Ground State Electronic Structures. from. Multi-Edge Analysis

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1 Ground State Electronic Structures from Multi-Edge Analysis Robert K. Szilagyi Montana State University, Bozeman, MT computational.chemistry.montana.edu

2 Reminders: unique research opportunities (no other spectroscopic technique for S and Cl) facilities (beamlines, instrumentation, sample prep. expertise) semi-empirical theory (effective nuclear charge, transition dipole, covalency

3 On a gloomy and snowy November afternoon

4 On a gloomy and snowy November afternoon

5 Nitrosated β-subunit of human hemoglobin βcys93 N.-L.CHAN,P.H.ROGERS,A.ARNONE 1.9 Å CRYSTAL STRUCTURE OF THE S-NITROSO FORM OF LIGANDED HUMAN HEMOGLOBIN BIOCHEMISTRY, 1998, 37, 16459

6 RSNO compounds (CCDB)

7 RSNO compounds: geometric structure

8 RSNO compounds: electronic structure large sulfur contribution S-N double (π) bond S-C single (σ) bond Biochemical and Biophysical Research Communications, 2005, 330(1), S-N single (σ) bond

9 S K-edge XAS of S-nitrosated glutathione (GSNO) 1.4 normalized XAS intensity (FF/I0) Biochemical and Biophysical Research Communications, 2005, 330(1), calibrated (thiosulfate) photon energy, ev

4 normalized XAS intensity (FF/I0) 1.2 1.0 0.

5 ev 2473.4 ev 2475.0 ev S-C σ* (4.0 ev) (0.

10 S K-edge XAS of S-nitrosated glutathione (GSNO) 1.4 normalized XAS intensity (FF/I0) ON-S π* ON-S σ* (2.1 ev) ev ev ev S-C σ* (4.0 ev) (0.0 ev) calibrated (thiosulfate) photon energy, ev

11 S K-edge XAS of SNO compounds Normalized XAS Intensity S-NO π* S-NO σ* S-C σ* S-nitroso glutathione Photon Energy, ev GSNO SNAP N-acetyloxy-3-nitrosothiovaline

12 S K-edge XAS of S compounds Normalized XAS Intensity H-S σ* S-C σ* S-C σ* Na + - S-CH 2 -CH 3 NaSEt Cys H-S-CH 2 -CH S charge becomes less negative Z eff (S) increases Photon Energy, ev

13 S K-edge XAS of S compounds Normalized XAS Intensity H-S σ* ON-S σ* S-C σ* H-S-CH 2 -R S-C σ* Cys ON-S π* GSNO ON-S-CH 2 -R S charge becomes less negative ON Z eff (S) increases +- S-CH 2 -R Photon Energy, ev

14 S K-edge XAS of S compounds Normalized XAS Intensity ON-S π* ON-S σ* S-C σ* H-S σ* S-C σ* S-C σ* Cys NaSEt GSNO S charge becomes less negative Z eff (S) increases Photon Energy, ev

15 S K-edge XAS as detection method for SNO Normalized XAS Intensity SNO-hemoglobin ON-S S 1s p* ON-S fit π* fit First derivative Second derivative Photon Energy, ev Derivatives of XAS Intensity Biochemical and Biophysical Research Communications, 2005, 330(1),

16 Multi-edge XAS Conceptually NOT an original idea! Conscious exploitation of complementary ground state electronic structure information from multiple absorbers Molecular Orbital Theory: Experimentally probing the excitation of an absorber core electron (1s for K) to a unoccupied/virtual molecular orbital with some absorber contribution. Donor orbital: S 1s (localized on S, in MO picture as s.a.l.c.) Acceptor orbital: ϕ* = Σ c i φ i for a simple M-S bond: ϕ* = c M,d φ M (nd) + c M,s φ M (n+1 s) + c M,p φ M (n+1 p) c S,s φ S (3s) + c S,p φ S (3p) + c S,d φ S (3d)

Multi-edge XAS for a simple M-S bond: ϕ* = c M,d φ M (nd) + c M,s φ M

(3d) metal contribution/character ligand character/covalency for

1s L 2p metal L-edge XAS metal K-edge XAS ligand K-edge L-edge SSRL

17 Multi-edge XAS for a simple M-S bond: ϕ* = c M,d φ M (nd) + c M,s φ M (n+1 s) + c M,p φ M (n+1 p) c S,s φ S (3s) + c S,p φ S (3p) + c S,d φ S (3d) metal contribution/character ligand character/covalency for intense spectral features in absorption spectroscopy Δl = 1 M 2p M 1s L 1s L 2p metal L-edge XAS metal K-edge XAS ligand K-edge L-edge SSRL BL10-1/8-2 BL7-3/9-3/4-1/4-3 BL6-2/4-3 BL10-1/8-2 SSRL BL10-1 SSRL BL7-3 SSRL BL4-3

18 Multi-edge XAS

19 Multi-edge XAS at SSRL BL6-2/ eV 3000eV 4000eV 5000eV K edges excitation form n=1 orbital 2146eV P 2472eV S 2822eV Cl 3206eV Ar 3608eV K 4038eV Ca 4492eV Sc 4966eV Ti 5465eV V 2000eV 3000eV L edges excitations form n=2 orbitals 2007eV Sr 2156eV Y 2307eV Zr 2465eV Nb 2625eV Mo 2793eV Tc 2967eV Ru 3146eV Rh 3330eV Pd 2300eV 3000eV M edges excitations form n=3 orbitals 2365eV Hf 2469eV Ta 2575eV W 2682eV Re 2792eV Os 2909eV Ir 3027eV Pt

20 Multi-edge XAS: A non-biological, but simple example Cl P Pd Cl P LUMO Inorganica Chimica Acta, 2008, 361(4),

21 Multi-edge XAS: A non-biological, but simple example 2

22 Multi-edge XAS: phosphorous K-edge Phosphorous 3p character of the palladium-phosphorous bonds is determined from phosphorous K-edge XAS

23 Multi-edge XAS: chlorine K-edge Chlorine 3p character of the palladium-chlorine bonds is determined from chlorine K-edge XAS

24 Multi-edge XAS: palladium L-edge Metal 4d character of the palladium-ligand bonds is determined from palladium L-edge XAS (only L III edge is shown)

25 Multi-edge XANES: chloropalladium(ii/iv) K 2 Pd II Cl 4 K 2 Pd IV Cl 6 closed shell d 8 closed shell d 6

inorganic chemistry (Solomon) 1.4 Cu 3d x 2 -y 2 Normalized XAS Intensity 1.2 1.

26 Chlorine K-edge XANES: ϕ* = (1 α ) Cu 3d x 2 -y 2 _ α Cl 3p salc Cu(II) is the hydrogen atom of inorganic chemistry (Solomon) 1.4 Cu 3d x 2 -y 2 Normalized XAS Intensity Cl 1s Cl 3p salc NaCl Cs 2 ZnCl 4 T d 0.2 Cs 2 CuCl 4 D 4h Photon Energy, 2833 ev 2835

27 Multi-edge XANES: Cl Pd(II) is the hydrogen atom of organometallic chemistry Inorganica Chimica Acta, 2008, 361(4),

28 Multi-edge XANES: Pd Inorganica Chimica Acta, 2008, 361(4),

29 Experimental M-L covalency acceptor orbital donor orbital Ψ a = 2 ( 1 α ) φ α φ Ψd = c φ l,d ligands M l,d L φ = φ L c l,o ligands orbitals (donor is 1s for K-edge excitations) l,o electric dipole allowed transition/fermi golden rule: 2 I <Ψ Ψ > a r d I 2 (1 α ) cl,d < φm r φl,d > α cl,dc l,o < φl,o r φl,d > ligands ligands ligands orbitals ligand core/metal overlap 0 ligand core/ligand core overlap 0 2 for 1s np excitation JACS, 1992, 112(4), < Ψ Ψ > α 1 a r d cl,1s cl,np < Rad( Ψl,np) r Rad( Ψl,1 s) > 3 ligands < R > dipole integral I = <ΨM L(3p) r ΨL(1s) > = α < R > 3

30 Multi-edge XANES: chloropalladium(ii/iv) using I(Cl - t ) = 21.0 ev ~50% Cl covalency in both [PdII Cl 4 ] 2- and [Pd IV Cl 6 ] 2- from complementarity this corresponds to ~50% Pd covalency in each molecular orbital probed by XAS from area under pre-edge features at Pd L-edges we get I(Pd II ) = 20.8 (SSRL) 16.9 (ALS) ev I(Pd IV ) = 14.1 (SSRL) 11.9 (ALS) ev to test the transferability we used I(Pd II ) to determine the covalency of Pd-Cl bonds in PdCl 2 to be ~50% with a new transition dipole integral for I(Cl - b )16.4 (SSRL) 14.5 (ALS) Pd-Cl bond in organometallic chemistry is the Fe-S bond in coordination chemistry

31 Multi-edge XANES: non-innocent ligands 2+ - C - A) Crystal structure of [Ph 2 BP tbu 2 ]CuII (NTol 2 ) B) Structural overlay of reduced and oxidized forms C) Ligand based redox chemistry JACS, 2009, 131(11),

32 Multi-edge XANES: non-innocent ligands Normalized Intensity ev ev ev ev Cu K-edge first electric dipole allowed Cu 1s 4p transition {[Ph 2 BP tbu 2]Cu I (NTol 2 )} {[Ph 2 BP tbu 2]Cu II (NTol 2 )} anhydrous Cu II Cl 2 Cu I Cl Photon 8995 Energy, 9002 ev

33 Multi-edge XANES: non-innocent ligands Normalized Intensity {[Ph 2 BP tbu 2]Cu II (NTol 2 )} {[Ph 2 BP tbu 2]Cu I (NTol 2 )} PPh 3 P 1s P-C σ* P 1s P 4p ev ev ev P K-edge ev ev ev P 1s P 3p/4p based electric dipole allowed transitions Photon Energy, 2150 ev

34 Multi-edge XANES: non-innocent ligands Normalized intensity {[Ph 2 BP tbu 2]Cu II (NTol 2 )} {[Ph 2 BP tbu 2]Cu I (NTol 2 )} anhydrous Cu II Cl 2 Cu I Cl ev * * Cu 2p 3d transition ev Cu L III -edge Cu L backdonation transition envelopes Photon 937 Energy, 940 ev

35 Multi-edge XANES: quantitative treatment Normalized intensity {[Ph 2 BP tbu 2]Cu II (NTol 2 )} ev Cu L III -edge What is the Cu contribution to the redox active orbital? What is the % Cu character the blue vs. green areas correspond to? ev anhydrous Cu II Cl Photon 937 Energy, 940 ev

36 Multi-edge XANES: quantitative treatment Renormalized Intensity Cs 2 Cu II Cl 4 Cl K-edge 4 Cl absorbers Cl absorbers anhydrous Cu II Cl Photon 2970 Energy, 3020 ev

37 Multi-edge XANES: quantitative treatment Renormalized XAS Intensity D 2d Cs 2 CuCl 4 pre-edge area = ev ~ 30% Cl 3p Cs 2 Cu II Cl 4 anhydrous Cu II Cl 2 anhydrous CuCl 2 pre-edge area = ev ~ 35% Cl 3p Cl K-edge 4 Cl absorbers Cl absorbers Photon 2827 Energy, 2830 ev

38 Multi-edge XANES: quantitative treatment Normalized intensity 35% Cl 3p character with limited 4s mixing Cu 3d character is ~ 65% pre-edge area = ev {[Ph 2 BP tbu 2]Cu II (NTol 2 )} ev Cu L III -edge pre-edge area ev Cu 3d character ~14% ev 1.0 anhydrous Cu II Cl Photon 937 Energy, 940 ev

39 Calculated spin densities for [Ph 2 BP tbu 2 ]CuII (NTol 2 ) P tbu Ph 2 : 15% BPh 2 : 2% Cu: 13% (p-tol) 2 : 20% N: 49% JACS, 2009, 131(11),

40 State-of-the-Art S K-edge Data galactose oxidase HO HO CH 2 OH + O 2 O OH OH O CH + H 2 O 2 HO OH O OH OH 1GOG fungus Dactylium dendroides

41 State-of-the-Art S K-edge Data Tyr495 His581 His496 water Cu Tyr272 Cu 2+ / O(Tyr-Cys) 400 mv Cys228 Cu 2+ /O(Tyr-Cys) galactose oxidase 150 mv Cu + /O(Tyr-Cys)

42 State-of-the-Art S K-edge Data Tyr495 His581 His496 Cu Tyr272 water Cys228 galactose oxidase JACS, 2010, submitted GO samples: 93% Cu-loaded 150 μl mm In phosphate buffer w/2m urea, ph=7 50-fold excess of K 3 Fe(CN) 6 37±3% oxidation BL6-2 only! LHe cryojet only! 19 absorbers: 13 Met 4 Cys-Cys thioether crosslink

State-of-the-Art S K-edge Data 3.0 2.5 2.0 1.5 1.

dithionite reduced Tyr495 His581 His496 Cu Tyr272 water TyrCys 1- (Met 13 Cys 5 )

43 State-of-the-Art S K-edge Data Normalized XAS Intensity ferricyanide oxidized as isolated/semi reduced dithionite reduced Tyr495 His581 His496 Cu Tyr272 water TyrCys 1- (Met 13 Cys 5 ) * buffer contamination TyrCys 1- (Met 13 Cys 5 ) 0.5 Cys Photon Energy, ev

44 State-of-the-Art S K-edge Data Normalized XAS Intensity ferricyanide oxidized as isolated/semi reduced dithionite reduced presence of Tyr-Cys in Met 13 Cys 5 background renormalized pre-edge hhlw = 0.40 ev A = 0.78 thus D 0 = 0.31 TyrCys 1- (Met 13 Cys 5 ) oxidized-reduced XANES spectrum * buffer contamination TyrCys 1- (Met 13 Cys 5 ) Photon Energy, ev

45 State-of-the-Art S K-edge Data Experimental area D 0 = ev for N abs = 19 and n holes = 1. S character (α 2 ) is defined by the transition dipole expression 1 n D holes 2 0 = α (S 3p) I(S1s 3 N absorber 3p) I(S 1s 3p) for sulfide (formally Z=-2) 6.54 ev for thiolate (formally Z=-1) 8.47 ev for thioether (formally Z=0) 10.4 ev and with corrections for partial Cu loading and Tyr-Cys oxidation: S character (α 2 ) from XAS for oxidized holo GO is 24±11% (calc.: 22±2%) JACS, 2010, submitted from EPR for oxidized apo GO is 20±3% (calc: 15±1%)

NAME: SECOND EXAMINATION

1 Chemistry 64 Winter 1994 NAME: SECOND EXAMINATION THIS EXAMINATION IS WORTH 100 POINTS AND CONTAINS 4 (FOUR) QUESTIONS THEY ARE NOT EQUALLY WEIGHTED! YOU SHOULD ATTEMPT ALL QUESTIONS AND ALLOCATE YOUR