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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

)Π

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

(

√

2ξ

1

) + V

M

_

1

√

2

(−ξ

1

+

√

3ξ

2

)

_

+ V

M

_

L −

1

√

2

(ξ

1

+

√

3ξ

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.

References

[1] G. S. Ezra, H. Waalkens and S. Wiggins. Microcanonical rates, gap times,

and phase space dividing surfaces. J. Chem. Phys., 130:164118, 2009.

[2] N. DeLeon and B. J. Berne. Intramolecular rate process: Isomerization

dynamics and the transition to chaos. J. Chem. Phys., 75:3495–3510, 1981.

[3] P. J. Robinson and K. A. Holbrook. Unimolecular Reactions. Wiley, New

York, 1972.

[4] W. Forst. Theory of Unimolecular Reactions. Academic, New York, 1973.

[5] R. G. Gilbert and S. C. Smith. Theory of Unimolecular and Recombination

Reactions. Blackwell Scientiﬁc, Oxford, 1990.

[6] T. Baer and W. L. Hase. Unimolecular Reaction Dynamics. Oxford Uni-

versity Press, New York, 1996.

[7] W. L. Hase. Some recent advances and remaining questions regarding

unimolecular rate theory. Acc. Chem. Res., 31:659–665, 1998.

[8] H.-H. Kausch. Polymer Fracture. Springer Verlag, New York, 1987.

[9] B. Crist. The Ultimate Strength and Stiﬀness of Polymers. Ann. Rev.

Mater. Sci., 25:295–323, 1995.

[10] L. Garnier, B. Gauthier-Manuel, E. W. van der Vegte, J. Snijders, and

G. Hadziioannou. Covalent bond force proﬁle and cleavage in a single

polymer chain. J. Chem. Phys., 113:2497–2503, 2000.

[11] A. M. Saitta and M. L. Klein. First-principles study of bond-rupture of

entangled polymer chains. J. Phys. Chem. B, 104:2197–2200, 2000.

11

[12] A. M. Saitta and M. L. Klein. First-principles molecular dynamics study

of the rupture processes of a bulklike polyethylene knot. J. Phys. Chem.

A, 105:6495–6499, 2001.

[13] A. M. Maroja, F. A. Oliveira, M. Ciesla, and L. Longa. Polymer fragmen-

tation in extensional ﬂow. Phys. Rev. E, 63:Art. No. 061801, 2001.

[14] U. F. Rohrig and I. Frank. First-principles molecular dynamics study of a

polymer under tensile stress. J. Chem. Phys., 115:8670–8674, 2001.

[15] D. Gersappe and M. O. Robbins. Where do polymer adhesives fail? Euro-

phys. Lett., 48:150–155, 1999.

[16] A. E. Filippov, J. Klafter, and M. Urbakh. Friction through dynamical

formation and rupture of molecular bonds. Phys. Rev. Lett., 92:Art. No.

135503, 2004.

[17] D. Aktah and I. Frank. Breaking bonds by mechanical stress: When do

electrons decide for the other side? J. Am. Chem. Soc., 124:3402–3406,

2002.

[18] D. Kruger, R. Rousseau, H. Fuchs, and D. Marx. Towards “mechanochem-

istry”: Mechanically induced isomerizations of thiolate-gold clusters.

Angew. Chem. Intl. Ed., 42:2251–2253, 2003.

[19] M. K. Beyer and H. Clausen-Schaumann. Mechanochemistry: The Me-

chanical Activation of Covalent Bonds. Chem. Rev., 105:2921–2948, 2005.

[20] E. Evans. Probing the relation between force – lifetime – and chemistry

in single molecular bonds. Ann. Rev. Biophys. Biomol. Struct., 30:105–28,

2001.

[21] P. M. Williams. Analytical descriptions of dynamic force spectroscopy:

behaviour of multiple connections. Anal. Chim. Act., 479:107–115, 2003.

[22] S. A. Harris. The physics of DNA stretching. Contemp. Phys., 45:11–30,

2004.

[23] I. Tinoco. Force as a useful variable in reactions: Unfolding RNA. Ann.

Rev. Biophys. Biomol. Struct., 33:363–385, 2004.

[24] Y. V. Pereverzev and O. V. Prezhdo. Force-induced deformations and

stability of biological bonds. Phys. Rev. E, 73(5):050902, 2006.

[25] J. N. Stember and G. S. Ezra. Fragmentation kinetics of a Morse oscillator

chain under tension. Chem. Phys., 337:11–32, 2007.

[26] D. G. Truhlar, B. C. Garrett, and S. J. Klippenstein. Current Status of

Transition-State Theory. J. Phys. Chem., 100:12711–12800, 1996.

12

[27] D. Chandler. Introduction to Modern Statistical Mechanics. Oxford Uni-

versity Press, New York, 1987.

[28] B. Crist, J. Oddershede, J. R. Sabin, J. W. Perram, and M. A. Ratner.

Polymer Fracture - A Simple Model for Chain Scission. J. Polymer Sci.

Polymer Physics, 22:881–897, 1984.

[29] H. Goldstein, C. Poole, and J. Safko. Classical Mechanics. Addison-Wesley,

San Francisco, 3rd edition, 2002.

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

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