi idual spec um gene a ed
o each snapsho . The simula ed spec um is ob ained by a e aging o e 1000 indi idual EXAFS spec um, whe eas
o XANES 100 indi idual spec a a e enough.
RESULTS AND DISCUSSION.
Second hyd a ion shell de e mina ion
The high cha ge o i alen ansi ion me al ca ions, such as C (III), Rh(III) o I (III) in aqueous solu ions joined
wi h he high kine ic s abili y o hei co esponding aquaions lead o expec a s uc u al o de beyond he i s
hyd a ion shell o hese ca ions. Second hyd a ion shell has been de e mined o se e al i alen and di alen me al
ca ions om X- ay and neu on di ac ion echniques o highly concen a ed aqueous solu ions. Mo e ecen ly, we
ha e p oposed ha e ined analysis o
EXAFS
da a may also gi e in o ma ion on he second hyd a ion shell o highly
dilu ed aqueous solu ions o i alen me al ca ion such as C (III) o Rh(III)[17, 18, 2]. A pa adigm o ine aquaion
622
k(A"')
FIGURE 1. Con ibu ion o he c-space EXAFS
spec um o he Single Sca e ing due o he second
shell (solid line) and he mul iple sca e ing (dashed
line) o he i s shell o C (III), Rh(III) and I (III)
in aqueous solu ion.
E(eV)
FIGURE 2. I Lm-edge XANES expe imen-
al and simula ed spec a. The simula ed ones
use a se o snapsho s including only he 1s .
shell (^cu o ^^-1 ^) '^^ ^^° hyd a ion shells
(^cu o 6-0A).
is he hexahyd a e o I (III) ha exhibi s he longes mean li e ime o he i s -shell wa e molecules a 298K, ^ 300
yea s.
Con a y o wha is expec ed, he second hyd a ion shell can no be de e mined om I Lm EXAFS spec a. Da a
analysis o
EXAFS
unc ion show ha he ampli ude o he second shell (SS) con ibu ion is oo small compa ed o he
i s -shell muhiple sca e ing (MS) con ibu ion which appea s a simila dis ances. Figu e
1
shows he compa ison o
hese wo con ibu ions o he cases o
C (III),
Rh(III) and
I (III).
In he wo i s cases he SS:MS con ibu ion a io is
oughly 1:2 whe eas o he I (III) his a io dec eases o 1:4, hus a oiding he s uc u al de e mina ion o
he
second
shell
[4].
This di e en ial beha io is due o he hea ie na u e o
he
i idium a om compa ed o hodium o ch omium
which esuhs in he backsca e ing ampli ude o
he
pa hs including I as an in e media e s ep (i.e. jus he MS pa hs)
o become highe han he ones no including i .
Figu e 2 shows he expe imen al I Lm XANES spec um co esponding o he same dilu e I (III) aqueous solu ions
oge he wi h he simula ed spec a based on a MD simula ion o
I (III),
wo di e en cu o
adii,
3.1 A and 6.0 A o
he s uc u e conside ed o each snapsho , we e employed. In he i s case, he simula ed XANES spec um is only
due o con ibu ions om he i s shell, whe eas in he second spec um he second shell con ibu ion is aken in o
accoun . Con a y o he EXAFS analysis, he expe imen al hump appea ing 16 eV abo e he main esonance is well
ep oduced when he second hyd a ion shell is included in he s uc u es employed o simula e he XANES spec um
om he s a is ical ajec o ies. Simila beha io is obse ed when he XANES spec a o C (III) o Rh(III) aqueous
solu ions a e examined[2]. The spec oscopical eason which hampe ed he de e mina ion o he second hyd a ion in
EXAFS o he i idium case is s ongly educed in he case o XANES due o he ac he dependence o he Debye-
Walle ac o wi h he ec o k has exponen ial cha ac e . Thus, since XANES in ol es low k
alues,
he sensi i i y o
his pa o
he
XAS spec um is much smalle , and ea u es o
he
second hyd a ion shell become ele an .
623
The In isibili y o some hyd a ion egions o XAS
Pd(II) ca ion o ms a squa e-plana e ahyd a e in wa e solu ion. Due o his ac he second hyd a ion shell
adop s a c own-like shape enclosing he aquaion and lea ing he axial egion (abo e and below he molecula plane)
spa sely popula ed. Ne e heless, esul s om Classical MD[5], QM/MM MD[6] and CPMD[12] simula ions show he
exis ence o a ce ain hyd a ion s uc u e in his axial egion {meso-shell), i s beha iou being a mo e dynamic han
o he second sol a ion shell. Could such a meso-shell s uc u e be de e mined by means o
XAS
echniques? Based
on ou p e ious knowledge employing EXAFS and XANES o simila aims, ce ainly i would be di icul , when no
impossible, o obse e he meso-shell using EXAFS spec a analysis, since he meso-shell is a less s uc u ed egion
han he second shell. Bu s ill he e exis s he possibili y o s udy i h ough XANES analysis.
Figu e 3 plo s he K-edge XANES expe imen al spec um o Pd(II) in aqueous solu ion, oge he wi h simula ed
spec a om he ajec o ies o Classical and Ca -Pa inello MD simula ions. Al hough bo h simula ed spec a i he
expe imen al one qui e well, he CPMD esul ep oduces be e he slope o he second esonance owing o he ac
ha CPMD wa e molecules a e lexible and pola izable, and hus cons i u e a be e app oxima ion o he beha iou o
eal wa e molecules. Gi en ha he meso-shell is be e s uc u ed in he Classical MD simula ion, we can decompose
he co esponding spec um in o he con ibu ions s emming om he i s hyd a ion shell, and om he i s shell plus
he meso-shell a oms. Inclusion o
he
second sol a ion shell al eady yields he comple e spec um, so i is no plo ed
in he igu e. The e is no ea u e in he spec a ha can be assigned o he meso-shell. Howe e , ea u es due o he
second sol a ion shell can be iden i ied. The e o e, in spi e o he p esence o basic s uc u al di e ences be ween
he hyd a ion pa e ns o hexahyd a es (sphe ical symme y, de ailed abo e) and Pd(II) e ahyd a e (c own-like plus
meso-shell) hei second hyd a ion shells seem o be equi alen when app oaching hei s udy h ough analysis o hei
XANES spec a, and delica e ea u es such as he meso-shell emain in isible o XANES sc u iny.
Selec ing an In e molecula Po en ial on he Basis o XANES Spec a
The s uc u al in o ma ion on anion sol a ion in ap o ic sol en s is sca ce and usually he quan i a i e alues ound
in he li e a u e co e a wide ange. The sol a ion numbe s o b omide and iodide anions in ap o ic and no e y pola
sol en s a e es ima ed in he ange 1-9. I is hen clea ha he de elopmen o speci ic in e molecula po en ials o
be used in Compu e Simula ions appea s as an impo an ool o help in s uc u al cha ac e iza ion o hese sys ems.
Howe e , due o he sca ce expe imen al in o ma ion, he alida ion o he de eloped po en ials is no as easy as in
he case o aqueous solu ions. Figu e 4 shows he expe imen al B K-edge XANES spec um o a dilu e ace oni ile
solu ion o a b omide sal eco ded by Wa anabe e al.[19] On he same igu e he co esponding simula ed XANES
spec a de i ed om h ee MD simula ions which employed he h ee B -ACN po en ials men ioned in he Me hods
Sec ion ha e been plo ed. The compa ison be ween simula ed and expe imen al XANES spec a indica es ha Po . C
is he mos app op ia e in e molecula po en ial. As a as he XANES ag eemen implici ly deno es simila s uc u es,
he analysis o he MD esul s gi e us a quan i a i e desc ip ion o he sol a ion o B ^ anion in ace oni ile. This
halide in ace oni ile o ms a a he elaxed i s sol a ion shell o med by '^10 ACN molecules whe e one o he
hyd ogen a oms o he me hyl g oup is placed close o he anion, 2.7-2.9 A, han he o he wo hyd ogen a oms o he
me hyl g oup(ca.
A.2-A..
A) due o he ben o ien a ion o
he
ACN molecules ('~ 130°) wi h espec o he B ^ anion.
CONCLUDING REMARKS.
The in e play be ween compu e simula ions and XAS p o ides a powe ul ool o s udy ions in solu ion. In his pape
we ha e shown how he compa a i e analysis o expe imen al and simula ed spec a allows, o highly cha ged ca ions
in solu ion, he de e mina ion o s uc u al pa ame e s o he second hyd a ion shell accu a ely enough. Howe e ,
ea u es due o poo s uc u ed egions wi h a high dynamical componen can no be iden i ied om ei he expe imen al
o simula ed spec a al hough hey appea well-de ined in he Compu e simula ion esul s. Mo eo e , he combined
use o expe imen al and simula ed spec a can help us in he de elopmen o eliable ion-sol en in e ac ing po en ials
o be used in MD simula ions o ions in solu ion.
624

ID
• 9
"3
13550
E(eV)
E (keV)
FIGURE 3. Compa ison o he Pd K-edge
XANES expe imen al and simula ed spec a. The
simula ed ones use snapsho s om a CPMD o a
classical MD simula ion. Changes in he ea u es o
he spec um wi h he hyd a ion shells conside ed in
he snapsho s a e p esen ed o he case o classical
MD simula ion.
FIGURE 4. Compa ison o he B K-edge
XANES expe imen al spec um o b omide in ace-
oni ile and h ee simula ed spec a using h ee
di -
e en in e molecula po en ials in he MD simula-
ion.
ACKNOWLEDGMENTS
Spanish Go e nmen (CTQ2005-03657) and Jun a de Andalucia (g oup FQM282) a e acknowledged o inancial
suppo . RAE hanks CSIC o a pos doc o al I3P ellowship.
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