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31. T. L. Poulos, J. Kraut, J. Biol. Chem. 255, 81998205 (1980).

32. T. H. Yosca et al., Science 342, 825829 (2013).
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Chem. Soc. 114, 65926593 (1992).
34. P. Vidossich et al., J. Phys. Chem. B 114, 51615169 (2010).
ACKN OWLED GMEN TS

We thank D. Collison for assistance with EPR, P. Ortiz de Montellano

for discussions on the mechanisms, S. Fisher for assistance with
the joint x-ray/neutron refinement, and the University of Leicester
BioMedical Workshop for custom building of microspectrophotometry
equipment, and J. Devos and the D-lab for experimental support.
Atomic coordinates have been deposited in the Protein Data
Bank under accession codes 4CVI for ferric CcP and 4CVJ
for compound I. This work was supported by The Leverhulme
Trust (grant F/00 212/Q to E.L.R./P.C.E.M.), Biotechnology and
Biological Sciences Research Council (grant BB/C001184/1 to
E.L.R./P.C.E.M., and a studentship to E.J.M.), The Wellcome Trust
(grant WT094104MA to P.C.E.M./E.L.R.), an Institut Laue-Langevin
studentship (to C.M.C.) and beam time at LADI-III and BIODIFF

CATALYSIS

Assessing the reliability of calculated

catalytic ammonia synthesis rates
Andrew J. Medford,1,2 Jess Wellendorff,1,2 Aleksandra Vojvodic,1 Felix Studt,1
Frank Abild-Pedersen,1 Karsten W. Jacobsen,3 Thomas Bligaard,1 Jens K. Nrskov1,2*
We introduce a general method for estimating the uncertainty in calculated materials
properties based on density functional theory calculations. We illustrate the approach for
a calculation of the catalytic rate of ammonia synthesis over a range of transition-metal
catalysts. The correlation between errors in density functional theory calculations is
shown to play an important role in reducing the predicted error on calculated rates.
Uncertainties depend strongly on reaction conditions and catalyst material, and the relative
rates between different catalysts are considerably better described than the absolute
rates. We introduce an approach for incorporating uncertainty when searching for
improved catalysts by evaluating the probability that a given catalyst is better than a
known standard.

ith the surge in density functional theory (DFT) calculations of chemical and
materials properties, the question of the
reliability of calculated results becomes
increasingly urgent (1), particularly when
calculations are used to make predictions of new
materials with interesting functionality (25).
Evaluating the reliability of DFT calculations has
relied mainly on comparisons to experiments
or to data sets of higher-level calculations to provide a measure of the expected accuracy of directly calculated properties such as bond strengths,
bond lengths, or activation energies of elementary processes. The question is how such intrinsic
uncertainties in calculated microscopic properties transform into error bars on calculated complex properties, defined here as properties that
depend on several microscopic properties in a
1

SUNCAT Center for Interface Science and Catalysis, SLAC

National Accelerator Laboratory, Menlo Park, CA 94025,
USA. 2SUNCAT Center for Interface Science and Catalysis,
Department of Chemical Engineering, Stanford University,
Stanford, CA 94305, USA. 3Center for Atomic-scale Materials
Design (CAMD), Department of Physics, Technical University
of Denmark, DK-2800 Lyngby, Denmark.
*Corresponding author. E-mail: norskov@stanford.edu

SCIENCE sciencemag.org

complex way (6). Examples of such properties

include mechanical strength (7), phase stability
(8), and catalytic reaction rates (5).
We estimate the reliability of DFT energies
by choosing an ensemble of exchange-correlation
functionals to represent the known computational errors for a set of adsorption energies (911).
This ensemble of energies is used to calculate
the rates of the ammonia synthesis reaction via
microkinetic modeling. We choose this process
because it is well described both experimentally
and theoretically (1216) and has enough complexity to bring out important aspects of error
propagation through multiple layers of simulation. This approach directly captures correlations between systematic errors in the underlying
energetics, revealing that uncertainties on the
calculated rates exhibit a nontrivial dependence
on the reaction conditions as well as the material and that trends in catalytic activity are
considerably better described than the absolute rates.
To calculate energies and estimated errors, we
apply the Bayesian error estimation functional
with van der Waals correlation (BEEF-vdW), a
recent exchange-correlation density function-

(EU FP7 NMI3-II grant 283883), Bruker UK (Sponsorship of

A.J.F. and M.G.C.), and beam time at LADI-III and BIODIFF.
P.C.E.M., M.P.B., and E.L.R. designed the research; C.M.C., A.G.,
M.P.B., A.O., S.C.M.T, T.E.S., C.L.M., E.J.M., and P.C.E.M. performed
crystallographic experiments; C.M.C., A.G., M.P.B., S.C.M.T., A.O.,
T.E.S., E.L.R., and P.C.E.M. analyzed crystallographic data; C.M.C.,
A.J.F., M.G.C., J.B., and P.C.E.M. performed spectroscopic
experiments; C.M.C., A.G., A.J.F., M.G.C., E.L.R., and P.C.E.M.
analyzed spectra; and E.L.R., M.P.B., and P.C.E.M. wrote the paper,
with contributions from all authors.
SUPPLEMENTARY MATERIALS

www.sciencemag.org/content/345/6193/193/suppl/DC1
Materials and Methods
Figs. S1 to S6
Tables S1 and S2
References (3548)
4 April 2014; accepted 29 May 2014
10.1126/science.1254398

al tailored for surface chemistry with built-in

error estimation capabilities (11). The functional
was fitted to describe several different properties, including common adsorbate-surface bond
strengths, and an ensemble of density functionals
around BEEF-vdW was generated. This Bayesian
error estimation (BEE) ensemble was designed
to reproduce known energetic errors by mapping
them to uncertainties on the exchange-correlation
model parameters. Figure 1 illustrates this. Uncertainties on new calculations may then be estimated
by mapping back again: Random sampling of a
probability distribution for fluctuations of the
model parameters leads to a large ensemble of
different predictions of the same quantity. The
statistical variance of those predictions defines
the
error estimate on the BEEF-vdW result, sBEE
p
Var
p , where the ensemble predictions are
stacked in vector
p . Further details are provided
in (11, 17). This approach to quantitative error
estimation in DFT can be viewed as a structured
analysis of the sensitivity of DFT results to the
choice of exchange-correlation approximation.
An appropriately designed ensemble also captures correlated variations between DFT total energies and offers a consistent approach to keeping
track of possible sources of error when data from
multiple calculations are folded in composite postDFT frameworks, such as microkinetic models
used to analyze catalytic reactions.
For the ammonia synthesis reaction, microkinetic models provide the link between the calculated microscopic properties and the reaction
rate or turnover frequency (TOF). Here, we use
a relatively simple kinetic model based on N2
dissociation as the rate-limiting step, following
the mechanism described by Honkala et al. (16).
This model has previously been shown to capture the experimentally observed trends in catalytic activity for different catalysts (18); details
of the model can be found in (17, 18). We first
consider in some detail the rates of ammonia
synthesis over stepped Fe and Ru surfaces, which
are the industry-standard catalysts (14, 19, 20).
The calculated ammonia synthesis rate over iron
per active (step) site (the TOF) is shown in Fig.
2A as an Arrhenius plot at industrial conditions.
The red shaded area indicates that the estimated
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197

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20. H. Hori, T. Yonetani, J. Biol. Chem. 260, 349355 (1985).

21. S. L. Edwards, H. X. Nguyen, R. C. Hamlin, J. Kraut,
Biochemistry 26, 15031511 (1987).
22. A. E. Pond, G. S. Bruce, A. M. English, M. Sono, J. H. Dawson,
Inorg. Chim. Acta 275276, 250255 (1998).
23. J. E. Erman, T. Yonetani, Biochim. Biophys. Acta 393, 350357
(1975).
24. J. E. Huyett et al., J. Am. Chem. Soc. 117, 90339041 (1995).
25. Y. T. Meharenna, T. Doukov, H. Li, S. M. Soltis, T. L. Poulos,
Biochemistry 49, 29842986 (2010).
26. A. J. Sitter, C. M. Reczek, J. Terner, J. Biol. Chem. 260,
75157522 (1985).
27. H. B. Dunford, Peroxidases and Catalases: Biochemistry,
Biophysics, Biotechnology, and Physiology (Wiley, Chichester,
UK, ed. 2, 2010).
28. E. Derat, S. Shaik, J. Phys. Chem. B 110, 1052610533
(2006).
29. S. Shaik, D. Kumar, S. P. de Visser, A. Altun, W. Thiel, Chem.
Rev. 105, 22792328 (2005).
30. I. Efimov et al., J. Am. Chem. Soc. 133, 1537615383 (2011).

R ES E A RC H | R E PO R TS

error in TOF is generally less than one order of

magnitude, although there is a nontrivial dependence on reaction conditions that results in
larger uncertainties at extreme temperatures.
We also investigated the ammonia synthesis
rate over a stepped Ru surface for which there
are detailed experiments for comparison (Fig. 2B).
In this case, the magnitude of the prediction uncertainty is somewhat greater, around two orders of magnitude, and again varies with reaction
conditions. The calculated apparent activation
barrier (17) and N2 dissociation barrier are compared with experimental results in the inset of
Fig. 2B; the experimental value is within the
uncertainty of the calculation, corroborating the
surface and kinetic models employed.
One interesting feature of error propagation
through the kinetic model is the cancellation of
errors arising from correlation between model
inputs. To assess this effect, we compared the
uncertainty inferred by the BEE ensembles (red)
to uncorrelated ensembles (gray) in Fig. 2 [see
(17) for details]. The uncorrelated ensembles
substantially overestimate the error at low temperatures because the TOF varies monotonically
with the product of the rate constant (k) and the
free site coverage (q* ). The rate constant varies
exponentially with the activation energy and, in
regimes of intermediate adsorbate coverage, q*
will be very sensitive to variations in the energy
of the most abundant surface intermediate. A
positive covariance between the transition-state
energy and the energies of all intermediates (see
table S2) implies that an exchange-correlation
functional that predicts a strong binding of the
surface-bound species (lower q* ) will also yield a
very stable transition state (higher k), hence the
cancellation of possible errors. This reasoning is
general to other surfaces, reactions, and kinetic
models, although the magnitude of the effect will
depend on the details of the system.
Next, we compare catalytic rates and error
estimates for several different metal catalysts
calculated using the chosen kinetic model (see
Fig. 3A). As previously indicated, the uncertainty on the TOF depends considerably on the
catalyst. For the unreactive metals, the uncertainty is large, whereas it is considerably smaller
for the most active catalysts, Ru and, in particular, Fe. Furthermore, Fig. 3B
that
 demonstrates

TOF
and relative
error bars on relative TOFs TOF@Fe
nitrogen adsorption energies (EN EN@Fe) are
substantially smaller than on the absolute materials properties. This decrease in uncertainty is the
result of the correlation of errors between various
transition-metal surfaces (see table S3). Exchangecorrelation functionals that bind a given intermediate or transition state stronger on one metal
are likely to bind it stronger on another, and the
BEEF-vdW exchange-correlation ensemble captures this effect quantitatively. Figure 3B demonstrates that we can make statistically significant
predictions about the relative ammonia synthesis rates on different metals. The predictions are
in agreement with experimental data showing
that Ru and Fe are the most active catalysts for
ammonia synthesis at these conditions (14, 21).
198

11 JULY 2014 VOL 345 ISSUE 6193

Fig. 1. BEEF-vdW
functional and
ensemble. BEEF-vdW
prediction errors for 17
experimental adsorption
energies (blue horizontal
lines) and distribution
of adsorption energy
perturbations (shaded
histogram) that result
from applying perturbed
exchange-correlation
functionals from the
BEEF-vdW ensemble to
those systems. The inset
illustrates the exchange
part of the perturbed
functionals (red lines) in
terms of exchange
enhancement factor, Fx,
as a function of the
reduced electron density
gradient, s. The BEEF-vdW
Fx is shown in blue. Fluctuations
within the ensemble of functionals
are scaled such that the variance
of the resulting energy perturbations,
s2, reproduces the average square prediction error realized by BEEF-vdW. The original ensemble from (11)
reproduces errors on several properties.The present work concerns surface chemistry, so the fluctuations are
rescaled to reflect the expected prediction error for surface adsorption energies only [see (17)].

Fig. 2. Simulated Arrhenius plots. Arrhenius plot for ammonia synthesis on Fe(211) (A) and Ru(0001)
(B) step site as calculated with BEEF-vdW and the described microkinetic model at industrial conditions
(100 bar, 50% approach to equilibrium).The shaded red area corresponds to error estimates, and the gray
area corresponds to an uncorrelated model [see (17)]. In the inset of (B), the N2 dissociation barrier is
plotted against the apparent Arrhenius activation barrier for the Ru(0001) step site under conditions
comparable to (15). The principal component ellipses [see (17)] of the correlated (red) and uncorrelated
(gray) ensembles are shown, and the predictions are compared to experimental measurements taken
from (15, 19) (black error bars).

The nitrogen adsorption energy at the active

site is a good descriptor of ammonia synthesis
activity due to a set of linear scaling relations

between the adsorption energy of nitrogen and

the adsorption energies of the other intermediates, H, NH, NH2, and the NN transition state
sciencemag.org SCIENCE

RE S EAR CH | R E P O R T S

Fig. 3. Ammonia
synthesis rate trends.
Absolute TOFs on metallic
step sites of selected
metals plotted as a
function of nitrogen
adsorption energy (A)
and TOFs divided by the
TOF of Fe as a function of
nitrogen adsorption
energy relative to Fe
(B). The rate activity
map obtained from
linear scaling relations
between the adsorption
energy of nitrogen and
other intermediates is
shown in (C), where
the red line/area
corresponds to the
uncertainty on the
absolute/relative rate,
respectively. Linear
regression between the
dissociative adsorption
energy of N2 (2EN) and
the NN transition-state
energy is shown in the
inset, along with principal
component ellipses of
the metal ensembles
[see (17)].The probability
that a rate volcano has
an optimum at a given
nitrogen adsorption
energy is presented in
(D). The temperature is
673 K, total pressure is
100 bar, and approach to
equilibrium is fixed at 10%.

(18, 2224). Given these relations, the nitrogen

adsorption energy determines all other energies
in the problem (to within the accuracy of the
scaling relations), and the rate can be calculated
as a function of nitrogen adsorption energy. In
Fig. 3C, we apply such an approach to each density functional in the BEEF-vdW ensemble to
evaluate the consequence of an imperfect representation of exchange-correlation effects on a
descriptor-based model of surface chemistry. The
linear regression parameters between the nitrogen adsorption energy and the NN transition
state exhibit much smaller standard deviations
than the underlying energies used to construct
them (Fig. 3C, inset). The lower uncertainty on
scaling parameters results from cancellation of
error due to correlated energetics (tables S2 and
S3) and is general to the other intermediates in
the system, as shown in fig. S2. The resulting
ensemble of rate maps (Fig. 3C) shows that the
volcano-type relation between rate and nitrogen adsorption energy is well determined by the
SCIENCE sciencemag.org

Fig. 4. Rate probability map. The probability that

the ammonia synthesis TOF of a given catalyst is
higher than the TOF of iron step sites (calculated
with the self-consistent BEEF-vdW energetics) as a
function of nitrogen adsorption energy relative to
that of iron. Reaction conditions are given in Fig. 3.
The line corresponds to linear regression between
the adsorption energy of nitrogen and other intermediates as described in Fig. 3C and fig. S2.

calculations. Comparing Fig. 3, B and C, it is also

evident that the calculated rates for individual
metals agree with the descriptor-based model to
within the BEE uncertainty.
The descriptor-based analysis provides a simple method for computational design of new
catalysts (3, 5). Once a set of descriptors is identified and a mapping between the descriptors
and the catalytic activity has been constructed,
the search for new catalysts is reduced to finding
new materials with descriptor values near the
optimum. An essential question is how well the
position of the maximum in such activity maps
is determined (25). Figure 3D shows the relative
probability that the maximum of the ammonia
synthesis rate occurs at a given nitrogen adsorption energy. The position of the maximum
is 0.58 eV, with a standard deviation of 0.08 eV.
This uncertainty in the predicted optimum is considerably smaller than the >2 eV range spanned
by the nitrogen adsorption energies of the metals
included in this study. The optimum descriptor

value is therefore precisely determined relative

to the energetic differences between transitionmetal catalysts.
In computational materials design, the magnitude of the uncertainty associated with a given
predicted property is of less importance than
the confidence with which one can evaluate a
hypothesis. For ammonia synthesis catalysts,
for instance, we could look for materials that exhibit higher TOFs than the industry-standard
iron catalyst. Our analysis allows an evaluation of
the probability that a given catalyst has a TOF
greater than that of iron. The results in Fig. 4
provide support to the notion that despite uncertainties of several orders of magnitude in absolute values of predicted TOFs, it is possible to
draw strong scientific conclusions about which
new materials are promising for ammonia synthesis. The probabilities shown in Fig. 4 reflect
only the expected magnitude of uncertainty on
energetics from exchange-correlation effects and
neglect all other possible sources of error, such
as the surface model, reaction mechanism, and
descriptor-based dimensionality reduction. Nonetheless, the present analysis indicates an upper
bound to the reliability of theoretical predictions
for ammonia synthesis TOFs, and the probabilistic approach provides a convenient framework
for including additional sources of uncertainty.
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Data reported herein are available in the supplementary materials.

Support from the U.S. Department of Energy Office of Basic Energy

Ultrafast low-energy electron diffraction

in transmission resolves polymer/
graphene superstructure dynamics
Max Gulde,1 Simon Schweda,1 Gero Storeck,1 Manisankar Maiti,1 Hak Ki Yu,2
Alec M. Wodtke,2,3 Sascha Schfer,1 Claus Ropers1*
Two-dimensional systems such as surfaces and molecular monolayers exhibit a
multitude of intriguing phases and complex transitions. Ultrafast structural probing of
such systems offers direct time-domain information on internal interactions and couplings
to a substrate or bulk support. We have developed ultrafast low-energy electron diffraction
and investigate in transmission the structural relaxation in a polymer/graphene bilayer
system excited out of equilibrium. The laser-pump/electron-probe scheme resolves the
ultrafast melting of a polymer superstructure consisting of folded-chain crystals registered
to a free-standing graphene substrate. We extract the time scales of energy transfer
across the bilayer interface, the loss of superstructure order, and the appearance of an
amorphous phase with short-range correlations. The high surface sensitivity makes this
experimental approach suitable for numerous problems in ultrafast surface science.

1
4th Physical Institute, University of Gttingen, 37077
Gttingen, Germany. 2Max Planck Institute for Biophysical
Chemistry, 37077 Gttingen, Germany. 3Institute for Physical
Chemistry, University of Gttingen, 37077 Gttingen,
Germany.

*Corresponding author. E-mail: cropers@gwdg.de

200

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SUPPLEMENTARY MATERIALS

www.sciencemag.org/content/345/6193/197/suppl/DC1
Materials and Methods
Figs. S1 and S2
Tables S1 to S3
References (2628)

ACKN OWLED GMEN TS

IMAGING TECHNIQUES

he investigation of atomic-scale dynamics

with high spatiotemporal resolution yields
insights into ultrafast structural reorganizations associated with energy transfer
or phase transitions. Substantial progress
was made in establishing methods for the timeresolved structural analysis of bulk media, including
ultrafast implementations of x-ray crystallography (13), high-energy electron diffraction (46),
and microscopy (79), as well as time-resolved
x-ray and electron spectroscopy (10, 11). In contrast, structural dynamics at surfaces, interfaces,
and ultrathin films remain largely elusive, as the
surface signal in both x-ray and high-energy electron diffraction is typically masked by large bulk
contributions. This limits our ability to study
quasitwo-dimensional (2D) systems exhibiting
characteristic phase transitions and topologically
controlled ordering (12, 13), as well as the dy-

Science to the SUNCAT Center for Interface Science and

Catalysis is gratefully acknowledged. A.J.M. is grateful for
support by the U.S. Department of Defense through the
National Defense Science and Engineering Graduate
Fellowship Program.

namics of surface reconstructions and complex

adsorbate superstructures (14, 15). Ultrafast electron scattering in grazing incidence enhances the
surface signal (14, 16) but faces particular challenges in quantitative diffraction analysis.
Optimal surface sensitivity would be attained
with an ultrafast implementation of low-energy
electron diffraction (LEED). At electron energies of tens to a few hundreds of electron volts,
scattering cross sections are strongly increased,
which allows for probing depths of only a few
monolayers and has made LEED a widely used
tool for surface structure determination. However,
at such low energies, it has proven exceedingly
difficult to implement pulsed electron sources
that fulfill the requirements of an ultrafast diffraction experiment (1719), that is, short pulse
duration and low beam emittance. Laser-triggered
electron emission from nanoscale photocathodes
(20, 21) is expected to resolve some of these issues
(2224), providing well-collimated low-energy
electron pulses and a temporal resolution that is
comparable to state-of-the-art ultrafast x-ray or
high-energy electron diffraction. Motivated by these
prospects, we have undertaken the development
of a new diffraction apparatus.

17 March 2014; accepted 2 June 2014

10.1126/science.1253486

We have developed transmission ultrafast

LEED (T-ULEED) based on a nanometric needle
photocathode and demonstrate its capability to
resolve atomic-scale structural dynamics of surfaces and monolayer films with a temporal resolution of a few picoseconds. Specifically, we
studied the ultrafast laser-driven dynamics of a
polymer superstructure on freestanding monolayer graphene.
In the laser-pump/electron-probe scheme
(Fig. 1A), the sample is excited out of equilibrium
by amplified femtosecond laser pulses (800 nm
wavelength, 80-fs pulse duration, repetition rate
10 kHz, focal diameter about 100 mm). To minimize hot electron emission from graphene (25),
the pump pulse is temporally stretched to 3 ps by
dispersion, which, however, is still sufficiently
short to resolve the processes described below.
The pump-induced structural dynamics are probed
by ultrashort electron pulses emitted from a sharp
tungsten tip (50-nm radius of curvature), triggered by the second harmonic of the laser. These
electron pulses (up to 100 electrons per pulse) are
collimated and focused onto the sample at variable electron energies using an electrostatic lens
assembly in a geometry that we have recently
studied numerically (22). Scattered electrons are
subsequently recorded in a transmission geometry by a phosphor screen microchannel plate
detector (MCP, Hamamatsu F2226-24P). With our
laser-triggered low-energy electron source, diffraction patterns can also be recorded in backreflection and for a range of electron energies,
as demonstrated in the supplementary materials
(26) (figs. S6 to S8).
The electron pulse duration and the spatial
and temporal overlap (delay time, Dt = 0) of the
laser-pump and electron-probe pulses are determined via a transient-electric-field effect near a
bare transmission electron microscopy (TEM)
copper grid. Upon excitation of a single copper
grid bar with high peak intensity (fluence up to
30 mJ/cm2, unstretched pump pulses), a dense
electron cloud is emitted (25, 27), which may lead
to a spatial deflection of the passing electron pulse
(Fig. 2A). Projection images of the grid before
and after Dt = 0 are shown in Fig. 2B, acquired by
defocusing the pulsed electron beam. The central
distortion in the lower image indicates the extension of the pump-induced electron cloud. Using a
collimated electron beam passing a single mesh
sciencemag.org SCIENCE

Assessing the reliability of calculated catalytic ammonia synthesis

rates
Andrew J. Medford et al.
Science 345, 197 (2014);
DOI: 10.1126/science.1253486

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