INSIGHTS | P E R S P E C T I V E S
COMBUSTION CHEMISTRY
A radical approach to soot formation
Chain reactions of resonance-stabilized radicals turn molecules into clusters and nanoparticles
By Murray Thomson and Tirthankar Mitra
H
umans have used the high-temper-
ature synthesis of carbon particles as
a source of pigments since prehistoric
times (1), and today, “carbon blacks”
are used in tires, inks, coatings, plas-
tics, and electrical applications. For
most substances, solid particles become gases
when heated, but solid soot forms from gas-
eous molecules at high temperature through
a mechanism that is still not understood.
The high-temperature synthesis of carbon
particles (see the figure) occurs under oxy-
gen-starved conditions where simple hydro-
carbons can grow into larger molecules,
especially polycyclic aromatic hydrocarbons
(PAHs), in the gas phase. These large mol-
ecules cluster into carbon nanoparticles, a
process often referred to as soot inception.
From gas to soot
The initial formation of solid nanoparticles from gas molecules is a missing pathway in soot formation.
Johansson et al. propose a mechanism in which chain reactions of resonance-stabilized radicals (RSRs)
account for the growth of polyaromatic hydrocarbons (large RSRs) and their cluster growth.
Air
Air O OH Oxygen-species
Soot
oxidation OH
O
Air
Soot
growth
Air
Soot
nucleation
Missing pathways to nucleation?
PAH
growth
Pyrolysis
Fuel Flame zones
An overall picture of soot
formation shows a fame that
evolves from a blue fuel-rich
zone to the orange soot zone.
978 7 SEP TEMBER 2018 • VOL 361 ISSUE 6406
The carbon nanoparticles then grow and ag-
gregate to form larger, fractal-like structures.
On page 997 of this issue, Johansson et al. (2)
propose a new mechanism based on chain
reactions of resonance-stabilized radical
(RSR) species to explain this transition from
gas-phase molecules to nanoparticles.
Most models of soot inception use the
approach of Frenklach and Wang (3), who
modeled soot nucleation based on the
irreversible collision of PAH species that
link together to form a dimer. A dimer
would be better described as a molecular
cluster rather than soot, so it is not pos-
sible to define a clear moment when the
growing cluster becomes soot. Thus, many
models group dimers, clusters, incipient
soot, and mature soot into the soot model.
In later work, Eaves et al. (4) modeled the
formation of the dimer as a reversible pro-
RSR growth mechanism
Fractal
attack clusters
Further
Growing RSR growth
particle
.....
Soot
nuclei
Ring closure,
RSR regeneration
Chain elongation
Cyclopentadienyl
radical (initial RSR)
Radicals to the rescue
Molecules such as cyclopentadiene (bottom)
can form radicals that undergo chain reactions
and build up large RSRs (middle) and ultimately
fractal clusters of these larger molecules (top).
Published by AAAS
cess to be consistent with thermodynam-
ics. However, many researchers have noted
that PAH dimers held together by physical
forces (e.g., van der Waals interactions) are
not stable at high temperatures (5), and the
PAH dimers will break apart.
Thus, chemical bonds between the PAH
molecules in the cluster or particle are es-
sential to maintain particle stability at the
high flame temperatures. Several research-
ers have proposed pathways for covalent
bond formation, but these pathways use
Downloaded from http://science.sciencemag.org/ on September 6, 2018
irreversible reactions with high-energy bar-
riers. The challenge is to provide a detailed
reaction mechanism that explains the rapid
clustering yet is consistent with fundamen-
tal thermodynamics principles.
Johansson et al. propose a new mechan-
ism to overcome this challenge and pro-
vide pathways to rapid particle formation
that are fully consistent with fundamental
scientific principles. The CHRCR (cluster-
ing of hydrocarbons by radical-chain reac-
tions) mechanism invokes chain reactions
of RSR species. These RSR species are
radicals and highly reactive. Every step in
this sequence forms a more stable RSR,
and thus the reaction moves forward. The
chain reactions can begin with small RSR
species such as the cyclopentadienyl rad-
ical. The species growth is fast because the
reactions of these RSRs with other radical
and closed-shell hydrocarbons readily re-
generate larger RSRs. There is no need for
additional hydrogen-abstraction reactions
that can have a high energy barrier. The
large resonantly stabilized p-radical can
then undergo s-dimerization to form a
molecular cluster.
Although this dimerization process
forms a stable cluster, the cluster can re-
gain its radical character by losing an H
atom and form products with higher sta-
bility. Thus, the radical pool never gets
depleted. The proposed reaction steps are
very exothermic (they release energy) and
should be effectively irreversible. The clus-
ter can continue to grow via reactions with
other RSRs, unsaturated aliphatic species,
GRAPHIC: A. KITTERMAN/SCIENCE
or nonradical aromatic species. This pro-
cess would result in the fast and irrevers-
ible growth of large molecular clusters that
eventually leads to soot particles.
Department of Mechanical and Industrial Engineering, University
of Toronto, Canada. Email: murray.thomson@utoronto.ca
sciencemag.org SCIENCE
 The CHRCR mechanism proposed by Jo-
hansson et al. may eventually resolve the
mystery of how soot inception occurs. How-
ever, to test this hypothesis, there is a need to
establish detailed reaction rates for the many
reactions between RSRs and other radical
and stable hydrocarbon species, as well as for
the reactions forming the initial clusters and
the growth pathways of these clusters. Fur-
ther research is also necessary to identify how
these clusters transition into three-dimen-
sional solid structures. Once these reaction
rates are determined, the model predictions
can be validated quantitatively against soot
and gas-phase species measurements in lab-
oratory reactors and flames. These laboratory
experiments will need to span the wide range
of gas compositions, temperatures, and pres-
sures in which these carbon nanoparticles
are formed in practical applications. This
process is likely to iterate between model
improvement and validation. However, the
short lifetime of the RSRs may make their ex-
perimental measurement more challenging.
The issue of carbon particle formation is
not only of industrial interest. Soot or smoke
is unintentionally formed in combustion ap-
plications and in wildfires, and if released
“Further research is also
necessary to identify how
these clusters transition
into three-dimensional solid
structures.”
to the environment, soot contributes to air
pollution and climate change. Space dust in
interstellar regions is believed to form from
carbon-containing stars through a mechan-
ism similar to that for soot (6). Now that Jo-
hansson et al. have proposed an innovative
and promising new approach to understand-
ing soot inception, the hard work will be fill-
ing in the details of the model that should
help solve a mystery that has challenged re-
searchers for at least the last 40 years. j
REFERENCES
1. M.-J. Wang, C. A. Gray, S. R. Reznek, M. Mahmud,
Y. Kutsovsky, Carbon Black, in Encyclopedia of Polymer
Science and Technology (Wiley, 2003); https://doi.
org/10.1002/0471440264.pst477.
2. K. O. Johansson, M. P. Head-Gordon, P. E. Schrader,
K. R. Wilson, H. A. Michelsen, Science 361, 997 (2018).
3. M. Frenklach, H. Wang, Symp. Int. Combust. 23, 1559
(1991).
4. N. A. Eaves, S. B. Dworkin, M. J. Thomson, Proc. Combust.
Inst. 35, 1787 (2015).
5. T. S. Totton, A. J. Misquitta, M. Kraft, Phys. Chem. Chem.
Phys. 14 , 4081 (2012).
6. A. G. G. M. Tielens, Annu. Rev. Astron. Astrophys. 46, 289
(2008).
10.1126/science.aau5941
SCIENCE sciencemag.org
ASTROPHYSICS
Computational
astrophysics for the future
An open, modular approach with agreed standards
would facilitate astrophysical discovery
By Simon Portegies Zwart
S
cientific discovery is mediated by
ideas that, after being formulated in
hypotheses, can be tested, validated,
and quantified before they eventually
lead to accepted concepts. Computer-
mediated discovery in astrophysics
is no exception, but antiquated code that
is only intelligible to scientists who were
involved in writing it is holding up scien-
tific discovery in the field. A bold initiative
is needed to modernize astrophysics code
and make it transparent and useful beyond
a small group of scientists.
Scientific software is like a prototype in
a laboratory experiment; it must stimulate
experimentation. The eventual code is a
description of concepts and their relation-
ships, which are imperative for reproduc-
ibility and validating the results. In recent
decades, hardware performance and com-
puter languages have both changed dra-
matically. Software engineering has also
experienced major advances, such as multi-
lingual implementations and the introduc-
tion of design patterns. Industry and large
scientific endeavors, such as CERN, have
embraced these changes; in addition, their
software is built on various assisting pack-
ages to vitalize modularity, platform inde-
pendency, and message brokering. Although
leading to a better structure, these develop-
ments also lead to higher complexity (1) and
a sharp increase in the number of code lines
(2). The latter is particularly noticeable in
the growth of the Linux kernel (3).
Astronomical source code remains tiny
by industrial standards, and its structure
is characterized by developments dur-
ing the “software crisis” of 1965 to 1985,
when software was written as a long list
of instructions without formal structure
(4). The relative simplicity of these “dino-
source” codes facilitates their survival but
frustrates further development. Scientific
source code is experimental in much the
same way as laboratory experiments; it is
not a final concept and is never ideally or-
Leiden Observatory, Leiden University, 2300 RA Leiden,
Netherlands. Email: spz@strw.leidenuniv.nl
Published by AAAS
ganized because it is intended to mediate
exploration. By contrast, industrial code is
mature but restrains experimentation. Fur-
thermore, industry can afford dedicated
teams to design and maintain software,
whereas astronomical software develop-
ment is organized in indigent “families”
of researchers. A modular approach with
Downloaded from http://science.sciencemag.org/ on September 6, 2018
agreed standards is essential to embolden
astrophysical discovery by computer.
CITING AND SHARING
The simple structure of astronomical soft-
ware packages has enabled them to survive,
some even since the 1970s. Although this di-
nosource code is often written in an ancient
dialect, the underlying physics has hardly
changed. About 58% of these codes are
publicly available (5), but many are obfus-
cated because they have received multiple
updates in the form of patches, keeping the
deprecated code for backward compatibil-
ity. Existing code therefore forms no suit-
able basis for building a general framework.
We know little about undisclosed codes, but
it is unlikely that they are different.
Authors may decide not to distribute
their source code; this is generally moti-
vated by a desire to preserve a head start on
the competition, or for fear that erroneous
results produced by others discredit their
efforts. Such secretly developed codes are
of no help to the community and produce
unverifiable results. In experimental sci-
ences, failure to publish laboratory details
is equivalent to failure in properly describ-
ing an experiment (6), and this cannot be
much different for source code. But so long
as public codes are copied, adapted, or ex-
panded and eventually released under a
different name, one can hardly expect the
community to change its behavior. The ap-
parent lack of trust that sufficient credit
is given to code development can only be
lifted by enabling codes to be cited directly.
The Astrophysics Source Code Library
(7) provides a platform that mediates shar-
ing and citing of astronomical source code,
but it does not assign a digital object iden-
tifier (DOI). Such a service is provided by
Zenodo (8), and all ingredients to organize
the community are in principle available.
7 SEP TEMBER 2018 • VOL 361 ISSUE 6406 979
A radical approach to soot formation
Murray Thomson and Tirthankar Mitra

Science 361 (6406), 978-979.

DOI: 10.1126/science.aau5941

Downloaded from http://science.sciencemag.org/ on September 6, 2018

ARTICLE TOOLS http://science.sciencemag.org/content/361/6406/978

RELATED http://science.sciencemag.org/content/sci/361/6406/997.full
CONTENT

REFERENCES This article cites 5 articles, 1 of which you can access for free
http://science.sciencemag.org/content/361/6406/978#BIBL

PERMISSIONS http://www.sciencemag.org/help/reprints-and-permissions

Use of this article is subject to the Terms of Service

Science (print ISSN 0036-8075; online ISSN 1095-9203) is published by the American Association for the Advancement of
Science, 1200 New York Avenue NW, Washington, DC 20005. 2017 © The Authors, some rights reserved; exclusive
licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. The title
Science is a registered trademark of AAAS.