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Isomerization kinetics of a strained Morse oscillator ring

Joseph N. Stember
a,1
, Gregory S. Ezra
a,2,∗
a
Department of Chemistry and Chemical Biology
Baker Laboratory
Cornell University
Ithaca
NY 14853
Abstract
Isomerization kinetics are studied for a 3-atom linear Morse chain under
constant strain. Cyclic boundary conditions render the problem isomorphic to
an isomerizing system of particles on a ring. Both RRKM (fully anharmonic,
Monte Carlo) and RRK (harmonic appproximation) theories are applied to pre-
dict isomerization rates as a function of energy for a particular strain value.
Comparison with isomerization rates obtained from trajectory calculations of
flux correlation functions shows that the harmonic approximation significantly
overestimates the rate constant, whereas the anharmonic calculation comes con-
siderably closer to the simulation result. The energy range over which a rate
constant has dynamical meaning is delineated.
Keywords:
Mechanochemistry, Isomerization kinetics, Statistical theories
PACS: 82.20.Db, 34.10.+x, 83.20.Lp
1. Introduction
Isomerization reactions are of great importance in chemistry, and are central
to many condensed phase and biological processes. Study of the dynamics of
isomerization provides a venue for exploring issues of statisticality and the ef-
fectiveness of statistical theories. (For a brief survey of some relevant literature,
see [1].) For example, the classic work of De Leon and Berne [2] examined the
dynamics of a symmetrical two-well potential, adjusting the energy and degree
of coupling in the system. For energies just above the activation barrier, RRKM
behavior [3–7] was found for sufficiently large coupling. However, for energies
significantly above the barrier, even with large coupling, oscillatory recrossing

Corresponding author
Email address: gse1@cornell.edu (Gregory S. Ezra)
1
Present address: NYU Langone Medical Center, 550 First Ave, New York, NY 10016
2
Tel: 607-255-3949; Fax: 607-255-4137
Preprint submitted to Elsevier September 13, 2010
motions led to non-exponential decay of reactive flux, so that an isomerization
rate constant was no longer defined.
A fundamental understanding of the intramolecular dynamics and kinetics of
fragmentation (bond dissociation) of atomic chains subject to a tensile force is
needed to provide a solid foundation for theories of material failure under stress
[8, 9], polymer rupture [10–14], adhesion [15], friction [16], mechanochemistry
[17–19] and biological applications of dynamical force microscopy [20–24]. (For
more detailed discussion of this topic, see the previous paper [25].)
In the present paper we study numerically the kinetics of bond breaking in
single atomic chains under stress. The dissociation of a 1-D chain subject to
constant tensile force is a problem in unimolecular kinetics, and a fundamental
issue concerns the applicability of statistical approaches such as RRKM [3–7]
or transition state theory [26]. In previous work, we have studied the applica-
bility of statistical theories to describe the dissociation rate of tethered linear
chains under tensile stress [25]. In the present work we impose cyclic boundary
conditions on the chain, so that it is mapped onto a ring polymer under strain.
For small strains, the potential surface has a single minimum, whereas at higher
strains a bifurcation occurs to yield several distinct minima. The reaction of
interest now corresponds to isomerization between the various minima. Stan-
dard methods involving the reactive flux can be employed to study the kinetics
of isomerization [27]
Section 2 describes the system to be studied and the form of the potential
surface as a function of the strain. In section 3 we discuss the methods used
to compute the isomerization rate constant based on the reactive flux approach
[27]. Section 4 discusses the results of our trajectory simulations, while sta-
tistical (RRK and RRKM) computations of the rate are reported in section 5.
Section 6 concludes.
2. Isomerizing system
The isomerizing system we consider is a cyclic version of the tethered linear
chain treated previously [25]. Our system consists of P identical atoms on a line
confined to a “box” of length L. We assume that adjacent atoms interact via
Morse potentials, and impose cyclic boundary conditions, so that our setup can
be mapped onto a system consisting of P atoms on a ring with circumference
L. That is, we map a linear chain to a strained ring. Taking the length L to be
a constant, we have P −1 = N degrees of freedom for a P-atom system.
A unique equilibrium structure exists for L ≈ Pr
eq
, r
eq
being the equilibrium
bond distance in the unstrained Morse potential. All bond distances are equal
in such a structure. As L increases in the strained chain to the point where the
value of L/P significantly exceeds the equilibrium value r
eq
, a bifurcation occurs
wherein the number of equilibrium structures goes from 1 to P, at which point
the initial (symmetric) equilibrium structure becomes a global maximum of the
potential [28]. A schematic of the two isomers forming in a strained N = 1 ring
is shown in Figure 1.
2
In terms of single-particle coordinates x = {x
k
}, the potential energy is
given by
V ({x
i
}
P
i=1
; L) =
P−1

i=1
V
M
(x
i+1
−x
i
) + V
M
(L −(x
P
−x
1
)), (1)
where the Morse potential is
V
M
(r) = D
0
[1 −exp(−β(r −r
eq
))]
2
. (2)
For all calculations, we measure energy in units of the pairwise dissociation
energy D
0
, and length in units of the equilibrium bond distance r
eq
.
In bond coordinates the potential is
V ({r
i,i+1
}
P−1
i=1
; L) =
P−1

i=1
V
M
(r
i,i+1
) + V
M
(L −
P−1

i=1
r
i,i+1
), (3)
where r
i,j
≡ x
j
−x
i
.
2.1. Diatomic chain: N = 1
For the diatomic case (P = 2, N = 1) the potential is simply
V (r
12
) = V
M
(r
12
) + V
M
(L −r
12
). (4)
As L increases from 1 to 10, the potential curve bifurcates, going from having
one well to two wells, both corresponding to a stable isomer (Figure 2). The
large L regime is of interest from the point of view of isomerization dynamics.
Denoting the left well A and that on the right well B, the energetic barrier to
isomerization is given by V (r

12
) − V (r
A/B
12
) = E

L
, where r
A/B
12
could be the
position of either well A or well B (which have the same potential energy.)
To simplify our calculations, we transform coordinates x → ˜ x such that the
kinetic energy takes the simple diagonal form
T =
1
2
N

i=1
˜ p
2
i
. (5)
The generating function [29] for the desired transformation to Jacobi coordinates
(X, ξ) is
F(x
1
, x
2
, P, Π) = a(x
1
+ x
2
)P + b(x
2
−x
1
)Π, (6)
which gives the relations
X =
∂F
∂P
= a(x
1
+ x
2
) (7a)
ξ =
∂F
∂Π
= b(x
2
−x
1
) (7b)
P =
1
2a
(p
1
+ p
2
) (7c)
Π =
1
2b
(p
2
−p
1
). (7d)
3
The kinetic energy is
1
2
(p
2
1
+ p
2
2
) = a
2
P
2
+ b
2
Π
2
, (8)
so that, with a = b = 1/

2, we have
T =
1
2
(P
2
+ Π
2
), (9)
and the Hamiltonian takes the form
H = V
M
(

2ξ) + V
M
(L −

2ξ) +
1
2
P
2
+
1
2
Π
2
. (10)
Of particular note is that
˙
P = −
∂H
∂X
= 0, so that the momentum P conjugate
to X is a constant of the motion. In other words, integration of the equations
of motion should ideally preserve the center of mass momentum P(t), so that if
we choose only trajectories such that P(t = 0) = 0, then every such trajectory
should have P(t) = 0 ∀ t. For N = 2 we find numerically that our symplectic
integrator generates |P(t)| values on the order of 10
−18
or smaller.
Choosing P(0) = 0 =
1

2
(p
1
+p
2
) implies that p
1
(0) = ±

T, p
2
(0) = ∓

T.
Motion of the system consists of trivial oscillation between the two wells when
E > E

L
, and within one well when E ≤ E

L
.
2.2. Triatomic: N = 2
In terms of bond coordinates, the potential for P = 3, N = 2 is
V (r
12
, r
23
) = V
M
(r
12
) + V
M
(r
23
) + V
M
(L −(r
12
+ r
23
)). (11)
As L increases from 2 to 10, we again see a bifurcation, this time into a three-
well system (Figures 3 and 4). Each pair of wells is separated by an activation
barrier, as in the N = 1 case. All three activation energies are equivalent. There
is also a global maximum in the potential, situated symmetrically with respect
to the three wells, which represents the energetically unfavorable configuration
wherein all three bonds are extended equally to a value considerably greater
than r
eq
.
For all our calculations, we use β = 1 and L = 10. This yields the activation
energy E

L=10
= 0.882, which is close to that of the tethered linear chain studied
previously with β = 1 and f = 0.02 [25]. Potential energy surfaces (β =
1, L = 10) in bond coordinates and Jacobi coordinates, together with saddle
points, are displayed in Figures 4(a) and 4(b), respectively. We use the following
nomenclature for our wells: let A be the lower left well in Figure 4(a), B the
lower right well in Figure 4(a) and C the upper left well in Figure 4(a). Then,
the transition state separating wells A and B for instance will be labeled ‡
AB
.
The full Hamiltonian in terms of bond coordinates is
H = V
M
(r
12
) + V
M
(r
23
) + V
M
(L −(r
12
+ r
23
)) + p
2
r12
+ p
2
r23
−p
r12
p
r23
, (12)
4
where we have set the center of mass momentum P equal to zero. In terms of
single-particle coordinates, the Hamiltonian is given by
H = V
M
(x
2
−x
1
) +V
M
(x
3
−x
2
) +V
M
(L−(x
3
−x
1
)) +
1
2
_
p
2
1
+ p
2
2
+ p
2
3
_
. (13)
The generating function for the tranformation to Jacobi coordinates (X, ξ
1
, ξ
2
)
is
F(x
1
, x
2
, x
3
, P, Π
1
, Π
2
) = a(x
1
+x
2
+x
3
)P +b(x
2
−x
1

1
+c(x
3

1
2
(x
1
+x
2
))Π
2
,
(14)
so that we have
X =
∂F
∂P
= a(x
1
+ x
2
+ x
3
) (15a)
ξ
1
=
∂F
∂Π
1
= b(x
2
−x
1
) (15b)
ξ
2
=
∂F
∂Π
2
= c(x
3

1
2
(x
1
+ x
2
)) (15c)
P =
1
3a
(p
1
+ p
2
+ p
3
) (15d)
Π
1
=
1
2b
(p
2
−p
1
) (15e)
Π
2
=
1
3c
(2p
3
−p
2
−p
1
). (15f)
The kinetic energy is
T =
1
2
(p
2
1
+ p
2
2
+ p
2
3
) =
3a
2
2
P
2
+ b
2
Π
2
1
+
3c
2
4
Π
2
2
, (16)
so that, setting a =
1

3
, b =
1

2
and c =
_
2
3
, we have T =
1
2
(P
2
+ Π
2
1
+ Π
2
2
)
and resulting Hamiltonian
H =
1
2
(P
2
+ Π
2
1
+ Π
2
2
) + V
M
(


1
) + V
M
_
1

2
(−ξ
1
+


2
)
_
+ V
M
_
L −
1

2

1
+


2
)
_
. (17)
As for the case N = 1, the center of mass momentum is a constant of the motion,
i.e.,
˙
P = −
∂H
∂X
= 0.
3. Isomerization kinetics and rate constant for N = 2
We now analyze the kinetics of isomerization in the triatomic chain subject
to cyclic boundary conditions. We follow the derivation for the two-well system
given, for example, in Chandler [27].
5
3.1. Phenomenological kinetics
Isomerization reactions occurring in our system are
A
kAB
−−−→B (18a)
A
kAC
−−−→C (18b)
B
kBA
−−−→A (18c)
B
kBC
−−−→C (18d)
C
kCA
−−−→A (18e)
C
kCB
−−−→B. (18f)
Since the shape and depth of each well is identical, all the rate constants (as-
suming we are in a parameter regime in which a rate constant has meaning) are
equal, i.e. k
AB
= k
BA
= k
AC
= k
CA
= k
BC
= k
CB
= k.
The concentrations of A,B and C are therefore determined by the linear rate
equations
˙ c
A
(t) = −2kc
A
(t) + kc
B
(t) + kc
C
(t) (19a)
˙ c
B
(t) = kc
A
(t) −2kc
B
(t) + kc
C
(t) (19b)
˙ c
C
(t) = kc
A
(t) + kc
B
(t) −2kc
C
(t). (19c)
In matrix notation we have
˙ c(t) = Kc(t), (20)
where c(t) = [c
A
(t), c
B
(t), c
C
(t)] is the concentration vector and
K =
_
_
−2k k k
k −2k k
k k −2k
_
_
, (21)
is the rate constant matrix, with eigenvalues {0, −3k, −3k}. Differential equa-
tion (20) has the solution
c(t) = exp(Kt)c
0
, (22)
where c
0
= c(t = 0).
Assuming an initial condition with all species in well A, and setting the
initial concentration equal to unity, i.e. c
0
= [1, 0, 0], we obtain
c(t) = exp(Kt) c
0
=
_
_
1
3
+
2
3
exp(−3kt)
1
3

1
3
exp(−3kt)
1
3

1
3
exp(−3kt)
_
_
. (23)
6
3.2. Isomerization rates and concentration fluctuations
Standard arguments based upon the regression hypothesis [27] relate the
relaxation behavior of the concentration c
A
(t) of species in well A, for example,
to the decay of fluctuations of the corresponding equilibrium concentration:
∆c
A
(t)
∆c
A
(0)
=
C(t)
C(0)
=
δn
A
(0)δn
A
(t)
δn
A
(0)
2

, (24)
where ∆c
A
(t) = c
A
(t)−c
A
(t →∞) = c
A
(t)−c
A
and C(t) ≡ δn
A
(0)δn
A
(t) is
the equlibrium concentration fluctuation correlation function. The microscopic
quantity n
A
(t) is the average number of systems in well A as determined by
averaging over the (trajectory) ensemble, and δn
A
(t) = n
A
(t) − n
A
, where
n
A
is the long time (equilibrium) average value of n
A
(t).
Our analysis of the phenomenological kinetics of isomerization shows that
∆c
A
(t)
∆c
A
(0)
= exp(−3kt), (25)
so that the value of the isomerization rate coefficient k can in principle be
extracted from a trajectory simulation evaluation of C(t).
The population n
A
(t) is defined by the integral over the trajectory ensemble
of the characteristic function H
A
= Θ(r

12
−r
12
)Θ(r

23
−r
23
), where r

12
, r

23
mark
the positions of the saddle points dividing A from B and A from C, respectively.
By definition, the quantity H
A
[r
12
(t), r
23
(t)] is equal to 1 when the trajectory
is in well A, and 0 when outside of A. We observe that H
A
= H
2
A
= x
A
=
1
3
,
the equilibrium fraction of A. We have
C(0) = δn
A
(0)
2
= (H
A
(0) −x
A
)
2
= x
A
(1 −x
A
) = x
A
(x
B
+x
C
) =
2
9
. (26)
The numerator of the right hand side of Equation (24) is
δn
A
(0)δn
A
(t) = n
A
(0)n
A
(t) −n
2
A
= n
A
(0)n
A
(t) −x
2
A
. (27)
Taking the time derivative of both sides of Equation (24) leads to the more
useful form (cf. [27])

2
3
k exp(−3kt) = H
A
(0)
˙
H
A
(t) = −
˙
H
A
(0)H
A
(t). (28)
We now observe that
d
dt
H
A
[r
12
(t), r
23
(t)] = ˙ r
12

∂r
12
H
A
[r
12
(t), r
23
(t)] + ˙ r
23

∂r
23
H
A
[r
12
(t), r
23
(t)] .
(29)
Then, recalling our definition H
A
[r
12
(t), r
23
(t)] ≡ Θ(r

12
−r
12
(t))Θ(r

23
−r
23
(t)),
we have
˙
H
A
(0) = −
_
˙ r
12
(0)Θ(r

23
−r
23
(0))δ(r
12
(0) −r

12
)
+ ˙ r
23
(0)Θ(r

12
−r
12
(0))δ(r
23
(0) −r

23
)
_ (30)
7
so that
k exp(−3kt) = −
3
2
__
˙ r
12
(0)Θ(r

23
−r
23
(0))δ(r
12
(0) −r

12
)
+ ˙ r
23
(0)Θ(r

12
−r
12
(0))δ(r
23
(0) −r

23
)
_
H
A
(t)
_
,
(31)
where the average over initial conditions is taken over the full available phase
space, spanning the 3 wells. Note that the minus sign in Equation (31) is
correct; at very short times only those trajectories crossing into well A, for
which ˙ r
1k
< 0, k = 2, 3, will contribute to the integral.
The microcanonical density of states for well A is
ρ(E) =
1
3
_
well A ∪ well B ∪ well C
dr
12
dp
r12
dr
13
dp
r13
δ(E −H(r
12
, p
r12
, r
13
, p
r13
)),
(32)
where the microcanonical partition function is obtained by averaging over all
the available phase space (wells A, B and C), and is just three times the parti-
tion function for an individual well, since all 3 wells are identical (as is evident
from Figure 4(b)). From Equation (31), we therefore obtain via standard ma-
nipulations [27] the result
k exp(−3kt) = −
1
2ρ(E)
_
_
‡AB,H(z)=E
dr
23
dp
r23
sign [ ˙ r
12
(0)] H
A
(t)
+
_
‡AC,H(z)=E
dr
12
dp
r12
sign [ ˙ r
23
(0)] H
A
(t)
_
.
(33)
4. Trajectory simulations and extraction of rate coefficient
To go from the integral form of k exp(−3kt) given in Equation (33) to the
expression that we actually use to compute the fluxes, we sum over discrete
contributions ˙ r
12
(0)H
A
(t) and ˙ r
23
(0)H
A
(t):
k(E) exp(−3k(E)t) = −
1
2ρ(E)
×
_

TAB
_
N

AB
(E −E

L
)
n
traj
_
sign [ ˙ r
12
(0)] H
A
(r
12
(t), r
23
(t))
+

TAC
_
N

AC
(E −E

L
)
n
traj
_
sign [ ˙ r
23
(0)] H
A
(r
12
(t), r
23
(t))
_
,
(34)
where T
ij
is the set of initial conditions on transition state ‡
ij
. N

ij
(E −E

L
) is
the phase space volume-like quantity that gives the area in the (r
ij
, p
r
ij
) plane
of phase points that satisfy the microcanonical condition H(z) = E, where ij
is the degree of freedom that lies “along” the ij transition state.
8
Since N

AB
(E − E

L
) = N

AC
(E − E

L
) by symmetry, and because we are
interested chiefly in the rate of exponential flux decay, we may disregard constant
factors and rewrite our rate constant equality more simply as a proportionality
relation
k(E) exp(−3k(E)t) ∝
_
_

trajs,AB
sign [ ˙ r
12
(0)] H
A
(r
12
(t), r
23
(t))
+

trajs,AC
sign [ ˙ r
23
(0)] H
A
(r
12
(t), r
23
(t))
_
_
.
(35)
In a regime where the flux computed using Equation (35) exhibits exponential
decay, the decay exponent is just 3k(E).
Initial conditions are selected at random on the two configuration space
transition states, i.e., with equal probability for phase points lying on either
transition state. Two line segments define the transition states AB and AC,
and are obtained by solving the equations
V (r

12
, r
23
) ≤ E
max
(36a)
and
V (r
12
, r

23
) ≤ E
max
, (36b)
for r
23
and r
12
, respectively, where E
max
is our maximum energy of interest,
which we set equal to 1.0 for β = 1 and L = 10. The configuration space
transition states are shown in Figure 5. Associated conjugate momenta p
r23
or p
r12
are sampled uniformly in the appropriate range corresponding to total
energy E.
In practice, for parameters β = 1 and L = 10 we use a modified characteristic
function H
A
(t) = Θ(r

12
−r
12
(t))Θ(r

23
−r
23
(t))Θ(8−(r
12
(t) +r
23
(t))) to ensure
that only phase points actually in well A are included by the characteristic
function.
Having selected r
12
, r
23
, p
r12
and p
r23
we convert to single-particle coordi-
nates via
x
1
= 0 (37a)
x
2
= x
1
+ r
12
(37b)
x
3
= x
2
+ r
23
(37c)
p
1
= −p
r12
(37d)
p
2
= p
r12
−p
r23
(37e)
p
3
= p
r23
, (37f)
where we have arbitrarily set x
1
= 0 since the potential depends only on relative
particle displacements (bond distances). Trajectories are integrated using a
second-order symplectic integrator as in our previous work on linear tethered
9
chains [25], and the integration algorithm is simpler in single-particle coordinates
due to the diagonal kinetic energy. A sample trajectory initiated near transition
state AB is shown in Figure 6. We can see various bonds forming, breaking and
reforming.
Initial positions on transition states AB, AC are chosen with probability
1
2
,
and corresponding momenta are taken to have random signs (±). We calculate
the reactive flux at energies {E = E

L
+ i∆E}
M
i=1
, where M = 10 and ∆E =
(E
max
− E

L
)/M. For each energy, we integrate n
traj
= 3 × 10
3
trajectories for
n
step
= 6×10
4
time steps. Our trajectory time step value is τ = 10
−2
τ
0
, where
τ
0
is the unit of time associated with our choice of units for energy, length and
mass.
As we can see from Figure 7, for lower energies the nontransient flux shows
exponential decay, but the dynamics become more oscillatory with increasing
energy. For these higher energies, the rate constant ceases to have meaning,
so we restrict ourselves to energies less than E

L
+ ∆E. We calculate fluxes for
{E = E

L
+i∆E

}
M
i=1
, where M = 10 and ∆E

= ∆E/10, the fine-grained energy
increment. The flux decay for one of these fine-grained energies, E = E

L
+4∆E

,
is plotted in Figure 8.
5. RRK and RRKM calculations
For comparison with our simulation rate constant, we compute RRK (har-
monic) and RRKM (anharmonic) rate constants following the procedures de-
scribed previously [25]. The region of reactant configuration space sampled for
the reactant sum of states calculation is shown in Figure 9. Since k
AC
= k, the
RRKM rate constant is given by
k
RRKM
=
N

AC
(E −E

L
)
ρ
A
(E)
, (38)
where ρ
A
(E) is the density of states for well A.
A comparison between the flux rate constants and the RRK, RRKM results
is given in Figure 10. We find good agreement between the statistical and
simulation rate constants for energies near the activation barrier, with some
divergence at larger energies.
6. Summary and conclusions
We have computed harmonic, anharmonic and trajectory rate constants for
isomerization of a triatomic Morse chain under strain, subject to cyclic bound-
ary conditions. Computation of the rate coefficient via trajectory simulation
requires us to determine the rate of exponential decay of fluxes across the two
transition states of interest. Initial conditions are sampled uniformly on the
energy shell, and trajectories integrated using a second-order symplectic inte-
grator.
10
For our microcanonical calculations, we see good agreement between the
statistical and simulation rate constants for energies near the activation barrier,
with some divergence at larger energies. Compared to the tethered chain dis-
cussed previously [25], recrossing is more significant for the ring system treated
here. An isomerization rate constant exists only within a somewhat narrow
energy range above the isomerization barrier. At higher energies, the simula-
tions reveal oscillating patterns of flux among the wells. In other words, as was
observed for the tethered chain [25], the dynamics are statistical only within
a narrow range of energy per mode. For both systems, reactive events have
non-exponential lifetime distributions at high energies.
There are several possibilities for future work. One might involve computing
isomerization rate constants for longer chains, P > 3, N > 2. One complication
that arises for P > 3 is the presence of nonequivalent rate coefficients for inter-
well transitions. Another possibility is to consider chains composed of different
atoms, for which the symmetry of the problem is reduced.
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13
Figure captions
Figure 1: Schematic illustration of the formation of 2 ‘isomers’ via bifurcation for the strained
diatomic chain, P = 2, L > 2req.
Figure 2: 2-atom potential curves for β = 1 and (a) L = 2, (b) L = 3, (c) L = 4, (d) L = 5
and (e) L = 10
Figure 3: 3-atom potential energy surfaces for β = 1 and (a) L = 3, (b) L = 4, (c) L = 5 and
(d) L = 6.
Figure 4: 3-atom potential energy surface for β = 1 and L = 10 with saddles ‡
AB
(red), ‡
AC
(green) and ‡
BC
(blue). (a) Single particle coordinates. (b) Jacobi coordinates.
Figure 5: Sampling of transition states AB (vertical) and AC (horizontal) for β = 1, L = 10
and E = Emax.
Figure 6: Coordinates x
1
(red), x
2
(green) and x
3
(blue) versus time t for N = 2, β = 1 and
L = 10. The trajectory was initiated near transition state AB.
Figure 7: Isomerizing flux versus time for N = 2, β = 1, L = 10. (a) E = E

L
+ ∆E, (b)
E = E

L
+ 3∆E, (c) E = E

L
+ 5∆E, (d) E = E

L
+ 7∆E, (e) E = E

L
+ 9∆E and (f)
E = E

L
+ 10∆E. The energy parameters are as defined in the text.
Figure 8: Isomerizing flux versus time for N = 2, E = E

L
+ 4∆E
fg
, β = 1 and L = 10.
Figure 9: Configuration space projection of the Monte Carlo sampling for the reactant region
(well A) sum of states (light blue) in Jacobi coordinates, N = 2, β = 1 and L = 10. Also
shown are ‡
AB
(red), ‡
AC
(green), ‡
BC
(blue) and the global potential maximum (purple).
Figure 10: Rate coefficients k
RRK
(red), k
RRKM
(blue) and k
flux
(green) versus energy above
activation for N = 2, β = 1 and L = 10.
14
FIGURE 1 (J. N. Stember & G. S. Ezra)
15
0 2 4 6 8 10
r
12
1
2
3
4
5
V
0 2 4 6 8 10
r
12
1
2
3
4
5
V
0 2 4 6 8 10
r
12
1
2
3
4
5
V
0 2 4 6 8 10
r
12
1
2
3
4
5
V
0 2 4 6 8 10
r
12
1
2
3
4
5
V
FIGURE 2 (J. N. Stember & G. S. Ezra)
16
0 1 2 3 4 5 6
0
1
2
3
4
5
6
r
12
r
2
3
0 1 2 3 4 5 6
0
1
2
3
4
5
6
r
12
r
2
3
0 1 2 3 4 5 6
0
1
2
3
4
5
6
r
12
r
2
3
0 1 2 3 4 5 6
0
1
2
3
4
5
6
r
12
r
2
3
FIGURE 3 (J. N. Stember & G. S. Ezra)
17
0 2 4 6 8 10
0
2
4
6
8
10
r
12
r
2
3
0 2 4 6 8
0
2
4
6
8
Ξ
1
Ξ
2
FIGURE 4 (J. N. Stember & G. S. Ezra)
18
0 2 4 6 8 10
0
2
4
6
8
10
r
12
r
2
3
FIGURE 5 (J. N. Stember & G. S. Ezra)
19
1 2 3 4 5 6
x
20
40
60
80
100
t
FIGURE 6 (J. N. Stember & G. S. Ezra)
20
100 200 300 400 500 600
t
500
0
500
1000
1500
flux
E E
L

E
100 200 300 400 500 600
t
500
0
500
1000
1500
flux
E E
L

3E
100 200 300 400 500 600
t
500
0
500
1000
1500
flux
E E
L

5E
100 200 300 400 500 600
t
500
0
500
1000
1500
flux
E E
L

7E
100 200 300 400 500 600
t
500
0
500
1000
1500
flux
E E
L

9E
100 200 300 400 500 600
t
500
0
500
1000
1500
flux
E E
L

10E
FIGURE 7 (J. N. Stember & G. S. Ezra)
21
100 200 300 400 500 600
t
500
0
500
1000
1500
flux
FIGURE 8 (J. N. Stember & G. S. Ezra)
22
0 2 4 6 8
0
2
4
6
8
Ξ
1
Ξ
2
FIGURE 9 (J. N. Stember & G. S. Ezra)
23
0.002 0.004 0.006 0.008 0.010 0.012
EE
L

0.0005
0.0010
0.0015
0.0020
0.0025
0.0030
0.0035
k
FIGURE 10 (J. N. Stember & G. S. Ezra)
24