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Interplay of computer simulations and x-ray absorption spectra in the study of the bromide hydration structure

Merkling, Patrick J.; Ayala Espinar, Regla; Martínez Fernández, José Manuel; Rodríguez Pappalardo, Rafael; Sánchez Marcos, Enrique

Abstract

X-ray absorption spectra (EXAFS and XANES) were generated from snapshots of a Monte Carlo (MC) simulation of a bromide ion aqueous solution and from model structures. The MC simulation relies on a recently developed and tested polarizable potential based on ab initio potential energy surfaces. A comparison with the experimental K-edge Br spectrum of a 0.3 M YBr3 aqueous solution was performed. XANES spectra are reproduced acceptably only if statistical fluctuations are included, which is performed in this work by using snapshots from computer simulation. As expected, single scattering BrO contributions are dominant in the case of the EXAFS region. Due to this fact, Br- in water is a good model system for studying the influence of the distribution of distances on the determination of structural parameters. Then, a parallel study of the data analysis procedure of the experimental EXAFS spectrum and those theoretically computed from the structures supplied by the MC simulation, was carried out. The shape of the distribution function and its asymmetry must be taken into account in a practical way to obtain a more accurate determination of the BrO first-shell distance. A further refinement consists in using the computer simulation to extrapolate the BrO distance from the experimental EXAFS spectrum. In this way, a BrO distance of 3.44±0.07 Å and a coordination number of 6±0.5 were determined

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I n e p lay o c o m pu e si m u la i on s a nd x - ay a b s o p i on s p ec a i n h e s ud y o h e b o m i d e h y d a i on s u c u e P a ick J . M e kli ng, R eg l a A y a l a, J o s e ´M . M a ı ´ ne z , R a ae l R . P appa l a do, and E n i que S a ´ n c he z M a c o s a ) Depa amen o de Qu ı ´m i ca F ı ´ s i ca, Un i e s i dad de Se ill a, 41012-Se ill a, Spa i n R ece i ed 4 Ap il 2003 ; accep ed 1 J u l y 2003 X- ay ab s o p i on s pec a EXA FS and XANE S we e gene a ed o m s nap s ho s o a M on e C a l o M C s i m u l a i on o a b o m i de i on aqueou s s o l u i on and o m m ode l s uc u e s . The M C s i m u l a i on e li e s on a ecen l y de e l oped and e s ed po l a i zab l e po en i a l ba s ed on ab i n i i opo en i a l ene gy s u ace s . A co m pa i s on w i h he expe i m en a l K -edge B s pec u m o a 0.3 M Y B 3aqueou s s o l u i on wa s pe o m ed. XANE S s pec a a e ep oduced accep ab l y on l y i s a i s i ca l fl uc ua i on s a e i nc l uded, wh i ch i s pe o m ed i n h i s wo k by u s i ng s nap s ho s o m co m pu e s i m u l a i on. A s expec ed, s i ng l e s ca e i ng B O con i bu i on s a e do m i nan i n he ca s e o he EXA FS eg i on. Due o h i s ac , B i n wa e i s a good m ode l s y s e m o s udy i ng he i n fl uence o he d i s i bu i on o d i s ance s on he de e m i na i on o s uc u a l pa a m e e s . Then, a pa a ll e l s udy o he da a ana l y s i s p ocedu e o he expe i m en a l EXA FS s pec u m and ho s e heo e i ca ll y co m pu ed o m he s uc u e s s upp li ed by he M C s i m u l a i on, wa s ca i ed ou . The s hape o he d i s i bu i on unc i on and i s a s y mm e y m u s be aken i n o accoun i n a p ac i ca l way o ob a i n a m o e accu a e de e m i na i on o he B O fi s - s he ll d i s ance. A u he e fi ne m en con s i s s i n u s i ng he co m pu e s i m u l a i on o ex apo l a e he B O d i s ance o m he expe i m en a l EXA FS s pec u m . In h i s way, a B O d i s ance o 3.44 0.07 Å and a coo d i na i on nu m be o 6 0.5 we e de e m i ned. © 2003 Ame i can In s i u e o Phy s i c s .DOI : 10.1063 / 1.1603719 I. I NTR O DUCT I O N The s uc u e o i on i c s o l u i on s ha s been a m a e o i nc ea s i ng i n e e s o m expe i m en a l and heo e i ca l po i n s o i ew.1–3 The m a i n expe i m en a l echn i que s o s uc u a l s ud i e s o s uch s y s e ms a e x- ay d i ac i on X R D , neu on d i ac i on ND , and x- ay ab s o p i on s pec o s copy XA S . A l hough X R D and ND can y i e l d s uc u a l i n o m a i on abou d i s o de ed s y s e ms li ke m o s li qu i d s , he i accu acy dec ea s e s s ong l y i n he ca s e o m u l i co m ponen s y s e ms X R D o equ i e s con s i de ab l e s yn he i c e o s o pe o m he i s o op i c s ub s i u i on s ND .4,5 Th i s ac e s i c s he i u s e, a s doe s he need o e l a i e l y h i gh concen a i on s . Si nce he 1980 s , one o he XA S echn i que s , ex ended x- ay ab s o p- i on fi ne s uc u e EXA FS , ha s been app li ed o de e m i ne he p s eudopa i a l pa i co e l a i on unc i on s o a o ms i n bo h c y s a lli ne and a m o phou s s y s e ms .6 B ecau s e XA S i s e l e m en - s pec ifi c, he l oca l s uc u e a ound one ype o a o m can be ob a i ned by EXA FS . Add i i ona ll y, i can be app li ed o a l a ge ange o concen a i on s , ang i ng yp i ca ll y o m a ew m illi m o l a o s e e a l m o l a . X- ay ab s o p i on s pec o s copy ha s ad i i ona ll y been s ubd i i ded, acco d i ng o wo ene gy eg i on s o a s pec u m : x- ay ab s o p i on nea -edge s uc u e XANE S , wh i ch co e- s pond s o he nea -edge eg i on ha ex end s o m he h e s h- o l d o abou 50 eV abo e he edge, and EXA FS , wh i ch ex- end s o m ene g i e s o abou 50 o m o e han 1000 eV abo e he edge. Si nce he k i ne i c ene gy o he pho oe l ec on i s l ow i n he XANE S eg i on, m u l i p l e s ca e i ng M S e ec s a e do m i nan , ha i n he pa i cu l a ca s e o i on i c s o l u i on s a e m o s l y due o s ca e i ng pa hway s be ween a o ms o he fi s and s econd s o l a i on s he ll s a ound he ab s o be a o m . In he XANE S eg i on, bo h geo m e i ca l and e l ec on i c de a il s a - ec he s hape o a s pec u m , and he e o e he e i s no gen- e a l , d i ec , e l a i on s h i p be ween s pec u m and geo m e y a s i n he ca s e o EXA FS .7Th i s i s why he echn i que i s o en u s ed a s a fi nge p i n o cha ac e i z i ng he ne i ghbo hood o he ab s o be a o m .8 In he EXA FS eg i on, he s ca e ed pho oe l ec on ha s a h i gh k i ne i c ene gy, s o ha s i ng l e back s ca e i ng p oce ss e s a e do m i nan . Howe e , m u l i p l e s ca e i ng pheno m ena m ay con i bu e no i ceab l y o he s pec u m , m ak i ng i s i n e p e a- i on m o e d i fi cu l . In o de o ex ac i n o m a i on con a i ned i n an EXA FS s pec u m , a nu m be o s i m p li y i ng a ss u m p- i on s ha e o be m ade. B ea i ng i n m i nd ha he nu m be and co e l a i on o a i ab l e s needed i n he EXA FS ana l y s i s i s o en s upe i o o he i n o m a i on con a i ned i n he EXA FS s pec u m ,7,9–11 he u s e o i n o m a i on de i ed o m o he s ou ce s , li ke co m pu a i ona l m e hod s , i s o s pec i a l i n e e s . Th i s p ocedu e ha s p o en o be s ucce ss u l i n m any s ud i e s o s uc u a l e l uc i da i on o s o li d and li qu i d s y s e ms .12–17 The a i m o h i s wo k i s o ob a i n he b o m i de hyd a i on s uc u e by m ean s o he co m b i na i on o expe i m en a l i n o - m a i on de i ed o m XA S echn i que s and heo e i ca l da a o m co m pu e s i m u l a i on s . When dea li ng w i h he s uc u a l de s c i p i on o i on i c s o l u i on s , he pa e n s o he ca i on and an i on hyd a i on a e a o m s i m il a , m o s l y due o wo ea- s on s . Fi s o a ll , an i on en i on m en i s m a i n l y de e m i ned by he e s u l an o ce o he co m pe i i on be ween i on–d i po l e i n- aE l ec on i c m a il: s anchez@ s i m u l ux.u s .e s J OU R NAL O F C HE M I C AL P HY S I C S VOLU M E 119, NU M B E R 13 1 O C TO B E R 2003 66470021 - 9606/2003/119 ( 13 ) /6647/8/$20.00 © 2003 A m e ic an In s i u e o P h ysics R eu s e o A I P P ub lis h i ng c on en is s ub j e c o he e ms : h p s ://pub lis h i ng.a i p.o g/au ho s / i gh s- and - pe missi on s . D o w n l oaded o I P : 150.214.182.116 O n: W ed, 19 O c 2016 14:53:39 e ac i on s , wh i ch end o a o s y mm e i c hyd ogen a o ms a ange m en s a ound he an i on-oxygen ax i s , and hyd ogen bond i ng o he an i on, wh i ch a o s an a s y mm e i c a ange- m en o i s s u ound i ng wa e m o l ecu l e s o m ax i m i ze he hyd ogen bond i n e ac i on. The s econd ea s on i s ha he e l ec on den s i y d i s i bu i on i s m o e expanded a ound he nuc l eu s i n he an i on ca s e wha e s u l s i n m o e i m po an fi s - and s econd-o de pe u ba i on s w i h e s pec o he l oca l e l ec i c fi e l d s . The s e wo ea s on s an i c i pa e no i ceab l e d i e - ence s i n he s o l en o gan i za i on a ound ca i on s and an i on s , i n pa i cu l a o m onoa o m i c o s i m p l e i on s . In add i i on, he weak b o m i de–wa e i n e ac i on s i m p l y ex e m e l y a s s o l en -exchange a e s o he fi s s o l a i on s he ll . A ll he s e ea s on s m ake he XA S s udy o he b o m i de hyd a i on qu i e d i e en o m he s udy o h i gh l y cha ged ca i on s p e i ou s l y ca i ed ou by ou g oup.18–25 Ob i ou s l y, he s en s i i i y o he EXA FS echn i que o he d i s o de m ake s he s uc u a l ana l y s i s o h i s s y s e m m o e d i fi cu l . Thu s , he u s e o heo- e i ca l i n o m a i on i s expec ed o s hed li gh on i . S e e a l au ho s ha e p e i ou s l y exa m i ned he b o m i de hyd a i on w i h he he l p o heo e i ca l oo l s . Wa ll en e a l .26 u s ed m o l ecu l a dyna m i c s s i m u l a i on s o gene a e heo e i ca l EXA FS s pec a w i h he p og a m F E FF and he e o l u i on a s a unc i on o p e ss u e and e m pe a u e o EXA FS and XANE S s pec a wa s ana l yzed. D’Ange l oe a l .27 s ud i ed a l s o EXA FS s pec a w i h he p og a m GNXA S , and co m b i ned M D s i m u l a- i on e s u l s w i h a s ho ange m ode l d i s i bu i on ba s ed on Ga mm a unc i on s o fi he EXA FS s pec u m . Howe e , none o he m ca l cu l a ed he b o m i de XANE S s pec u m . One o he m o s co mm on a ss u m p i on s m ade o ca l cu l a e XA S s pec a i s o educe he s y s e m o a s i ng l e s uc u e. Ne e he l e ss , he con i bu i on o m m o l ecu l e s and a ange- m en s i n s an aneou s l y d i s o ed ha s an i m po an e ec on he a e age s pec u m ,22,25 e s pec i a ll y i n l ab il e s uc u e s li ke he b o m i de i on hyd a i on. In h i s s en s e, he po ss i b ili y o con s i de i ng s a i s i ca l i n o m a i on m ake s he ana l y s i s p oce- du e ea s i e . A ecen l y de e l oped b o m i de–wa e i n e ac i on po en i a l , wh i ch i nc l uded he po l a i zab ili y o pa i c l e s ba s ed on ab i n i i oda a and who s e good beha i o ha s ecen l y been checked by co m pu e s i m u l a i on s ,28 w ill be e m p l oyed i n h i s co m b i ned expe i m en a l – heo e i ca l s udy. I i s wo h po i n - i ng ou ha he heo e i ca l s pec a a e co m pu ed o m fi s p i nc i p l e s , s i nce no e m p i i ca l pa a m e e s we e i n oduced ne i he i n he i n e m o l ecu l a po en i a l s , no i n he co m pu a- i on o he XA S s pec a. The XANE S s pec u m w ill be co m - pu ed o m a ep e s en a i e s e o geo m e i e s ex ac ed o m he s a i s i ca l a j ec o y. W i h e s pec o he EXA FS ana l y s i s , on one s i de he M D po en i a l s ha ll be p obed, on he o he s i de, de a il s o he s uc u a l de e m i na i on w ill be i n e s i - ga ed. II. M E TH O D O L OG Y Theo e i ca l XANE S and EXA FS s pec a o he B K -edge 13 474 eV a e ca l cu l a ed by a co m b i na i on o s a- i s i ca l and quan u m - m echan i ca l ca l cu l a i on s . The s udy o he b o m i de hyd a i on wa s pe o m ed u s i ng h ee ap- p oache s : i co m pu a i on o XANE S s uc u e s o m quan u m - m echan i ca ll y m i n i m i zed c l u s e s w i hnwa e m o l - ecu l e s (4 n7) ; ii co m pu a i on o XANE S s pec a ak- i ng i n o accoun he s a i s i c s h ough M on e C a l o s i m u l a- i on s nap s ho s ; iii ana l y s i s o EXA FS s pec a i n wo way s : on he one hand, he expe i m en a l s pec u m wa s co m pa ed o a heo e i ca ll y co m pu ed one o m M on e C a l o s i m u l a i on s nap s ho s ; on he o he hand, he fi i ng p ocedu e o he EXA FS s pec u m wa s ca i ed ou on bo h s pec a, he ex- pe i m en a l one and he one co m pu ed o m M on e C a l o s i m u l a i on s . The co m pa i s on o he fi s wa s ca i ed ou w i h he a i m o e s i ng he a li d i y o he m ode l s uc u e s u s ed o de s c i be he b o m i de hyd a i on. The expe i m en a l B K -edge XA S s pec a u s ed i n h i s wo k o 0.3 M aqueou s s o l u i on s o Y B 3we e m ea s u ed a bea m li ne B L12 C o he P ho on F ac o y i n T s ukuba, J apan. The i ng cu en wa s 300 m A, and he i ng ene gy 2.5 GeV. A h i gh e s o l u i on Si 311 channe l -cu m onoch o m a o wa s u s ed. C a li b a i on wa s ca i ed ou w i h he L 2-edge o a Au o il 13734 eV . Da a we e co ll ec ed i n an sm i ss i on m ode u s i ng i on i za i on cha m be s a s de ec o s . The quan u m - m echan i ca ll y op i m i zed s uc u e s u s ed o ob a i n i ng XANE S s pec a we e aken o m a p e i ou s s udy on he m i c o s o l a i on o he b o m i de i on i n wa e , m e hano l , and ace on i il e.29 In h i s s udy, B (H2O)nc l u s e s (1 n8) we e op i m i zed a he B 3LY P l e e l w i h doub l e- ba s i s s e s aug m en ed w i h po l a i za i on and d i u s e unc i on s . S a i s i ca l i n o m a i on wa s ob a i ned o m M on e C a l o M C s i m u l a i on s u s i ng fi s -p i nc i p l e s b o m i de–wa e i n e - ac i on po en i a l s ecen l y de e l oped by ou g oup.28 F o h i s po en i a l , he M ob il e C ha ge Den s i y i n Ha m on i c O s c ill a- o s M ode l wa s e m p l oyed o de s c i be b o m i de an i on and wa e s pec i e s , bo h o he m be i ng po l a i zab l e, and he wa e fl ex i b l e. The wa e –wa e i n e ac i on s we e de s c i bed by a M C DHO po en i a l p e i ou s l y de s c i bed by he C ue na aca g oup, M ex i co.30 The e li ab ili y o he e s u l s de i ed o m nu m e i ca l s i m u l a i on s depend s c i i ca ll y on he po en i a l m ode l de s c i b i ng he i n e ac i on s a m ong he s i e s de fi n i ng he s y s e m . The i n e ac i on po en i a l u s ed ha s a l eady been e s ed i n p e i ou s s ud i e s ,28 whe e he s i m u l a ed s y s e ms s how a good ag ee m en w i h expe i m en a l e s i m a i on s . The M C s i m u l a i on s we e ca i ed ou w i h he M C HANG p og a m de e l oped by he g oup o C ue na aca.31 The s y s e m s i m u- l a ed con s i s s o 1 B 211 wa e m o l ecu l e s i n he NVT en s e m b l e a 300 K u s i ng he P OT–2 i n e ac i on po en i a l o m R e . 28. P e i od i c bounda y cond i i on s we e app li ed, and l ong- ange i n e ac i on s we e co m pu ed by he Ewa l d s u m m e hod, i nc l ud i ng a e m o accoun o he ne cha ge o he s y s e m .32,33 F u he de a il s abou he M C s i m u l a i on s a e g i en i n R e . 28. K -Edge XANE S s pec a o B i n wa e we e ca l cu l a ed o m 40 s nap s ho s aken e e y 120 K (K 103) con fi gu a- i on s o a M C s i m u l a i on. The s i m u l a ed XANE S s pec u m i s an a e age o e he s pec a o he s nap s ho s . XA S s pec a ha e been co m pu ed w i h he F E FF 8.10 p og a m code34 de e l - oped by R eh ’ s g oup. The po en i a l ca l cu l a i on s u s e he Hed i n–Lundq i s s e l -ene gy app ox i m a i on.35 A s e l - con s i s en fi e l d p ocedu e S C F wa s e m p l oyed. A 6.0 Å cu - o ad i u s wa s cho s en o he S C F ea m en and o he u ll - m u l i p l e s ca e i ng pa h s , en s u i ng he i nc l u s i on o he s econd s o l a i on s he ll i n he co m pu a i on o he s pec a. A m u fi n- i n po en i a l wa s app li ed w i h o e l ap c i e i a o 1.0 6648 J . C he m . P h ys ., V o l . 119, N o. 13, 1 O c obe 2003 M e kli ng e a l . R eu s e o A I P P ub lis h i ng c on en is s ub j e c o he e ms : h p s ://pub lis h i ng.a i p.o g/au ho s / i gh s- and - pe missi on s . D o w n l oaded o I P : 150.214.182.116 O n: W ed, 19 O c 2016 14:53:39 ouch i ng s phe e s , 1.15 and 1.15 o B , O, and H a o ms , e s pec i e l y. The s e c i e i a we e de e m i ned ad hoc bu cou l d be j u s ifi ed w i h he i on i c na u e o he ab s o b i ng a o m . I wa s ound ha he S C F ad i u s cou l d be l owe ed o 5.0 Å w i hou a ec i ng he e s u l s . A XANE S s pec u m ca l cu l a ed o m 200 s nap s ho s aken e e y 250 K con fi gu a i on s and S C F cu o o 5.0 Å y i e l d s e y s i m il a e s u l s . In p e i ou s s ud i e s on ca i on hyd a i on s uc u e,12,22,24,25 he i nc l u s i on o hyd ogen a o ms p o ed nece ss a y o ob a i n i ng a ea li s i c back s ca e i ng po en i a l bu l ed o a s en s i b l e deg ada i on o he s pec u m when hey we e i nc l uded a s back s ca e e s . D i fi cu l i e s a e m a i n l y a ss o- c i a ed w i h an o e e s i m a i on o he back s ca e i ng con i bu- i on, bu h i s doe s no a ec he i o l e i n he s e l -con s i s en fi e l d ca l cu l a i on o he po en i a l .16 In he ca s e o b o m i de hyd a i on s uc u e, ou e s u l s u s i ng he F E FF p og a m i nd i - ca ed ha he s i m u l a ed s pec a a e m o e s i m il a o he ex- pe i m en a l one s bo h EXA FS and XANE S when hyd ogen a o ms a e i nc l uded a s back s ca e e s . O he au ho s , who do no u s e he s a m e m e hodo l og i ca l app oach o co m pu e he EXA FS s pec a, wo k w i h he a ss u m p i on o u s i ng hyd o- gen a o ms a s back s ca e e s i n bo h an i on and ca i on s ud i e s .17 The d i e en s a egy hand li ng ca i on and an i on hyd a i on, apa o m i s heu i s i ca l j u s ifi ca i on a s s een i n Fi g s . 3 and 4, cou l d be unde s ood by he p e s ence o a c l o s e s hyd ogen s he ll a ound he an i on. The b o m i de i on i nduce s he p e s ence o a s e o hyd ogen a o ms o fi s - s he ll wa e m o l ecu l e s i n i s c l o s e s i c i n i y, wh i ch a e ound o p l ay a s i gn ifi can o l e i n bo h he pho oe l ec on s ca e i ng pheno m enon and he de e m i na i on o e l ec on i c wa e unc- i on s o he b o m i de c l u s e s . A s i m p lifi ed exp e ss i on o he EXA FS unc i on i s g i en by6 k j N j kR j 2S0 2k F j k e 2 j 2k2e2R j / (k) s i n 2kR j j k, 1 whe e (k) i s he o a l a m p li ude a s a unc i on o he ec o kand he s u mm a i on goe s o e a ll pa h s j . N j i s he coo d i - na i on nu m be , R j i s ha l o he pa h l eng h, S0 2(k) i s he a m p li ude educ i on ac o , F j (k) i s he back s ca e i ng a m - p li ude, j 2 i s he s econd-o de cu m u l an known a s he Debye–Wa ll e DW ac o , (k) he m ean ee pa h o he pho oe l ec on, and j (k) he pha s e- s h i . In Eq. 1 , he d i s o de i s de s c i bed by he DW ac o . None he l e ss , when heo e i ca l i n o m a i on de i ed o m nu- m e i ca l s i m u l a i on s i s con s i de ed, s uc u a l fl uc ua i on s a ound he an i on a e i m p li c i w i h i n he s a m p li ng o he con- fi gu a i ona l s pace. Then, he EXA FS unc i on can be a l e - na i e l y exp e ss ed a s 22 k1 N s i s uc j pa h s N j kR ij 2S0 2k F j k e 2R i j / (k) s i n 2kR i j j k, 2 whe e N s i s he nu m be o s uc u e s con s i de ed i n h i s ca s e 10 000 s uc u e s e en l y s paced o e 50 M ( M 106) M C con fi gu a i on s , i goe s o e he s uc u e s de i ed o m he s a i s i ca l s a m p li ng, and j o e he pa h s . The o l e p l ayed by he exponen i a l con a i n i ng he DW ac o o Eq. 1 i s e- p l aced by an a e age o e s uc u e s i n Eq. 2 . In o de o check he con e gence o he e s u l s , a co m pu a i on w i h 40000 s uc u e s e en l y s paced o e 200 M con fi gu a i on s wa s a l s o pe o m ed. No d i e ence s we e ound be ween bo h a e aged s pec a. F u he exa m p l e s o h i s a e ag i ng o e s i m u l a ed s pec a m ay be ound i n R e s . 12, 15, 26, 36, and 37. The cu -o ad ii s e l ec ed we e he s a m e a s ho s e cho s en i n he XANE S s pec a. The con s i de ed pa h s we e e s i c ed o a l eng h o up o 7.0 Å and an a m p li ude o a l ea s 9% o he i n en s i y o he s ho e s B H pa h. S uc u a l pa a m e e s we e ob a i ned o m bo h expe i - m en a l and heo e i ca l s pec a by m ean s o fi i ng a m ode l s uc u e o Eq. 1 . C on ac i on pa i s cou l d be exc l uded, a s appea ed a s we ll o m he ana l y s i s o he Y K -edge.38 Thu s , he m ode l s uc u e cho s en i s he hexahyd a ed c l u s e cde- p i c ed i n Fi g. 1. EXA FS da a we e ana l yzed w i h he F E FF IT 2.55 s o wa e package.39 The fi i ng o he expe i m en a l EXA FS s i gna l o Eq. 1 i s ba s ed on a s anda d non li nea l ea s s qua e s echn i que we ll -e s ab li s hed i n he li e a u e.40 III. R ES ULT S AND D I S CU SS I O N A . X AN ES s p ec a C a l cu l a ed XANE S s pec a o m a s e i e s o quan u m - m echan i ca ll y m i n i m i zed s uc u e s con a i n i ng be ween 4 and 7 wa e m o l ecu l e s a e d i s p l ayed i n Fi g. 2 a and co m pa ed w i h he expe i m en a l s pec u m . The geo m e i e s o he s uc- u e s s e l ec ed a e s hown i n Fi g. 1. The ca l cu l a ed XANE S s pec a s how no i ceab l e d i e ence s , e s pec i a ll y w i h e s pec o he e l a i e i n en s i y o he e s onance s . To he con a y, he ene gy a l ue s o he fi s wo e s onance s wh i ch appea a 13 472 and 13 489 eV, e s pec i e l y, a e ep oduced ea s on- ab l y we ll by a ll o he m and a e i n ag ee m en w i h he ex- pe i m en a l s pec u m . The co m pa i s on w i h he expe i m en a l s pec u m s how s ha he a i o o he he i gh s o he e s o- nance s i s no ep oduced. Wha i s m o e, he m a i n e s onance o he expe i m en a l s pec u m i s w i de and h i ghe han he one s o he co m pu ed s pec a. XANE S s pec a a e gene a ll y con s i de ed o be i n s en s i - i e o d i s o de , bu cha ac e i s i c o he coo d i na i on geo m - e y. In he ca s e o b o m i de hyd a i on, whe e he hyd a i on s uc u e i s no we ll de fi ned, he s en s i i ene ss o he XANE S s pec u m o he i n s an aneou s geo m e i e s can be ill u s a ed on h ee s uc u e s p i cked ou o he 40 con s i de ed o ca l cu- F IG. 1. Geo m e i e s o he quan u m - m echan i ca ll y op i m i zed s uc u e s u s ed o ca l cu l a e XANE S s pec a o Fi g. 2 a . 6649 J . C he m . P h ys ., V o l . 119, N o. 13, 1 O c obe 2003 B o mi de h y d a i on s u c u e R eu s e o A I P P ub lis h i ng c on en is s ub j e c o he e ms : h p s ://pub lis h i ng.a i p.o g/au ho s / i gh s- and - pe missi on s . D o w n l oaded o I P : 150.214.182.116 O n: W ed, 19 O c 2016 14:53:39 l a e he a e age s a i s i ca l s pec u m Fi g. 2 b . On he one hand, and un li ke he ca s e o he quan u m - m echan i ca ll y op i - m i zed c l u s e s , s o m e o he i nd i i dua l s pec a exh i b i m o e i n en s e e s onance s han he expe i m en a l one. On he o he hand, he i nd i i dua l XANE S s pec a d i e m o e be ween each o he , han ho s e co m pu ed o m quan u m - m echan i ca l s uc u e s . Th i s s en s i i i y o he XANE S s pec a o geo- m e i ca l change s o m he fl uc ua i on s o he s y s e m s up- po s s ong l y he need o i nc l ude s a i s i ca l i n o m a i on i n he s i m u l a i on o XANE S s pec a o b o m i de s o l u i on s . I a un i que m ode l s uc u e had been aken i n o con s i de a i on, he d i s c epanc i e s be ween heo e i ca l and expe i m en a l s pec- a wou l d ha e been a s c i bed o he app ox i m a i on s con s i d- e ed i n he quan u m co m pu a i on s needed o gene a e he s pec u m , and e en ua ll y, he s e m i e m p i i ca l app ox i m a i on s i n oduced i n ob a i n i ng s o m e o he pa a m e e s . In he s a m e fi gu e, he co m pu ed s pec a u s i ng he s uc u e s unca ed o he fi s s o l a i on s he ll a e s hown. The i nd i i dua l s pec a a e s ong l y a ec ed by he unca i on, wha ill u s a e s how XANE S i s s en s i i e o he s o l a i on beyond he fi s s he ll , a s a l eady ob s e ed i n he ca s e o ca i on hyd a i on.24,25 In Fi g. 3, he co m pa i s on o he a e aged ca l cu l a ed s pec u m o m s a i s i ca l i n o m a i on and he expe i m en a l one i s s hown. B o h he po s i i on o he wo m a i n e s onance s and he a i o o he i he i gh s ag ee. A s expec ed o m he qua li a i e ana l y s i s o he m e hodo l ogy u s ed, he w i d h o he m a i n e s onance o he a e aged s a i s i ca l s pec u m i s m o e s i m il a o he expe i m en a l one han ha ob a i ned o m a un i que s uc u e. Ne e he l e ss , he ac ha he i n en s i y o he m a i n e s onance i nc ea s e s when a g ea nu m be o s pec a de i ed o m d i e en s uc u e s i s i nc l uded, i s s i k i ng. In o de o s udy he s en s i i i y o he XANE S eg i on o he ab s o be -back s ca e e d i s ance, he XANE S s pec u m ha s been eca l cu l a ed con s i de i ng he s a m e po i n s o he con- fi gu a i ona l s pace, bu i nc l ud i ng on l y s o l en m o l ecu l e s o he fi s s o l a i on s he ll . Acco d i ng o he ad i a l d i s i bu i on unc i on o he M C s i m u l a i on s ,28 a m o l ecu l e be l ong s o he fi s s o l a i on s he ll when he B O d i s ance i s l owe han 4.1 Å. The a e aged s pec u m ob a i ned i s i nc l uded i n Fi g. 3 s ho da s hed li ne and d i e s s li gh l y o m he one con a i n- i ng m o e han one hyd a i on s he ll da s hed li ne . Th i s beha - i o i s d i e en o m he one ound by ou g oup i n he s udy o ca i on hyd a i on.22,24,25 In he l a e ca s e, s pec a ca l cu- l a ed o m s uc u e s ha con a i ned on l y one s o l a i on s he ll p e s en ed a m o e i n en s e m ax i m u m , and a s li gh d i s p l ace- m en and na ow i ng o he m a i n e s onance wa s ob s e ed. The e ec o he wa e m o l ecu l e s beyond he fi s hyd a i on s he ll on he a e aged XANE S s pec u m i s sm a ll i n he ca s e o he b o m i de hyd a i on, un li ke wha i s ob s e ed when co m pu i ng he e ec o h i ghe s he ll s o i nd i i dua l s nap- s ho s . Thu s , i doe s no s ee m po ss i b l e o e i e e non i i a l s uc u a l i n o m a i on beyond he fi s hyd a i on s he ll o h i s an i on i n s ud i e s o s o l u i on che m i s y. The ca l cu l a ed XANE S s pec u m u s i ng a cu o ad i u s o 6.0 Å, whe e hy- d ogen a o ms we e no i nc l uded a s back s ca e e s , i s a l s o p l o ed i n Fi g. 3 do ed li ne s . Th i s co m pu ed s pec u m d i - e s s i gn ifi can l y o m he o he s pec a i nc l uded i n he fi g- u e. B . EX AF S s p ec a The co m pa i s on o he expe i m en a l and heo e i ca l EXA FS s pec a i n e ms o (k)k2 i s d i s p l ayed i n Fi g. 4. The ag ee m en be ween bo h s pec a i s s a i s ac o y, e s pe- c i a ll y con s i de i ng ha no e m p i i ca l pa a m e e s we e i n- c l uded i n he co m pu a i on o he heo e i ca l s pec u m . When H a o ms a e exc l uded a s back s ca e e s , he ag ee m en i s ound o be a o m s a i s ac o y, s uppo i ng he i m po ance o hyd ogen a o ms i n he XA S s pec a o he ha li de aqueou s s o l u i on s .41–44 A s h i gh li gh ed i n he s e p e i ou s wo k s , h i s i s F IG. 2. Expe i m en a l B K -edge XANE S s o li d li ne and he one s co m pu ed o m quan u m - m echan i ca ll y op i m i zed s uc u e s s hown i n Fi g. 1. b Ind i - i dua l XANE S s pec a co m pu ed o d i e en s nap s ho s , e i he e s i c ed o fi s hyd a i on s he ll da s hed li ne s o no s o li d li ne s . F IG. 3. Expe i m en a l B K -Edge XANE S s o li d li ne and co m pu ed o m M C s i m u l a i on s , e i he u s i ng fi s hyd a i on s he ll s ho da s hed li ne , o up o 6 Å l ong da s hed li ne . The hypo he i ca l ca s e whe e H a o ms a e no i nc l uded a s back s ca e e s i s s hown i n do ed li ne s . 6650 J . C he m . P h ys ., V o l . 119, N o. 13, 1 O c obe 2003 M e kli ng e a l . R eu s e o A I P P ub lis h i ng c on en is s ub j e c o he e ms : h p s ://pub lis h i ng.a i p.o g/au ho s / i gh s- and - pe missi on s . D o w n l oaded o I P : 150.214.182.116 O n: W ed, 19 O c 2016 14:53:39 due o he nea l y li nea a li gn m en o a o ms B HO and a s a con s equence, he hyd ogen a o m ha s a ocu s i ng e ec o he pho oe l ec on wa e. Fi gu e 5 a d i s p l ay s he expe i m en a l s pec u m and i s fi u s i ng a s a m ode l s uc u e c l u s e ‘‘c’’ o Fi g. 1. In Fi g. 5 b , he pha s e-co ec ed F ou i e an s o m F T a l ong w i h i s fi a e p l o ed. A s u mm a y o he s uc u a l pa a m e e s ob a i ned i n he fi p ocedu e i s s hown i n he ‘‘expe i m en a l ’’ a m e o Tab l e I. A s s een i n he ab l e, he a l ue s co m pa e we ll w i h expe i m en a l e s u l s ob a i ned by o he au ho s . M u l i e l ec on exc i a i on s a e expec ed a ound 5, 7.3, and 8.22 Å 1.38 They can be de ec ed expe i m en a ll y i he d i e ence s pec u m be ween expe i m en a l s pec u m and fi exh i b i s peak s ap- p ox i m a e l y a he i nd i ca ed k- a l ue s . Th i s i s no he ca s e, and he e o e m u l i e l ec on exc i a i on s we e no i nc l uded i n he ana l y s i s . S o m e au ho s s udy i ng b o m i de conc l uded ha m u l i e l ec on exc i a i on s we e no i m po an ,38,41 wh il e o h- e s eached a h i ghe e s i m a e o m u l i e l ec on exc i a i on s and eco mm ended he i i nc l u s i on i n he da a ana l y s i s .45,46 The ac ili y o hand l e i ndependen s uc u a l i n o m a i on o s a i s i ca l na u e on he s y s e m unde s udy enab l e s u s o unde ake a s econd EXA FS da a ana l y s i s wh i ch co e s pond s o he co m pu ed EXA FS s pec u m o m he M C s nap s ho s da s hed li ne i n Fi g. 4 . Th i s ype o s a egy ha s a l eady been pe o m ed i n p e i ou s wo k s dea li ng w i h ca i on hyd a i on.22,25 A fi s s i gh , h i s cou l d be en i s aged a s an unna u a l p ocedu e o ob a i n he s uc u a l i n o m a i on, a s he d i ec exa m i na i on o d i s i bu i on unc i on s de i ed o m M C s ee ms o o e a m o e d i ec way o do i . Howe e , he a p i o i know l edge o he s uc u a l e s u l s g i e s u s an i dea l a m ewo k o check he u s ua l da a ana l y s i s p ocedu e o ex- ac h i s i n o m a i on o m an EXA FS s pec u m . Fi gu e s 5 a and 5 b s how he co m pa i s on be ween he heo e i ca ll y co m pu ed s pec u m and i s fi . The fi ed s pec u m and i s F T a e i n qu i e good ag ee m en w i h he i co e s pond i ng heo- e i ca l s pec a. F o he pu po s e o he fi , s i ng l e s ca e i ng pa h s B O and B H and he m u l i p l e s ca e i ng pa h s B HO and B HOH we e con s i de ed. To educe he nu m be o fi pa a m e e s , a ll DW ac o s o he B O and B H pa h s we e a ss u m ed o be i den i ca l , a s s ugge s ed by he s i m u l a i on a l - ue s ( B O 20.055 i n Tab l e I and B H 20.059). In he ca s e o he heo e i ca l s pec u m , he coo d i na i on nu m be wa s fi xed o he m ean a l ue o he s i m u l a i on. S0 2, he a m p li ude educ- i on ac o , wa s s e o 1. The ‘‘ heo e i ca l ’’ a l ue s g i en i n Tab l e I a e a ll ob a i ned o m he M on e C a l o s i m u l a i on e s u l s . The ‘‘ M C s i m u l a- i on’’ li ne g i e s d i ec e s u l s co m pu ed o m he s a i s i ca l s i m u l a i on. ‘‘ Fi o heo e i ca l s pec u m ’’ gene a e s an EXA FS s pec u m o m he s i m u l a i on s nap s ho s and fi s h i s s pec u m , u s i ng o no he h i d o de cu m u l an . The s e wo fi s un pa a ll e l o he ‘‘ Fi o expe i m en a l s pec u m ,’’ he m a i n d i e ence be i ng ha he EXA FS unc i on ana l yzed i s ha ob a i ned o m he s nap s ho s o he M C s i m u l a i on. In he ab l e, he e s u l s o wo fi s o he heo e i ca l s pec u m can be co m pa ed : he fi s con s i de s on l y cu m u- l an s up o s econd o de , he s econd i nc l ude s he h i d o de cu m u l an , wh i ch i s con s a i ned w i h he s econd o de cu m u- l an a l ue by fi x i ng he s kewne ss a i o3 / (2)3 / 2] o a a l ue o 0.37. Th i s nu m be a i s e s o m he s i m u l a i on a s exp l a i ned be l ow. The d i e ence be ween he fi ed B O d i s - ance s a e w i h i n 0.1 Å due o he i n oduc i on o he h i d o de cu m u l an . The s a m e p ocedu e pe o m ed on he ex- pe i m en a l s pec u m y i e l d s s i m il a conc l u s i on s . C o m pa ab l e fi nd i ng s we e ob a i ned by D’Ange l oe a l . i n a s udy o b o- m i de i n m e hano l .42 The d i s ance i n he fi o he co m pu ed s pec u m i s 0.1 Å F IG. 4. C o m pa i s on o he expe i m en a l s o li d li ne and co m pu ed l ong da s hed li ne k2-we i gh ed EXA FS unc i on. When H a o ms a e no i nc l uded a s back s ca e e s , he EXA FS unc i on wou l d be ep e s en ed by he s ho da s hed li ne. F IG. 5. a Expe i m en a l EXA FS s pec u m and i s be s fi w i h he pa a m - e e s i nc l uded i n Tab l e I. b P ha s e-co ec ed F ou i e an s o m o he s pec- u m and i s fi . 6651 J . C he m . P h ys ., V o l . 119, N o. 13, 1 O c obe 2003 B o mi de h y d a i on s u c u e R eu s e o A I P P ub lis h i ng c on en is s ub j e c o he e ms : h p s ://pub lis h i ng.a i p.o g/au ho s / i gh s- and - pe missi on s . D o w n l oaded o I P : 150.214.182.116 O n: W ed, 19 O c 2016 14:53:39 l a ge han he co e s pond i ng expe i m en a l one 3.44 e s u s 3.34 . On one hand, h i s d i s c epancy cou l d be a s c i bed o he m o l ecu l a po en i a l m ode l s . On he o he hand, he d i s c ep- ancy cou l d a i s e o m he fi i ng p ocedu e i s e l a s d i s cu ss ed be l ow. C . An alysis o h e p o ce du e o ob ai n h e g e o m e ical p a a m e e s o m a non i g i d d is i bu i on a ound h e e e e n ce a o m The EXA FS s pec u m o he b o m i de an i on i n wa e i s a concep ua ll y i n e e s i ng ca s e o m e hodo l og i ca l s ud i e s be- cau s e he s pec u m i s do m i na ed by he B O back s ca e i ng con i bu i on. The p e s en s udy co obo a e s ha con i bu- i on s o m m u l i p l e s ca e i ng pa h s excep ed he ‘‘ ocu s - i ng’’ pa h B HO and s i ng l e s ca e i ng con i bu i on s o m a o ms a d i s ance s l a ge han 5.0 Å p l ay a m i no o l e.26,27 The B O d i s i bu i on o d i s ance s i s , howe e , qu i e b oad and a s y mm e i c. The e o e, a m ode l s uc u e s hou l d be a li d, i i wa s ab l e o ep oduce e ss en i a ll y he p obab ili y d i s i bu i on unc i on o he B O d i s ance s . In h i s s ec i on, he ana l y s i s w ill be pe o m ed exc l u s i e l y on he heo e i ca ll y co m pu ed s pec u m , s o ha expe i m en a l con s i de a i on s do no need o be aken i n o accoun and he d i s i bu i on i s known. The a i m i s o m on i o ho ough l y how he EXA FS de e m i na i on can ep oduce he geo m e i ca l d i s i bu i on, wha wa s u s ed e e s e l y o gene a e he EXA FS s pec u m . A s i k i ng ea u e o he s uc u a l de e m i na i on by EXA FS s pec o s copy i s ha d i s ance s a e u s ua ll y s li gh l y s ho e han expec ed, and / o ob a i ned by o he echn i que s .1 S uch a d i e ence i s a l s o ob s e ed be ween he d i s ance ob- a i ned by a e ag i ng he M C s i m u l a i on s nap s ho s and he fi ed d i s ance o he heo e i ca l s pec u m o exa m p l e, R B O 3.54 e s u s 3.44 Å . In ac , he coo d i na i on d i s ance ob a i ned o m he EXA FS fi i s nu m e i ca ll y e y c l o s e o he m ax i m u m o he g( ) unc i on s hown o i n s ance i n R e . 28. Th i s ob s e a i on app li e s a l s o o he ca s e o he s econd s he ll o R h3and C 3.24,25 In he b o m i de s udy, he fi ed DW ac o s a e on l y ough l y ha l o he a l ue ound i n he s i m u- l a i on 0.037 e s u s 0.055 Å2), wh il e he coo d i na i on nu m - be i s m a i n a i ned fi xed. The s y s e m a i c unde e s i m a i on o d i s ance s e en when he ‘‘co ec ’’ h i d o de cu m u l an i s u s ed enab l e s a s li gh e fi ne m en o he e s i m a ed expe i m en- a l d i s ance ba s ed on a an s e ab ili y o he d i e ence ob- a i ned o m he heo e i ca l co m pu a i on. Th i s s hou l d be wa - an ed i he s hape o he d i s i bu i on o he s i m u l a i on co e s pond s o he ea l one, R heo RM C Si m u l a i on R Fi o heo w i h3 3.54 3.44 Å 0.1 Å. Then, Rexp– heo R Fi o exp w i h3R heo 3.34 0.1 Å. The e o e, ou e s i m a e o he a e age fi s s he ll B O d i s - ance o m he expe i m en a l s pec u m i s 3.44 0.07 Å. In o de o fi nd ou m o e abou he ea s on s o h i s d i - e ence i n he fi s hyd a i on s he ll , s e e a l a e m p s we e m ade u s i ng on l y he i n o m a i on abou he d i s i bu i on i n h i s s he ll . The s uc u a l i n o m a i on u s ed i n a ll he s e ca l cu l a- i on s i s ha ob a i ned o m he M C e s u l s . Tab l e I g i e s he i n eg a i on nu m be , a e age B O d i s ance and i s DW ac o (2). F o he pu po s e o he ana l y s i s , he B O fi s peak had o be i s o l a ed s o m ewha a b i a il y, s i nce he d i s i bu i on unc i on doe s no d op o ze o. The cho s en c i e i u m wa s o u s e a s w i ch i ng unc i on, cen e ed a ound he m i n i m u m o he d i s i bu i on unc i on, ha b i ng s he d i s i bu i on o ze o a c angen l y be ween 3.8 and 4.2 Å. I a s i c cu o c i e- i u m i s cho s en i n s ead, he qua li a i e conc l u s i on s d awn he e a e no a ec ed. The e e ence d i s i bu i on i n a ll he s e ca l cu l a i on s i s g i en by he p obab ili y d i s i bu i on unc i on P D F , p l o ed i n Fi g. 6 s o li d li ne . Th i s unc i on i s d i ec l y e l a ed o he ad i a l d i s i bu i on unc i on (g(R)), P D F R B O N g s wR B O R B O 2, 3 whe e he s upe s c i p ‘‘ s w’’ e e s o he s w i ched g(R) and N i s a no m a li za i on con s an . TA B LE I. B e s fi d i s ance s , Debye–Wa ll e ac o s , and coo d i na i on nu m be s a ound he b o m i de an i on ob a i ned o m he ana l y s i s o he EXA FS s pec a and o he M C s i m u l a i on u s i ng 10 000 s nap s ho s . N OR B O / Å B O 2 / Å23 / Å3 Expe i m en Fi o expe i m en a l s pec u m 5.84a3.27 0.04 0.035 0.002 Fi o expe i m en a l s pec u m w i h30.37( B O 2)3 / 2 5.84a3.34 0.03 0.034 0.002 0.0023 0.0002 R e . 26 7.2 0.4 3.36 0.01 0.027 0.002 0.0014 0.0006 R e . 27 6.9 3.34 0.04 0.0065 R e . 50 6a3.19 0.016 R e . 48 6a3.20 0.022 0.0034 R e . 41 5.1 0.5 3.29 0.04 0.026 0.03 0.0020 0.0020 Theo y M C s i m u l a i on 5.84 0.3 3.54 0.01 0.055 0.005 0.0036 0.0002 Fi o heo e i ca l s pec u m 5.84a3.37 0.03 0.037 0.002 Fi o heo e i ca l s pec u m w i h30.37( B O 2)3 / 2 5.84a3.44 0.03 0.036 0.002 0.0025 0.0004 Fi o 1 s - s he ll P D F 7.0 0.1 3.50 0.01 0.065 0.001 Fi o 1 s - s he ll P D F w i h36.9 0.1 3.54 0.01 0.058 0.001 0.0052 0.0005 a Fi xed a l ue. 6652 J . C he m . P h ys ., V o l . 119, N o. 13, 1 O c obe 2003 M e kli ng e a l . R eu s e o A I P P ub lis h i ng c on en is s ub j e c o he e ms : h p s ://pub lis h i ng.a i p.o g/au ho s / i gh s- and - pe missi on s . D o w n l oaded o I P : 150.214.182.116 O n: W ed, 19 O c 2016 14:53:39 To o ll ow he s ep s o an EXA FS da a ana l y s i s , he F ou- i e an s o m o he P D F wa s u s ed a s i npu o he fi o he o ll ow i ng exp e ss i on : 47 P D F k A exp i R B Ok2k2 / 2 i 3k3 / 6 4 wh i ch y i e l d s ‘‘e ec i e cu m u l an s .’’ Tab l e I g i e s wo s e s o e s u l s , con s i de i ng o no he h i d o de cu m u l an . ‘‘ Fi o 1 s s he ll P D F ’’ u s e s he B O d i s i bu i on unc i on and fi s coo d i na i on nu m be , d i s ance, and DW ac o i n a m anne de a il ed i n he nex s ec i on. ‘‘ Fi o 1 s s he ll P D F w i h3’’ add i i ona ll y fi s he h i d o de cu m u l an . The h i d o de cu m u l an i s ound o be 0.0052 Å3 s ee Tab l e I , ha i s , 0.37( 2)3 / 2. C on s a i n i ng he s kewne ss o a a l ue o 0.37 i n a ll he fi s en s u e s ha he d i s i bu i on s ound a e co m pa a- b l y a s y mm e i ca l . Th i d o de cu m u l an s fi na ll y d i e g ea l y be ween au ho s and m e hod s u s ed. A d i ec fi o he EXA FS s pec u m i s s ub j ec o h i gh unce a i n i e s : Wa ll en e a l .26 de e m i ne a nega i e a l ue, wh il e Si m one e a l .41 ob a i n a a l ue i n ag ee m en w i h ho s e ob a i ned by o he au ho s u s i ng a l e na e app oache s .48 D’Ange l oe a l .27 ob- a i n a s kewne ss o 0.81. W i h i n he i app oach, howe e , h i ghe o de cu m u l an s a l s o p l ay a s i gn ifi can o l e. In h i s wo k, a d i ec ca l cu l a i on o 3 o m he M C s i m u l a i on y i e l d s 0.0036, ha i s a s kewne ss o 0.28, bu i we wan o neg l ec h i ghe o de cu m u l an s , i i s m o e i n e e s i ng o m ake u s e o an e ec i e a l ue. When s econd and h i d o de cu m u l an s a e i nc l uded, he a e age d i s ance de e m i ned i n he fi o he P D F i s equa l o he e e ence one 3.54 Å . The co e s pond i ng d i s i bu i on i s p l o ed i n Fi g. 6 do ed li ne . When he fi i nc l ude s on l y s econd o de cu m u l an s , he d i s ance de e m i ned i s 3.50 Å l ong da s hed li ne . Tha i s , a s ho en i ng o he d i s ance i s ob s e ed. Th i s a l ue i s qu i e d i e en o m he one ob a i ned by fi i ng o he co m pu ed EXA FS unc i on 3.44 o 3.37 Å, e s pec i e l y . Ano he e s o he m e hod o he de e m i na i on o he s uc u e li e s i n he i n e s i ga i on o he po ss i b l e a i ac a s - s oc i a ed o he gene a i on o he EXA FS unc i on i a he F E FF/F E FF IT m e hod o m he s nap s ho s o he M C s i m u l a- i on. Two nu m e i ca l exa m i na i on s ha e been de s i gned. The fi s con s i s ed i n gene a i ng a heo e i ca l EXA FS s pec u m a i s i ng s o l e l y o m s i ng l e s ca e i ng con i bu i on s o he fi s s he ll o oxygen a o ms . The fi i nc l uded on l y B O s i ng l e s ca - e i ng pa h s and s econd o de cu m u l an s , y i e l d i ng a d i s ance o 3.36 Å. The s econd exa m i na i on wa s he gene a i on o an EXA FS s pec u m ba s ed on m ode l s uc u e s o he geo m e y ‘‘c’’ o Fi g. 1, whe e he po s i i on o he wa e m o l ecu l e s wa s s y mm e i ca ll y m od ifi ed be ween 2.8 and 4.2 Å o he B O d i s ance. The s e s pec a we e we i gh ed by he P D F o he fi s peak. Th i s heo e i ca l s pec u m bea s a c l o s e e s e m b l ance o he one ob a i ned by he a e ag i ng o s pec a o m M C s nap- s ho s , and he fi pa a m e e s a e e y s i m il a . Th i s i s a s ong i nd i ca i on ha he ea s on o he d i s c epancy i s no due o m u l i p l e s ca e i ng e ec s o he p e s ence o hyd ogen a o ms c l o s e o he b o m i de, bu i s a he o be ound i n he s hape o he d i s i bu i on and he i nab ili y o ad j u s i w i h DW ac o s . I V . C O NCLUD I N G R E MARK S XANE S and EXA FS s pec a o B K -edge o b o m i de i n wa e we e ca l cu l a ed o m s i m u l a i on s nap s ho s and, i n he ca s e o XANE S , quan u m - m echan i ca ll y m i n i m i zed c l u s e s we e a l s o p obed. Whe ea s he quan u m - m echan i ca l c l u s e s do no co m pa e we ll w i h expe i m en a l da a i n s o l u i on, he s e o s i m u l a i on da a l ead s o a good ag ee m en . The d i s - c epanc i e s be ween XANE S s pec a ca l cu l a ed o m quan u m - m echan i ca l s uc u e s and M C s i m u l a i on s s ugge s he need o i nc l ud i ng s a i s i ca l i n o m a i on i n he co m pu- a i on. In h i s s en s e, i i s e ss en i a l o u s e a s a i s i ca l d i s i - bu i on o wa e m o l ecu l e s a ound he b o m i de an i on de i ed o m a conden s ed m a e s y s e m whe e i on–wa e and wa e –wa e i n e ac i on s p l ay a s i gn ifi can o l e. B ea i ng i n m i nd ha i n e m o l ecu l a po en i a l s we e fi ed oab i n i i o ca l cu l a i on s o s i m il a l e e l han ho s e u s ed o he s uc u e op i m i zed quan u m - m echan i ca ll y, he m a i n ea s on o j u s i y he d i e ence m u s be he s a i s i ca l ac o s . In he ca s e o he EXA FS co m pu a i on s o b o m i de hy- d a i on, he m a i n con i bu i on s a e due o s i ng l e s ca e i ng o m he fi s hyd a i on s he ll and, due o h i s ea s on, can be hand l ed ea li s i ca ll y by a one-d i m en s i ona l d i s i bu i on o m ode l s uc u e s . Th i s i s a s i m p lifi ed p i c u e o he m o e ea li s i c s ca e i ng pheno m enon whe e B HO pa h s and B H pa h s a e be i ng con s i de ed. The b oad and a s y mm e i c d i s i bu i on o B O d i s ance s i n he s i m u l a i on wa s de s c i bed i n e ms o an a s y mm e y pa a m e e o 0.37 s kewne ss i n o de o be ab l e o ob a i n s econd and h i d o de cu m u l an s w i h l ow i nde e m i na i on s o he fi o he EXA FS s pec u m . Th i s a s y mm e y pa a m - e e wa s ob a i ned by fi i ng he B O d i s i bu i on o he s i m u- l a i on i nk- s pace. The d i s c epanc i e s ha appea be ween he heo e i ca l EXA FS s pec u m and i s fi u s i ng cu m u l an s i nd i ca e ha s y s e ms w i h s i gn ifi can geo m e i ca l d i s o de i n he c l o s e en i on m en o he ab s o be a o m , li ke he fi s hyd a i on s he ll o he b o m i de an i on, can ha d l y be de s c i bed by cu- m u l an s li m i ed o h i d o ou h o de .49 Due o he cha - ac e i s i c s o he p obab ili y d i s i bu i on unc i on, d i s ance s ob a i ned by a con en i ona l fi p ocedu e o he EXA FS s pec- u m a e ob s e ed o be c l o s e o he m ax i m u m o he ad i a l d i s i bu i on unc i on when s o l e l y DW ac o s a e con s i de ed, F IG. 6. B O p obab ili y d i s i bu i on unc i on s P D F o m M C s i m u l a i on s o li d li ne , o m fi o heo e i ca l EXA FS s pec u m w i h3da s hed , and o m wo fi s o he M C P D F: w i h cu m u l an s up o 2 l ong da s hed and up o 3 do ed . 6653 J . C he m . P h ys ., V o l . 119, N o. 13, 1 O c obe 2003 B o mi de h y d a i on s u c u e R eu s e o A I P P ub lis h i ng c on en is s ub j e c o he e ms : h p s ://pub lis h i ng.a i p.o g/au ho s / i gh s- and - pe missi on s . D o w n l oaded o I P : 150.214.182.116 O n: W ed, 19 O c 2016 14:53:39 and a l s o a ll s ho when h i d o de cu m u l an s a e i n o- duced. The s y s e m a i c unde e s i m a i on o d i s ance s e en when he ‘‘co ec ’’ h i d o de cu m u l an i s u s ed enab l e s a s li gh e fi ne m en o he e s i m a ed expe i m en a l d i s ance. I we a ss u m e ha he d i s i bu i on o d i s ance s o m he s i m u- l a i on i s co ec , we ob a i n ha he a e age B O d i s ance de e m i ned i n he expe i m en a l fi 3.34 Å i s unde e s i m a ed by 0.1 Å. The e o e, ou be s gue ss o he expe i m en a l d i s - ance i s 3.44 0.07 Å. 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