Internal Structure of Incipient Soot from Acetylene

Pyrolysis obtained via Molecular Dynamics Simulations

Khaled Mosharraf Mukuta , Anindya Gangulyb , Eirini Goudelib , Georgios
A. Kelesidisc,d , Somesh Roya,∗
a
Department of Mechanical Engineering, Marquette
University, Milwaukee, Wisconsin, 53233, USA
b
Department of Chemical Engineering, University of Melbourne, Victoria, Australia
c
Nanoscience and Advanced Materials Center (NAMC), Environmental and
Occupational Health Science Institute, School of Public Health, Rutgers, The State
University of New Jersey, 170 Frelinghuysen Road, , Piscataway, New Jersey,
08854, U.S.A.
d
Particle Technology Laboratory, Institute of Process Engineering, Department of
Mechanical and Process Engineering, ETH Zürich, Sonneggstrasse 3, CH-8092
Zürich, Switzerland

Abstract
A series of reactive molecular dynamics simulations is used to study the
internal structure of incipient soot particles obtained from acetylene pyroly-
sis. The simulations were performed using ReaxFF potential at four different
temperatures. The resulting soot particles are cataloged and analyzed to ob-
tain statistics of their mass, volume, density, C/H ratio, number of cyclic
structures, and other features. A total of 3324 incipient soot particles were
analyzed in this study. Based on their structural characteristics, the incip-
ient soot particles are classified into two classes, referred to as type 1 and
type 2 incipient soot particles in this work. The radial distribution of density,
cyclic (5-, 6-, or 7-member rings) structures and C/H ratio inside the parti-
cles revealed a clear difference in the internal structure between type 1 and
type 2 particles. These classes were further found to be well represented by
the size of the particles with smaller particles in type 1 and larger particles
in type 2. The radial distributions of ring structures, density, and C/H ratio
indicated the presence of a dense core region in type 2 particles, whereas no
clear evidence of the presence of a core was found in type 1 particles. In type

∗
Corresponding author: [Link]@[Link]

Preprint submitted to Carbon January 24, 2024

 2 incipient soot particles, the boundary between the core and shell was found
to be around 50%–60% of the particle radius of gyration.
Keywords:
Soot, Molecular Dynamics, Core-Shell structure, ReaxFF, Machine learning

1 1. Introduction
2 Soot is a harmful carbonaceous nanoparticle generated during combus-
3 tion of hydrocarbon fuels. Soot, also known as black carbon, can cause
4 serious health issues [1, 2] and acts as a major forcing factor in climate
5 change[3, 4]. The exact mechanism of the formation of soot particulates
6 from gaseous precursors is still unknown due to the complex chemical na-
7 ture of the hydrocarbon reaction network and time- and length-scale of the
8 soot formation processes. According to the present understanding, soot for-
9 mation occurs by a series of complex physicochemical events such as the
10 formation of gas-phase soot precursors including, but not limited to, poly-
11 cyclic aromatic hydrocarbons (PAHs), nucleation of incipient soot particles,
12 growth and maturation of incipient soot particles due to surface reactions,
13 aggregation by coagulation or coalescence, and decay of the particles by
14 fragmentation and oxidation [5, 6, 7, 8, 9]. The inception of soot particles
15 is arguably the least understood phenomenon among these processes and
16 the exact chemical reaction pathways of soot inception are not completely
17 known yet. Researchers agree that soot formation starts with forming small
18 gas-phase precursor molecules such as acetylene which leads to PAHs like
19 benzene, pyrene, and coronene [10, 11, 12]. The freshly formed PAHs then
20 combine to form the solid or liquid-like incipient soot particles [13, 14, 15].
21 These particles then start to grow by surface reactions and coalescence to
22 form larger soot particles [13, 16, 17, 18, 19].
23 Due to the complexity and scale of incipient soot particles, their exact
24 internal structures are not very well characterized yet. Recent studies have
25 shown incipient soot particles tend to have a condensed core of ring-like struc-
26 tures surrounded by a shell of chain-like structures [20]. As these incipient
27 particles mature, their internal structures evolve, which in turn affects their
28 physical and chemical properties.
29 There have been some recent breakthroughs in the experimental explo-
30 ration of the internal structure of incipient soot. For example, Chang et
31 al. [21] employed high-resolution transmission electron microscopy (HRTEM)

2
32 and scanning electron microscopy (SEM) to investigate the structural evolu-
33 tion and fragmentation of coal-derived soot and carbon black particles under
34 high-temperature air oxidation conditions. They also explored the onset
35 of micropores and the internal graphitic microcrystals using X-ray diffrac-
36 tion (XRD) and Raman spectra. Morajkar et al. [22] utilized HRTEM,
37 XRD, Raman spectroscopy, and inductively coupled plasma mass spectrom-
38 etry (ICPMS) to examine the transmission of trace metals from biodiesel
39 fuels to soot particles and the nanostructural irregularities of the soot. In
40 their study, Gleason et al. [23] indicated that the formation of soot nuclei in
41 an ethylene/nitrogen flame can be attributed exclusively to aromatic com-
42 pounds comprising one or two rings. Carbone et al. [24] conducted a compre-
43 hensive investigation of soot inception in a laminar premixed ethylene flame
44 and found that soot particles undergo an aging transformation from being
45 nearly transparent in the visible spectrum to a more graphitic-like composi-
46 tion. Using low-fluence laser desorption ionization (LDI) in conjunction with
47 HRTEM, Jacobson et al. [25], investigated the molecular composition of soot
48 particles to determine the PAH concentration in soot particles. The capabil-
49 ities of atomic force microscopy (AFM) were exploited by Barone et. al. [26]
50 to calculate particle size distribution functions under different sampling con-
51 ditions. In their study, Schulz et al. [27] conducted an investigation into
52 the initial phases of soot formation using AFM and observed the presence of
53 multiple aromatic compounds, some of which displayed noticeable aliphatic
54 side chains. Commodo et al. [28] investigated the initial phases of soot forma-
55 tion using X-ray, ultraviolet photoemission spectroscopy (UPS), UV-visible,
56 and Raman spectroscopy to show the coexistence of sp3 carbon and a more
57 advanced graphitic structure, which exhibits a slightly larger aromatic is-
58 land, a reduced band gap, and an increased density of states. In another
59 study, Commodo et al. [29] identified a noteworthy occurrence of aliphatic
60 pentagonal rings in the early stages of soot formation, particularly in close
61 proximity to the outer region of aromatic soot molecules, and it has been
62 suggested that the elimination of hydrogen from these molecules can result
63 in the creation of resonantly stabilized π-radicals [30]. This phenomenon has
64 also been theorized by Johansson et al. [31], Gentile et al. [32], and Rundel
65 et al. [33].
66 Even with such recent advancement in experimental findings, there is
67 still a lot of unknowns about the internal structure of soot. The limita-
68 tions of experimental methods can be compensated and complemented by
69 first-principle modeling such as molecular dynamics. With the development

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 70 of high-performance computational resources, reactive molecular dynamics
71 (RMD) simulation has become more affordable for studying complex reactive
72 networks. For soot-relevant RMD studies, the reactive force field (ReaxFF)
73 potential developed by van Duin et al. [34] for carbon, hydrogen, and oxygen
74 chemistry (CHO-parameters [35, 36]) is a popular choice. The ReaxFF poten-
75 tial can capture the physicochemical evolution of hydrocarbon systems in an
76 extensive range of temperatures and pressures. It is based on the bond order
77 between different atoms, which carry information related to bond breakage
78 and formation. In recent years, RMD simulations have been used to investi-
79 gate soot nucleation by pyrene dimerization [37], to shed light into the nucle-
80 ation and growth of incipient soot from PAHs, such as naphthalene, pyrene,
81 coronene, ovalene and circumcoronene [16], to explore the initial mechanism
82 of soot nanoparticle formation [38] and to examine the effect of oxygenated
83 additives on the reduction of diesel soot emissions [39].
84 Since RMD simulation provides detailed structural information at the
85 atomic scale, it can be an excellent tool for analyzing the internal structure
86 of incipient soot particles. For example, recently Pascazio et al. [40] looked
87 into the internal structure and the mechanical properties of incipient soot
88 particles using RMD simulation and quantified the amount of cross-linking
89 in the core and shell region of developing and mature soot particles. Mature
90 soot primary particles exhibit a distinct core-shell structure with a disorderly
91 condensed core of ring-like structures surrounded by a shell of chain-like
92 structures [20, 41].
93 Process temperature plays an important role in the development and
94 aging of soot particles. For example, in a recent study, Pathak et. al. [42]
95 studied graphitization induced structural transformation of candle soot at
96 different temperatures and found that increasing the temperature increases
97 the rate of graphitization that leads to more spherical and mature soot and
98 weakening of the correlation between graphitic nanostructure and surface
99 functional groups (SFGs). SFGs have been found to be connected to the
100 characteristics of soot aggregates, including the fractal dimension [43]. Since
101 soot morphology, maturity and reactivity are expected to be influenced by
102 temperature during acetylene pyrolysis [44], it is important to study the
103 internal structure of incipient soot particles at different temperatures.
104 In the present study, a series of isothermal RMD simulations using the
105 ReaxFF potential is conducted mimicking acetylene pyrolysis at different
106 temperatures (1350, 1500, 1650, and 1800K). A variety of physicochemical
107 features of these RMD-generated soot particles are then analyzed to shed

4
108 light on different types of incipient soot particles and to characterize the
109 internal structure of these particles obtained from RMD simulations.

110 2. Numerical Methodology

111 2.1. Simulation configurations
112 Following the methodology described in [45], 1000 acetylene molecules are
113 randomly placed in a cubic domain (75Å × 75Å × 75Å) at four different tem-
114 peratures, i.e., 1350, 1500, 1650, and 1800 K. The temperatures are chosen to
115 capture soot particles from various thermally activated systems. For statisti-
116 cal significance, at leach temperature, simulations are performed for at least
117 five times with different initial configurations. In total, 24 RMD simulations
118 were performed for four different temperatures. The RMD simulations are
119 performed using the Large-scale Atomic/Molecular Massively Parallel Simu-
120 lator (LAMMPS) [46] software. ReaxFF potential for hydrocarbons [34, 47]
121 is used to capture the chemical changes (bond breakage and formation) due
122 to reactive molecular collisions during acetylene pyrolysis. The bond length
123 between individual atoms is calculated at each timestep (0.25 fs) based on
124 the changes in the chemical environment to describe bond cleavage and for-
125 mation accurately [36]. This helps the model capture the chemical reactions
126 leading to radical formation during soot nucleation. Periodic boundary con-
127 ditions are assumed in all three dimensions. The coordinates of each atom are
128 calculated and updated using the velocity-Verlet algorithm [48] in conjunc-
129 tion with the Nose-Hoover thermostat [49]. A constant number, volume, and
130 temperature (NVT) ensemble strategy are used to run each simulation up to
131 10 ns. The simulation results are probed every 0.05 ns and the clusters of hy-
132 drocarbons that resembles primary soot particles are isolated, tabulated, and
133 analyzed. Each of these extracted clusters has at least 20 carbon atoms and
134 at least one 5-, 6-, or 7-membered ring structure following an earlier study
135 by Mukut et al.[50]. Features such as surface area and volume of primary
136 particles are calculated using MSMS software developed by Sanner [51] and
137 other physicochemical characteristics are analyzed mostly using MAFIA-MD
138 [52]. The open visualization tool (OVITO) [53] is used for visualization of
139 the molecular clusters.

140 2.2. Workflow

141 The workflow in this study can be summarized as:

5
142 1. Conduct RMD simulations at different temperature with various initial
143 configurations. and extract incipient soot particles from the trajectory
144 results.
145 2. Calculate chemical and morphological characteristics such as the num-
146 ber of atoms, C/H ratio, the radius of gyration, atomic fractal dimen-
147 sion, density, surface area, and volume.
148 3. Classify the soot particles based on all the calculated features using
149 machine learning techniques such as k-means clustering [54] and t-
150 distributed stochastic neighbor embedding (t-SNE) [55].
151 4. Investigate the internal distribution of several relevant features such as
152 distribution of cyclic/non-cyclic molecules, C/H ratio, density etc. and
153 find identifiable patterns in the distribution.

154 2.3. Extraction of physicochemical properties

155 From the RMD simulations, we extract the coordinates of each atom
156 present in the simulation box at regular time intervals via the trajectory file.
157 Each individual timestep is investigated separately by analyzing the atom
158 coordinates within the entire simulation domain, which contains both large
159 molecular clusters and small molecules. The large soot-like molecular clusters
160 are identified as the ones that have more than 20 carbon atoms and have at
161 least one 5-, 6-, or 7-member ring [50]. It is noted that in our case, the
162 smallest such cluster was found to have 65 carbon atoms. These clusters are
163 isolated using the cluster analysis tool from the OVITO Python module [53]
164 implemented in a unified Python script developed inhouse. Then the isolated
165 clusters are analyzed individually to calculate their physical, morphological
166 and chemical attributes. Some attributes are obtained trivially from the
167 trajectory files, e.g., number of atoms (N ), carbon to hydrogen ratio (Θ ),C/H

168 mass (Mp ), and molar mass (M ). Some other attributes like the radius of
169 gyration (Rg ), atomic fractal dimension (Df ), and density (ρ) are extracted
170 by simple algebraic and geometric analysis or by using empirical correlations
171 proposed in the literature and listed in Appendix B. The volume and the
172 surface area of incipient particles are calculated using MSMS software [51]
173 using a probe radius of 1.5 Å.
174 The identification and analysis of 5- /6- /7-member ring structures are
175 done using MAFIA-MD [52]. MAFIA-MD can analyze RMD trajectory files
176 to identify cyclic/ring structures in an atomic cluster. Not all cyclic struc-
177 tures identified are necessarily aromatic. As discussed in [52], it is difficult
178 to exactly confirm which cyclic structures are aromatic as the information

6
179 about aromaticity requires some approximations regarding the bond order
180 of aromatic bonds and establishment of planarity. To remove any confusion,
181 therefore, we used the terms “ring” or “cyclic” in this work instead of aro-
182 matic when discussing these internal structures in the soot clusters. The
183 numbers of 5-, 6-, and 7-member rings are denoted as N5 , N6 , N7 , respec-
184 tively, and the total number of rings is denoted as N© . Similarly, the number
185 of carbons in rings is denoted as N© and the number of non-cyclic carbons
186 in a particle is denoted as N¢ .
187 A sample of two particles and a list of their respective properties are pro-
188 vided in Appendix C. This entire set of features is used in the classification
189 of particles as discussed in Sec. 3.2. It must be noted here that while all the
190 above-mentioned properties were evaluated for each particle, this article only
191 focuses on the internal structure of the particles, which are characterized as
192 discussed in Sec. 2.4. Therefore, beyond their use in the classification of
193 particles, the detailed analysis of physical and morphological features such
194 as volume, surface area, radius of gyration, and atomic fractal dimension are
195 not the focus of this work.

196 2.4. Characterization of internal structure

197 We analyzed the internal structure of soot particles via the radial distri-
198 bution of carbon atoms, C/H ratio, and density inside the particle. In order
199 to compare different-sized particles on the same scale, we first normalized
200 the radius of particles by scaling each particle by its radius of gyration (Rg ).
201 Then each particle is divided in equal number of radial bins. Each radial
202 bin creates a spherical shell or strip as shown by the shaded yellow region of
203 interest in Fig. 1. We calculate various internal features in these spherical
204 strips and present them as a function of the normalized radial distance from
205 the center of mass of each spherical strip (r∗ = r/Rg ).
206 For example, let’s consider a strip of width ∆r, whose midplane is distance
207 r away from the center of mass. The number of cyclic and non-cyclic carbon
208 atoms in this strip (i.e., within a radial distance of r ± ∆r/2) are counted and
209 represented as a function of the normalized radius of the midplane (r∗ = r/Rg ),
210 as n© (r∗ ) and n¢ (r∗ ), respectively. The radial distribution of cyclic and non-
211 cyclic carbon per unit area (indicated by ′′ ) at a normalized distance r∗ are
212 then, respectively:

′′ n© (r∗ ) n¢ (r∗ )
N© (r∗ ) = ; N¢′′ (r∗ ) = (1)
4π(r∗ × Rg )2 4π(r∗ × Rg )2

7
 Figure 1: Schematic representation of the calculation of radial distribution of internal
features in the soot particle.

213 In a similar manner, the radial distribution of C/H ratio is also analyzed
214 for each particle. The C/H ratio of the entire particle is calculated as Θ = C/H

NC/N , where N and N

215 H C H are number of carbon and hydrogen atoms in the
216 entire particle, respectively. This C/H ratio is termed as the particle C/H
217 ratio (Θ ) to differentiate from the local C/H ratio (θ ), which is calculated
C/H C/H

218 using the number of carbon and hydrogen atoms in the spherical strips as
219 shown in Fig. 1. The local C/H ratio (θ ) is determined by calculating
C/H

220 the number of carbon (nC (r∗ )) and hydrogen (nH (r∗ )) atoms in a spherical
221 strip with the midplane at a normalized distance r∗ from the center of mass
222 (θ (r∗ ) = nC (r∗ )/nH (r∗ )). Finally, the local C/H ratio is normalized by the
C/H

223 corresponding particle C/H ratio

θ (r∗ )
θ∗ (r∗ ) =
C/H
(2)
C/H
Θ C/H

224 Similarly, the radial distribution of local density is also evaluated by di-
225 viding the simulated density of the thin spherical strip using Eqn. B.3 for the
226 strip (referred as local density, $(r∗ )) by the simulated density of the particle
227 (ρs ) as
$(r∗ )
ρ∗s (r∗ ) = (3)
ρs

8
228 3. Results and Discussion
229 3.1. Formation of incipient soot particles in RMD
230 During the RMD simulations, the system of atoms goes through differ-
231 ent chemical and physical interactions resulting in the formation of larger
232 atomic clusters due to the pyrolysis of acetylene. The evolution of one of
233 these atomic clusters is depicted in Fig. 2. Carbon and hydrogen atoms
234 are represented using black and red dots, respectively. First, the acetylene
235 molecules combine to form small linear chains (Fig. 2B: linearization) and
236 then transform into cyclic structures (Fig. 2C: cyclization). After cyclization,
237 the small clusters start growing due to both bond formation at the surface
238 and internal reorganization. These larger atomic clusters resemble incipient
239 soot particles (Fig. 2D–F). It is important to note that, the collisions are
240 stochastic in nature and the time required for an event, i.e. linearization,
241 cyclization, surface growth. etc., varies based on the initial configurations,
242 and therefore are omitted from the figure for generality. A similar formation
243 mechanism is also reported by Zhang et al. [56] for carbon-black simulations
and Sharma et al [45] for acetylene pyrolysis simulations.

Figure 2: A general representation of steps during the formation and evolution of incipient
soot cluster during acetylene pyrolysis (from a simulation performed at 1650 K).
244

9
245 The incipient soot clusters are extracted from the RMD simulations at
246 different timesteps to capture the growth. Each simulation is run at least
247 five times with a velocity field initialized randomly in each case to generate
248 soot particles with different evolutionary histories. In total, 3324 individ-
249 ual soot clusters are isolated from the RMD simulations (number of carbon
250 atoms ranging from 65 to 1503). The C/H ratios (Θ ) of these particles are
C/H

251 compared to the theoretical limits for PAHs in Fig. 3. Based on the com-
252 pactness, the PAHs can be classified into two categories: (a) peri-condensed
253 PAHs, where the carbon atoms in the aromatic structures can be shared by
254 more than two aromatic rings and (b) cata-condensed PAHs, where the car-
255 bon atoms in the aromatic structure can be shared by at most two aromatic
256 rings. Siegmann and Sattler [57] proposed a relationship between the number
257 of carbon and hydrogen atoms for both peri-condensed and cata-condensed
258 PAHs. Fig. 3 presents the C/H ratio and molar mass of the soot clusters
259 from different temperatures and compares it with the peri-condensed and
260 cata-condensed PAH zones derived from [57]. As observed from Fig. 3, the
261 soot clusters fall between the peri-condensed and cata-condensed boundaries,
262 indicating an intricate network of different types of aromatic and aliphatic
263 structures in incipient particles.
264 Using atomic force microscopy Commodo et. al. [29] showed that smaller
265 aromatic clusters (number of carbon atoms ranging from 6 to 55, lower than
266 what studied in this work) in the early stage of soot formation in a slightly
267 sooting premixed ethylene flame tend to be close the peri-condensed line.
268 However, in this work, we find that large clusters lie closer to cata-condensed
269 limit than peri-condensed limit, potentially indicating significant presence of
270 non-aromatic (i.e., aliphatic and alicyclic) structures.

271 3.2. Classification of incipient soot particles

272 We tagged, extracted, or calculated the physicochemical features (such
273 as Temperature, number of carbon atoms, number of hydrogen atoms, and
274 molar mass) for each particle. The complete set of features used in this study
275 is listed in Appendix C.1, and two sample particles with the entire feature
276 set are shown in Appendix C.2.
277 Our initial observation of trends of various internal and physicochemi-
278 cal features revealed a wide variation, indicating that these particles can be
279 classified into multiple groups based on their features. The classification of
280 the incipient soot particles is depicted in Fig. 4. We attempted two unsu-
281 pervised machine-learning techniques to extract unique classifications that

10
 Figure 3: C/H ratio vs. molar mass of soot clusters at different temperatures.

282 may exist in the incipient particle sample space. The first method is the
283 k-means clustering algorithm [54], which is used to label particles of differ-
284 ent classes based on all extracted features of the particles. Then we used
285 the t-dispersion stochastic neighbor embedding (t-SNE)[55] plot to display
286 the particle properties on a 2D map. In the t-SNE diagram, similar clusters
287 (i.e., potentially belonging to the same class) are expected to be close to each
288 other. Although the number of classes was not known a priori, trial and error
289 with k-means clustering revealed good results with two classes. For identifi-
290 cation purposes, these two classes are referred to as “type 1” and “type 2”
291 particles, respectively. The resulting t-SNE diagram is shown in Figure 4(a).
292 Looking closely at the two classes, we see that the particles exhibiting
293 similarity fall into a nearly continuous size range. For example, in the first
294 class, (type 1) the incipient particles have a lower total number of carbon
295 atoms (65 − 818) whereas in the second class (type 2) the particle have a
296 higher number of total atoms (759 − 1503). This essentially points to the
297 fact that the characteristics of the incipient particles change after a certain
298 level of growth: smaller particles (type 1) show different features and trends
299 than larger particles (type 2). It should be noted here that the number of
300 total carbon atoms is not a unique marker of the threshold between type 1

11
(a) A t-SNE diagram generated using all the 3324 incipient soot clusters with two different
k-means clusters.

(b) Some example particles from each class obtained from RMD sim-
ulations. The non-cyclic carbon atom structures are shown in purple
dots and the cyclic structures are shown in black. Hydrogen atoms are
omitted from the visualization for clarity.

Figure 4: Classification of incipient soot particles

12
301 and type 2 – as indicated by a small overlap in the number of carbon atoms
302 range between the types – but acts as a very good surrogate for threshold
303 identifier. In total, we have obtained 670 type 1 and 2654 type 2 incipient
304 particles from a total of 3324 particles. Fig. 4(b) depicts some example
305 particles from the analyzed sample space. Here, the non-cyclic carbon atom
306 structures are shown in purple dots and the cyclic structures are shown in
307 black, while hydrogen atoms are omitted from the visualization for clarity.

308 3.3. Comparison with experimental data

309 The particles obtained in the current study show very good match with
310 experimentally observed properties of incipient soot particles as reported in
311 the literature. For example, the mean density of the particles is our study is
312 calculated to be 1.53 ± 0.08 g/cm3 , which is is an excellent match with the
313 empirical soot density of by Johansson et al [58], who reported the value to
314 be 1.51 g/cm3 . More detailed comparison of average particle properties are
315 presented in [59].

316 3.4. Internal structure of incipient soot particles

317 The radial distributions of various quantities relevant to the analysis of
318 the internal structure of the incipient particles are presented as box and
319 whiskers plots in subsequent figures. In this visualization, every box includes
320 the data points within the second and third quartiles, the horizontal line
321 inside the box indicates the median value and whiskers represent the range
322 of the data. The statistics were found to be insensitive to the process tem-
323 perature. Hence aggregate data for all temperatures is presented here.
324 The radial distribution of cyclic and non-cyclic carbon atoms per unit area
325 for type 1 (Figs. 5(a)-5(b)) and type 2 (Figs. 5(c)-5(d)) incipient particles
326 as a function of the normalized radial distance from the center of mass is
327 shown in Fig. 5. The blue vertical line depicts the location where the radial
328 distance becomes equal to the radius of gyration (Rg ) of individual particles.
329 For type 1 particles, an abundance of non-cyclic carbon atoms is observed in
330 the central (e.g., less than 50% Rg ) region. The number of non-cyclic carbon
331 atoms is almost twice the number of carbon atoms in cyclic structures in
332 type 1 particles. Almost all the carbon atoms reside near the central region
333 of type 1 particles and the number of carbon atoms quickly drops to zero as
334 we go away from the center of mass. This indicates that in type 1 particles,
335 i.e., at the very early stages of soot formation, the number of non-cyclic
336 structures is significantly higher than the number of cyclic structures.

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 (a) (b)

(c) (d)

Figure 5: Radial distribution of (a,c) non-cyclic and (b,d) cyclic carbon atoms (N¢′′ (r∗ )
′′
and N© (r∗ )) in (a,b) type 1 and (c,d) type 2 soot particles as a function of the normalized
radial distance (r∗ = Rrg ) from the center of mass. The blue vertical line is at a radial
distance equivalent to Rg .

337 The type 2 particles, on the other hand, show a different trend where a
338 very concentrated region of cyclic carbon atoms is observed in the central
339 region of the particles. The concentration of cyclic carbon atoms slowly
340 decreases as the distance from the center of mass increases. The number of
341 non-cyclic carbon atoms increases from a very low value in the central region,
342 then reaches a steady value near the radius of gyration and then gradually
343 drops to zero as the distance increases beyond the radius of gyration. This
344 indicates that the non-cyclic carbon atoms are more likely to be present in the
345 outer region (what can be presumably considered near the particle surface)
346 of the type 2 incipient particles while the central region is dominated by the
347 cyclic carbon atoms.
348 Figure 5 suggests that the internal chemical structure of incipient soot
349 particles changes as the particles transition from type 1 to type 2. This in-

14
350 dicates the development of core-shell structures as the incipient soot grows
351 and matures. The presence of such core-shell structure has been theorized in
352 the literature. For example, Michelsen et. al. [60] used a fractal core-shell
353 model to explain the changes in the structure of soot aggregates and primary
354 particles at different heights of a laminar co-flow ethylene-air flame. Kholghy
355 et. al. [61] proposed a surface shell formation model to predict maturity of
356 soot primary particles. More directly, recently Botero et. al. [20] studied the
357 internal structure of soot particles using high-resolution transmission elec-
358 tron microscopy (HRTEM) to identify the PAH structures in the core and
359 shell regions, and suggested the presence of a stabilized core region indicat-
360 ing nano-structural mobility. Pascazio et. al. [40] utilized RMD simulation
361 and identified different levels of crosslinking in core and shell in hypotheti-
362 cal soot particles. Kelesidis et al. [62] also investigated oxidation dynamics
363 of carbonaceous nanoparticles having various core-shell structures using lat-
364 tice Monte Carlo simulations. The clear difference in the radial distribution
365 of cyclic and non-cyclic carbon atoms between type 1 and type 2 particles
366 supports these findings.
367 The changes in chemical properties inside the incipient soot particles can
368 also be observed in the radial distribution of carbon to hydrogen ratio. The
369 normalized local C/H ratio for type 1 (Fig. 6(a)) and type 2 (Fig. 6(b))
370 particles are plotted as a function of the normalized radial distance from the
371 center of mass in Fig. 6 using box and whisker plots. The blue vertical line
372 depicts the location where the radial distance becomes equal to the radius of
373 gyration (Rg ) of individual particles. The red horizontal line indicates where
374 the local C/H ratio is equal to the particle C/H ratio.
375 The normalized local C/H ratio increases up to a certain distance from
376 the center of mass and then starts to drop. For type 1 particles, the increase
377 in the local C/H ratio take longer distance from the center of mass, and the
378 median value gradually reaches a peak value slightly higher than the particle
379 C/H ratio (about 1.3 times). After that, the local C/H ratio starts to drop
380 and the median value reaches a value close to the particle C/H ratio at around
381 65% of the radius of gyration. The value stays close to the particle C/H ratio
382 up to the radius of gyration, and then slowly drops to zero. This indicates
383 a very small or no dense core region in type 1 particles. The demarcation
384 between the core and shell regions is not clear in type 1 particles because
385 of the absence of a pronounced core as the local C/H ratio remains close to
386 the particle C/H ratio. For type 2 particles, however, the local C/H ratio
387 increases rapidly in the central region and the median value reaches a peak

15
 (a)

(b)

∗ θC/H (r ∗ )
Figure 6: Radial distribution of normalized C/H ratio (θC/H (r∗ ) = Θ ) in incipient
C/H
∗ r
particles as a function of normalized radial distance (r = Rg ) from the center of mass.
C
The blue vertical line is at a radial distance equivalent to Rg . The H ratio of the strip
and the particle are the same along the red horizontal line.

16
388 value of about 1.7 times the particle C/H ratio. After that, the local C/H
389 ratio starts to drop and reaches a value equal to the global C/H ratio at
390 the radius of gyration. Unlike type 1 particles, the region where the median
391 of the normalized local C/H ratio is close to unity is very narrow in type 2
392 particles. This indicates that the dense core region of type 2 particles is
393 well-developed and the separation between the core and shell regions is more
394 pronounced than in type 1 particles.

(a)

(b)

∗
Figure 7: Radial distribution of normalized local density (ρ∗ (r∗ ) = "(r )
ρs ) inside incipient
∗ r
particles as a function of normalized radial distance (r = Rg ) from the center of mass.
The blue vertical line is at a radial distance equivalent to Rg . The density of the strip and
the particle are the same along the red horizontal line.

395 The radial distribution of the normalized density inside type 1 (Fig. 7(a))

17
396 and type 2 (Fig. 7(b)) incipient soot particles is presented in Fig. 7 as a
397 function of the normalized radial distance from the center of mass of soot
398 particles (r∗ ) as box and whisker plots. For type 1 particles, Fig. 7 shows a
399 very small dense central region that extends up to about 40% of the radius of
400 gyration. The local density of type 1 particles is maximum near the center of
401 mass, and it drops gradually as the distance from the center of mass increases.
402 For type 2 particles, on the other hand, the dense core region is larger and
403 extends up to about 50-60% of the radius of gyration. The local density of
404 type 2 particles stays close to the particle density up to around 60% of the
405 radius of gyration, and then it quickly drops.

406 3.5. The boundary between the core and shell

407 The results discussed so far indicate the presence of a core and shell
408 structure in incipient soot particles. This is further examined by looking
409 at the median values of normalized local density (ρ∗s ), normalized C/H ratio
410 (θ∗ ), and radial distribution of carbon atoms (N©
C/H
′′
and N¢′′ ) in Fig. 8 for both
411 type 1 (in red) and type 2 (in blue) incipient soot particles. No significant
412 trend is noticed from the radial distribution of non-cyclic carbon per unit
413 area (Fig. 8(d)). However, the normalized density (Fig. 8(a)), C/H ratio
414 (Fig. 8(b)) and the radial distribution of cyclic carbon atoms per unit area
415 (Fig. 8(c)) demonstrate unique common trends in type 2 particles, which is
416 not observed in type 1 particles. All of these quantities
417 1. reach a maximum value near the center of mass and decrease gradually
418 to a local minimum at a distance of about 50% of the radius of gyration,
419 2. show the presence of a plateau region between 50% and 60% of the
420 radius of gyration,
421 3. and drop monotonously after approximately 60% of the radius of gy-
422 ration.
423 The first region or the central region can be identified as the core of the
424 soot as it is near the center of mass, it is denser and contains more rings
425 than other regions (as seen in Fig. 5(b) and 5(d)). The local minima mark
426 the beginning of the boundary between the core and the shell. The narrow
427 plateau region can be thought of as the boundary region between core and
428 shell regions. And finally, the gradual descent of these quantities indicates
429 the shell region. In the type 1 particles, we can only see the gradual descent
430 stage, indicating that the core-shell demarcation is not yet developed, i.e.,
431 there is no developed core. The reason for such a trend in density, C/H

18
 (a) (b)

(c) (d)

Figure 8: Identification of core and shell based on the radial distribution of normalized
medians (a) density, (b) C/H ratio and radial distribution of the number of (c) cyclic and
(d) non-cyclic carbon atoms per unit area in incipient particles as a function of normalized
radial distance (r∗ = Rrg ) from the center of mass.

19
432 ratio and ring structures can be explained by the nature of the stacking of
433 cyclic molecules (disordered and ordered), as shown in Fig. 9. As observed
434 in the schematic in Fig. 9, the core region comprises an interconnected cross-
435 linked network of cyclic molecules while the shell region contains sheet-like
436 organization of cyclic molecules. Such structural differences in core and shell
437 are also supported by results presented by Pascazio et al. [40]. The core
438 size of 0.5 − 0.60Rg obtained here is also consistent with the core size of
439 0.5 − 0.75Rg suggested by lattice Monte Carlo simulations [62].

Figure 9: Schematic of core and shell structure of incipient particles.

440 4. Conclusion
441 A series of reactive molecular dynamics (RMD) simulations were per-
442 formed to study the evolution of incipient soot particles during acetylene
443 pyrolysis at four different temperatures. A total of 3324 incipient soot par-
444 ticles were obtained at different stages of evolution from these simulations.
445 The mass, volume, surface area, radius of gyration, density, C/H ratio, and
446 the number of cyclic structures were calculated for each particle. The inter-
447 nal structures of RMD-derived soot and their classification were investigated.
448 Using unsupervised machine-learning techniques, the incipient soot particles
449 are classified into two types – type 1 and type 2 – based on their morpho-
450 logical and chemical features. This classification was found to be very well

20
451 predicted by the size of the particles with smaller particles in the type 1 class
452 and larger particles in type 2. The internal structures of type 1 and type 2
453 particles show clearly distinct trends and features, indicating the two types
454 correspond to early and late stages of incipient soot. The internal structure
455 of the incipient particles from this investigation shows no direct or obvious
456 sensitivity to temperature for temperature ranging from 1350 to 1800 K.
457 Other conclusions drawn from the study are
458 1. Incipient soot particles comprise both cyclic and non-cyclic structures.
459 2. The core of type 1 particles is dominated by non-cyclic structures while
460 the core of type 2 particles is dominated by cyclic or ring structures.
461 3. The internal distribution of ring and non-ring structures indicates the
462 presence of a dense core region and a less dense shell region in type 2
463 incipient particles.
464 4. The core comprises an interconnected cross-linked network of cyclic
465 molecules while the shell region contains a sheet-like organization of
466 cyclic molecules.
467 5. The core of type 2 particles extend up to approximately 0.5 − 0.6Rg ,
468 followed by the shell region beyond 0.6Rg .
469 6. The core and core-shell demarcation is not developed in type 1 particles.

470 5. Acknowledgments
471 The research benefited from computational resources provided through
472 the NCMAS, supported by the Australian Government, The University of
473 Melbournes Research Computing Services and the Petascale Campus Ini-
474 tiative. K.M.M. and S.R. acknowledge funding support from the National
475 Science Foundation as some of this material is based upon work supported
476 by the National Science Foundation under Grant No. 2144290.

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733 [64] J. Theiler, Estimating fractal dimension, J. Opt. Soc. Am. A, JOSAA
734 7 (6) (1990) 1055–1073. doi:10.1364/JOSAA.7.001055.

735 [65] S. R. Forrest, T. A. Witten, Jr., Long-range correlations in smoke-

736 particle aggregates, J. Phys. A: Math. Gen. 12 (5) (1979) L109. doi:
737 10.1088/0305-4470/12/5/008.

738 Appendix A. Symbols and nomenclature

739 a: A parameter in Eqn B.4
740 A: Surface area of a particle (Å2 )

29
741 c: A parameter in Eqn B.4
742 Df : Atomic fractal dimension of a particle
743 mp,i : Mass of ith particle (kg)
744 M : Molar mass of a particle (kg/kmol)
745 Mp : Mass of a particle (kg)
746 n© : Number of cyclic carbon atoms at a specific location
747 n¢ : Number of non-cyclic carbon atoms at a specific location
748 N : Total number of atoms in the entire particle
749 N© : Number of rings in the entire particle
750 N5 : Number of 5-membered rings in the entire particle
751 N6 : Number of 6-membered rings in the entire particle
752 N7 : Number of 7-membered rings in the entire particle
753 NC : Number of carbon atoms in the entire particle
754 NH : Number of hydrogen atoms in the entire particle
755 N© : Number of cyclic carbon atoms in the entire particle
756 N¢ Number of non-cyclic carbon atoms in the entire particle
757 r: Local radius (Å)
758 Req : Volume equivalent radius (Å)
759 Rg : Radius of gyration (Å)
760 ρs : Simulated density of a particle (kg/m3 )
761 ρe : Empirical density of a particle (kg/m3 )
762 $: Local (actual) density (kg/m3 )
763 T : Temperature (K)
764 θ : Local C/H ratio
C/H

765 Θ : C/H ratio of the entire particle

C/H

766 V : Volume of a particle (Å3 )

767 wC : Mass of a carbon atom (kg)
768 wH : Mass of a hydrogen atom (kg)
769

770 Superscripts:
771 ∗: Denotes normalized value
772 ′′: Denotes per unit area value

773 Appendix B. Expressions for physical properties of soot particles

774 The trajectory files obtained from RMD simulations contain coordinates
775 of each atom with reference to a global reference frame. This coordinate
776 information along with the mass of each atom is used to calculate the coor-

30
777 dinate of the center of mass of each particle. The mass of a particle Mp is
778 calculated by summing up the mass of the atoms in the cluster. The volume
779 (V ) is calculated using MSMS [51] with a pore size of 1.5 Å. The volume
780 equivalent radius of a particle with volume V is calculated via Eqn. B.1.
! "1/3
3V
Req = (B.1)
4π

781 The radius of gyration (Rg ) is calculated following the standard definition
782 using Eqn. B.2. #$
N 2
i=1 mp,i ri
Rg = $N , (B.2)
i=1 mp,i

783 where ri is the distance of the ith atom from the center of mass, mp,i is the
784 mass of individual atoms, and N is the total number of atoms in the cluster.
785 The simulated density (ρs ) is calculated using the particle mass (Mp ) and
786 volume (V ) of the incipient particle using Eqn. B.3.
Mp
ρs = (B.3)
V
787 Empirical (bulk) density [58, 63] of an incipient particle is calculated using
788 Eqn. B.4.
% &
2 −1 wC Θ +wH
ρe = (0.260884a c) Θ +1
C/H

C/H
, (B.4)

789 where wC and wH are the molar masses of a carbon and hydrogen atoms, a
790 is the length of the graphite unite cell in the basal plane, c is the interlayer
791 spacing in Angstroms, and Θ represents the carbon to hydrogen ratio of
C/H

792 the cluster. More details can be found in [58, 63].

793 The atomic fractal dimension (Df ), following the approach used in [45],
794 is calculated using the sandbox method [64, 65] using Eqn. B.5.

log Mp (r)
Df = , (B.5)
log r
795 where Mp (r) is the mass of atoms in the cluster as a function of radial distance
796 from the center of mass. Please note that this “atomic” fractal dimension
797 is for a single incipient particle and is different from the traditional fractal
798 dimension used in aggregate characterization [45].

31
799 Appendix C. Physicochemical data used and analyzed in this study
800 Appendix C.1. Feature set
801 The feature set used in this study for each particle includes the following
802 1. Temperature (T )
803 2. Number of carbon atoms (NC )
804 3. Number of hydrogen atoms (NH )
805 4. Number of atoms (N )
806 5. Molar mass (M )
807 6. C/H ratio (Θ )C/H

808 7. Radius of gyration (Rg )

809 8. Atomic fractal dimension (Df )
810 9. Simulated density (ρs )
811 10. Empirical density (ρe ) (also referred to as the bulk density in literature)
812 11. Total number of cyclic structures (N© )
813 12. Fraction of cyclic carbon atoms (N©/NC )
814 13. Fraction of 5-member rings (N5/N© )
815 14. Fraction of 6-member rings (N6/N© )
816 15. Fraction of 7-member rings (N7/N© )
817 16. Surface area (A)
818 17. Volume (V )
819 18. Area to volume ratio (A/V )

820 Appendix C.2. Sample data

821 Figure C.10 shows two sample soot clusters and their properties as ex-
822 amples. These clusters, labeled as A and B, were extracted from a simulation
823 at 1500 K at two different times. The left side shows the molecular structure
824 of the particle and the three-dimensional volumetric representation by con-
825 structing a surface mesh using OVITO [53] (this is what the incipient particles
826 would actually look like). The physicochemical properties of these particles
827 as analyzed in this work for classification via machine-learning are tabulated
828 on the right side of the figure.

32
Figure C.10: Two sample soot particles and their attributes investigated in this study

33