We report experimental results on the diffractive imaging of three-dimensionally aligned 2,5-diiodothiophene molecules. The molecules were aligned by chirped near-infrared laser pulses, and their structure was probed at a photon energy of 9.5 keV (λ ≈ 130 pm) provided by the Linac Coherent Light Source. Diffracted photons were recorded on the Cornell–SLAC pixel array detector, and a two-dimensional diffraction pattern of the equilibrium structure of 2,5-diiodothiophene was recorded. The retrieved distance between the two iodine atoms agrees with the quantum-chemically calculated molecular structure to be within 5%. The experimental approach allows for the imaging of intrinsic molecular dynamics in the molecular frame, albeit this requires more experimental data, which should be readily available at upcoming high-repetition-rate facilities.

1.
P. W.
Allen
and
L. E.
Sutton
, “
Tables of interatomic distances and molecular configurations obtained by electron diffraction in the gas phase
,”
Acta Crystallogr.
3
,
46
72
(
1950
).
2.
I.
Hargittai
and
M.
Hargittai
,
Stereochemical Applications of Gas-Phase Electron Diffraction
(
VCH Verlagsgesellschaft
,
Weinheim, Germany
,
1988
).
3.
R.
Henderson
, “
The potential and limitations of neutrons, electrons and x-rays for atomic-resolution microscopy of unstained biological molecules
,”
Q. Rev. Biophys.
28
,
171
193
(
1995
).
4.
K.
Lonsdale
, “
The structure of the benzene ring in C6(CH3)6
,”
Proc. R. Soc. London, Ser. A
123
,
494
515
(
1929
).
5.
D.
Crowfoot
,
C. W.
Bunn
,
B. W.
Rogers-Low
, and
A.
Turner-Jones
, “
The x-ray crystallographic investigation of the structure of penicillin
,” in
Chemistry of Penicillin
, edited by
H. T.
Clarke
(
Princeton University Press
,
Princeton
,
1949
), Chap. XI, pp.
310
366
.
6.
J.
Watson
and
F.
Crick
, “
Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid
,”
Nature
171
,
737
738
(
1953
).
7.
J. C. H.
Spence
, “
XFELs for structure and dynamics in biology
,”
IUCrJ
4
,
322
339
(
2017
).
8.
A. H.
Zewail
, “
4D ultrafast electron diffraction, crystallography, and microscopy
,”
Annu. Rev. Phys. Chem.
57
,
65
103
(
2006
).
9.
R.
Neutze
,
R.
Wouts
,
D.
van der Spoel
,
E.
Weckert
, and
J.
Hajdu
, “
Potential for biomolecular imaging with femtosecond x-ray pulses
,”
Nature
406
,
752
757
(
2000
).
10.
F.
Filsinger
,
G.
Meijer
,
H.
Stapelfeldt
,
H.
Chapman
, and
J.
Küpper
, “
State- and conformer-selected beams of aligned and oriented molecules for ultrafast diffraction studies
,”
Phys. Chem. Chem. Phys.
13
,
2076
2087
(
2011
); arXiv:1009.0871 [physics].
11.
A.
Barty
,
J.
Küpper
, and
H. N.
Chapman
, “
Molecular imaging using x-ray free-electron lasers
,”
Annu. Rev. Phys. Chem.
64
,
415
435
(
2013
).
12.
H.
Ihee
,
V.
Lobastov
,
U.
Gomez
,
B.
Goodson
,
R.
Srinivasan
,
C.
Ruan
, and
A. H.
Zewail
, “
Direct imaging of transient molecular structures with ultrafast diffraction
,”
Science
291
,
458
462
(
2001
).
13.
G.
Sciaini
and
R. J. D.
Miller
, “
Femtosecond electron diffraction: Heralding the era of atomically resolved dynamics
,”
Rep. Prog. Phys.
74
,
096101
(
2011
).
14.
C. J.
Hensley
,
J.
Yang
, and
M.
Centurion
, “
Imaging of isolated molecules with ultrafast electron pulses
,”
Phys. Rev. Lett.
109
,
133202
(
2012
).
15.
N. L. M.
Müller
,
S.
Trippel
,
K.
Długołęcki
, and
J.
Küpper
, “
Electron gun for diffraction experiments on controlled molecules
,”
J. Phys. B: At., Mol. Opt. Phys.
48
,
244001
(
2015
); arXiv:1507.02530 [physics].
16.
J.
Yang
,
M.
Guehr
,
T.
Vecchione
,
M. S.
Robinson
,
R.
Li
,
N.
Hartmann
,
X.
Shen
,
R.
Coffee
,
J.
Corbett
,
A.
Fry
,
K.
Gaffney
,
T.
Gorkhover
,
C.
Hast
,
K.
Jobe
,
I.
Makasyuk
,
A.
Reid
,
J.
Robinson
,
S.
Vetter
,
F.
Wang
,
S.
Weathersby
,
C.
Yoneda
,
M.
Centurion
, and
X.
Wang
, “
Diffractive imaging of a rotational wavepacket in nitrogen molecules with femtosecond megaelectronvolt electron pulses
,”
Nat. Commun.
7
,
11232
(
2016
).
17.
J.
Yang
,
X.
Zhu
,
T. J. A.
Wolf
,
Z.
Li
,
J. P. F.
Nunes
,
R.
Coffee
,
J. P.
Cryan
,
M.
Gühr
,
K.
Hegazy
,
T. F.
Heinz
,
K.
Jobe
,
R.
Li
,
X.
Shen
,
T.
Veccione
,
S.
Weathersby
,
K. J.
Wilkin
,
C.
Yoneda
,
Q.
Zheng
,
T. J.
Martínez
,
M.
Centurion
, and
X.
Wang
, “
Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction
,”
Science
361
,
64
67
(
2018
).
18.
J.
Küpper
,
S.
Stern
,
L.
Holmegaard
,
F.
Filsinger
,
A.
Rouzée
,
A.
Rudenko
,
P.
Johnsson
,
A. V.
Martin
,
M.
Adolph
,
A.
Aquila
,
S.
Bajt
,
A.
Barty
,
C.
Bostedt
,
J.
Bozek
,
C.
Caleman
,
R.
Coffee
,
N.
Coppola
,
T.
Delmas
,
S.
Epp
,
B.
Erk
,
L.
Foucar
,
T.
Gorkhover
,
L.
Gumprecht
,
A.
Hartmann
,
R.
Hartmann
,
G.
Hauser
,
P.
Holl
,
A.
Hömke
,
N.
Kimmel
,
F.
Krasniqi
,
K.-U.
Kühnel
,
J.
Maurer
,
M.
Messerschmidt
,
R.
Moshammer
,
C.
Reich
,
B.
Rudek
,
R.
Santra
,
I.
Schlichting
,
C.
Schmidt
,
S.
Schorb
,
J.
Schulz
,
H.
Soltau
,
J. C. H.
Spence
,
D.
Starodub
,
L.
Strüder
,
J.
Thøgersen
,
M. J. J.
Vrakking
,
G.
Weidenspointner
,
T. A.
White
,
C.
Wunderer
,
G.
Meijer
,
J.
Ullrich
,
H.
Stapelfeldt
,
D.
Rolles
, and
H. N.
Chapman
, “
X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser
,”
Phys. Rev. Lett.
112
,
083002
(
2014
); arXiv:1307.4577 [physics].
19.
S.
Stern
,
L.
Holmegaard
,
F.
Filsinger
,
A.
Rouzée
,
A.
Rudenko
,
P.
Johnsson
,
A. V.
Martin
,
A.
Barty
,
C.
Bostedt
,
J. D.
Bozek
,
R. N.
Coffee
,
S.
Epp
,
B.
Erk
,
L.
Foucar
,
R.
Hartmann
,
N.
Kimmel
,
K.-U.
Kühnel
,
J.
Maurer
,
M.
Messerschmidt
,
B.
Rudek
,
D. G.
Starodub
,
J.
Thøgersen
,
G.
Weidenspointner
,
T. A.
White
,
H.
Stapelfeldt
,
D.
Rolles
,
H. N.
Chapman
, and
J.
Küpper
, “
Toward atomic resolution diffractive imaging of isolated molecules with x-ray free-electron lasers
,”
Faraday Discuss.
171
,
393
(
2014
); arXiv:1403.2553 [physics].
20.
M. P.
Minitti
,
J. M.
Budarz
,
A.
Kirrander
,
J. S.
Robinson
,
D.
Ratner
,
T. J.
Lane
,
D.
Zhu
,
J. M.
Glownia
,
M.
Kozina
,
H. T.
Lemke
,
M.
Sikorski
,
Y.
Feng
,
S.
Nelson
,
K.
Saita
,
B.
Stankus
,
T.
Northey
,
J. B.
Hastings
, and
P. M.
Weber
, “
Imaging molecular motion: Femtosecond x-ray scattering of an electrocyclic chemical reaction
,”
Phys. Rev. Lett.
114
,
255501
(
2015
).
21.
H. N.
Chapman
,
P.
Fromme
,
A.
Barty
,
T. A.
White
,
R. A.
Kirian
,
A.
Aquila
,
M. S.
Hunter
,
J.
Schulz
,
D. P.
Deponte
,
U.
Weierstall
,
R. B.
Doak
,
F. R. N. C.
Maia
,
A. V.
Martin
,
I.
Schlichting
,
L.
Lomb
,
N.
Coppola
,
R. L.
Shoeman
,
S. W.
Epp
,
R.
Hartmann
,
D.
Rolles
,
A.
Rudenko
,
L.
Foucar
,
N.
Kimmel
,
G.
Weidenspointner
,
P.
Holl
,
M.
Liang
,
M.
Barthelmess
,
C.
Caleman
,
S.
Boutet
,
M. J.
Bogan
,
J.
Krzywinski
,
C.
Bostedt
,
S.
Bajt
,
L.
Gumprecht
,
B.
Rudek
,
B.
Erk
,
C.
Schmidt
,
A.
Hömke
,
C.
Reich
,
D.
Pietschner
,
L.
Strüder
,
G.
Hauser
,
H.
Gorke
,
J.
Ullrich
,
S.
Herrmann
,
G.
Schaller
,
F.
Schopper
,
H.
Soltau
,
K.-U.
Kühnel
,
M.
Messerschmidt
,
J. D.
Bozek
,
S. P.
Hau-Riege
,
M.
Frank
,
C. Y.
Hampton
,
R. G.
Sierra
,
D.
Starodub
,
G. J.
Williams
,
J.
Hajdu
,
N.
Timneanu
,
M. M.
Seibert
,
J.
Andreasson
,
A.
Rocker
,
O.
Jönsson
,
M.
Svenda
,
S.
Stern
,
K.
Nass
,
R.
Andritschke
,
C.-D.
Schröter
,
F.
Krasniqi
,
M.
Bott
,
K. E.
Schmidt
,
X.
Wang
,
I.
Grotjohann
,
J. M.
Holton
,
T. R. M.
Barends
,
R.
Neutze
,
S.
Marchesini
,
R.
Fromme
,
S.
Schorb
,
D.
Rupp
,
M.
Adolph
,
T.
Gorkhover
,
I.
Andersson
,
H.
Hirsemann
,
G.
Potdevin
,
H.
Graafsma
,
B.
Nilsson
, and
J. C. H.
Spence
, “
Femtosecond x-ray protein nanocrystallography
,”
Nature
470
,
73
(
2011
).
22.
J. C. H.
Spence
,
U.
Weierstall
, and
H. N.
Chapman
, “
X-ray lasers for structural and dynamic biology
,”
Rep. Prog. Phys.
75
,
102601
(
2012
).
23.
J. C. H.
Spence
and
R. B.
Doak
, “
Single molecule diffraction
,”
Phys. Rev. Lett.
92
,
198102
(
2004
).
24.

At infinite resolution, cross-correlation terms between the individual molecules could theoretically be measured.

25.
M.
Liang
,
G. J.
Williams
,
M.
Messerschmidt
,
M. M.
Seibert
,
P. A.
Montanez
,
M.
Hayes
,
D.
Milathianaki
,
A.
Aquila
,
M. S.
Hunter
,
J. E.
Koglin
 et al, “
The coherent x-ray imaging instrument at the linac coherent light source
,”
J. Synchrotron Radiat.
22
,
514
519
(
2015
).
26.
T.
Kierspel
,
J.
Wiese
,
T.
Mullins
,
J.
Robinson
,
A.
Aquila
,
A.
Barty
,
R.
Bean
,
R.
Boll
,
S.
Boutet
,
P.
Bucksbaum
,
H. N.
Chapman
,
L.
Christensen
,
A.
Fry
,
M.
Hunter
,
J. E.
Koglin
,
M.
Liang
,
V.
Mariani
,
A.
Morgan
,
A.
Natan
,
V.
Petrovic
,
D.
Rolles
,
A.
Rudenko
,
K.
Schnorr
,
H.
Stapelfeldt
,
S.
Stern
,
J.
Thøgersen
,
C. H.
Yoon
,
F.
Wang
,
S.
Trippel
, and
J.
Küpper
, “
Strongly aligned molecules at free-electron lasers
,”
J. Phys. B: At., Mol. Opt. Phys.
48
,
204002
(
2015
); arXiv:1506.03650 [physics].
27.
A. T. J. B.
Eppink
and
D. H.
Parker
, “
Velocity map imaging of ions and electrons using electrostatic lenses: Application in photoelectron and photofragment ion imaging of molecular oxygen
,”
Rev. Sci. Instrum.
68
,
3477
3484
(
1997
).
28.
U.
Even
,
J.
Jortner
,
D.
Noy
,
N.
Lavie
, and
N.
Cossart-Magos
, “
Cooling of large molecules below 1 K and He clusters formation
,”
J. Chem. Phys.
112
,
8068
8071
(
2000
).
29.
P.
Hart
,
S.
Boutet
,
G.
Carini
,
M.
Dubrovin
,
B.
Duda
,
D.
Fritz
,
G.
Haller
,
R.
Herbst
,
S.
Herrmann
,
C.
Kenney
,
N.
Kurita
,
H.
Lemke
,
M.
Messerschmidt
,
M.
Nordby
,
J.
Pines
,
D.
Schafer
,
M.
Swift
,
M.
Weaver
,
G.
Williams
,
D.
Zhu
,
N.
Van Bakel
, and
J.
Morse
, “
The CSPAD megapixel x-ray camera at LCLS
,”
Proc. SPIE
8504
,
85040C-1
85040C-11
(
2012
).
30.
H.
Stapelfeldt
and
T.
Seideman
, “
Colloquium: Aligning molecules with strong laser pulses
,”
Rev. Mod. Phys.
75
,
543
557
(
2003
).
31.
I.
Nevo
,
L.
Holmegaard
,
J. H.
Nielsen
,
J. L.
Hansen
,
H.
Stapelfeldt
,
F.
Filsinger
,
G.
Meijer
, and
J.
Küpper
, “
Laser-induced 3D alignment and orientation of quantum state-selected molecules
,”
Phys. Chem. Chem. Phys.
11
,
9912
9918
(
2009
); arXiv:0906.2971 [physics].
32.
S.
Stern
, “
Controlled molecules for x-ray diffraction experiments at free-electron lasers
,” Dr. rer. nat. dissertation (
Universität Hamburg
,
Hamburg, Germany
,
2013
).
33.
N. L. M.
Müller
, “
Electron diffraction and controlled molecules
,” Dr. rer. nat. dissertation (
Universität Hamburg
,
Hamburg, Germany
,
2016
).
34.
T.
Kierspel
, “
Imaging structure and dynamics using controlled molecules
,” Dr. rer. nat. dissertation (
Universität Hamburg
,
Hamburg, Germany
,
2016
).
35.
M. S.
Gordon
and
M. W.
Schmidt
, “
Advances in electronic structure theory: GAMESS a decade later
,” in
Theory and Applications of Computational Chemistry: The First Forty Years
, edited by
C. E.
Dykstra
,
G.
Frenking
,
K. S.
Kim
, and
G. E.
Scuseria
(
Elsevier
,
Amsterdam
,
2005
).
36.

The scattering vector s is defined by s = sin(Θ)/λ, with the scattering angle Θ; therefore, 2Θ is defined between the axis of the XFEL and a point on the detector.

37.
M.
Berger
,
J.
Hubbell
,
S.
Seltzer
,
J.
Chang
,
J.
Coursey
,
R.
Sukumar
,
D.
Zucker
, and
K.
Olsen
, XCOM: Photon Cross Section Database, version 1.5,
2010
.
38.
Y.-P.
Chang
,
D. A.
Horke
,
S.
Trippel
, and
J.
Küpper
, “
Spatially-controlled complex molecules and their applications
,”
Int. Rev. Phys. Chem.
34
,
557
590
(
2015
); arXiv:1505.05632 [physics].
39.
S.
Trippel
,
M.
Johny
,
T.
Kierspel
,
J.
Onvlee
,
H.
Bieker
,
H.
Ye
,
T.
Mullins
,
L.
Gumprecht
,
K.
Długołęcki
, and
J.
Küpper
, “
Knife edge skimming for improved separation of molecular species by the deflector
,”
Rev. Sci. Instrum.
89
,
096110
(
2018
); arXiv:1802.04053 [physics].
40.

χRed2=n=1N(ynf(n)σn)2N1, where N is the total number of considered radial bins, n is x-value corresponding to a radial bin, y is the corresponding experimentally determined value with a standard deviation σ, and f(n) is the corresponding value from the simulated diffraction pattern.

41.
L.
Holmegaard
,
J. L.
Hansen
,
L.
Kalhøj
,
S. L.
Kragh
,
H.
Stapelfeldt
,
F.
Filsinger
,
J.
Küpper
,
G.
Meijer
,
D.
Dimitrovski
,
M.
Abu-samha
,
C. P. J.
Martiny
, and
L. B.
Madsen
, “
Photoelectron angular distributions from strong-field ionization of oriented molecules
,”
Nat. Phys.
6
,
428
(
2010
); arXiv:1003.4634 [physics].
42.
S.
Trippel
,
J.
Wiese
,
T.
Mullins
, and
J.
Küpper
, “
Communication: Strong laser alignment of solvent-solute aggregates in the gas-phase
,”
J. Chem. Phys.
148
,
101103
(
2018
); arXiv:1801.08789 [physics].
43.
A.
Owens
,
A.
Yachmenev
, and
J.
Küpper
, “
Coherent control of the rotation axis of molecular superrotors
,”
J. Phys. Chem. Lett.
9
,
4206
4209
(
2018
); arXiv:1807.04016 [physics].
44.
S.
Trippel
,
T.
Mullins
,
N. L. M.
Müller
,
J. S.
Kienitz
,
K.
Długołęcki
, and
J.
Küpper
, “
Strongly aligned and oriented molecular samples at a kHz repetition rate
,”
Mol. Phys.
111
,
1738
(
2013
); arXiv:1301.1826 [physics].
45.
B.
Deppe
,
G.
Huber
,
C.
Kränkel
, and
J.
Küpper
, “
High-intracavity-power thin-disk laser for alignment of molecules
,”
Opt. Express
23
,
28491
(
2015
); arXiv:1508.03489 [physics].
You do not currently have access to this content.