Cheistron School, SPring8, November 2009

Filming molecular reactions with short X-ray pulses
Michael Wulff (wulff!@esrf(wulff!@esrf.fr)
fr)

European Synchrotron Radiation Facility, Grenoble

Synchrotron emits intense 100 ps X-ray pulses withup to ~1010 ph per pulse

Can be used to visualize atomic motions ofmolecules “at work”.

circumference = 844.1 m, orbit time = 2.816 μs

Pump-probe
Pumpprobe set-ups
set ups atESRF, KEK, APS, SPring8, SLS, ALSExpected motions of hemoglobin – upon photolysis ‐ from static crystalstructures

Conformational changes inhibited by crystal constraints
2

Pump‐probe method•

Diffraction and scattering•••

Goal:
Observe transient structures in molecules
Ultimately design molecules with specific properties

CCD camera
laser pulse

X-ray pulse

Overview of ID09

Synchrotron wall
Electron beamControl hutches
Hutch 2(TR)

U17

U20X
X-raybbeam
Optics hutch

Hutch1(HP)

Monochromator
Femto and nanosecond laser

Goniostat and CCD detector

New: Frelon CCD

High-speed chopper

Focusing mirror

Heatload chopper

2 in-vac undulators

U d l t spectrum(U17)
Undulatort(U17)

Pulse shape

3.5E-070.8

2.3 109 ph/pulse(5mA)
0.7

3.0E-070.6

intensity (a.u.)

intensity (AAmp)

2.5E-072.0E-07ML(3%)

1.5E-07

0.5

100ps

0.4

0.3
1.0E-070.2
5.0E-080.1

0.0E+00
1015

20

25

30

0.0
-200-150

energy(keV)

75% of experiments use the 3% pink beam for high intensity.
intensity-100-500time (p(ps))

50100

150200High-speed chopper rotates at 986.3Hz(600m/s)
Minimum open-time is 200 nsTunnel(0.14 mm)step

3 kHz modechopper out

Single pulse selection(16 bunch mode)-176 ns

176 nstunnel(( 200-450ns))
1.5 mmΔ t = 250 nst

Step (0-20μs)

Three choppers control the pulse structure of the pink beam

176 nsPulse train from16 bunch modeheat-load chopper

1 ms

high-speed chopper

50 μs

0.3-20 μs
ms-chopper
Single X-ray pulse(100 ps)

1.5 msPulse lengths: 50 ps to 50 us, Pulse frequency: 0-1000 Hz

Lasers for pump-probe experiments

New FReLoN Camera gives 5-10 times more images per hours .
More averaging, more time delays , more samples per day.

1/ Readout,
2/ Spatial correction,
3/ Radial integration & scattering corrections
4/ Data storage
0.04

δS / S0

done in 0.8 s

Delay 800ns

Average of 76
curves1200 S(q,S(q t) curves measured per hour with 2 s
exposure time.
-5x 25 (noise floor 2 x 10 )0.02

[Ir2(dimen)4]3+

0.00

-0.02
03

6-1

Q(Å )
Data from M. Christensen et al. CMM, Copenhagen

9Measuring the time delay with a GaAs photodetector.
Laser delay shifted electronicallyelectronically.
150 ps resolution leads to an uncertainty in τ of 15‐30 ps

Author - Title (Footer)10Ch i l reactions
Chemicaltiini solutionl tiscattering
tt i experimentsitSet-up for liquid diffraction

Marccdnozzle
GaAs

liquid sheet(0.3 mm) thick)Scattering from a liquid: probing atom-atom distances with 100 ps resolution

laser on (τ)

laser offTh two images
Thei
are scaledl d to 1 at theh edge
d off theh CCD andd subtracted.
bd
laser on (τ) – laser off

Diffraction from a moleculeλrij2θrijDebye equation for gas scattering:S ( q) = ∑ f i ( q) f j ( q)sin( q rij )qriji, jÆ{CCD(∑Z )2ii∑ f (q)2ii

for q → 0for q → ∞

12000
1000

I2 (2.67 Å) ÆI 2* (3.05 Å)

I2 (X; r = 2.67 Å)
10000

0

I2 (A; r = 3.05 Å)-1 0 0 0

ΔS(eeu/I )22S((eu/I )

8000

6000

2I

I2*(3.05 Å)

4000-2 0 0 0I2(2.67 Å) Æ 2 I-3 0 0 0-4 0 0 0I2(2.67 Å)-5 0 0 0

2000

ΔS= S(excited) - S(non-excited)-6 0 0 0001234567-1Q (A n g )89100123456-1Q (A n g )78910

Fourier transform of ΔS(q,ΔS(q τ) is a measure of the change in radial electron density

ΔS [r,,τ ] ≡1∞

dq
q q ΔS (q,τ ) sin((q r )
∫
2π r
20

The difference in radial electron density is obtained from the FT of ΔS(q, t)
ΔS [r,τ ] ≡1∞

2π 2 r ∫030

d q ΔS (q,τ ) sin(dqi (q r )30I2(X) Æ 2 I (10%)

20I2(X) Æ I2(A) (20%)

20
Liquid phase (cage)

1010I..Cl00-10-10Gas phase

ΔS[rr]

ΔS[rr]

Liquid phase (cage)-20-20-30-30-40-40-50-50-60-60-70-70
0 1 2

3 4 5 6 7r(Ang)

8 9 100 1 2

3 4 5 6 7

8 9 10r(Ang)

The solvent structure around new molecules is measured! Can be simulated by MD.

CCl4

Structure of the C2H4I intermediate
100ps

bridged structure

C2H4I + I0.03

123456789100TheoryExperimentq (Å )r (Å)

anti structure

anti structure
0.01
TheoryExperiment

0.00

0.01

12345678910-0.01

ΔS(r)

ΔS(q)

6I-I-1

0.00

-0.02

123456789-0.01

TheoryExperiment

-0.03

-0.02

-0.04
-1
1q (Å )

Ir (Å)

C2H4

C2H40.03

0.01
TheoryExperiment

0.02

0.00
00.01

12345678910-0.01

ΔS(r)C2H4 + 2I

5C-I-0.04

0C

490CC80.03

ΔS(q)C3-0.03

0.02

II

7-0.02C2H4I + I2-0.02

0.00

-0.01

C1-0.01

ΔS(r)

ΔS(q)

0.01

0C2H4I2+hν

0.00
0IC0.01

TheoryExperiment

0.02

bridged structure

0.00

-0.02

0123456789-0.01-0.03-00.0202-00.0404-1q (Å )The bridged structure C2H2I is formed!
Ihee, Science, 309, 1223-1225, (2005)

TheoryExperimentr (Å)

Transient structures of C2H4I2 and C2F4I2 in methanol

C2H4I2

C2F4I2

Red curve = exp

BridgedAnti-structure

Bridge structure

Anti-structure

Molecular dynamics movie of I2 dissociation

Film by Rodolphe VuilleumierWatching the formation of a diatomic molecule with 100 picosecond X-ray pulses

ESRF June 27, 2007

1. δt = 0 ps (time zero): the molecule explodes after being hit by a laser flash. 2. δt = 0.3 ps. Iodine atoms collide with the nearest liquid molecules

Laser flash

3. δt= 1ps. A strongly vibrating molecule is formed.

4. δt= 100ps. The molecule is cooling down, becoming smaller.
Energy is transferred to the solvent.

Laser dissociation of a diatomic molecule in a liquid (I2)

{I2(x) + hv (520nm) Æ I2*(FC) ÆI2
Δ tvib=156
156 fsI2*(X)(X)Æ I2(X) ; 0.14ns
0 14nsI2(A/A’) Æ I2(X) ; 2.7ns
Æ I2(X) ; 25 ns

2I

4.0

3

3.8

B
3.6

disst ( I , I ) Ang

total energy(eV)

21πu

pump

A/A'

34
3.4

rmax

3.2

3.0

1

2.8

2.4

v=1
v=00
2.0

rmin

2.6

X

2.5

3.0r (Ang)

3.5

4.0

4.5

01020304050t ( ps )

60

70

80

90100

The dissociation and recombination of I2 in CCl4(1:500) probed 100 ps after excitation
excitation.
30

35000

S(Q, τ)

30000

ΔS(Q, τ)25000

CCl4 + I2

20

CCD coounts/5s

20000
15000
1010000
5000
00-5000Sc∝ exc
N2 IB-10000-15000-20000-10laser on – laser off-20-25000-30000Plech et al. , PRL, 92, 12, p 125 505, 2004-30

-35000012345Q = 4 π sin(θ) / λ6789

How to subtract the heat from the data
CCl4 curve measured by exciting the C-Cl bondElongated Br2Elongated I2Author - Title (Footer)

23Recombination of iodine atoms in CCl4 cage
Slicing the 100 ps X-ray pulse by a 1 ps laser pulse(530nm)

τ = - 25ps
Liquid sample
100 ps X
X-rayray pulse

1 ps laser pulse

7.5
0.080

7.0

FT

0.075
500ps(24)

6.5

0.070
300ps(24)

6.0

0.065
200ps(26)

55
5.5

0 060
0.060
100ps(95)

5.0

0.050

ΔS
S[r,dS[r]
τ]

4.5

dS(Q)
ΔS
S(Q,τ)

0.055

60ps(93)
40ps(93)

4.0

30ps(7)

3.5
3.0
2.5

0.035

10ps(90)

0.030
0.025
0.020

-10ps(95)

1.5

0.040

20ps(95)0ps(142)2.00.045

0 015
0.015
-20ps(142)1.00.010-30ps(149)0.50.005-40ps(140)0.00.000-0.5012345Q(Å-1)

Q(Å-1)

6789-0.005
0246r(Å)

R (Å)

81012

I2 bond formation measured by deconvoluting laser-sliced data
(Jae Hyuk Lee, Savo Bratos et al. , unpublished)

3Energy[eV]

B

2

1

020
2.0γ(22 ns)

1πu
β (2700 ps)

hν

A/A'

25
2.5

30
3.0α(140ps)

35
3.5

40
4.0

Interatomic distance (A)Work in progress25454.5

Expected motions of hemoglobin – upon photolysis ‐ from static crystal
structures

Conformational changes inhibited by crystal constraints
26

tertiary change

quaternary change

28

29

30

31

32

33

34

Flash photolysis of Hemoglobin probed by SAXS/WAXS
Cammarata et al, Nature Methods, 5, 2009

R04 COhντ = 2 μs

T04 CO
4 CO

R4D

T-jump

1.1

pump.

1

R4

0.9

fracctional population

ΔS [arb. units]

T 0 -R 4

temp.

0.6
0.5

289.7
289 2
289.2

0.3

288.7

0.1

288.2

-0.1
0.20.40.60.811.2
q [Å -1 ]

1.4

1.6

1.822.2

290.2

0.4

00290.7

T00.70.2

R 0 -R 4

291.2

R00.8291.7

1E 8
1E-8

287.7
1E 7
1E-7

1E 6
1E-6

1E 5
1E-5

1E-4
1E
4time [s]

1E 3
1E-3

1E 2
1E-2

1E 1
1E-1

1E 0
1E+0Population dynamics of time-independent excited states

temp. [K]B

Protein dynamics in solution probed by time resolved SAXS/WAXS(ID09B, Cammarata et al. )Filming the dissociation of CO from MbCO by Laue diffraction(L29F mutant)Phe29

distal
His64
COhemeFe22+proximal
His93
Ribbon presentation

Van-der-Waals presentation
CO seemingly trapped in protein

MbCO : C823 H1045 Fe N222 O221 S3 , 2305 atoms, 153 amino acids

Laue diffraction from myoglobin (resolution dmin = 1.7 A)(Ef= 15.0 keV, delta E/E = 3%, 16 single‐pulse images accumulated on a CCD detector)

Setup

Timing200
1000-100-200-300-400-500
300
400ps psps

MovieScience, 300, 1944
(20 Jun 2003)

100 psPhe29
Hi 64
His64
H2O100 psCOPhe29
Hi 64
His64
H2O

COFe
Hi 93
His93

100 psIle107heme
Leu104

316 ps

1 ns

3.16 ns

Hi 64
His64

31.6 ns

316 ns

3.16 us

Author - Title (Footer)51

Dissociation pathways for HgI2 in methanol

II

Hg I

Dissociation(267nm)

I

I
Recombination(< 1ps)

HgI2

Hg

HgI + I{

Non geminate recombination 68 ns
Reation:{

HgI2*

HgI2 ÆÆ

HgI + I Æ{

Non geminate recombination 22 ns

HgI2
Hg

HgI2
I
0.5 x ( HgI +I2)

Hg IIII

HgI2

2HgI + I2Structure of HgI2* in methanol 100 ps after dissociation(267nm)(solvent: δT = 1.2 K, δP = 14 atm)

I Hg

I Hg I

Q-space

FTA

Real-space
B

I-I

Hg-I

Difference Inntensity, rΔS
S(r)Experimental
TheoryDifference In
Dntensity, qΔS
S(q)I

SoluteCage
Solvent

024q (Å-1)

680246r (Å)

8 10 12 14Structural Dynamics of HgI2 in methanol(CH3OH)
1.8

0.0

1.6

2.0HgI2 (parent)

1.5HgI (transient)I
I2

1.0HgI2 (non-geminated)

05
0.5

1.4-0.51.2
1.0-1.0

0.8
0.60.4-11.5
50.2

0.00.0-15

10-14

10-13

10-1210-1110-1010-910-810-710-6-2.0-15

1010Time delay (s)-1410-1310-12

10-1110-10

10-9-91010-8-710-810-6

1010-710Time delay (s)

140

20
18120

16

Presssure (atm)Hea
at (J/mol)

100
80
60
40

14
12
1086420

20-15-14-13-12-11-10-9-8-7-610 10 10 10 10 10 10 10 10 10Time delay (s)

-15

10-14

10-1310-1210-1110-101010

Time delay (s)-6Density (kg/mm 3)

2.5

Temperaturre (K)Concentration
Cn (mM)

3.0

Solvent hydrodynamics (Cammarata, Pontecorvo et al)

Liquid jetΔT(K)laserr2R

Acoustic horizon

IR excitation of C-H and O-H bonds

CH3OH

Δρ(kg/m3)

Model: interaction between experiment and theory

Excited-state structures
DFT

Solvation cageMD

ΔS(q t)ΔS(q,pump-probe

Global fitting of ΔS(q, t)

Structures(t)Stt(t)
Concentration(t)
ρ(t)
T(t)
()
P(t)

Hydrodynamics
IR pump-probe

CCM, Copenhagen, April 27, 2009

Visions for pico- and femtosecond pump-probe experiments
Marco Cammarata(CMM/ESRF), Michael Wulff(ESRF),

ESRF1

ESRF2 (2009-2018)
Belledonne
extension(ID31-ID02)

Chartreuse
extensiontiVercors
extension(ID06-ID09)

PeninsulaExtension(ID20-ID22)(ID27-ID30)

pq

M= q / p, F = M S

p =100m=100m, q =1m Æ M=0.01
M=0 01
Sy = 120um Æ Fy = 1.2 um
Sz = 30um Æ Fz = 0.3 um

Acknowledgement 1: The Liquid & Laue TeamFriedrich Schotte
Maciej Lorenc
Tae Kyu Kim
Jae Hyuky Lee
Marco Cammarata
Qingyu KongFriederike Ewald,
Savo Bratos

Michael Wulff
Philip Anfinrud
Hyotcherl Ihee
Manuela Lo Russo+ former ID09 staff!

Acknowledgements
ESRF
Marco Cammarata
Friederike Ewald
Qingyu Kong
Emanuele Pontecorvo
Laurent Eybert
Laurent Claustre
Sebastien Petitdemange
Ernesto Paiser
Wolfgang Reichenbach
ESRF support staff
External
Philip Anfinrud (NIH)Friedrich Schotte (NIH)
Harry Ihee (Kaist)
Savo Bratos (Uni Paris)
Rodolphe Vuilleumier (Uni Paris)
Anton Plech (KFA, Karlsruhe)
Richard Neutze(Uni Goteborg)
Martin Meedom Nielsen(Uni Copenhagen)Robert Feidenhans’l (Uni Copenhagen)