MNRAS 481, 3052–3062 (2018) doi:10.

1093/mnras/sty2215

Molecular hydrogen formation in the interstellar medium: the role of

polycyclic aromatic hydrocarbons analysed by the reaction force and
activation strain model

Downloaded from https://academic.oup.com/mnras/article-abstract/481/3/3052/5105891 by University of Canberra user on 23 September 2018

César Barrales-Martı́nez,1 Diego Cortés-Arriagada2 and Soledad Gutiérrez-Oliva1‹
1 Laboratorio de Quı́mica Teórica Computacional (QTC), Departamento de Quı́mica-Fı́sica, Facultad de Quı́mica, Pontificia Universidad Católica de Chile,
Av. Vicuña Mackenna 4860, 7810000, Macul, Santiago, Chile
2 Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, PO Box

8940577, San Joaquı́n, Santiago, Chile

Accepted 2018 August 5. Received 2018 August 4; in original form 2017 December 27

ABSTRACT
The formation of H2 onto pyrene (from hydrogen atoms) was studied in the framework
of the Eley–Rideal mechanism, which was fully analysed for all the adsorption sites of
pyrene. The structural and electronic contributions to the activation energies were characterized
through the reaction force and activation strain model (ASM). The reaction force indicates
that the activation process of the hydrogen chemisorption is dominated by the structural
rearrangements of reactants rather than by electronic reordering. Furthermore, the ASM shows
that the structural rearrangements are driven by the approach of hydrogen to the pyrene surface,
which generates a strong repulsive interaction. However, the changes in the geometry of the
surface generate a minimal increase of the total energy, being negligible at the absorption
sites at the edge of the surface. For that reason, the process is most kinetically favoured at
the edge sites, which have lower activation energies (∼1–3 kcal mol–1 ) than the internal ones
(∼6 kcal mol–1 ). On the other hand, the recombination of hydrogen atoms for the subsequent
H2 formation is a barrier-less process, no matter the adsorption site of the carbonaceous
surface. The ASM analysis shows that the attractive interactions take place at the beginning
of the recombination process, they avoid that the energy barrier can be generated by structural
distortions. Both the chemisorption and the abstraction of the adsorbed hydrogen atom by
an incoming H atom, throughout the entire surface, are highly exoenergetic processes, with
reaction energy values in the range of −12 to −36 kcal mol–1 and −84 to −60 kcal mol–1 ,
respectively.
Key words: astrochemistry – molecular processes – ISM: molecules.

1 I N T RO D U C T I O N
Molecular hydrogen (H2 ) is the most abundant molecule in the
interstellar medium (ISM), and as such it is expected to play an
important role in the formation of more complex molecules. The
H2 formation process has not been well characterized to date, how-
ever, and has been an important focus of discussion in astrophysics.
The association reaction of two hydrogen atoms to form H2 has a
−1
low rate coefficient of k ∼ 10−29 cm3 s in the gas phase (Vidali
2013), and therefore this mechanism is unlikely to be responsible
for the high amount of H2 in the ISM at lower temperatures. It has
been proposed that interstellar dust grains could act as catalysts in
the formation of H2 , because the hydrogen atoms could easily ad-
 E-mail: msg@uc.cl
sorb and diffuse over these surfaces (Vidali 2013). It is known that
polycyclic aromatic hydrocarbons (PAHs) are components of dust
grains (Tielens 2008). They are present in many different environ-
ments in the ISM (Lau et al. 2016; Roser & Ricca 2015; Peeters
et al. 2017), and several theoretical studies have considered PAHs as
catalysts of H2 formation (Rauls & Hornekær 2008; Hirama, Ishida
& Aihara 2003; Rasmussen, Henkelman & Hammer 2011). PAHs
have been experimentally detected in the ISM as a mix of several
sizes (small species such as anthracene, pyrene and coronene, and
larger ones of more than 100 carbon atoms) and have been pro-
posed to be responsible for some diffuse interstellar bands (DIBs)
in the visible and near-infrared regions (Tielens 2008; Roser &
Ricca 2015). Previous theoretical works have shown that hydrogen
atoms can be chemisorbed on PAHs with low activation energies,
which range from ∼1 to ∼10 kcal mol–1 (Rauls & Hornekær 2008;
Goumans 2011; Wang et al. 2012; Denis & Iribarne 2009; David-

C 2018 The Author(s)

Published by Oxford University Press on behalf of the Royal Astronomical Society


Figure 1. Potential energy (red), E(ξ ), and reaction force (blue), F(ξ ), pro-
files of a single-step reaction. The green dashed lines delimit the transition-
state region, and the orange dashed line indicates the transition-state position.
son et al. 2014; Cortés-Arriagada et al. 2014). Experimentally, it
has been found that the H chemisorption onto highly oriented py-
rolytic graphite (HOPG) has an activation energy of 4.61 kcal mol–1
(Aréou et al. 2011), confirming the presence of an energy barrier.
Subsequently, H2 can be formed barrierless via the Eley–Rideal
mechanism (Rauls & Hornekær 2008; Bonfanti et al. 2011). How-
ever, the reaction still lacks a thorough analysis, especially regard-
ing the physical factors that give rise to the activation energies. The
Eley–Rideal mechanism of H2 formation onto PAHs consists of two
steps: (i) H chemisorption, and (ii) abstraction of the chemisorbed
hydrogen atom by another one that is not chemisorbed, forming H2
by recombination. In this paper, a complete analysis of both steps,
chemisorption and abstraction, is presented. The focus is on the
physical factors that govern the activation and relaxation processes.
Moreover, in order to understand why PAHs are good substrates
for the formation of the H2 molecule under ISM conditions, two
theoretical approaches to rationalize the activation energy barriers
are used.
2 R E AC T I V I T Y M O D E L S
2.1 Reaction force
Introduced by Toro-Labbé (1999), the reaction force is defined as
the negative of the derivative of the potential energy profile, E(ξ ),
with respect to the reaction coordinate (ξ ):
 
∂E(ξ )
F (ξ ) = − . (1)
∂ξ
F(ξ ) provides the elements to characterize the various reaction
mechanisms that might be operating along the reaction coordinate.
The reaction force profile presents two critical points for any el-
ementary step represented by an energy profile (Fig. 1 in red), in
which reactants (R) and products (P) are separated by an energy
barrier: a minimum at ξ 1 , and a maximum at ξ 2 (Fig. 1 in blue).
A natural partition of the reaction path into three reaction regions
emerges (Toro-Labbé et al. 2007, 2009; Politzer et al. 2005), where
the energy involved in each region is governed by different phys-
ical phenomena. The first region is termed the reactant region. It
is dominated mainly by structural rearrangements and is located
between ξ R and ξ 1 , as shown in Fig. 1. The second region is termed
the transition-state (TS) region. It ranges from ξ 1 to ξ 2 and con-
tains the TS structure at ξ TS . In this region, electronic reordering
dominates, with bond-forming and bond-breaking processes. The
Molecular hydrogen formation 3053
third region, termed the product region (defined between ξ 2 and
ξ P ), is also structurally intensive, and is where geometry relaxation
processes allow reaction products to be created.
If the F(ξ ) profile is integrated in the three regions, the energy
involved in each of them can be quantified:
 ξ1  ξET
W1 = − F (ξ ) dξ > 0, W2 = − F (ξ ) dξ > 0, (2)
ξR ξ1
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 ξ2  ξP
W3 = − F (ξ ) dξ < 0, W4 = − F (ξ ) dξ < 0. (3)
ξET ξ2
This allows a natural partition of the activation energy into two
contributions, which give insights about the physical nature of the
activation energy:
E ‡ = W1 + W2 . (4)
The first term on the right-hand side in equation (4), W1 , is the
necessary energy to bring the reactant molecules as close as possible
to each other in order to activate the reaction, and therefore its
character is mostly structural. On the other hand, W2 corresponds to
the energy necessary to reach the TS from ξ 1 . Because it is defined
within the TS region, W2 accounts mainly for electronic processes.
In this context, the relative weights of W1 and W2 in the activation
energy provide insight into its physical nature.
2.2 Activation strain model
Developed by Bickelhaupt and co-workers (Bickelhaupt 1999; van
Stralen & Bickelhaupt 2006; van Zeist et al. 2008; van Zeist &
Bickelhaupt 2010; Wolters & Bickelhaupt 2015; Kubelka & Bick-
elhaupt 2017; Bickelhaupt & Houk 2017), the ASM allows a parti-
tion of the total energy into two components. The first component is
termed the strain energy (Estr ), and takes into account the energy
cost to distort the reactants along the reaction coordinate without
interaction between them; the second component, termed the inter-
action energy (Eint ), is the energy absorbed or released when the
distorted reactants interact:
E(ξ ) = Estr (ξ ) + Eint (ξ ). (5)
The reaction force and ASM have been used to characterize the
reactivity of the Diels–Alder cyclo-addition reaction in order to
identify and quantify the driving and retarding forces that govern
chemical reactions (Politzer et al. 2014). These two models have
also been used to analyse the HCN/CNH isomerization reaction in
an astrophysical context (Dı́az et al. 2017). When combining these
models, the reaction work can be expressed in terms of strain and
interaction energies, as:
W1 = Estr,1 + Eint,1 , (6)
W2 = Estr,2 + Eint,2 . (7)
This decomposition of reaction works will be used to characterize
the physical phenomena underlying the activation process.
3 C O M P U TAT I O N A L D E TA I L S
All the calculations were performed at the density functional theory
(DFT) level, with the PBE functional (Perdew, Burke & Ernzer-
hof 1996) in combination with the Dunning correlation-consistent
polarized double-zeta basis set (cc-pVDZ) (Dunning 1989). The
PBE functional has performed well in describing non-covalent
MNRAS 481, 3052–3062 (2018)
3054 C. Barrales-Martı́nez, D. Cortés-Arriagada and S. Gutiérrez-Oliva
Figure 2. Labels of some carbon atoms on pyrene; the adsorption sites
appear with red numbers (1−5).
interactions of graphene-type surfaces with different adsorbates
(Cortés Arriagada, Sanhueza & Wrighton 2013b; Cortés-Arriagada,
Sanhueza & Santander-Nelli 2013a). In addition, the pure DFT func-
tional PBE describes with good accuracy the H chemisorption onto
carbonaceous surfaces in comparison with the hybrid functional
PBE0, indicating the negligible effects of exact exchange in the
functional (Rasmussen et al. 2011). Dispersion force corrections for
energies were included by means of the pairwise dispersion method
DFT-D3 (Grimme et al. 2010; Grimme, Ehrlich & Goerigk 2011)
with the Becke–Johnson damping scheme. In the DFT-D3 scheme,
the dispersion correction (Edisp ) is added to the SCF-DFT energy
(ESCF−DFT ), which is obtained with the PBE exchange-correlation
functional; then, the corrected total energies are expressed as a sum
of electronic and dispersion contributions as EDFT−D3 = ESCF−DFT
+ Edisp . Basis-set superposition errors (BSSEs) were corrected with
the geometrical counterpoise method (Kruse & Grimme 2012) and
using the gCP-D3 web service (http://wwwtc.thch.uni-bonn.de/).
The nature of the optimized structures of reactants (R) and prod-
ucts (P) was confirmed through vibrational frequency analysis,
which gives no imaginary frequencies for all the vibrational modes.
TSs were optimized according to the quadratic synchronous tran-
sit (QST3) methodology (Peng et al. 1996), and confirmed with
only one imaginary vibrational frequency. Potential energy profiles
were obtained by means of the intrinsic reaction coordinate (IRC)
methodology in reduced mass-weighted units (ξ R = 0 and ξ P =
1) (Fukui 1981). Natural bond orbital (NBO) analysis (Foster &
Weinhold 1980; Reed, Curtiss & Weinhold 1988) was performed
to obtain natural atomic charges, atomic spin densities and Wiberg
bond orders. Note that the H2 formation reaction is expected to
occur mainly inside dense interstellar clouds, where the molecules
are exposed to low-UV fluxes, this is without contribution from
excited states (Van Dishoeck 2014). Hence, the ground and lowest
spin states were used for all the systems involved in the H2 forma-
tion reaction. The open-shell systems were treated by unrestricted
calculations (UPBE). Calculations were carried out using the GAUS-
SIAN09 program (Frisch et al. (2009); dispersion corrections were
obtained using the ORCA 3.0.1 program (Neese 2012).
4 R E S U LT S A N D D I S C U S S I O N
4.1 Adsorption of a single hydrogen atom on pyrene
The first step of the hydrogen formation reaction to be analysed is the
adsorption of a single hydrogen atom onto pyrene. According to its
D2h symmetry, pyrene has five positions where chemisorption can
take place (Fig. 2). The reaction and activation energies associated
with this process are shown in Table 1.
MNRAS 481, 3052–3062 (2018)
For each internal adsorption site (1 and 2 in Fig. 2), the initial
physisorption takes place on the top (on the corresponding C atom)
and hollow (over the center of the 6-member ring) sites of pyrene, as
observed in related PAHs (Davidson et al. 2014; Ferullo, Domancich
& Castellani 2010; Bonfanti et al. 2007); however, our simulations
show that the chemisorption starts from the physisorption onto the
top sites. It is worthwhile to note that the most stable physisorption
states are those on the hollow position. However, in this study we
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are interested in analysing the reactions taking place on the top sites
because these are the ones from which chemisorption processes
initiate. Henceforth, any physisorption analysis will be referred to
the top one.
Physisorption occurs at interatomic distances of 3.1 Å with re-
spect to the adsorbent carbon atom (Ci , i = 1−5), with energies in
the range of −0.61 to −0.32 kcal mol–1 (Table 1). These physisorp-
tion energies are in reasonable agreement with those determined
from experimental studies of hydrogen adsorbed on a (0001) sur-
face of a graphite single crystal through atomic beam scattering
in ultra-high-vacuum (UHV) conditions (−0.92 kcal mol–1 ) (Ghio
et al. 1980). In addition, theoretical studies indicate that hydrogen
physisorption onto internal sites of coronene takes place at 3.0 Å
from the Ci atom, with an energy of −0.74 kcal mol–1 according to
PW91-D3 (Ferullo et al. 2010), −1.08 kcal mol–1 according to PBE-
D3 (Davidson et al. 2014) and −0.79 kcal mol–1 according to the
MP2 method (Bonfanti et al. 2007). Likewise, hydrogen physisorp-
tion onto anthracene takes place at 3.1 Å, with a physisorption en-
ergy ranging from −0.42 to −0.28 kcal mol–1 as determined from
PBE-D3 calculations (Ferullo, Castellani & Belelli 2016), where
the anthracene adsorption sites are analogous to the external sites
of pyrene. The less stable physisorption state is obtained on the
external sites (3−5) because dispersion effects are favoured over
the sites 1 and 2 rather than at the edges of pyrene. This is because
dispersion effects increase with the number of pairwise interactions
between atoms within a molecule. After the physisorbed state is
reached, five reaction paths (R1−R5, Fig. 3a) were analysed for the
chemisorption process according to the different adsorption sites
(C1 −C5 ).
The activation energies for hydrogen chemisorption onto the ad-
sorption sites 3−5 are in the range ∼1.26−2.83 kcal mol–1 , while
the adsorption barriers in the internal sites 1 and 2 are 5.54 and
6.38 kcal mol–1 , respectively. Hence, hydrogen atom chemisorption
is kinetically favoured onto the external sites of pyrene. In the TS
structures, the Ci −H distance is ∼2 Å when adsorption occurs on the
external sites, which is in agreement with the 2.15 Å reported by Fer-
ullo and co-workers onto anthracene (Ferullo et al. 2016), while the
Ci −H distance is 1.75 Å in the TS structure when adsorption occurs
onto the internal sites, which is similar to the reported value onto
pyrene and coronene (1.76 Å) (Cortés-Arriagada et al. 2014). On the
other hand, E◦ values indicate that chemisorption onto the edge
sites (R3−R5) is more exoenergetic. These differences are related to
the geometry that the mono-hydrogenated pyrene adopts once reac-
tion is completed because of the hybridization change of the Ci atom
(sp2 −→ sp3 ). The product of reaction R3−R5 is almost planar, al-
lowing a complete delocalization of the unpaired electron along the
whole π-system, whereas the geometric structure is distorted (not
planar) in the product of R1 and R2, and the electronic delocaliza-
tion is interrupted. This makes the edge-mono-hydrogenated pyrene
molecules the most stable species. The E◦ values reported in Ta-
ble 1 are in agreement with energy barriers and reaction energy val-
ues reported for hydrogen adsorption onto anthracene (Ferullo et al.
2016), pyrene (Rasmussen et al. 2011; Cortés-Arriagada et al. 2014)

Table 1. Physisorption energy Ephys , reaction energy E◦ , activation energy E‡, reverse activation energy Erev
and the works Wn from the reaction force model. Each work value has in parentheses their respective contribution to
‡
E‡ and Erev as appropriate. Ephys = E(pyr − H)physisorbed − (Epyr + EH ); E = E(pyr − H)chemisorbed − (Epyr + EH );
‡
E ‡ = E(pyr−H)ts − (Epyr + EH ); Erev = E(pyr−H)ts − E(pyr−H)chemisorbed . All energies are in kcal mol–1 .
Site Ci (i = 1−5) Ephys E◦ E‡
1 −0.61 −12.25 5.54
2 −0.52 −12.03 6.38
3 −0.36 −35.78 1.26
4 −0.32 −22.88 2.83
5 −0.38 −32.12 1.74
Figure 3. Potential energy profiles (a) and reaction force profiles (b) for
H chemisorption onto a pyrene surface. Different colours represent the
different adsorption sites.
and coronene (Rauls & Hornekær 2008; Cortés-Arriagada et al.
2014).
‡
The reverse activation energies (Erev ) are also reported in
Table 1; these are related to the hydrogen desorption process, reach-
ing values in the range of 37.04−17.79 kcal mol–1 . Desorption
from the external sites has a higher barrier than from the internal
ones, with R4 having a slightly lower barrier than the other exter-
nal sites. For comparison purposes, the hydrogen desorption energy
barrier from highly oriented pyrolytic graphite (HOPG) (analo-
gous to the internal sites of pyrene) is 13.8 kcal mol–1 as deter-
mined from experimental thermal desorption spectra (TDS) analysis
(Zecho et al. 2002); this value is in agreement with the thermal (at
10 K) corrected and zero-point energy-corrected (ZPE-corrected)
‡ remain almost unchanged in the reactant region, with an increase
reverse barriers for R1 of Grev = −15.65 kcal mol–1 (see Table
S3 in the Supporting Information), which is in agreement with a
theoretical study of a hydrogen atom desorbing from an internal
Molecular hydrogen formation 3055
‡
‡
Erev W1 W2 −W3 −W4
17.79 3.75 (68%) 1.79 (32%) 8.39 (47%) 9.40 (53%)
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18.41 4.37 (69%) 2.01 (31%) 8.14 (44%) 10.27 (56%)
37.04 0.79 (62%) 0.47 (38%) 21.81 (59%) 15.23 (41%)
25.71 1.90 (67%) 0.93 (33%) 14.47 (56%) 11.24 (44%)
33.86 1.15 (66%) 0.59 (34%) 19.38 (57%) 14.48 (43%)
site of a pyrene surface, showing a E‡ value of 14.5 kcal mol–1
(including ZPE; Cortés-Arriagada et al. 2014).
It should be noted that these energy profiles correspond to the
minimum energy path (shown in Fig. 3) connecting reactants to
products. However, other reaction paths were obtained as a function
of the angle of inclination of the hydrogen atom as it approaches
the surface. It was found that the reactions are very sensitive to
changes in this angle. For example, the minimum energy path for
reaction in site 1 is obtained when hydrogen approaches the surface
with an angle of 94◦ and the activation energy is 5.54 kcal mol-1
(Table 1); however when H approaches the surface with lower in-
clination angles the activation energy increases (see Table S1 in
the Supplementary Information), which could be high enough for
the reaction to occur in cold regions of the ISM. For the external
sites, dependence on the angle is lower. For example, for site 3
the minimum energy path is obtained when the H atom approaches
with an angle of 73◦ , and the activation energy is 1.26 kcal mol-1
(Table 1); but when the angle changes to 40◦ and 20◦ , the activa-
tion energy increases to 5.53 and 16.62 kcal mol–1 , respectively
(Table S1).
The reaction force and ASM were used to rationalize the nature
of the energy barriers. Three reaction regions were defined from the
critical points located on the F(ξ ) profile (Fig. 3b): the reactant (R),
transition state (TS) and product (P). The reaction works involved in
the energy barriers are depicted in Table 1, where W1 and W2 repre-
sent the works involved in the chemisorption barrier (E‡). Because
the hydrogen uptake above the TS distance [dCi −H (ξTS ) ≈ 1.8 − 2.0
Å] is driven mainly by dispersion forces, the work associated with
electronic effects (W2 ) is expected to be less than the structural
one (W1 ) in the chemisorption barrier. Indeed, the E‡ values are
governed mainly by structural changes, where the W1 parameter
represents 62–68 per cent of the required energy to reach the TS
structure. In addition, the ASM analysis (Fig. 4) shows that the
reaction energy in the reactant region is dominated mainly by the
repulsive interaction between the π-system of pyrene and the in-
coming hydrogen atom. A very small contribution from the surface
distortion of pyrene [Estr, 1 ∼ 1 kcal mol–1 ] is found for R1 and
R2 near the end of the reactant region, whereas the strain energy is
almost zero along the whole reactant region for R3−R5 (Table 2).
Moreover, Fig. 5 shows the changes in the geometrical parameters
of pyrene along the reaction coordinate, which are associated with
its surface reconstruction. The >Ci − Cj − Ck − Cl dihedral angle
is displayed to measure the changes in the pyrene planarity (>Ci −
Cj − Ck − Cl (ξ R ) = 180◦ ), and dCi −Cj is the distance between the
Ci atom and its adjacent carbon atoms (Cj ). The Ci −Cj distances
of only ∼0.01 Å with respect to the free pyrene. In contrast, the
>Ci − Cj − Ck − Cl angle decreases in the early stages of the
MNRAS 481, 3052–3062 (2018)
3056 C. Barrales-Martı́nez, D. Cortés-Arriagada and S. Gutiérrez-Oliva

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Figure 4. E(ξ ) (black line), Estr (ξ ) (red line) and Eint (ξ ) (blue line) profiles of (a) R1 and (b) R3 along the reaction coordinate. The vertical green dotted
lines delimit the transition-state (TS) region, and the orange dotted line shows the TS position. Panels (c) and (d) depict a zoom of the region ranging from ξ R
to ξ TS for R1 and R3, respectively. The R1 and R3 profiles are representative for the reactions onto internal and external sites, respectively.

Table 2. Energetic parameters from the ASM for the activation process. Estr,1 = Estr (ξ 1 ) − Estr (ξ R ); Estr,2 =
Estr (ξ TS ) − Estr (ξ 1 ); Estr = Estr,1 + Estr,2 ; Eint,1 = Eint (ξ 1 ) − Eint (ξ R ); Eint,2 = Eint (ξ TS ) − Eint (ξ 1 ); Eint =
Eint,1 + Eint,2 . All values are in kcal mol–1 .

Site Estr,1 Eint,1 Estr,2 Eint,2 W1 W2 Estr Eint E‡

Ci (i = 1 − 5)

1 0.94 2.81 1.51 0.28 3.75 1.79 2.45 3.09 5.54

2 1.06 3.31 1.51 0.50 4.37 2.01 2.57 3.81 6.38
3 0.07 0.72 0.36 0.11 0.79 0.47 0.43 0.83 1.26
4 0.18 1.72 0.74 0.19 1.90 0.93 0.92 1.91 2.83
5 0.11 1.04 0.44 0.15 1.15 0.59 0.55 1.19 1.74

chemisorption in reactions R1 and R2, with a decrease of at least 5◦
until the end of the reactant region. However, when the adsorption
occurs on the edges of pyrene (R3−R5), the decrease in the >Ci −
Cj − Ck − Cl angle is lower, with a change of only 2◦ entering in
the TS region. Therefore, the magnitude of W1 is associated with
the hydrogen approximation to pyrene with a minimal contribution
of the required substrate reconstruction of carbonaceous surfaces
under hydrogen chemisorption.
The main electronic events that are characterized by works W2
and W3 take place entering into the TS region, which ranges in
Ci −H distances from dC−H (ξ 1 ) ≈ 2.0 to dC−H (ξ 2 ) ≈ 1.3 Å for
systems R1−R2, and from dC−H (ξ 1 ) ≈ 2.3 to dC–H (ξ 2 ) ≈ 1.4 Å
for systems R3−R5. W2 is involved in the activation energy, and it
represents the non-spontaneous electronic work required to reach
the TS. In that region, positive (repulsive) Eint (ξ ) reaches a max-
imum value before the TS at dCi−H ≈ 1.8 Å for R1−R2 and at
dCi−H ≈ 2.2 Å for R3−R5, and then starts to decrease, indicating
that some attractive interactions begin to occur, which could be re-
lated to the Ci −H bond-forming process. Note that these attractive
interactions act later in the internal sites of pyrene: this is when
the hydrogen atom is closer to Ci , and where the surface is more
distorted. Thus, the breaking of the electronic delocalization along
the whole π-system of pyrene (its reconstruction) takes place in
the region characterized by W2 (from ξ 1 to ξ TS ). It reduces the re-
pulsive interactions, allowing the attractive interactions to begin to
act, so that the Ci −H bond process takes place, especially in the
internal sites of pyrene. Once the TS is reached, the >Ci − Cj −
Ck − Cl is ∼172◦ and ∼176◦ in systems R1−R2 and R3−R5, re-
spectively. After the TS is reached, the chemisorption is driven by
spontaneous electronic rearrangements characterized by W3 , which

MNRAS 481, 3052–3062 (2018)


Figure 5. Structural parameters of the pyrene molecule along the reaction path for the adsorption of a single hydrogen atom on its surface.
‡ tion. Conversely, the dihedral angle continues to decrease in R1 and
represents 44−59 per cent of the reverse energy barrier (Erev ). The
contribution of the electronic work W3 is at least 10 per cent higher
in systems R3−R5 than in R1 and R2. This is because several charge
displacements in the ξ TS −ξ 2 range are taking place, as noted from
the charge profiles (Fig. S6), creating strong attractive interactions,
such as seen in the Eint,3 values (Table 3), which are due to the
Ci −H bond-forming process.
At the beginning of the product region, some electronic activ-
ity (mainly associated with Ci rehybridization) is still taking place,
reaching the final state between ξ 2 and ξ P . However, it is important
to note that the energy released in this region is related to the spon-
taneous structural relaxation owing to the change in the planarity
(see the dihedral angle >Ci − Cj − Ck − Cl in Fig. 5) caused by the
Ci −H bond, which provides a high stabilization energy as reflected
in the Eint,4 values. The higher adsorption stability in the edge sites
of systems R3−R5 is caused by the fact that the mono-hydrogenated
pyrene is planar at ξ P . For that reason, the desorption process (re-
verse reaction) from edge positions is a highly unfavourable reac-
Molecular hydrogen formation 3057
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R2, forming an almost tetrahedral structure inside of pyrene, so that
desorption can take place at a lower energetic cost as depicted by
‡
the Erev values. In summary, the structural work is the main con-
tribution in the chemisorption barrier (W1 > W2 ). Otherwise, the
contribution is dependent on the desorption site in the desorption
process: W3 < W4 if desorption occurs from the internal sites, while
the electronic rearrangements dominate if the desorption occurs
from the edge sites (W3 > W4 ), enhancing the desorption barrier
‡
(Erev ). However, the stability of the products is high enough that
the desorption process is avoided at lower temperatures, allowing
recombination in further steps.
4.2 H2 formation via the Eley–Rideal mechanism
The next step in the reaction mechanism is the abstraction of the
chemisorbed hydrogen atom by an incoming H atom, resulting
in the formation of H2 and the recovery of the pyrene molecule.
MNRAS 481, 3052–3062 (2018)
3058 C. Barrales-Martı́nez, D. Cortés-Arriagada and S. Gutiérrez-Oliva
Table 3. Energetic parameters from the activation strain model for the activation process. Estr, 3 = Estr (ξ 2 ) − Estr (ξ TS );
Estr,4 = Estr (ξ P ) − Estr (ξ 2 ); Estr,rev = Estr,3 + Estr,4 ; Eint,3 = Eint (ξ 2 ) − Eint (ξ TS ); Eint,4 = Eint (ξ P ) − Eint (ξ 2 );
Eint, rev = Eint,3 + Eint,4 . All values are in kcal mol–1 .
Site Estr,3 Eint,3 Estr,4
Ci (i = 1−5)
1 4.30 −12.69 15.19
2 3.91 −12.05 16.58
3 6.19 −28.00 22.69
4 5.99 −20.46 22.47
5 5.84 −25.21 23.31
Figure 6. Various mono-hydrogenated pyrene molecules. The reaction be-
tween an H atom and the molecule is called (a) R1, (b) R2, (c) R3, (d) R4
and (e) R5.
Because H2 is expected to be formed by recombination between
a chemisorbed and a physisorbed hydrogen atom (considering a
low-temperature environment), the Eley–Rideal mechanism was
adopted (Cazaux & Tielens 2002). According to the five possible
mono-hydrogenated pyrene molecules (Fig. 6), there are at least
five possible ways to recombine hydrogen atoms to form H2 .
The reaction to be analysed is represented as:
H − pyrene · +H· −→ pyrene + H2 (Fig. 7). At this point, it
is necessary to point out that the reactant structure (H − pyrene ·
+ H ·), from which the recombination takes place, must behave as
a birradical because both H − pyrene and the hydrogen atom are
open-shell systems. However, the final products (pyrene + H2 ) are
closed-shell systems in their ground states. In order to account for
these considerations, a broken-symmetry wavefunction approach
was implemented to allow for a high-spin and low-spin structure
in reactants and products, respectively. This is a singlet open-shell
electronic structure along all the path of the H2 recombination
reaction. In this sense, Fig. 8(a) shows the potential energy profile
for this reaction according to three electronic schemes, where the
reaction is assumed to proceed in (i) a triplet state, (ii) a singlet
closed-shell state, and (iii) a singlet open-shell state. Because the
H atom is assumed to approach mono-hydrogenated pyrene from
an infinite distance, the singlet and triplet states must be degenerate
states. Because the singlet closed-shell state does not describe the
beginning of the process properly, a singlet open-shell state is
adopted instead. Only at the end of the reaction does the singlet
closed shell give a good description of the process. From the
energy profiles in Fig. 8(b), it is clear that hydrogen recombination
is a barrierless process, as has been previously reported (Rauls
& Hornekær 2008; Hirama et al. 2003; Rasmussen et al. 2011),
MNRAS 481, 3052–3062 (2018)
‡
Eint,4 W3 W4 Estr,rev Eint,rev Erev
−24.59 8.39 9.40 19.49 −37.28 17.79
−26.85 8.14 10.27 20.49 −38.90 18.41
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−37.92 21.81 15.23 28.88 −65.92 37.04
−33.72 14.47 11.25 28.46 −54.18 25.71
−37.79 19.38 14.48 29.15 −63.00 33.86
indicating that attractive interactions govern the process from the
beginning of the reaction.
Table 4 displays the reaction works, where it can be seen that the
process is dominated mainly by structural relaxation once the bonds
are formed, with a higher contribution of W4 to the whole potential
energy. The profiles depicted in Fig. 8(b) show that this part of the
reaction (ξ 2 −ξ P ) is quite similar for all the reactions, indicating
that the surface reconstruction is independent of the adsorption site
(all reactions have a similar W4 contribution to E◦ ). A previous
theoretical study showed, for a group of 12 diatomic dissociation
processes, that the structural contribution to the dissociation energy
is 73 per cent, indicating that there are some differences between a
diatomic dissociation process and the H abstraction via the Eley–
Rideal mechanism (Toro-Labbé et al. 2007).
Because of the nature of the abstraction reaction, the ASM anal-
ysis was performed in two partition schemes according to the
stages of the reactions, as has been previously implemented in the
HCN/CNH isomerization reaction assisted by water (Dı́az et al.
2017). Fig. 9(a) shows the ASM profile considering the H atom and
hydrogenated pyrene as fragments, which is useful for analysing
the first recombination step (hydrogen approaching H-pyrene). In
addition, Fig. 9(b) shows the ASM analysis considering H2 and the
pyrene molecule as fragments, which is useful for analysing the H2
desorption process, where the profile begins at the products. For the
H-approaching process (Fig. 9a), the Estr contribution is almost
zero until the maximum of the reaction force (ξ 2 ); therefore, the
first stage of the recombination is dominated by a high stabilization
energy, which is generated by strong attractive interactions between
reactants in the early stages of the reaction. In this case, the F(ξ )
maximuma (ξ 2 ) indicates where the Ci −H bond begins to break and
H2 begins to desorb.
Fig. 9(b) shows that the H2 desorption process is governed by a
repulsive interaction between it and pyrene, which spontaneously
drives the process. Moreover, this process is favoured owing to the
return of the π-system on pyrene, allowing a complete electronic
delocalization over its surface. These two factors favour stability,
as noted from the W4 values (Table 4).
Once the H2 molecule is formed, it reaches a physisorbed state,
which has a similar stability for all the different starting reactants
(Table 4); however, H2 is placed onto the Ci atom (top) for reactions
in internal sites and onto the centre of the carbon ring (hollow) for
reactions onto external ones (Fig. 10). These results are in agree-
ment with theoretical studies of PAH−H2 interactions, where H2
approaches perpendicular to the PAH plane (Heine, Zhechkov &
Seifert 2004; Tran et al. 2002). These Ephys values are very small
with respect to the high E◦ released at the end of the reaction;
therefore, H2 molecule can easily desorb to the gas phase. It should
be noted that this reaction takes place in the absence of an energy
 Molecular hydrogen formation 3059

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Figure 7. Reaction scheme of H2 formation via the Eley–Rideal mechanism from a mono-hydrogenated (C1) pyrene molecule. The spin density of reactants
is shown, where violet and cyan colors indicate the alpha and beta spin density respectively (isosurface = 0.015 a.u.).

Figure 9. E(ξ ) (black line), Estr (ξ ) (red line) and Eint (ξ ) (blue line)
profiles of the (a) forward and (b) reverse reaction on site 1 as representative
Figure 8. (a) Potential energy profiles obtained in three different spin mul-
(all the reactions show similar profiles). The vertical green dotted lines
tiplicities: triplet state (green), singlet closed shell (red) and singlet open
indicate the maximum of F(ξ ), ξ 2 .
shell (black). (b) Potential energy profile for the abstraction and H2 forma-
tion onto mono-hydrogenated pyrene in the five possible sites.
barrier, regardless of the angle of the H approximation to the H atom
chemisorbed on the surface.

Table 4. E◦ values, reaction works W3 and W4 for the five different 5 A S T RO P H Y S I C A L I M P L I C AT I O N S
reactions, physisorption energies (Ephys ) for H2 over the pyrene molecule,
and the distance between H2 and the pyrene molecule in the physisorbed
This study has established that the H2 molecule can be formed on
state (in Å). All energetic parameters are in kcal mol–1 (Ephys = EH2 + a pyrene molecule in high-density regions of the ISM with low-
Epyrene − Epyrene−H2 (physisorbed) ). UV flux, for example in dense molecular clouds, where PAHs are
expected to be in their neutral form (Allamandola, Tielens & Barker
Site E◦ −W3 −W4 Ephys d(H2 − pyrene) 1989). These results indicate that the hydrogen chemisorption is
Ci (i = 1−5) the rate-determining step of the reaction. The reactivity models
employed in this study indicate that it is not surface distortions that
1 −83.86 32.87 (39%) 50.99 (61%) 0.93 2.81 (top)
are the main cause of the energy barriers in this kind of reaction, but
2 −84.08 34.88 (41%) 49.20 (59%) 0.90 2.85 (top)
rather the repulsive interaction between the reactants that can take
3 −60.33 22.91 (38%) 37.42 (62%) 0.94 2.78 (hollow)
4 −73.22 23.67 (32%) 49.55 (68%) 0.95 2.77 (hollow)
place in the early stages of reactions. For this reason, the process
5 −63.99 24.49 (38%) 39.50 (62%) 0.94 2.77 (hollow) is more efficient at the edge sites of PAHs than at the internal
ones. Once the hydrogen atom is chemisorbed on pyrene, it remains

MNRAS 481, 3052–3062 (2018)

3060 C. Barrales-Martı́nez, D. Cortés-Arriagada and S. Gutiérrez-Oliva
Figure 10. Representation of top and hollow physisorption states.
bonded to the surface unless another incoming atom can react with
it; that is, it cannot spontaneously return to the gas-phase under the
conditions found in dense molecular clouds (low temperature and
low UV flux). On the other hand, the H2 recombination, following
the Eley–Rideal mechanism, is a barrierless process. This is because
of the birradical character of reactants, which means that an initial
repulsive interaction between them is avoided. Furthermore, the
low E◦ values for this reaction indicate that the H2 molecule
returns to the gas phase. These results, in combination with the high
abundance of hydrogen atoms in comparison with other atoms and
molecules present in the ISM, makes the Eley–Rideal mechanism
a feasible explanation for the high abundance of this molecule in
dense molecular clouds.
Figure 11. Energetic scheme of the whole reaction.
MNRAS 481, 3052–3062 (2018)
Moreover, the use of the reaction force and ASM analysis has
a big advantage, which is that the conditions of the reaction (the
chemical nature of PAHs) can be modified in order to make the
process more kinetically favourable. In this regard, because the
chemisorption barrier is dominated by structural rearrangements,
specifically the hydrogen atom approximation to pyrene, charge
doping can be used as a strategy to tailor the interaction energy to
become less repulsive between the surface and a hydrogen atom.
Downloaded from https://academic.oup.com/mnras/article-abstract/481/3/3052/5105891 by University of Canberra user on 23 September 2018
This explains why hydrogen chemisorption is a barrierless process
onto cationic anthracene and pyrene (Hirama et al. 2003), indi-
cating that charge doping avoids the repulsive interaction between
reactants, and therefore does not produce an important increase in
the energy of the systems. Hence, W1 and W2 should decrease or
even vanish. Furthermore, doping with atoms of higher atomic radii
than carbon is able to reduce the surface reconstruction during the
chemisorption (Fukushima et al. 2011) and to break the complete
planarity, and therefore the electronic delocalization of the carbona-
ceous surfaces, allowing a decrease of Estr , Eint and, therefore,
E‡ values. Finally, the energy released when H2 is formed (in the
recombination reaction) ranges from 60 to 84 kcal mol–1 (highly ex-
oenergetic) and is responsible for the surface heating, as proposed
by Duley & Williams (1993), Minissale et al. (2016), Garrod et al.
(2006) and Dulieu et al. (2013). This allows the desorption of any
other molecule formed on the PAH surface to occur; for example,
methanol, which has been proposed to form on dust grains, can
desorb aided by the H2 formation process on the same surface, ex-
plaining why methanol has been detected in the gas phase (Willacy,
Williams & Duley 1994; Friberg et al. 1988).
6 CONCLUSIONS
At the PBE-D3/cc-pVDZ level of theory, it was found that the re-
action of hydrogen chemisorption onto pyrene has to overcome an
energy barrier to take place, which is different if the reaction is
carried out on an internal or an external site of the surface. Fol-
lowing a complete analysis of the reaction mechanism (Fig. 11), it
was found that the reaction force analysis indicates that it is mostly
the structural rearrangements that contribute to this reaction bar-
rier. In addition, the ASM shows that the most important structural
change in the system is the shortening of the H–pyrene distance,
generating an initial repulsive interaction between reactants, which

operates until the TS is reached. This interaction is stronger in reac-
tions in which the H atom is chemisorbed onto internal sites of the
carbonaceous surface, leading to these reactions presenting higher
activation energies. On the other hand, the abstraction reaction and
H2 formation is a barrierless process in any of the five possible
sites of a mono-hydrogenated pyrene molecule. This is because
of the strong attractive interaction that governs the reaction from
the beginning, as revealed by ASM analysis. As the H–H bond
forms, a H–pyrene bond breaks, and the H2 molecule passes from
a chemisorbed state to a physisorbed one with small physisorption
energies, which can be overcome by the high energy released (in all
sites) once the reaction is complete. This is mainly because of the
recovery of the planarity of the pyrene surface, allowing complete
electronic delocalization over it and the formation of the H–H bond.
Both processes release a high amount of energy.
AC K N OW L E D G E M E N T S
The authors acknowledge financial support from FONDECYT
through project no. 1141098 and thank Professor Alejandro Toro-
Labbé for useful comments and discussions. CB-M acknowledges
a CONICYT PhD fellowship. The authors wish to thank Miss
Alessandra Misad for helping with the writing of the manuscript.
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S U P P O RT I N G I N F O R M AT I O N
Supplementary data are available at MNRAS online.
Table S1. Activation energies for the H chemisorption reaction for
various approaching angles.
Table S2. Energetic parameters with zero-point energy corrections
of the H chemisorption onto pyrene.
Table S3. Gibbs free energy of the H chemisorption onto pyrene.
Table S4. Dihedral angle (>Ci –CN –CN –CN ) at the five key points
along the reaction coordinate.
Table S5. Interatomic distances (dCi-H ) between Ci and H at the five
key points along the reaction coordinate.
Figure S1. Representation of some H atom approach angles to the
pyrene surface for an internal site.
MNRAS 481, 3052–3062 (2018)
3062 C. Barrales-Martı́nez, D. Cortés-Arriagada and S. Gutiérrez-Oliva
Figure S2. Representation of some H atom approach angles to the Figure S7. Molecular electrostatic potential for the five mono-
pyrene surface for an external site. hydrogenated pyrene molecules.
Figure S3. Wiberg bond order derivatives for the adsorption of a
single hydrogen atom onto the pyrene surface. Please note: Oxford University Press is not responsible for the
Figure S4. Hybridization of the Ci atom along the reaction path for content or functionality of any supporting materials supplied by
the five reactions. the authors. Any queries (other than missing material) should be
Figure S5. Spin density of the chemisorbed H atom along the directed to the corresponding author for the article.
reaction path for the five reactions.

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Figure S6. NPA (Natural Population Analysis) charge of the
chemisorbed hydrogen atom along the reaction path for the five
reactions. This paper has been typeset from a TEX/LATEX file prepared by the author.

MNRAS 481, 3052–3062 (2018)