Femtochemistry and femtobiology: ultrafast events in molecular science

544 Pages·2004·15.307 MB·English

by  Monique Martin, James T Hynes

PREFACE
This book reflects the heights of knowledge of ultrafast chemical processes attained in these
early years of the XXIst century: the latest research in femtosecond and picosecond
molecular processes in Chemistry and Biology, carried out around the world, is described
here in more than 110 articles. The results were presented and discussed at the Vlth
International Conference on Femtochemistry, in Paris, France, from July 6 to July 10, 2003.
The articles pubhshed here were reviewed by referees selected from specialists in the
Femtochemistry community, guaranteeing a collective responsability for the quality of the
research reported in the next 564 pages.
Femtochemistry is an ever-growing field, where new research areas are constantly opening
up, and one which both stimulates and accompanies the development of ultrafast
technologies. The award of the Nobel Prize to Ahmed H. Zewail in 1999 testifies to the
world-wide recognition of this field of Chemistry. Since the first Femtochemistry Conference,
held in Berlin in 1993, the studies of primary molecular events have quickly expanded to
include a large variety of molecular media —isolated molecules and clusters in supersonic
jets, solutions and liquids, polymers, solids and nanoparticules, nanostmctures and surfaces—
and an increasing variety of molecular systems with a clear growth in the number of studies
devoted to complex molecular ensembles and biological molecules. Progress in determining
molecular routes and mechanisms as well as in femtosecond optical pulse shaping has helped
to propel advances in the control of molecular dynamics, including complex molecular
systems and biological molecules in condensed phases. The increasing interest in
femtobiology and chemistry at the frontier with biology is an obvious indicator of the present
impact of life sciences in our society. New materials and reactions at surfaces are also some
of the relatively new topics that promise rapid developments. New methodologies and
technologies for probing and following in real time molecular dynamical phenomena have
appeared within the last ten years or so. These methods, based on multidimensional IR
spectroscopies, ultrafast X-ray and electron diffraction techniques, are well represented in this
book. Of ever-improving performance, they are now applied to the characterization of
structural dynamics of an increasing number of chemical and biological systems.
This book reports the state of research in Femtochemistry and Femtobiology presented at
Paris, at the Maison de la Chimie, in July 2003, representing the tenth anniversary of the
VI
conference. The five previous meetings of the series were held in various cities of Europe :
Berlin (1993) organized by Jorn Manz, Lausanne (1995) by Majed Chergui, Lund (1997) by
Villy Sundstrom, Leuven (1999) by Frans De Schryver and Toledo (2001) by Abderrazzak
Douhal. We wish to thank them all here for their help and support, with a particular
acknowledgment to our immediate predecessor Abderrazzak Douhal who was so generous
with his advice.
Among the novel research efforts presented at the Paris meeting were the Keynote Lecture
given by Ahmed Zewail (USA) and the six Plenary Lectures given by Huib Bakker (The
Netherlands), Herschel Rabitz (USA), Robin Hochstrasser (USA), Michael Wulff (France),
Graham Fleming (USA) and Gerhard Ertl (Germany). We thank them all for their
contributions.
We express our sincere thanks, for their generous contribution to the success of the
meeting, to the distinguished senior scientists who chaired a session at the meeting : Savo
Bratos (France), Guy Buntinx (France), A.Welford Castleman (USA), David Clary (England),
Frans De Schryver (Belgium), Ken Eisenthal (USA), Yann Gauduel (France), Bertrand Girard
(France), Joshua Jortner (Israel), Takayoshi Kobayashi (Japan), Karl Kompa (Germany), Jorn
Manz (Germany), Claude Rulliere (France).
We also express our gratitude to Pierre Potier, member of the French Academy of
Sciences, President of the Foundation of Maison de la Chimie for having honored us by his
presence at the opening of the Conference and his warm welcome to his "house". We also
express our appreciation to Pascale Briand, who was the joint Director of Ecole Normale
Superieure for Sciences during the preparation of the meeting, for her support and her
heartening and visionary talk at the opening session. Let both receive our warmest thanks.
The organization of the meeting in Paris gave us the opportunity to gather French experts
of the field in a French Advisory Committee : Jean-Yves Bigot (Strasbourg), Savo Bratos
(Paris), Guy Buntinx (Lille), Alain Fuchs (Orsay), Geoffrey Gale (Palaiseau), Yann Gauduel
(Palaiseau), Bertrand Girard (Toulouse), Jean-Louis Martin (Palaiseau), Claude Rulliere
(Bordeaux), Benoit Soep (Saclay), Michael Wulff (Grenoble). Let them find here our deep
thanks for their advice, contibutions and help.
We are very grateful to the members of the Local Organization Committee: Irene
Burghardt (Paris), Pascale Changenet-Barret (Paris), Guilhem Gallot (Palaiseau), Thomas
Gustavsson (Saclay), Damien Laage (Paris), Isabelle Lampre (Orsay), Jean-Pierre Lemaistre
(Paris), Christian Ley (Paris), Severine Martrenchard (Orsay), Pascal Plaza (Paris) and
Vll
Rodolphe Vuillemier (Paris), who all worked hard in a collective effort so that the meeting
would run smoothly, and who exhibited examplary responsibility, solidarity and friendship.
We also thank three PhD students and a postdoctoral fellow, Agathe Espagne, Mathilde
Mahet, Olivier David and Bruno Nigro, for their active and cheerful help. We also express our
gratitude to Dominique Ho Tin Hoe and Sandrine Faure who worked efficiently and
enthusiastically, most often behind the scenes. We wish to emphasize Sandrine Faure's
dedication in helping for the preparation of the present book and wish to thank her here once
more. We are also thankful for the assistance at the Department of Chemistry of ENS-Paris,
from Yvon Poncel, Anne Halloppe, Cristelle Berezaie, Daniel Jaouen and Jean-Frangois
Sallefranque.
Finally we gratefully acknowledge financial support from the following Agencies,
Companies and Institutions : European Science Foundation, Scientific Programme on
Femtochemistry and Femtobiology ULTRA, Conseil regional d'lle-de-France, Fondation de la
Maison de la Chimie, Ministere Delegue a la Recherche et aux Nouvelles Technologies,
Departement des Sciences Chimiques du CNRS, Departement de Recherche sur I'Etat
Condense, les Atomes et les Molecules (DRECAM)/CEA/Saclay, Ecole Normale Superieure,
Departement des Sciences Physiques et Mathematiques du CNRS, Section Ile-de-France de la
Societe Frangaise de Chimie, Optoprim, Thales-Laser, Photon Lines, Hamamatsu France,
Laser 2000, Spectra-Physics, Coherent, Melles Griot Industrie, Newport Micro-Controle,
Excel Technology France, Clark-MXR Europe-jyhoriba GmbH, Gibert-Joseph Book Store,
Paris.
Monique M. Martin
UMR CNRS-ENS 8640, PASTEUR, Department of Chemistry, Ecole Normale Superieure,
Paris, France
James T. Hynes
UMR CNRS-ENS 8640, PASTEUR, Department of Chemistry, Ecole Normale Superieure,
Paris, France
and
Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
December 2003
Femtochemistry and Femtobiology
M.M. Martin andJ.T. Hynes (editors)
© 2004 Elsevier B.V. All rights reserved.
Ultrafast Electron Diffraction and Transient Complex Structures
— From Gas Phase to Crystallography
Ahmed H. Zewail
Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics,
California Institute of Technology, Pasadena, California 91125 U.S.A.
ABSTRACT
This article highlights the recent development of ultrafast electron diffraction at Caltech. This
development has made it possible to resolve transient structures both spatially (0.01 A) and
temporally (picosecond and now femtosecond) in the gas phase and condensed media,
surfaces and crystals, with wide ranging applications. We also present some advances made
in the studies of mesoscopic ionic solvation and biological dynamics and function.
1. ULTRAFAST ELECTRON DIFFRACTION (UED)
The dynamics of molecular systems has now been studied with atomic scale resolution,
spanning the very small (Nal) to the very large (DNA, proteins and their complexes) [1].
X-ray and electron diffraction, if endowed with ultrafast temporal resolution, can provide the
unique ability of revealing all intemuclear coordinates of transient structures with very high
spatial resolution. In our laboratory, the method of choice has been ultrafast electron
diffraction, for the following reasons: First, the cross-section for electron scattering is six
orders of magnitude larger compared to x-ray scattering. Second, UED experiments are
'tabletop' scale and can be implemented with ultrafast (femtosecond and picosecond) laser
sources. Third, electrons are less damaging to specimens per useful elastic scattering event.
Fourth, electrons, because of their short penetration depth arising from strong interaction with
matter, can reveal transient structures in gases, surfaces and (thin) crystals.
The development of UED has evolved through different phases. The "dreaming phase" was
conceptual and was followed by technical and theoretical advances in order to develop the
methodology and obtain our first UED images—the "exploration phase". The two phases
culminated in the breakthrough developments (in 2001) of the third-generation apparatus
(UED-3) for the gas phase [2] and (in 2003) the fourth-generation apparatus (UED-4) for the
condensed phase and biological systems [3, 4]. These two generations launched the
"explosion phase", where we have been able to image complex molecular structures in the
four dimensions of space and time with atomic-scale resolutions. The detection sensitivity of
structural change is as low as 1% in the gas phase, and less than a monolayer in the
condensed phase. A variety of phenomena have been studied (Fig. 1), and a comprehensive
review of the principles and some applications has recently been published [5]—original
citations of developments are in [4, 5].
In UED, several disparate fields of study are involved: femtosecond pulse generation,
electron beam optics, CCD detection systems, ultrahigh vacuum (UHV) technology and
advanced computation. For UED-3 of isolated reactions, output from a femtosecond laser is
split into a pump path and an electron-generation path. The pump laser proceeds directly into
the vacuum chamber and excites a beam of molecules. The probe laser is directed toward a
back-illuminated photocathode where the laser generates electron pulses via the photoelectric
effect; the electrons are accelerated, collimated, focused, and then scattered by the isolated
molecules. The resulting diffraction patterns are detected with a CCD camera, and the images
are stored on a computer for analysis. The UED-3 apparatus is also equipped with a time-of-
flight mass spectrometer (MS-TOF) to aid in the identification of species generated during
the course of chemical reactions.
In UED-4, the new features include three interconnected UHV chambers—the sample
preparation, load-lock and scattering chambers. The crystal is mounted on a computer-
controlled goniometer for high-precision (0.005°) angular rotation; it can be cooled to a
temperature of 100 K. The preparation chamber has sputtering and cleaning tools, and is also
equipped with low-energy electron diffraction (LEED) and Auger spectroscopy (AS) for
characterization of the crystal surface. Molecules can be studied on the surface either as
physisorbed or chemically functionalized entities.
In UED-4, as in UED-3, we have characterized the electron and light pulses used. For the
30-keV electrons, we used in situ streaking techniques and, for light, the now standard
autocorrelation method. We have obtained the fastest streaking speed of 140 ± 2 fs/pixel in
UED-4, thus approaching the state-of-the-art in streak cameras. For the extraction field of
10 kV/mm, the spreading time is -20 fs. The measured streaking broadening ("pulse width")
is 322 ± 128 fs. Using the same electron gun design, Jianming Cao, a former member of this
group and now at Florida State University, has achieved -300 fs pulses, albeit with a
streaking speed of 250 fs/pixel. Dwayne Miller's group in Toronto recently reported - 600 fs
resolution. The coherence time of electrons is 10 fs or longer giving a coherence length on
the order of a micron. The initiation laser pulse duration is typically 120 fs, and the overall
temporal resolution is determined by the geometry of the experiment and the relative widths
(shapes) and speeds of the two pulses (see Fig. 2).
The temporally and spatially resolved transient structures elucidated by UED include
structures in radiationless transitions, structures in non-concerted organic reactions, structures
in non-concerted organometallic reactions, structures of carbene intermediates, dynamic
pseudorotary structures, non-equilibrium structures and conformational structures on
complex energy landscapes, transient structures of surfaces and bulk crystals, and solid-to-
Conformations on Complex Energy Landscapes
Bifurcations
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Fig. 1. Scope of UED applications
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liquid phase transitions. These studies were reported in the references cited above; for
reviews see [4, 5]. Here we give one prototypical example for gas phase reactions and
another for crystal surface restructuring and melting.
1.1. Structures in Reactions
We have directly observed the structural dynamics of isolated chemical reactions via
changes in diffraction patterns, using what we have termed the diffraction image referencing
(diffraction-difference) method. A prototypical case is that of the non-concerted elimination
reaction of dihaloethanes. It demonstrates the UED methodology of using different electron
pulse sequences to isolate the reactant, intermediates in transition, and product structures. The
reaction involves the elimination of two iodine atoms from the reactant to give the product.
The structures of all intermediates were unknown, and the challenge lay in determining the
structural dynamics of the entire reaction. As detailed elsewhere, this was achieved by
referencing the diffraction to different time frames (-95 ps, 0 ps, and +5 ps). The temporal
evolution of the two steps of the reaction was also recorded; for the fmal step as a rise
(25 ± 7 ps) and for the intermediate as a decay (26 ± 7 ps).
The molecular structure of the C2F4I intermediate was determined from the diffraction-
difference curves AsM(t; 5 ps; s). Both the bridged and classical C2F4I structures were
considered in the analysis of the diffraction data. The theoretical curves for the classical
structures reproduce the experimental data very well, whereas the fit provided by the
theoretical bridged structure is vastly inferior. Thus, we conclude that the structure of the
C2F4I radical intermediate is, in fact, classical in nature—^the iodine atom does not bridge the
two carbons. The structural parameters of the C2F4I intermediate are given in Fig. 3. The C-I
and C-C distances of the C2F4I intermediate are, respectively, longer and shorter than those
of the reactant, while the C-F' intemuclear distance in the radical site (-CF'2) is shorter than
that of the -CF2I site. These results elucidate the increased C-C and decreased C-I bond order
resulting from the formation of the transient C2F4I structure. Moreover, the ZCCF' and
ZIF'CF' angles become larger than the corresponding angles of the reactant (by --9° and -12''
respectively), suggesting that the radical center (-CF'2) of the C2F4I intermediate relaxes
following loss of the first I atom. The structures and dynamics reported for this reaction are
vital in describing the retention of stereochemistry in such class of reactions, and this is the
first example of resolving such complex structures during the transition.
1.2. Structures of Surfaces and Crystals
In UED-4, we studied the temporal evolution of bulk and surface structures with
atomic scale spatial resolution. The first study was on crystals of silicon, with and without
adsorbates. Referencing the diffraction-difference (Fig. 4) to the ground-state structure shows
the changes in the structure caused by the initiating pulse, from ground state pattern at
negative time to the observed change at positive time. The structural change is evident in the
shift with time of the in-phase Bragg peak of the rocking curve, while the increase in
vibrational amplitude is reflected in the broadening. The evolution takes place as a rise to a
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are the difeaction from the crystal (top); diffraction image referencing of Bragg spots
(middle) and of amorphous-to-liquid transition (bottom).