Joseph N. Stember, Gregory S. Ezra
*
Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853, United States
Received 20 March 2007; accepted 6 June 2007
Available online 21 June 2007
Abstract
The bond dissociation kinetics of tethered atomic (Morse potential) chains under tensile stress is studied. Both RRKM (fully anhar
monic, Monte Carlo) and RRK (harmonic appproximation) theory are applied to predict bond dissociation rate constants as a function
of energy and tensile force. For chains with N P3 atoms a hybrid statistical theory is used involving a harmonic approximation for
motion in the transition state for bond dissociation. For chains with N = 2–5 atoms, while the RRK approximation signiﬁcantly over
estimates the dissociation rate constant, the fully anharmonic RRKM rate is quite close to simulation results. For the N = 2 chain, a
novel approach to the extraction of decay rate constants based on the classical spectral theorem is implemented. Good agreement
between the RRKM and dynamical rate constants is obtained for N = 2 despite the fact that the reactant phase space contains a signif
icant fraction of relatively shortlived trajectories.
Ó 2007 Elsevier B.V. All rights reserved.
PACS: 82.20.Db; 34.10.+x; 83.20.Lp
Keywords: Mechanochemistry; Fragmentation kinetics; Statistical theories
1. Introduction
A fundamental understanding of the intramolecular
dynamics and kinetics of fragmentation (bond dissocia
tion) of atomic chains subject to a tensile force is needed
to provide a solid foundation for theories of material fail
ure under stress [1,2], polymer rupture [3–7], adhesion [8],
friction [9], mechanochemistry [10–12] and biological appli
cations of dynamical force microscopy [13–17]. In chain
scission models for polymer ﬁber failure, the primary fail
ure events are breaking of covalent bonds within individual
chains [1,2,18,19]. Although trajectory studies on model
polyethylene chains suggest that complete intramolecular
vibrational energy redistribution (IVR) can occur on a
picosecond timescale [20,21], extensive theoretical work
has shown that the rate of bond breakage in single polymer
chains under constant stress/strain can be up to several
orders of magnitude slower than calculated on the basis
of statistical approaches such as transition state theory
[22–30]. Of course, studies of energy transfer and equipar
tition in single chains of coupled anharmonic oscillators
have a long history, beginning with the seminal work of
Fermi et al. [31,32]. (For some recent work on dynamics
of atomic chains see [33–38].)
In the present paper we study numerically the kinetics of
bond breaking in single atomic chains under stress. The
dissociation of a 1D chain subject to constant tensile force
is a problem in unimolecular kinetics. A fundamental issue
in unimolecular kinetics concerns the applicability of statis
tical approaches such as RRKM [39–43] or transition state
theory [44]. Previous theoretical work has suggested that
dissociation of atomic chains under stress is not amenable
to simple statistical approaches [22–30]. Early trajectory
simulations on the dynamics of Morse chains [22–25]
showed that correlated motions of $5–10 chain atoms
are necessary for bond breaking to occur. Moreover, sim
ple bond stretching or force criteria for bond rupture were
found to fail, in that apparently broken bonds were
observed to reform (bond healing). A signiﬁcant fraction
03010104/$  see front matter Ó 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.chemphys.2007.06.019
*
Corresponding author. Tel.: +1 607 255 3949; fax: +1 607 255 4137.
Email address: gse1@cornell.edu (G.S. Ezra).
www.elsevier.com/locate/chemphys
Chemical Physics 337 (2007) 11–32
of dissociative events occurred via a twostage process: an
initial, relatively persistent local bond stretching, followed
by rapid breaking of the stretched bond [24]. Simulations
of the fragmentation of 1D Lennard–Jones (LJ) chains at
constant strain with inclusion of a frictional damping term
and a stochastic force modelling interaction with a heat
bath show that, while fragmentation rate constants ﬁt an
Arrhenius form with activation energy consistent with a
static picture at constant strain [45], the magnitude of the
preexponential factor was at least three orders of magni
tude smaller than expected on the basis of naive dynamical
considerations [27] (see, however, Ref. [46]). Healing of
incipient breaks is highly eﬃcient. Comparison of polymer
rupture with singlebond dissociation dynamics for the
same damping/ﬂuctuating force via Kramers theory [47]
shows that stochastic forces are not responsible for the
bond healing. Bolton, Nordholm and Schranz (BNS) have
studied the dissociation of 1D Morse chains (N = 2–20)
under stress [28], following earlier work on the classical
dynamics of unstressed chains [48–50]. Nonexponential
decay, failure of RRKM theory, and extensive transition
state recrossing eﬀects were found. Interestingly, the pres
ence of lateral interchain coupling increased recrossing
eﬀects. Standard harmonic classical TST has been applied
to the dissociation of a 1D Morse chain [29,30], with the
transition state for dissociation of a given bond located
at the maximum of the eﬀective potential (see below).
The harmonic canonical TST rate constant did not agree
with molecular dynamics calculations, but eﬀects of anhar
monicity [43,28] on the predictions of TST were not sys
tematically investigated. Molecular dynamics studies on
thermal degradation in polyethylene [51] indicate that the
dependence of bond scission rate on average thermal exci
tation energy can be ﬁt with RRK theory [52], suggesting
that bending and torsional modes might play an important
role in establishing statistical behavior. (Refs. [53–56] are
representative studies of the role of torsional and bending
degrees of freedom in intramolecular dynamics.)
Dissociative trajectories in 1D LJ chains do not exhibit
the sensitive dependence on initial conditions expected for
chaotic systems [26]; this suggests a signiﬁcant degree of
regularity at the transition state (saddle point) for single
bond dissociation. Such regularity is analogous to that
found for isomerization reactions in clusters (see, for exam
ple, [57,58] and references cited therein).
In the present work classical trajectory simulations are
used to investigate the fragmentation kinetics and phase
space structure of short tethered atomic chains under con
stant tensile stress. Morse parameters in the simulations
can be chosen, for example, to model the eﬀective CH
2

CH
2
bond potential in polyethylene [51]. We focus on non
statistical aspects of the dissociation dynamics and the role
of anharmonicity.
In Section 2 we introduce the model Hamiltonian to be
studied, which consists of a tethered chain of identical
atoms interacting via pairwise Morse potentials subject to
constant tensile stress. Section 3 discusses application of
statistical theories such as RRKM and RRK (harmonic
approximation to RRKM) to our model. We describe the
numerical procedures used to implement a fully anhar
monic version of RRKM theory using Monte Carlo inte
gration to determine reactant and transition state phase
space volumes as a function of energy. (See also recent
work by Zhao and Du [59].) Section 4 outlines the proce
dures used to extract dissociation rate constants from clas
sical trajectory simulations of chain fragmentation. In
Section 5 we discuss in some detail the phase space struc
ture for the N = 2 case, as visualized through use of Poin
care´ surfaces of section [60]. For the N = 2 chain, there are
two distinct transition states corresponding to dissociation
of the two diﬀerent bonds, and we examine intersections of
the stable and unstable manifolds of the two transition
states in order to give a phase space picture of shorttime
(direct) dynamics in terms of reactive cylinders [61–65].
Section 6 compares the values of trajectory dissociation
rate constants with those obtained using statistical
approaches for the N = 2 chain. In Section 7 we explore
the possibility of making a more stringent comparison
between dynamical and statistical rate constants by intro
ducing corrections to the RRKM expression based on the
classical spectral theorem [66–73]. Section 8 presents a
comparison of statistical and dynamics rate constants
obtained for chains with N = 3–5 atoms, while Section 9
concludes.
2. Model potential and Hamiltonian
2.1. Potential energy surface
We consider ﬁrst a onedimensional Morse oscillator
plus potential linear in bond coordinate, describing a par
ticle tethered to a wall (inﬁnite mass) and acted on by a
constant tensile force f. The potential for this system takes
the form
V ðr; f Þ ¼ V
M
ðrÞ Àf ðr Àr
0
eq
Þ ð1aÞ
¼ D
0
½1 ÀexpfÀbðr Àr
0
eq
Þg
2
Àf ðr Àr
0
eq
Þ: ð1bÞ
Unless otherwise speciﬁed, we shall measure length in units
of r
0
eq
, the zeroforce Morse oscillator equilibrium bond dis
tance, and energies in units of D
0
, the unperturbed Morse
dissociation energy.
For the Br
2
molecule, for example, r
0
eq
¼ 2:28 A
˚
,
D
0
= 45.89 kcal/mol and b ¼ 4:432=r
0
eq
[28]. For the typical
tensile stress value of 25 kcal mol
À1
A
˚
À1
studied by Bolton
et al., f ¼ 1:24D
0
=r
0
eq
[28]. For the CC bond in model poly
ethylene (pe), r
0
eq
¼ 1:529 A
˚
, D
0
= 83 kcal/mol and
b ¼ 2:94=r
0
eq
[74,75,51,76]. At the representative tensile
stress value of 1 GPa [2], f ¼ 0:053D
0
=r
0
eq
. We have studied
Morse chains with b values in the range 1–3. All the calcu
lations reported here are carried out for the tensile stress
value f = 0.02.
The potential (1a) is plotted versus r in Fig. 1 for various
f values and b = 1. For f 6 f
crit
¼
b
2
, potential (1a) has two
12 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
stationary points, one at the potential minimum r = r
eq
and
one at the saddle point, r = r
à
: In general, the critical values
of the potential are given by
r
eq
¼
1
b
ln
b À
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
bðÀ2f þbÞ
_
f
_ _
þr
0
eq
ð2aÞ
r
z
¼
1
b
ln
b þ
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
bðÀ2f þbÞ
_
f
_ _
þr
0
eq
: ð2bÞ
As f increases, r
à
decreases while r
eq
increases slightly. The
depth of the potential well decreases from the zeroforce
value D
0
until f reaches the critical value f
crit
, at which
point the well disappears completely. For b = 1 and
f = 0.02, we have r
eq
= 1.010 and r
à
= 5.595.
Now consider a linear chain of N atoms. For this system
with N P2 degrees of freedom, the conversion from inter
nal (bond) coordinates r to external (labﬁxed) coordinates
x is given by (see Fig. 2)
x
k
¼
k
j¼1
r
j
; k ¼ 1; . . . ; N: ð3Þ
We assume that the potential between atoms is pairwise
Morse (nearest neighbors only) and that the tensile force
acts only on the outermost atom, giving a potential func
tion for the chain
V ðx; f Þ ¼ V
M
ðx
1
Þ þV
M
ðx
2
Àx
1
Þ þÁ Á Á þ
V
M
ðx
N
Àx
NÀ1
Þ Àf ðx
N
ÀNr
0
eq
Þ ð4aÞ
¼
N
i¼1
½V
M
ðr
i
Þ Àf ðr
i
Àr
0
eq
Þ: ð4bÞ
The force is distributed through the chain so that the po
tential in each bond coordinate r
k
has the same functional
dependence on bond length as the oneparticle potential
(1a). Hence the equilibrium bond length between any adja
cent pair of atoms at the global minimum in the N P2
chain is just the equilibrium bond length for the one
dimensional case. A similar equivalence holds for the crit
ical bond length. For example, the equilibrium and saddle
conﬁgurations corresponding to breaking bond 1 are
x
k;eq
¼ kr
eq
; k ¼ 1; . . . ; N; ð5aÞ
x
k;saddle
¼ r
z
þðk À1Þr
eq
; k ¼ 1; . . . ; N: ð5bÞ
For a single tethered atom, Fig. 1 shows the existence of a
welldeﬁned conﬁguration space transition state for bond
breaking located at the top of the eﬀective potential energy
barrier. For a chain of atoms under stress, there is an anal
ogous critical conﬁguration associated with the dissocia
tion of each bond. Detailed static analyses of polymer
chains subject to tensile force (both constant strain and
constant stress) have been given [45,77]. Although the static
analysis leads to a clear view of the nature of certain impor
tant cuts through the multibody potential (for example,
one bond stretched with all other bonds having equal dis
placements from equilibrium), it provides limited insight
into fracture dynamics.
Contours of the N = 2 potential energy surface (PES),
Eq. (4a), as a function of the singleparticle coordinates
x
1
and x
2
are plotted in Fig. 3a. There is a global minimum
corresponding to the bound chain and two saddle points
associated with the two possible bond dissociation path
ways. Along the minimum energy pathway for breaking
of bond 1, both x
1
and x
2
coordinates increase, while the
path for breaking of bond 2 is approximately a vertical
line, x
1
$ const. Bound motions at the respective transition
states are approximately perpendicular to the minimum
energy paths (see below).
The potential energy barrier to dissociation, i.e., the
activation energy E
a
¼ E
Ã
f
, is deﬁned to be
E
Ã
f
¼ V ðr
z
; f Þ ÀV ðr
eq
; f Þ: ð6Þ
For any particular value of the force f, all energies are mea
sured from the fdependent minimum energy V(x
eq
(f)). For
b = 1 and f = 0.02 we have E
a
= 0.8881.
2.2. Hamiltonian
In single particle coordinates, the Natom chain Hamil
tonian is simply
Hðx; f Þ ¼
N
i¼1
1
2m
i
p
2
i
þV ðx; f Þ; ð7Þ
2 4 6 8 10
x
0.5
1
1.5
2
V
Fig. 1. Potential V(r, f) for a tethered Morse particle under tensile stress,
Eq. (1a). The unit of length is r
0
eq
, the zeroforce Morse oscillator
equilibrium bond distance, and the unit of energy D
0
, the unperturbed
Morse dissociation energy. Force parameter f: f = 0 (black), f = 0.02 (red),
f = 0.04 (green), f = 0.06 (blue), f = 0.08 (purple), f = 0.1 (light blue). (For
interpretation of the references to colour in this ﬁgure legend, the reader is
referred to the web version of this article.)
1 2 3 4 f
x
1
x
2
Fig. 2. Deﬁnition of singleparticle coordinates {x
i
} for a tethered chain
of N = 4 atoms under tensile stress.
J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32 13
where p
i
is the momentum of particle i. We shall take all
particles to have the same mass m
i
= m. Fixing the unit
of mass speciﬁes a unit of time; with D
0
¼ r
0
eq
¼ m ¼ 1,
the period of the harmonic oscillation at the bottom of
the Morse potential well with b = 1 is s
HO
¼ 2p=
ﬃﬃﬃ
2
p
.
Although the overall magnitudes of dissociation rate con
stants depend on the value of the particle mass m, the ratios
of rate constants computed from two diﬀerent methods
(e.g., trajectory and RRK) do not (see Section 6.1).
In terms of bond coordinates, the Natom chain Hamil
tonian is
Hðr; f Þ ¼
1
2
p
2
r
1
þ
N
k¼2
p
2
r
k
À
NÀ1
k¼1
p
r
k
p
r
kþ1
þ
N
i¼1
ðV
M
ðr
i
Þ Àf ðr
i
Àr
0
eq
ÞÞ: ð8Þ
In terms of singleparticle coordinates the kinetic energy is
therefore separable while the potential energy is nonsepara
ble, whereas in bond coordinates the potential energy sep
arates while the kinetic energy has coupling terms Àp
r
k
p
r
kþ1
.
3. RRKM and RRK dissociation rate constants
3.1. RRKM theory
The RRKM expression for the E and fdependent
molecular fragmentation rate constant associated with
breaking of bond j is [39–43]
k
RRKM
j
ðE; f Þ ¼
N
z
j
ðE ÀE
Ã
f
Þ
qðEÞ
; ð9Þ
where N
z
j
ðE ÀE
Ã
f
Þ is the classical sum of states (phase
space volume) at the transition state for breaking of bond
j, E
Ã
f
is the forcedependent dissociation energy, and q(E) is
the classical density of states for the reactant region of
phase space,
qðEÞ ¼
dNðEÞ
dE
; ð10Þ
with NðEÞ the classical sum of states (phase space volume)
at total energy E.
For an Nmode system, q has dimensions (qp)
N
/
J = (Js)
N
/J = (Js)
NÀ1
· s. The classical transition state
sum of states N
z
is the phase space volume for an
(N À 1)degreeoffreedom system at the critical conﬁgura
tion, and has dimensions (qp)
NÀ1
= (Js)
NÀ1
. The ratio of
the two, which is the classical unimolecular rate dissocia
tion rate constant as deﬁned in (9), then has units of inverse
time, (Js)
NÀ1
/((J s)
NÀ1
· s) = s
À1
, as it should. The unit of
time used in our calculations, s
0
, is discussed in Section 4.1.
The quantum density of states q
Q
is obtained in the semi
classical limit by dividing q by the volume of a phase space
‘‘cell’’. For an N mode system, q
Q
= q/h
N
. Similarly, the
quantum transition state sum of states is N
z
Q
¼
N
z
=h
NÀ1
. We therefore have
k
RRKM
¼
N
z
q
¼
h
nÀ1
N
z
Q
h
n
q
Q
ð11aÞ
¼
1
h
N
z
Q
q
Q
; ð11bÞ
so that the usual expression for k
RRKM
, Eq. (11b), explic
itly contains Planck’s constant h [39–43]. The absence of
Planck’s constant in the formula (9) expressed in terms of
purely classical quantities is nevertheless appropriate and
entirely correct.
Broadly speaking, in order for the RRKM rate constant
expression to be valid it is necessary that k
rxn
(k
IVR
, i.e.,
the rate of intramolecular energy transfer should be greater
2 4 6 8 10 12
x
1
2
4
6
8
10
12
x
2
2 4 6 8 10 12
X
2
4
6
8
10
12
Fig. 3. Contour plot of the N = 2particle potential energy surface, Eq. (4a), with f = 0.02. Saddle points 1 (red) and 2 (green) are also shown. (a) Single
particle coordinates: {x
1
, x
2
}; (b) Jacobi coordinates: {n, X}. (For interpretation of the references to colour in this ﬁgure legend, the reader is referred to the
web version of this article.)
14 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
than the reaction rate. Many studies have been carried out
on the validity of RRKM theory (9) and the connection
between deviations from statisticality and intramolecular
dynamics (for example, the existence of bottlenecks to
intramolecular energy ﬂow) [66,78–83]. Our focus here is
on the validity of expression (9) for the particular case of
atomic chains under tensile stress [28–30].
We shall consider energies low enough so that the disso
ciation of two or more bonds is not energetically possible.
If the overall statistical rate constant for chain fragmenta
tion via single bond dissociation is
k
RRKM
¼
N
j¼1
k
RRKM
j
ð12Þ
where the total number of decay channels is equal to the
number of bonds in the chain, then N(t), the number of
bound molecules at time t, exhibits exponential decay,
NðtÞ ¼ Nð0Þ e
Àk
RRKM
t
: ð13Þ
In general we deﬁne the overall dissociation rate constant,
when it exists, by
k ¼ À
1
NðtÞ
_
NðtÞ ð14aÞ
¼
N
j¼1
k
j
ð14bÞ
¼ þ
1
NðtÞ
N
j¼1
_ n
j
ðtÞ; ð14cÞ
where n
j
(t) is the number of molecules that have dissociated
via channel j at time t. In a regime where the system exhib
its exponential decay, the rate constant for dissociation via
channel j is given in terms of the branching ratio b
j
as
k
j
¼
n
j
ðtÞ
N
m¼1
n
m
ðtÞ
k b
j
k: ð15Þ
3.2. RRK theory: a harmonic approximation to RRKM
theory
RRK theory is the harmonic limit of RRKM theory
[52]. We approximate the potential function V(x) by a sec
ond order expansion about the potential minimum and
saddle points. At these critical points, linear terms vanish,
and we have
V
crit
’ V ðx
crit
Þ þ
1
2
N
i¼1
N
j¼1
Dx
i
Dx
j
o
2
V
ox
i
ox
j
_ _¸
¸
¸
¸
x¼x
crit
þÁ Á Á
ð16Þ
There are N real normal mode (angular) frequencies for the
reactant, fx
i
g
N
i¼1
, and N À 1 real frequencies, fx
z
i
g
NÀ1
i¼1
, for
the transition state, together with a single imaginary fre
quency associated with unstable motion oﬀ the saddle.
For an rdimensional harmonic oscillator, frequencies
fx
i
g
r
i¼1
, the phase space volume NðEÞ at energy E is
NðEÞ ¼
ð2pÞ
r
r!
E
r
r
i¼1
x
i
; ð17Þ
so that the harmonic (RRK) approximation to the RRKM
rate constant (9) for dissociation via transition state a is
k
RRK
f
ðE; aÞ ¼
1
2p
N
i¼1
x
f ;i
NÀ1
i¼1
x
z
f ;i
ðaÞ
E ÀE
Ã
f ;a
E
_ _
NÀ1
; ð18Þ
where E
Ã
f ;a
is the critical energy for dissociation of bond a
under external force f. It should be noted that in our pres
ent model with all atoms identical, E
Ã
f ;a
E
Ã
f
is the same for
all transition states because b and r
0
eq
are the same for each
term in potential (4a).
3.3. Computation of RRKM rate constant
3.3.1. Reactant phase space volume
To compute k
RRKM
f
ðEÞ we must determine the reactant
phase space volume NðEÞ, from which the reactant density
of states can be obtained via Eq. (10). NðEÞ is the volume
of the region of phase space consisting of all points with
energy less than or equal to E:
NðEÞ ¼
_
dx
1
dp
1
dx
2
dp
2
Á Á Á dx
N
dp
N
HðE ÀHðx; pÞÞ ð19Þ
where H is the Heaviside step function. This integral has no
analytical solution for our system (cf. [84]), necessitating
use of either a harmonic approximation to the potential
or numerical (Monte Carlo) integration. As the validity
of the harmonic approximation versus the role of anhar
monicity in the reactant density of states is an important
question when assessing the validity of RRKM theory for
treating stressed polymer chains [28,29], for comparison
with the harmonic approximation we shall evaluate the
fully anharmonic reactant density of states and transition
state sum of states essentially exactly using a numerical
Monte Carlo approach.
To evaluate the phase space volume numerically, we
consider a region (‘‘hypercube’’) in phase space M
0
with
volume V
0
large enough to contain all reactant phase
points with energy E 6 E
MC
max
. To compute NðEÞ, the phase
space volume as a function of energy, we determine the vol
umes V
a
of subsets M
a
& M
0
containing phase points with
E 6 E
a
6 E
MC
max
, a = 1, 2, . . . , a
max
. If n
r
phase points
fx
i
; p
i
g
N
i¼1
2 M
0
are chosen randomly, and n
a
of these points
lie within M
a
, then, for large enough n
r
, the volume V
a
is
V
a
’
n
a
n
r
V
0
: ð20Þ
From the set of pairs fE
a
; V
a
g
amax
a¼1
, we can ﬁt the phase
space volume NðEÞ to a polynomial in E,
NðEÞ ’ E
N
ðc
0
þc
1
E þÁ Á ÁÞ; ð21Þ
that is, harmonic oscillator phase space volume plus anhar
monic corrections. The associated reactant density of states
is then obtained by diﬀerentiating the ﬁtted NðEÞ with re
spect to E. Details of the sampling procedure are further
discussed in Appendix A.
J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32 15
For N = 2, the conﬁgurational projection of M
0
is the
union of the rectangular region and adjacent triangular
region shown in Fig. 4. It should be noted that the sam
pling procedure used for N = 3–5, which employs a simpler
phase space hypercube, gives approximately the same den
sity of states for N = 2 as that obtained using the more
elaborate shape shown in Fig. 4.
Harmonic and anharmonic reactant densities of states
are shown for N = 2–5 in Fig. 5.
As mentioned above, we consider energies low enough
such that multiple bond breakages (3body dissociation
when N = 2) do not occur. For f = 0.02, b = 1, this means
that the maximum energy we consider is E
MC
max
¼ 1:5281
(with respect to the fdependent minimum energy).
3.3.2. Transition state sum of states
For determination of the phase space sum of states for
the transition state associated with channel 1, it is conve
nient to transform to Jacobi coordinates
X ¼
1
2
ðx
1
þx
2
Þ ¼ r
1
þ
1
2
r
2
ð22aÞ
n ¼ x
2
Àx
1
ð22bÞ
P ¼ p
1
þp
2
ð22cÞ
P ¼
1
2
ðp
2
Àp
1
Þ ð22dÞ
using the generating function [85,60]
F
2
ðx
1
; x
2
; P; PÞ ¼ Pðx
2
Àx
1
Þ þ
1
2
Pðx
1
þx
2
Þ: ð23Þ
The Hamiltonian in the transformed coordinates is then
HðX; P; n; PÞ ¼
P
2
4
þP
2
þV ðn; X; f Þ: ð24Þ
The PES in Jacobi coordinates (Fig. 3b) indicates that the
conﬁguration space transition state 1 can approximately be
deﬁned by X
z
¼
1
2
ðx
1
þx
2
Þ ¼
1
2
ðr
z
þðr
z
þr
eq
ÞÞ ¼ r
z
þ
1
2
r
eq
(=6.10 for f = 0.02 and b = 1), which is just the harmonic
approximation nonreactive normal mode. In single particle
2 4 6 8 10 12
x
1
2
4
6
8
x
2
Fig. 4. Conﬁguration space projection (light blue) of the phase space
region used for sampling of coordinates in the Monte Carlo determination
of reactant phase space volume NðEÞ. Contours of the potential energy
and the location of saddles (saddle 1 (red) and saddle 2 (blue)) are also
shown. (For interpretation of the references to colour in this ﬁgure legend,
the reader is referred to the web version of this article.)
0.25 0.5 0.75 1 1.25 1.5
E
20
40
60
80
100
120
140
N 2
0.25 0.5 0.75 1 1.25 1.5
E
100
200
300
400
500
N 3
0.25 0.5 0.75 1 1.25 1.5
E
200
400
600
800
1000
N 4
0.25 0.5 0.75 1 1.25 1.5
E
250
500
750
1000
1250
1500
N 5
Fig. 5. Harmonic approximation (red) and fully anharmonic Monte Carlo (blue) reactant density of states versus energy for (a) N = 2, (b) N = 3, (c)
N = 4 and (d) N = 5. (For interpretation of the references to colour in this ﬁgure legend, the reader is referred to the web version of this article.)
16 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
coordinates, the conﬁguration space projection of transi
tion state 1 lies along the line x
2
= Àx
1
+ 2r
à
+ r
eq
.
The 2D ‘‘hypercube’’ M
z
0
used to sample transition state
1 is deﬁned by conditions
X ¼ r
z
þ
1
2
r
eq
ð25aÞ
n 2 ½0; r
z
ð25bÞ
P ¼ 0 ð25cÞ
P 2 À
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
E
MC
max
ÀE
Ã
f
_
;
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
E
MC
max
ÀE
Ã
f
_ _ _
ð25dÞ
Thus the N = 2 transition state 1 hypercube has volume
V
z
0;1
¼ 2r
z
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
ðE
MC
max
ÀE
Ã
f
Þ
_
. The transition state 2 sampling
hypercube is deﬁned as
x
1
2 ½0; 3:303 ð26aÞ
x
2
¼ r
eq
þr
z
ð26bÞ
p
1
2 À
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2 E
MC
max
ÀE
Ã
f
_ _
_
;
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2 E
MC
max
ÀE
Ã
f
_ _
_ _ _
ð26cÞ
p
2
¼ 0; ð26dÞ
and has volume V
z
0;2
¼ 6:606
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2ðE
max
ÀE
Ã
f
Þ
_
. Again, the x
1
range endpoint of 3.303 marks the position of the barrier to
3body dissociation products from transition state 2 for
f = 0.02 and b = 1.
For both the reactant and transition state Monte Carlo
calculations, we used a
max
= 100, with n
rand
= 10
7
. Transi
tion state sums of states are ﬁtted to functions of the form
NðE ÀE
z
f
Þ ¼ ðE ÀE
z
f
Þ
NÀ1
½c
0
þc
1
ðE ÀE
z
f
Þ þÁ Á Á: ð27Þ
4. Classical trajectory simulations
4.1. Integration of trajectories
Classical equations of motion are
_ z ¼ L
H
z fz; HðzÞg: ð28Þ
with z = (x
1
, . . . , x
N
,p
1
. . . p
N
) and Hamiltonian H(z) given
by Eq. (7). Here, {Æ,Æ} denotes the usual Poisson bracket
[85,60]. We employ a simple reversible 2ndorder symplec
tic integrator [86,87] to integrate Eq. (28). A typical value
of the timestep used in our integrations is h = 0.1s
0
, where
s
0
is the unit of time associated with our choice of units for
energy, length and mass. In units of s
0
, the period of mo
tion of a unit mass in the harmonic potential obtained by
expanding the Morse potential about its minimum is
s
HO
¼ 2p=ðb
ﬃﬃﬃ
2
p
Þ. For example, using physical parameters
for model polyethylene [74,75,51,76] we have s
HO
’
1.5s
0
’ 46.4 fs. With h = 0.01 s
0
and n
step
= 8 · 10
3
time
steps, the length of our typical trajectory runs is then
approximately 55 harmonic oscillator periods ’2.5 ps.
For the tensile stress values used here, this timescale is long
enough to characterize the decay dynamics.
4.2. Sampling phase points on the energy shell
To compare the predictions of RRK and RRKM theory
at constant energy E with trajectory results, it is necessary
to sample trajectory initial conditions z = (x, p) distributed
with suitable measure on the energy shell H(z) = E. The
sampling procedure used is discussed in more detail in
Appendix B.
4.3. Extraction of rate coeﬃcient k(E)
Given a microcanonical ensemble of N(0) initial condi
tions fz
j
ð0Þg
Nð0Þ
j¼1
, and deﬁning N(t) 6 N(0) as the number
of trajectories that have not reacted by time t, we can com
pute an eﬀective rate constant k(E, f) if we assume that the
system exhibits exponential decay with timeindependent
rate constant. The associated lifetime distribution is
NðtÞ ¼ Nð0Þ exp½ÀkðE; f Þt: ð29Þ
For each energy we run N(0) = 50,000 trajectories and re
cord the times at which dissociation of each trajectory oc
curs (if it ever does for that trajectory). For f = 0.02 and
b = 1 the condition for dissociation of bond j is taken to be
r
j
> r
z
þ2r
0
eq
; j 2 ½1; . . . ; N: ð30Þ
The resulting data are histogrammed. Transient behavior
(the ﬁrst 350 time steps for b = 1 and f = 0.02) is ignored
and an exponential ﬁt to the histogram at longer times
gives approximate k(E, f) values.
It should be noted that the bond dissociation criterion
(30) is intended to ensure that recrossing eﬀects are
excluded from the numerical determination of the longtime
(asymptotic) decay rate, which is the quantity to be com
pared with statistical theories.
Values of the decay rate constants obtained via trajec
tory simulation are compared with the predictions of statis
tical theory below. We also compare these dynamical decay
rates with those obtained via an analysis based on the clas
sical spectral theorem [66–73].
5. Phase space structure and dynamics for N = 2
Before turning to a detailed comparison of RRKM and
trajectory dissociation rate constants, we examine the
phase space structure for the N = 2 chain. For the tethered
chain with N = 2 atoms, we can use the standard Poincare´
surface of section (SOS) construction [60] to examine the
system phase space at constant energy E.
5.1. Surfaces of section
5.1.1. SOS along a dissociative coordinate: PODS and
turnstiles
At constant energy E, we can deﬁne a SOS by the con
dition (given in terms of Jacobi coordinates)
P ¼ 0;
_
P > 0: ð31Þ
J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32 17
We will refer to this SOS as SOS
1
. Fig. 6 shows SOS
1
for
f = 0.02, b = 1 at energies E ¼ E
Ã
f
À0:4, E
Ã
f
, E
Ã
f
þ0:01
and E
Ã
f
þ0:1.
The overall shape of the separatrix [60] deﬁning the reac
tant phase space region [79] is clearly visible in Fig. 6b,
E ¼ E
Ã
f
. The critical conﬁguration for dissociation via tran
sition state 1 is located on SOS
1
at P = 0, X = 6.10. At
energies above the activation barrier, the periodic orbit
dividing surface (PODS [88–90]; see below) appears as an
unstable ﬁxed point on SOS
1
(Fig. 6c and d); the PODS
and its associated stable/unstable manifolds are computed
below. The points spilling out towards X !1 are reactive
trajectories that dissociate via breaking of bond 1.
For E > E
Ã
f
we also see ‘‘lobe’’ or ‘‘turnstile’’ structures
near the boundaries of the reactive complex region. The
turnstiles mediate transport between phase space regions,
and detailed analysis of turnstile dynamics can be used to
understand rates of intramolecular energy ﬂow and unimo
lecular dissociation [91,79,92]. Regions of lower trajectory
density in SOS
1
are associated with trajectories that disso
ciate through channel 2, and so do not return to the SOS
(see below).
Also evident in the interior of the complex region is an
area of bounded, regular behavior, which appears as a
transverse slice through a set of invariant tori [60]. Classical
trajectories with initial conditions on invariant tori do not
Fig. 6. Surfaces of section for the N = 2 chain (f = 0.02). Conjugate variables (X, P) are plotted when SOS
1
conditions P = 0,
_
P > 0 are satisﬁed. (a)
E ¼ E
Ã
f
À0:4; (b) E ¼ E
Ã
f
; (c) E ¼ E
Ã
f
þ0:01; (d) E ¼ E
Ã
f
þ0:1.
18 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
dissociate. The fact that a signiﬁcant proportion of the
tethered chain phase space volume is occupied by bound
trajectories means that, to obtain a more accurate predic
tion of the dissociation rate constant using statistical
assumptions, it is necessary to correct RRKM theory by
removing bound phase space regions from consideration
[93–95,79,96].
SOS
1
is symmetric about the line P = 0; this timerever
sal symmetry can be exploited to determine relevant peri
odic orbits [97,98]. (An analogous SOS suitable for
channel 2, SOS
2
, is deﬁned by the conditions p
1
= 0,
_ p
1
> 0. Whereas SOS
1
is symmetric about the line P = 0,
SOS
2
is symmetric about the line p
2
= 0.)
In the (X, P) plane of SOS
1
, the unstable ﬁxed point on
the line P = 0 is the intersection of the PODS [88–90] asso
ciated with the transition state for bond 1 cleavage with the
SOS. This hyperbolic ﬁxed point and its associated stable/
unstable manifolds (plus the analogous structures for reac
tion 2) are phase space structures that determine the disso
ciation dynamics of the N = 2 tethered chain.
Consider determination of the PODS for channel 1. To
locate the PODS, we sample a line of initial conditions on
SOS
1
along the symmetry line P = 0. The SOS conditions
on P and P imply that points on the symmetry line have
p
1
= p
2
= 0, so that these trajectories start on the classical
zerovelocity manifold V(x) = E. Any trajectory that
returns to the symmetry line in a single iteration of the
Poincare´ map is a periodic orbit [97,98]. The location of
the PODS on the symmetry line can therefore be deter
mined using a Newton–Raphson procedure [99].
Fig. 7 shows conﬁguration space projections of PODS
associated with both transition states at several energies.
The shapes of the PODS conform approximately to the har
monic prediction of a slanted line segment for transition
state 1 and an approximately horizontal line segment for
transition state 2. Close inspection of the PODS reveals that
they are in fact curved, an anharmonic dynamical eﬀect.
Numerical approximations to the stable/unstable mani
folds W
u=s
of the PODS are obtained by propagating phase
points close to the periodic orbit on the respective linear
ized manifolds (computed as outlined in Appendix C) for
wards/backwards in time [60]. To visualize W
u=s
, we select
1000 initial conditions along short segments of the linear
ized manifolds E
u/s
close to the PODS and propagate all
these phase points either forward or backwards in time.
The resulting manifolds for E
Ã
f
þ0:1 are shown in Fig. 8.
Taken together, these two manifolds deﬁne a bound com
plex region. One possible deﬁnition of a direct trajectory
is one that does not enter or exit the bound separatrix
region via a turnstile [79].
5.1.2. SOS in reactant region (r
1
= r
2
): reactive cylinders
An informative view of the dynamics is provided by the
SOS deﬁned by crossings of the hypersurface
R
+
{zr
1
= r
2
, _ r
2
> _ r
1
g. To formulate the crossing condi
tion in terms of a single variable, we consider a canonical
transformation to coordinates
X ¼
1
2
ðx
1
þx
2
Þ ð32aÞ
Dr ¼ r
2
Àr
1
¼ x
2
À2x
1
ð32bÞ
with generating function [60,85]
F ¼
1
2
ðx
1
þx
2
ÞP þðx
2
À2x
1
Þp
Dr
; ð33Þ
from which we deduce the relation between conjugate
momenta
P ¼
2
3
ðp
1
þ2p
2
Þ ð34aÞ
p
Dr
¼
1
3
ðp
2
Àp
1
Þ: ð34bÞ
1 2 3 4 5 6 7 8
x
1
6.4
6.6
6.8
7.2
7.4
7.6
7.8
x
2
Fig. 7. PODS shown together with potential energy contours for f = 0.02.
Saddle points 1 and 2 are marked as black dots, PODS
1
and PODS
2
are
shown at energies E ¼ E
Ã
f
þ0:1 (red), E
Ã
f
þ0:2 (green), E
Ã
f
þ0:3 (blue),
E
Ã
f
þ0:4 (yellow), E
Ã
f
þ0:5 (purple) and E
max
(black). (For interpretation
of the references to colour in this ﬁgure legend, the reader is referred to the
web version of this article.)
Fig. 8. SOS (green) at E ¼ E
Ã
f
þ0:1 deﬁned by P = 0,
_
P > 0; The stable
manifold W
s
(blue) and unstable manifold W
u
(red) of the PODS are also
shown. (For interpretation of the references to colour in this ﬁgure legend,
the reader is referred to the web version of this article.)
J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32 19
(Note that the momentum P conjugate to X in the {X, Dr}
coordinate system diﬀers from the momentum P in the
{X, n} coordinate system.) From the nondiagonal kinetic
energy
T ¼
P
2
4
À
Pp
Dr
2
þ
5p
2
Dr
2
; ð35Þ
we have
p
Dr
¼
1
10
P Æ
1
10
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
40T À9P
2
_
: ð36Þ
We select the positive branch of solutions for p
Dr
, which is
equivalent to imposing the surface crossing condition
p
Dr
>
1
10
P or
p
2
> 2p
1
; ð37Þ
which is just the condition p
2
À p
1
> p
1
i.e. _ r
2
> _ r
1
. Thus,
an equivalent deﬁnition of our surface is R
+
{zDr = 0,
p
Dr
¼
1
10
P þ
1
10
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
40T À9P
2
p
g. We examine the fate of trajec
tories initiated on a grid of initial conditions with
r
1
ð0Þ ¼ r
2
ð0Þ ¼ x
1
ð0Þ ¼
1
2
x
2
ð0Þ 2 ½0; 3:5 ð38aÞ
Pð0Þ 2 ½À2:6; 2:6; ð38bÞ
where r(0) and P(0) values are evenlyspaced. Initial mo
menta {p
1
(0),p
2
(0)} are obtained from
p
1
¼
P
2
À2p
Dr
ð39aÞ
p
2
¼
P
2
þp
Dr
; ð39bÞ
where the p
Dr
(0) values are chosen to be on the positive
branch of (36) so as to place the initial conditions on R
+
.
The resulting initial grid is shown in Fig. 9a, and the
SOS generated from this initial condition set is in Fig. 9b.
A plot of the grid of initial conditions on R
+
under one
iteration of the return map is shown in Fig. 9c. One note
worthy feature of Fig. 9b is the presence of ‘‘holes’’, regions
within the SOS structure that are either devoid of or spar
sely ﬁlled by iterates.
To elucidate the dynamical signiﬁcance of these holes,
we initiate trajectories on transition states 1 and 2 (that
is, distributed along the corresponding PODS), propagate
them forward in time, and examine their intersection with
R
+
. The successive intersections of these trajectories with
the SOS are shown in Fig. 10. Let R
u;j
m
& R
þ
be the region
corresponding to the mth intersection of R
+
by the set of
trajectories initiated on transition state j. (The superscript
u indicates that the region R
u;j
m
is bounded by the intersec
tion of the unstable mainfold of the PODS with R
+
.)
Fig. 10a shows that R
u;1
1
and R
u;2
1
are the two holes toward
the bottom of the SOS structure that contain no phase
points; that is, regions R
u;1
1
and R
u;2
1
are composed of phase
points with no preimage on R
+
. The regions R
u;1
2
and R
u;2
2
,
ﬁrst visible in Fig. 10b, are cross sections of cylindrical
structures in phase space, socalled reactive cylinders [61–
65]. Upon further iterations, shown in Fig. 10c–e, the cyl
inder cross sections stretch out, twist and generally spread
themselves through the reactive region. We infer that the
set of reactive phase points on R
+
is the closure of
2
j¼1
1
i¼1
R
u;j
i
.
Of equal importance to the sets R
u;j
m
, j = 1, 2, which react
through transition states 1 and 2, respectively, in negative
time, is the set of trajectories R
s;j
m
, which react in forward
time. We deﬁne R
s;j
m
to be the set of trajectories that react
through transition state j after undergoing m À 1 further
intersections with R
+
. (The superscript s indicates that
these trajectories are associated with the stable manifold
of the corresponding PODS; they are calculated by propa
gating backwards in time from the relevant transition
state.) In particular, we consider the regions R
s;j
1
, j = 1, 2,
which consist of phase points that react immediately in for
ward time, where immediate means without an intervening
intersection of the SOS.
Fig. 11a displays R
s;1
1
R
s;2
1
along with the grid of initial
conditions on R
+
that intersect R
+
for some positive time
value. Note that R
s;1
1
R
s;2
1
ﬁlls the ‘‘holes’’ in the SOS,
which consist of phase points that never return to the sur
face in positive time, and so react immediately.
It is informative to observe intersections between the
forward and backward direct reactive tubes, R
u;1
2
R
s;1
1
and R
u;2
2
R
s;2
1
. (One could just as well inspect the intersec
tions R
u;1
1
R
s;1
2
and R
u;2
1
R
s;2
2
, which appear in ure
Fig. 11b and are simply the timeevolved iterations of
R
u;1
2
R
s;1
1
and R
u;2
2
R
s;2
1
, respectively for one mapping of
R
+
.) To illustrate the information aﬀorded by these over
laps, the area AðR
u;1
2
R
s;1
1
Þ reﬂects the phase space volume
of trajectories that enter the reactant region through tran
sition state 1 and exit through transition state 1 after
2 + 1 À 1 = 2 intersections with the SOS R
+
. Hence,
AðR
u;1
2
R
s;1
1
Þ þAðR
u;2
2
R
s;1
1
Þ should correlate with the
fraction P
z
1;d
ðE ÀE
Ã
f
Þ of transition state 1 belonging to
direct trajectories, where direct trajectories could be
deﬁned as those having only two intersections with SOS
R
+
, noting that since R
i;u
1
R
s;j
1
for i, j = 1, 2 is zero, no
reactive trajectories cross R
+
only once.
We observe from Fig. 12 that the overlap areas
R
u;1
2
R
s;1
1
and R
u;2
2
R
s;2
1
both increase with increasing
energy, while R
u;2
2
R
s;1
1
and R
u;1
2
R
s;2
1
are zero for most
energies except those near E
max
, where a thin strip of non
zero overlap R
u;2
2
R
s;1
1
begins to emerge, as is evident in
Fig. 12d–f. Thus, there are virtually no trajectories that
enter through transition state m and exit through transition
state n, m5n, without crossing SOS R
+
at least three times.
6. Statistical theories compared with dynamical rate
constants
6.1. Ratios of rate constants are independent of choice of
mass unit
We shall compare absolute values of dissociation rate
constants obtained from classical trajectory simulations
with those calculated using RRKMtype theories. Recall
that our unit of time is deﬁned in terms of the choice of
20 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
mass unit, s
0
$
ﬃﬃﬃﬃ
m
p
. Although absolute values of dissocia
tion rate constants depend upon the value of m used, ratios
of rates do not. Thus, from Eq. (18) for the RRK rate con
stant, and recalling the mass dependence of harmonic oscil
lator frequencies, we see that
k
RRK
f
ðEÞ $
1
ﬃﬃﬃ
m
p
_ _
N
1
ﬃﬃﬃ
m
p
_ _
NÀ1
$
1
ﬃﬃﬃﬃ
m
p : ð40Þ
The RRKM rate constant is given by the ratio (9). Both the
reactant phase space volume and the density of states q(E)
scale in general as ð
ﬃﬃﬃﬃ
m
p
Þ
N
, where N is the number of degrees
of freedom, while N
z
ðE ÀE
Ã
f
Þ scales as ð
ﬃﬃﬃﬃ
m
p
Þ
NÀ1
. The
anharmonic RRKM rate constant therefore scales in the
same way with mass as the RRK rate constant, as 1=
ﬃﬃﬃﬃ
m
p
.
Finally, to determine the mass dependence of simulation
results k
sim
, we note that increasing m means that particles
are eﬀectively moving more slowly by a factor of 1=
ﬃﬃﬃﬃ
m
p
; we
therefore have k
sim
$ 1=
ﬃﬃﬃﬃ
m
p
.
Rate constants k
RRK
, k
RRKM
, and k
sim
therefore all
have the same mass dependence and the ratio of any two
of these k values is massindependent.
6.2. Comparison of RRK with RRKM and simulation rate
constants
RRK, RRKM and simulation rate constants for the
total dissociation rate for N = 2, f = 0.02, b = 1 are shown
Fig. 9. (a) Grid of initial conditions for E ¼ E
Ã
f
þ0:1 on SOS deﬁned by r
1
= r
2
, _ r
2
> _ r
1
. (b) SOS for E ¼ E
Ã
f
þ0:1 deﬁned by r
1
= r
2
, _ r
2
> _ r
1
. (c) First
iterate under Poincare´ map of initial conditions in panel (a).
J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32 21
Fig. 10. The nth crossing of SOS r
1
= r
2
, _ r
2
> _ r
1
for trajectories initiated on transition states 1 (red) and 2 (blue), E ¼ E
Ã
f
þ0:1. (a) n = 1; (b) n = 2; (c)
n = 3; (d) n = 4; (e) n = 10. (For interpretation of the references to colour in this ﬁgure legend, the reader is referred to the web version of this article.)
22 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
as functions of energy in Fig. 13a. While the harmonic
RRK approximation signiﬁcantly overestimates the
RRKM rate constant (cf. Refs. [27–29]), the RRKM value
is only slightly larger than the simulation results, with the
disparity growing larger at higher energies. This level of
agreement is perhaps surprising, given the nonnegligible
fraction of regular phase space occupied by invariant tori,
as noted above. We comment further on this point below.
6.3. Relative rate calculations
As the phenomenon of reactive selectivity is of central
interest in chemistry, it is important to examine the relative
rates of competing reactions. For N = 2, the two compet
ing reactions are the cleavage of bonds 1 and 2, respec
tively. We therefore study the ratio of rate constants k
2
/
k
1
. We consider the statistical predictions for the branching
ratio k
2
/k
1
and compare with simulation results.
6.3.1. RRK and RRKM calculations, N = 2
From expression (9) for k
RRKM
(E, f), the ratio of
RRKM rate constants for reactions 1 and 2 is simply
k
2
k
1
_ _
RRKM
¼
N
z
2
ðE ÀE
Ã
f
Þ
N
z
1
ðE ÀE
Ã
f
Þ
; ð41Þ
as the reactant density of states at energy E cancels out.
The ratio in the harmonic approximation is then
k
2
k
1
_ _
RRK
¼
x
z
1
x
z
2
; ð42Þ
where x
z
j
is the harmonic frequency of the nonreactive nor
mal mode taken about the jth saddle point.
6.3.2. Trajectory results
If k
sim
is the total rate constant for dissociation as deter
mined from trajectory simulation, the rate constants for
channels 1 and 2, k
1,sim
and k
2,sim
respectively, are given
in terms of the respective branching ratios multiplied by
the overall rate constant:
k
j;sim
¼
n
j
n
1
þn
2
k
sim
; j ¼ 1; 2 ð43Þ
where n
1
, n
2
are the number of trajectories that have re
acted through channels 1, 2 respectively at some relatively
long time (we use 2000 time steps) with all nonstatistical,
transient trajectories omitted. The rate ratio is then
k
2
k
1
_ _
sim
¼
n
2
n
1
: ð44Þ
6.3.3. Periodic orbit dividing surface actions
If the transition state of (locally) minimal ﬂux at energy
E is the phase space region A, then for the N = 2 case it
follows from the variational principle of classical mechan
ics [100] that the boundary oAof the region Ais a periodic
classical trajectory deﬁning the periodic orbit dividing sur
face (PODS) [88,89]. The associated ﬂux is then the action
of the PODS
N
z
PODS
ðE ÀE
Ã
f
Þ ¼
_
A
dp ^ dq ¼
_
oA
pdq ð45Þ
deﬁned as a line integral over one cycle of the PODS. Be
cause the PODS is a dynamically determined object and
N
z
PODS
ðE ÀE
Ã
f
Þ reﬂects the full anharmonic dynamics in
the vicinity of the saddle point, this method for calculating
the sum of states N
z
ðE ÀE
Ã
f
Þ provides a check on the accu
Fig. 11. (a) Grid of initial conditions of trajectories started on the SOS r
1
= r
2
, _ r
2
> _ r
1
, E ¼ E
Ã
f
þ0:1, and returning to the SOS at least once, is shown in
green. Trajectories in red and blue regions dissociate immediately through transition states 1 (red) and 2 (blue), respectively, in forward time. (b) Iterates of
initial conditions in panel (a) are shown in green. Additional red and blue regions are preimages of regions in panel (a) under Poincare´ map; that is, they
contain initial conditions for trajectories that dissociate after crossing the SOS once in forward time. (For interpretation of the references to colour in this
ﬁgure legend, the reader is referred to the web version of this article.)
J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32 23
Fig. 12. Red points are initial conditions for trajectories having at least one intersection with the SOS r
1
= r
2
, _ r
2
> _ r
1
. Green points are the iterates under
the Poincare´ map. E ¼ E
Ã
f
þDE. (a) DE = 0.1; (b) DE = 0.2; (c) DE = 0.3; (d) DE = 0.4; (e) DE = 0.5; (f) DE = 0.6. (For interpretation of the references to
colour in this ﬁgure legend, the reader is referred to the web version of this article.)
24 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
racy of the corresponding harmonic and Monte Carlo cal
culations. We evaluate the PODS sum of states at energy E
as
_
PODS
ðp
1
_ q
1
dt þp
2
_ q
2
dtÞ ¼
_
PODS
ðp
2
1
þp
2
2
Þj
H¼E
dt; ð46Þ
using PODS initial conditions obtained as described above.
Fig. 14 shows N
z
j
ðE ÀE
Ã
f
Þ, j = 1, 2, versus energy E for
the harmonic approximation, Monte Carlo integration and
the PODS action method just described. We see that the
anharmonic Monte Carlo areas agree essentially exactly
with the PODS actions (the true dynamical local ﬂuxes).
It is also evident that the harmonic approximation to the
transition sum of states is reasonably accurate, especially
at lower energies.
Fig. 15 shows the RRK and PODS branching ratios k
2
/
k
1
versus energy compared with simulation results. The
value of the RRK branching ratio ð
ﬃﬃﬃ
2
p
Þ is essentially deter
mined by the ratio of the reduced masses for breaking
bonds 1 and 2, and is independent of energy (cf. Ref.
[28]). To the extent that motion along the PODS (the
dynamically deﬁned conﬁguration space transition states)
corresponds to separable motion along the bond coordi
nates, the RRKM/PODS branching ratios will be identical
with the harmonic value. This is not quite the case, how
ever, as can be seen from the form of the PODS plotted
in Fig. 7, so that the branching ratios calculated from the
PODS are close to but not identical with the RRK value.
Only the ratio obtained from simulations exhibits any
signiﬁcant energy dependence; further analysis of its
dynamical origins will require a more detailed investigation
of ‘‘lobe dynamics’’ [92] via the surface of section shown in
Fig. 9.
7. Correcting RRKM theory
7.1. General considerations
While Fig. 6a–d show that a nonnegligible portion of the
reactant phase space is occupied by regular, bound trajec
tories, RRKM rate constants for bond dissociation calcu
lated using an anharmonic density of states are in fairly
close agreement with trajectory values, at least for N = 2
(see Fig. 13a–d). Given that the reactant phase space is cer
tainly not globally chaotic, and given the probable exis
tence of barriers to IVR in the vicinity of the regular
regions of phase space (cantori [91,79]), it is possible that
the good agreement between RRKM and trajectory rate
constants is to some degree fortuitous.
In order to explore this point further, and to make a
proper comparison between the ‘‘statistical’’ rate constant
and the dynamical result, we need to ensure that the inﬂu
ence of bound and direct trajectories on the RRKMtype
calculation is taken into account. A noteworthy discussion
of this problem has been given by Berblinger and Schlier in
the context of the dissociation of the H
þ
3
molecule [96].
0.1 0.2 0.3 0.4 0.5 0.6
E E
f
0.025
0.05
0.075
0.1
0.125
0.15
k
N 2
0.1 0.2 0.3 0.4 0.5 0.6
E E
f
0.02
0.04
0.06
0.08
k
N 3
0.1 0.2 0.3 0.4 0.5 0.6
E E
f
0.005
0.01
0.015
0.02
0.025
k
N 4
0.1 0.2 0.3 0.4 0.5 0.6
E E
f
0.005
0.01
0.015
0.02
k
N 5
a b
c d
Fig. 13. k
RRK
ðE ÀE
Ã
f
Þ (red), k
RRKM
ðE ÀE
Ã
f
Þ (blue) and k
sim
ðE ÀE
Ã
f
Þ (green) for (a) N = 2, (b) N = 3, (c) N = 4 and (d) N = 5. (For interpretation of the
references to colour in this ﬁgure legend, the reader is referred to the web version of this article.)
J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32 25
Barblinger and Schlier identify various properties of the
reactant phase space that should be taken into account
when computing a statistical, RRKMtype dissociation
rate constant. These factors are: (a) presence of direct reac
tive trajectories; (b) recrossing of the transition state(s); (c)
existence of bound (nonreactive) regions of reactive phase
space. After corrections for all these factors have been
made, any remaining discrepancies between RRKM theory
and simulation results can be presumably be attributed to
dynamical eﬀects such as slow IVR (existence of signiﬁcant
phase space bottlenecks) in the reactive portion of phase
space.
The analysis of Berblinger and Schlier can be summa
rized in the following formula for the corrected RRKM
dissociation rate constant [96,80]
k
RRKM
corrected
¼ k
RRKM
j
ð1 À/
z
direct
Þ
ð1 À/
bound
À/
direct
Þ
; ð47Þ
where /
bound
is the fraction of the reactant phase space re
gion occupied by bound (unreactive) trajectories, /
direct
is
the fraction of phase space occupied by direct (‘‘nonstatis
tical’’) trajectories, /
z
direct
is the fraction of the phase space
at the transition state occupied by direct trajectories, and j
is a factor that corrects for recrossing of reactive trajecto
ries at the transition state (the transmission coeﬃcient).
Rather than attempt to implement a corrected statistical
rate theory in the form given by Berblinger and Schlier, we
now discuss a related approach for the N = 2 chain based
on the classical spectral theorem [66–73].
7.2. Computation of statistical and dynamical rate constants
via the classical spectral theorem
In classical unimolecular rate theory it has been known
at least since the work of Thiele [66] that the appropriate
invariant measure on the energy shell for reactive trajecto
ries is given by the volume element (see also refs [67–73])
dr ¼ dq
z
^ dp
z
^ dt; ð48Þ
where (q
à
,p
à
) are canonical coordinates on the transition
state (we consider the N = 2 case for simplicity), and t is
the time along a trajectory initiated on the transition state
passing into the interior of the reactant region. The total
density of nonbound trajectories on the energy shell
H = E in the reactant region is therefore obtained by inte
grating the volume element dr over the transition state(s)
and over the gap time for each trajectory; this is the content
of the classical spectral theorem [66–73]. Thus, trajectories
initated on transition states j = 1, 2 are run backwards in
time until they either pass out of the reactant region or a
suitably large cutoﬀ time has elapsed. (Note that only a
set of measure zero of these trajectories initiated at the
transition state will remain trapped in the reactant region
forever.) The time interval between entry into and exit from
the reactant region is the gap time [101,66]. Details of the
sampling procedure and computation of gap times are
given in Appendix D.
For N = 2, the total density of nonbound trajectories
on the energy shell for H = E is then
q
nonbound
ðEÞ ¼ N
z
1
ðE ÀE
Ã
f
Þhti
1
þN
z
2
ðE ÀE
Ã
f
Þhti
2
; ð49Þ
where N
z
i
ðE ÀE
Ã
f
Þ is the sum of states for transition state i
and hti
i
is the average gap time for trajectories that leave
the reactant region via transition state i (in forward time)
0.1 0.2 0.3 0.4 0.5 0.6
E E
f
0.5
1
1.5
2
2.5
1
‡
0.1 0.2 0.3 0.4 0.5 0.6
E E
f
1
2
3
4
2
‡
Fig. 14. (a) Sum of states for transition state 1. N
z
1;HO
ðE ÀE
Ã
f
Þ (red),
N
z
1;anh
ðE ÀE
Ã
f
Þ (blue) and N
z
1;PODS
ðE ÀE
Ã
f
Þ (black circles) versus E; (b)
Sum of states for transition state 2. N
z
2;HO
ðE ÀE
Ã
f
Þ (red), N
z
2;anh
ðE ÀE
Ã
f
Þ
(blue) and N
z
2;PODS
ðE ÀE
Ã
f
Þ (black circles) versus E. (For interpretation of
the references to colour in this ﬁgure legend, the reader is referred to the
web version of this article.)
0.1 0.2 0.3 0.4 0.5 0.6
E–E
f
*
0.8
1.2
1.4
1.6
1.8
k
2
k
1
Fig. 15. Branching ratio k
2
/k
1
as a function of energy above threshold,
E ÀE
Ã
f
, f = 0.02. HO approximation (red); anharmonic Monte Carlo
(blue); PODS actions (black circles); trajectory simulation (green circles).
(For interpretation of the references to colour in this ﬁgure legend, the
reader is referred to the web version of this article.)
26 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
having entered through either channel. Eq. (49) may be
interpreted as an expression for the combined volume of
two (bifurcated) reactive cylinders [61–63] with crosssec
tional areas N
z
i
ðE ÀE
Ã
f
Þ and lengths hti
i
, i = 1, 2.
The density of states deﬁned in Eq. (49) excludes bound
regions of phase space, as bound trajectories by deﬁnition
do not pass through the transition state; direct trajectories,
however deﬁned, are still included.
By initiating trajectories on transition state j, we can
determine N
(j)
(t), the number (or fraction) of unbound spe
cies left at time t that will ultimately decay through channel
j. It is straightforward to show that, whereas products in
channel j appear at rate characterized by the constant k
j
,
the subpopulation of reactive species that dissociate
through channel j undergoes the same exponential deple
tion exp(Àk t) as the overall reactant concentration.
For those reactant species destined to dissociate through
channel j, a suitably normalized distribution of gap times is
(assuming an exponential distribution [66])
f
j
ðt; EÞ ¼
expðÀkðEÞtÞ
_
1
tc
exp½ÀkðEÞt
0
dt
0
; ð50Þ
where t
c
> 0 is a cutoﬀ time beyond which all transient,
nonexponential behavior has died out. The average gap
time for reaction through channel j is then given by
hti
j
ðE; t
c
Þ ¼
_
1
tc
t
0
f
j
ðt
0
; EÞdt
0
¼
1
kðEÞ
þt
c
; ð51Þ
and depends on the cutoﬀ time t
c
. The values of k(E) ob
tained with this method are denoted by k
PODSj
1
ðEÞ, where
the notation indicates that the intercept 1/k is in practice
obtained by ﬁtting the observed linear behavior of hti
j
at
large cutoﬀ times t
c
!1 and extrapolating back to ﬁnd
the intercept. A representative plot of hti
j
(E) versus t
c
(Fig. 16) shows transient, nonexponential behavior for
shorter t
c
values and linear behavior – corresponding to
exponential decay – for larger t
c
values.
Also of interest is the quantity k
0
(E), the statistical dis
sociation rate constant corrected for the presence of bound
regions of reactant phase space (and obtained via the spec
tral theorem with t
c
= 0). By deﬁnition of the average gap
time, q
(j)
(E), the portion of the reactant density of states
destined for dissociation through channel j, is given by
q
ðjÞ
ðEÞ ¼ N
z
j
ðE ÀE
Ã
f
Þhti
j
ðEÞ; ð52Þ
where hti
j
(E) is obtained with t
c
= 0, so that all ‘‘direct’’
trajectories are included in the average. The rate constant
k
0
(E) is obtained from
k
0
ðEÞ ¼
N
j¼1
N
z
j
ðE ÀE
Ã
f
Þ
N
j¼1
q
ðjÞ
ðEÞ
: ð53Þ
7.3. Comparison of statistical and dynamical dissociation
rates for N = 2
Total dissociation rate constants for N = 2, f = 0.02 and
b = 1 obtained using various methods are shown in Fig. 17.
We can see that there is a signiﬁcant (roughly threefold)
disparity between the RRK and the RRKM predictions,
representing a qualitative failure of the harmonic approxi
mation. This is not unexpected, as the harmonic approxi
mation is especially inadequate for the reactant region
(see Fig. 5a–d). At ﬁxed energy per mode, e = E/N, the dis
parity between harmonic and anharmonic statistical rate
theory increases with the number of atoms N (see below).
If we consider the reactant density of states for N = 2, it
should apparently always be the case that
q
ð1Þ
ðEÞ þq
ð2Þ
ðEÞ 6 qðEÞ; ð54Þ
as the RHS of (54) includes bound as well as nonbound
phase points, so that we expect the inequality
k
0
ðEÞ Pk
RRKM
ðEÞ ð55Þ
to hold. As we can see in Fig. 17, inequality (55) holds only
up to a certain energy, E ÀE
Ã
f
’ 0:4, above which the rate
20 40 60 80 100
t
c
50
100
150
200
250
300
〈t〉
1
Fig. 16. Plot of average gap time hti
1
(t
c
) as a function of cutoﬀ time t
c
for
trajectories initiated on PODS
1
, E ¼ E
Ã
f
þ0:4. Note linear behavior
consistent with exponential decay as t
c
!1.
0.1 0.2 0.3 0.4 0.5 0.6
E–E
f
*
0.025
0.05
0.075
0.1
0.125
0.15
k
Fig. 17. Rate constants k
RRK
ðE ÀE
Ã
f
Þ (red), k
RRKM
ðE ÀE
Ã
f
Þ (blue),
k
sim
ðE ÀE
Ã
f
Þ (green circles), k
0
ðE ÀE
Ã
f
Þ (black circles) and k
PODS1
1
ðE ÀE
Ã
f
Þ
(purple) versus energy above threshold, E ÀE
Ã
F
, for N = 2, f = 0.02 and
b = 1. (For interpretation of the references to colour in this ﬁgure legend,
the reader is referred to the web version of this article.)
J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32 27
constant k
0
(E) actually becomes smaller than the RRKM
rate constant. We resolve this apparent paradox by noting
that q(E) is calculated using the ﬁxed conﬁguration space
sampling region shown in Fig. 4, while the densities q
(j)
are obtained via the spectral theorem using the PODS.
As the PODS move progressively outwards from their
respective saddle points with increasing energy, the increase
of the associated densities of states with energy is suﬃcient
to outweigh the eﬀects of the presence of bound regions,
resulting in a violation of the inequality (55).
The anharmonic RRKM results are close to total disso
ciation rate constants determined via simulation. However,
the RRKM results begin to disagree with the simulation
rates with increasing energy, the disparity eventually reach
ing a factor of roughly three. This is perhaps not surpris
ing, given the lack of global chaos seen in the SOS for
N = 2. At the very highest energies, it becomes diﬃcult to
ﬁt the lifetime distributions to a pure exponential decay;
nevertheless, the ﬁts obtained for k
sim
and k
0
agree at these
energies.
Dissociation rate constants obtained using the classical
spectral theorem essentially match those obtained by simu
lation. Of course the spectral theorem approach, which is
based upon the distribution of gap times, must reﬂect the
same dynamical information as a standard trajectory sim
ulation. It is nevertheless gratifying to see that the two
approaches agree so well. It seems likely that the spectral
theorem approach will prove useful in the multimode case
(N P3 dof) in combination with the normal form based
analysis of the transition state of Uzer et al.[102,103].
8. N >3 atom chains
A signiﬁcant jump in dynamical complexity occurs in
going from N = 2 to N P3atom chains. For N > 2, the
dynamics and phase space structure cannot easily be visu
alized via a SOS [60,104]. Further, the transition states
for chain fragmentation are themselves (N À 1) P2degree
of freedom dynamical systems, making visualization and
accurate anharmonic sampling diﬃcult using the
approaches described above for N = 2 atom chains.
Accurate determination of transition states in Natom
chains under tensile stress is a problem that seems wellsui
ted to the application of recent advances in normal form
expansion techniques recently developed by Uzer
et al.[102,103,105]. In the present work, however, we
restrict ourselves to the computation of a ‘‘hybrid’’ har
monic–anharmonic rate constant for our statistical predic
tions of chain fragmentation rates.
As Fig. 14 shows, for N = 2 at least the harmonic tran
sition state sum of states is a close approximation to the
anharmonic result at energies close to the dissociation
threshold E
Ã
f
. We therefore combine a harmonic oscillator
approximation for the transition state sum of states with
a full numerical determination of the reactant density of
states to give our RRKM expression for N P3atom
chains:
k
RRKM=HO
ðEÞ ¼
N
z
HO
ðE ÀE
Ã
f
Þ
q
anh
ðEÞ
: ð56Þ
Total bond dissociation rate constants obtained using
RRK, RRKM and simulation with f = 0.02 and b = 1
are plotted as a function of energy E for N = 2–5 in
Fig. 13. To further examine the validity of the harmonic
and statistical approximations to the dynamical rate con
stant, we plot the ratios of harmonic (RRK) to anharmonic
(hybrid RRKM) and anharmonic to simulation results as a
function of energy per degree of freedom, E/N, in Figs. 18
and 19, respectively.
The ratios of RRK to hybrid RRKM rate constants are
simply the ratios of harmonic and anharmonic reactant
densities of states. Fig. 18 shows that, while the discrepancy
between the RRK and RRKM rate constants grows with
the number of atoms N at ﬁxed energy per mode, e = E/
N, at constant total energy E the ratio of RRK and RRKM
rate constants approaches unity (harmonic limit) as N
increases. For example, for total energy E = 1 the ratios
are 3.24(N = 2), 2.46(N = 3), 2.12(N = 4) and 1.89
(N = 5). RRKM total dissociation rate constants com
0.3 0.4 0.5 0.6 0.7
E
N
1.5
2
2.5
3
3.5
k
RRKM
k
sim
Fig. 19. Ratio k
RRKM
(E)/k
sim
(E) as a function of energy per mode, E/N,
for N = 2 (red), N = 3 (green), N = 4 (blue) and N = 5 (purple). (For
interpretation of the references to colour in this ﬁgure legend, the reader is
referred to the web version of this article.)
0.3 0.4 0.5 0.6 0.7
E
N
2.5
3
3.5
4
4.5
k
RRK
k
RRKM
Fig. 18. Ratio k
RRK
(E)/k
RRKM
(E) as a function of energy per mode, E/N,
for N = 2 (red), N = 3 (green), N = 4 (blue) and N = 5 (purple). (For
interpretation of the references to colour in this ﬁgure legend, the reader is
referred to the web version of this article.)
28 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
puted with an anharmonic reactant density of states are
within a factor of 2 of the simulation result. The ratio of
RRKM to simulation rate constant shows an overall
increasing trend with increasing E/N.
Finally, Fig. 20 shows the ratios (k
RRK
/k
RRKM
) and
(k
RRKM
/k
sim
) as a function of E/N, N = 2–5, for tethered
chains with potential parameters corresponding to model
polyethylene [74,75,51,76] and tensile force f = 0.02.
9. Summary and conclusions
In this work we have studied the bond dissociation
kinetics of tethered atomic (Morse potential) chains under
tensile stress. Our focus has been the nonstatistical aspects
of the dissociation kinetics and the role of anharmonicity.
Statistical theories of unimolecular dissociation rate con
stants, both RRKM and RRK (harmonic appproximation)
have been applied to predict bonddissociation rates as a
function of energy and tensile force. A fully anharmonic
version of RRKM theory is implemented using Monte
Carlo integration to determine reactant and transition state
phase space volumes as a function of energy. Comparison
of statistical predictions with dynamical dissociation rate
constants obtained using trajectory simulations for chains
with N = 2–5 atoms shows that, while the RRK approxi
mation signiﬁcantly overestimates the dissociation rate,
the fully anharmonic RRKM theory is quite accurate.
The eﬀects of anharmonicity are at least partly able to
rationalize discrepancies between trajectory results and
classical transition state theory noted previously [29].
For the twoatom chain, N = 2, we also carry out a
detailed examination of phase space structure using Poin
care´ surfaces of section. We note that good agreement
between the RRKM and dynamical rate constants is
obtained despite the fact that the reactant phase space con
tains a signiﬁcant fraction of relatively shortlived trajecto
ries (as judged by the number of intersections with the
SOS). For the N = 2 chain, we also implement a novel
approach to the extraction of decay rate constants based
on the classical spectral theorem. This approach corrects
for the presence of invariant bound (nonreactive) regions
of reactant phase space, and yields total dissociation rates
in close agreement with dynamical simulation.
Our statistical predictions for chains with N P3 atoms
are obtained using a hybrid statistical theory involving a
harmonic approximation for motion in the transition state
for bond dissociation. Further exploration of the dynamics
in the vicinity of the transition state in multimode chains
along the lines of the recent work by Uzer and Jaﬀe´
[102,103,105] would clearly be worthwhile, as would an
investigation of the applicability of the spectral theorem
approach.
Appendix A. Determining the reactant phase space volume
NðEÞ
For N = 2, the conﬁgurational projection of M
0
is the
union of the rectangular region and and adjacent triangular
region shown in Fig. 4. The shape of this region ensures
that phase points in the vicinity of transition states 1 and
2 are sampled appropriately while avoiding ‘‘leakage’’ of
sampled points into nearby exit channels.
For example, for f = 0.02 and b = 1 the line x
1
= 3.303
is taken to deﬁne a suitable boundary between sampling
regions in the vicinity of transition states 1 and 2 (see
Fig. 4). The line x
2
= Àx
1
+ 2r
à
+ r
eq
deﬁning transition
state 1 intersects this line at (3.303, 8.898). The phase space
sampling for the rectangular region is then
x
1
2 ½0; 3:303 ðA:1aÞ
x
2
2 ½0; r
eq
þr
z
ðA:1bÞ
p
j
2 À
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2E
max
_
;
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2E
max
_
_ _
; j ¼ 1; 2; ðA:1cÞ
while that for the triangular region is
x
2
2 ½0; 8:898 ðA:2aÞ
x
1
2 ½3:303; Àx
2
þ2r
z
þr
eq
ðA:2bÞ
p
j
2 À
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2E
max
_
;
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2E
max
_
_ _
; j ¼ 1; 2: ðA:2cÞ
The phase space region M
0
therefore has volume
0.3 0.4 0.5 0.6 0.7
E
N
2.5
3
3.5
4
4.5
5
k
RRK
k
RRKM
0.4 0.5 0.6 0.7
E
N
0.5
1.5
2
2.5
k
RRKM
k
sim
a
b
Fig. 20. (a) Ratio k
RRK
(E)/k
RRKM
(E) as a function of energy per mode E/
N for N = 2 (red), N = 3 (green), N = 4 (blue) and N = 5 (purple). (b)
Ratio k
RRKM
(E)/k
sim
(E) as a function of energy per mode E/N for N = 2
(red), N = 3 (green), N = 4 (blue) and N = 5 (purple). Morse parameters
correspond to model polyethylene. (For interpretation of the references to
colour in this ﬁgure legend, the reader is referred to the web version of this
article.)
J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32 29
V
0
¼ 2
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2E
max
_
_ _
2
3:303ðr
eq
þr
z
Þ þ
1
2
8:898ð2r
z
þr
eq
À3:303Þ
_ ¸
_ _
:
ðA:3Þ
For N = 2 the phase space volume NðEÞ is ﬁtted to the
form
NðEÞ ’ E
2
ðc
0
þc
1
E þ. . .Þ; ðA:4Þ
For N P3, dim(M
0
) = 2N and the region M
0
is deﬁned by
the following ranges of phase space coordinates:
x
j
2 ½x
jÀ1
; x
jÀ1
þr
z
; j ¼ 1; . . . ; N ðA:5aÞ
p
j
2 À
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2E
max
_
;
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2E
max
_
_ _
; j ¼ 1; . . . ; N: ðA:5bÞ
with x
0
= 0. Hence for the reactant region of phase space,
V
0
¼ ð2r
z
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2E
max
p
Þ
N
, and the function NðEÞ is ﬁtted to the
form
NðEÞ ’ E
N
ðc
0
þc
1
E þ. . .Þ; ðA:6Þ
that is, harmonic oscillator phase space volume plus anhar
monic corrections.
Appendix B. Sampling phase points on the energy shell
For N degrees of freedom, the phase space volume
element is
dz ¼ dxdp ¼ dx
1
Á Á Á dx
N
dp
1
Á Á Á dp
N
: ðB:1Þ
Introducing polar coordinates in momentum space, this
becomes
dz ¼ dx
1
Á Á Á dx
N
p
NÀ1
dpdx ðB:2Þ
where dx is the associated angular volume element. For
N = 2, dx = d/, with 0 6 / 6 2p, while for N = 3,
dx = sinhdh d/, with 0 6 h 6 p and 0 6 / 6 2p. To spec
ify phase points on the energy shell, we change variable
from p to E, using
oH
op
¼
oT
op
¼ p ðB:3Þ
(setting all masses m = 1) to obtain
dz ¼ dx
1
. . . dx
N
p
NÀ2
dEdx: ðB:4Þ
On the energy shell, the (2N À 1)dimensional element of
hypersurface area dr dz
H(z)=E
is therefore
dr ¼ dx
1
Á Á Á dx
N
p
NÀ2
dx: ðB:5Þ
The task is then to sample points distributed according to
the distribution function implied by (B.5) (see also
[106,28]).
B.1. N = 2 degrees of freedom
The situation for N = 2 dof is very straightforward. The
volume element is
dr
N¼2
¼ dx
1
dx
2
d/: ðB:6Þ
To sample phase points, we simply choose points uni
formly in some region R of conﬁguration space,
x ¼ ðx
1
; x
2
Þ 2 R. If V(x) 6 E, we determine the value of
the momentum magnitude p required to satisfy H = E.
Momentum components are then deﬁned according to
p = (psin/, pcos/), with angle / chosen at random in the
interval 0 6 / 6 2p.
B.2. N P3 degrees of freedom
The volume element in this case is
dr ¼ dx
1
dx
2
dx
3
pdx: ðB:7Þ
It is therefore necessary to weight momentum values
according to p rather than the natural 3D weighting p
2
.
To accomplish this we use a rejection method [99].
Points are sampled uniformly at random inside a region
Rof x = (x
1
,x
2
,x
3
) space. For any given energy E, there is a
maximum possible momentum magnitude P, which will be
determined by the value of the kinetic energy at the poten
tial minimum. For any sampled point x, provided
V(x) 6 E, we determine the associated scaled momentum
magnitude,
g
p
P
; 0 6 g 6 1: ðB:8Þ
Now choose a random number q between 0 and 1.
(1) If g < q, we reject the point.
(2) If g > q, we accept the point. Gaussian variates in 3D
are then used to compute a random orientation for
the momentum vector in 3D. If ^n is a randomly cho
sen vector on the 2sphere, the chosen phase point is
z ¼ ðx; p ¼ p^n ¼ gP^nÞ.
Analogous rejection procedures are used for sampling
the energy shell for N > 3.
Let N
trial
be the number of sampled points satisfying
V(x) 6 E; this is the total number of points sampled on
the energy shell, some of which will be rejected as above.
Let the number of accepted points {z
k
} be N
accept
. The
average value of any property F(z) is then
hF i ¼
k
F ðz
k
Þ
N
accept
ðB:9Þ
where the sum is over accepted points.
Appendix C. Stable and unstable manifolds of the PODS
The ﬁrst step in computing the full nonlinear stable and
unstable manifolds W
s=u
of the PODS is determination of
the linearized manifolds, E
s
and E
u
, respectively [107].
The monodromy matrix M corresponding to one trip
around the unstable periodic orbit PODS
1
provides a line
arized approximation to the iterated dynamics of a phase
point on the SOS displaced from the PODS by
Dz = (DX,DP),
30 J.N. Stember, G.S. Ezra / Chemical Physics 337 (2007) 11–32
MDz ¼
M
XX
M
XP
M
PX
M
PP
_ _
DX
DP
_ _
¼
DX
0
DP
0
_ _
¼ Dz
0
: ðC:1Þ
To determine M we propagate the displaced phase points
Dz
DX
= (DX,0) and Dz
DP
= (0,DP) for one iteration of the
SOS mapping. If Dz
DX
and Dz
DP
evolve to Dz
0
and Dz
00
respectively under the mapping, then DX M
XX
= X
0
, DX
M
PX
= P
0
and DP M
XP
= X
00
, DP M
PP
= P
00
. The matrix
M thus obtained can then be diagonalized to obtain eigen
values and eigenvectors.
For example, for E ¼ E
Ã
f
þ0:1, eigenvalues are
k
1
= 0.715, k
2
= 1.399 with corresponding stable and
unstable eigenvectors z
s
= (X
s
,P
s
) = (À0.9808,0.1948) and
z
u
= (X
u
,P
u
) = (À0.9808, À 0.1948), respectively. The
determinant of M is 1.00006, verifying symplecticity (area
conservation) of the linearized dynamics [60] to within rea
sonable numerical accuracy.
Points on the (nonlinear) manifolds W
u=s
are obtained
by propagating phase points close to the periodic orbit
on the respective linearized manifolds forwards/backwards
in time. To visualize W
u=s
, we select 1000 initial conditions
along short segments of E
s/u
close to the PODS and prop
agate all these phase points either forward or backwards in
time. The resulting manifolds for E
Ã
f
þ0:1 are shown in
Fig. 8. The bound complex region can be deﬁned to be
the phase space volume enclosed by these two manifolds
between the PODS and their ﬁrst intersection [79].
Appendix D. Computing average gap times
To calculate hti
1
(E), the average gap time for trajectories
exiting via transition state 1, initial coordinate values on
transiton state 1 are selected according to
nð0Þ 2 ½0; r
z
ðD:1aÞ
Xð0Þ ¼ X
PODS
1
ðEÞ; ðD:1bÞ
where X
PODS
1
ðEÞ is the average value of coordinate X for
PODS 1 at energy E. The initial momentum variable
P(t = 0) is selected in the range
Pð0Þ 2 À
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
Tð0Þ
_
;
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
Tð0Þ
_
_ _
; ðD:2Þ
where the kinetic energy is T(0) = E À V(X(0),n(0)). The
momentum P(0) is then Pð0Þ ¼ þ
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
4ðTð0Þ ÀPð0Þ
2
Þ
_
, where
the positive root is taken so that the trajectory will enter
the reactant region in negative time.
To calculate the average gap time hti
2
(E), we sample
x
1
(t = 0) and p
1
(t = 0) on transition state 2 by selecting ini
tial coordinate values in the ranges
x
1
ð0Þ 2 ½0; x
max
1
ðEÞ; ðD:3aÞ
x
2
ð0Þ ¼ x
PODS
2
2
ðEÞ ðD:3bÞ
where x
max
1
ðEÞ is a suitably chosen maximum value of coor
dinate x
1
, and x
PODS
2
2
ðEÞ is the average x
2
value for
PODS
2
(E). We sample initial momenta according to
p
1
ð0Þ 2 À
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2Tð0Þ
_
;
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2Tð0Þ
_
_ _
; ðD:4aÞ
p
2
ð0Þ ¼ Æ
ﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
2Tð0Þ Àp
1
ð0Þ
2
_
; ðD:4bÞ
where T(0) = E À V(x
1
(0),x
2
(0)). We select only the posi
tive solution for p
2
(0) so that again our trajectories will
propagate into the reactant region in negative time.
For both average gap time calculations, the dissociation
criterion is that either XðÀtÞ > X
PODS
1
ðEÞ (reaction 1) or
x
2
ðÀtÞ > x
PODS
2
2
ðEÞ, x
1
ðÀtÞ < x
max
1
ðEÞ (reaction 2). For
channel i, we therefore compute the average gap time for
trajectories that, in forward time, enter the reactant region
from either transition state and exit only through transition
state i. For both calculations we integrate n
traj
= 10
4
trajec
tories for energies E ¼ E
Ã
f
þ0:1; E
Ã
f
þ0:2; E
Ã
f
þ0:3; E
Ã
f
þ
0:4; E
Ã
f
þ0:5 and E
max
. Each trajectory is integrated with
time step s = À10
À1
s
0
for n
step
= 5 · 10
5
time steps or until
reaction has occurred. A negligible number of trajectories
fail to react within n
step
timesteps.
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