Overall rotation due to internal motion in the three-body problem: Applications in molecular dissociation and collisions

Florence J. Lin University of Southern California Department of Mathematics, KAP 108 3620 S. Vermont Avenue Los Angeles, CA 90089-2532 California American Physical Society 2007 Lawrence Berkeley National Laboratory Berkeley, CA October 27, 2007

Abstract
As a result of the conservation of total rotational angular momentum in an N-body system, an internal motion with nonzero orbital angular momentum produces a net overall rotation of a generalized Eckart frame of a polyatomic molecular system in the center-of-mass frame, regardless of whether or not the total rotational angular momentum vanishes. Examples appear in a net rotation of 20 degrees in the recoil angle of an atom departing from a dissociating triatomic molecule and in a net overall rotation of 42 degrees in 100,000 reduced time units in the computational dynamics of a protein. While the diatomic molecule in atom-diatomic molecule scattering has previously been treated as a point mass, this approach describes the contribution to the deflection angle of the atom due to rotation of the diatomic target molecule. When an N-body system returns to its original shape over the time interval, the net rotation due to internal motion is an example of a classical geometric phase. Other applications appear in the dissociation of polyatomic molecules, in the separation of overall rotation and internal motions of N-body systems, and in the dynamics of molecular rotors and machines.
References: F. J. Lin, Hamiltonian dynamics of atom-diatomic molecule complexes and collisions, Discrete and Continuous Dynamical Systems, Supplement, vol. 2007, 655 666 (2007). J. E. Marsden, R. Montgomery, and T. Ratiu, Reduction, symmetry, and phases in mechanics, Memoirs of the American Mathematical Society, vol. 88, no. 436, (American Mathematical Society, Providence, RI, 1990).

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

Introduction

Traditionally, molecular motions have been separated into translation, rotation, and internal motions [15]. Symplectic reduction [11-14] provides a systematic method to obtain reduced phase spaces and has been applied to describe N-body molecular dynamics [7-9]. The first reduction by translational symmetry parameterized by the total linear momentum leads to dynamics in the center-of-mass frame; a second reduction by rotational symmetry parameterized by the orbital angular momentum leads to dynamics in the internal frame. While the total rotational angular momentum is conserved, the orbital angular momentum is not conserved and couples the dynamics of overall rotation with the internal motions. The net overall rotation in the center-of-mass frame due to the internal dynamics follows from [9] (i) the conservation of the total rotational angular momentum in the center-of-mass frame and, equivalently, from (ii) Hamiltons equations in the center-of-mass frame. This net rotation can be described in terms of various internal coordinates and is massdependent. After describing various observations of this net rotation [3, 5, 16] and describing the net rotation in terms of Jacobi coordinates, the net rotation is described in terms of Eckart generalized coordinates for a generalized Eckart frame as a reduced internal phase space [9]. When the total rotational angular momentum vanishes, then the coordinates of overall rotation and internal motions are separated when the internal angular momentum vanishes.

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

Outline
(1) The dynamics in the internal reduced phase space can be described in various internal coordinates (2) The internal dynamics are coupled to the overall rotation in the center-of-mass frame; i.e., net overall rotation due to internal motions at zero total angular momentum has been observed (a) in a differential geometric study of a triatomic molecule, (b) in the net rotation of the recoil angle of the departing O atom in the dissociation of NO2, (c) in the net overall rotation in a computer simulation of a three-helix bundle protein. (3) In Jacobi coordinates, the net overall rotation due to internal motions (a) can be derived from the conservation of total rotational angular momentum, (b) can be derived from Hamiltons equations in the center-of-mass frame, using reduction theory. (4) In generalized Eckart coordinates, the net overall rotation due to internal motions can be derived from the conservation of total rotational angular momentum. (5) Further applications (a) The net rotation of the recoil angle of a departing atom in a triatomic dissociation at nonzero total angular momentum is due to internal motions of the diatomic fragment. (b) The deflection angle of the scattered atom in atom-diatomic molecule scattering includes a contribution due to the internal motion, e.g., rotation, of the diatomic molecule. (6) Geometric formulation (a) The geometric phase is the holonomy of a molecular connection. (b) The geometric phase is expressed in terms of a molecular gauge potential. (7) Summary

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

Various internal coordinates can be used to describe the dynamics of three-body to N-body molecular systems:
Guichardet coordinates Internuclear distances

(Tachibana and Iwai, 1986)

Jacobi coordinates

Bond angles, bond lengths, dihedral angles,

(Zhou, Cook, and Karplus, 2000)

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

Background: Observations of net rotation at zero total rotational angular momentum

(a) Net overall rotation in a differential geometric study of triatomic molecular dynamics (Guichardet, 1984)
At zero total angular momentum a purely vibrational motion, i.e., an internal motion, can take a molecule with a specified initial shape to a final configuration with the same shape but differing from the initial configuration by a net rotation
=

a dq
k k

a2 = m2 (m2 + m3 )q3 / D(q)

2 1

a1 = m1m2 q3 / D(q)

a3 = m2 (m1q1 + (m2 + m3 )q2 ) / D(q) + 2m1m2 q1q2

D(q ) = m1 (m1 + m3 )q + m2 (m2 + m3 ) q + q

2 2

2 3

(Tacbibana and Iwai, 1986)

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

Background: Observations of net rotation at zero total rotational angular momentum

(b) Net rotation of the recoil angle of the O atom in the photodissociation of NO2 (Demyanenko, Dribinski, Reisler et al., 1999)
At zero total angular momentum when the (remaining) NO fragment rotates by an angle , the direction of the recoil velocity vector R of the departing O atom rotates by an angle R with net rotation R:
mr 2 R = 2 d 20o 2 i mr + R
C

m=

m1m2 m1 + m2

(m1 + m2 )m3
m1 + m2 + m3

Jacobi coordinates m1 = O, m2 = N, m3 = 0

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

Background: Observations of net rotation at zero total rotational angular momentum

(c) Net overall rotation in the dynamics of a model three-helix bundle protein (Zhou, Cook, and Karplus, 2000)
At zero total angular momentum, the flexible protein molecule rotates by 42 degrees in 105 reduced time steps due to internal motions, i.e.,

= 42 degrees

(Zhou, Cook, and Karplus, 2000)

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

Jacobi coordinates for three-body systems, e.g., NO2 or an atom-diatomic molecule complex

m3 R R m1

m2

r
r m1 = O, m2 = N, m3 = O or m1 = Cl, m2 = H, m3 = Ar

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

The net rotation R of a generalized Eckart frame due to internal motions corresponds to the orbital angular momentum:
(Lin, 2007)

The total rotational angular momentum is conserved. The total rotational angular momentum is the sum of two terms (Delves,1960), i.e.,
& & & & Jtot = l + j = R2R + mr2r = R2 + mr2 R + mr2
= r R
mm m= 1 2 m1 + m2 ,

The net rotation of a generalized Eckart frame

R ( R )dyn + ( R )geom

has dynamic and geometric terms

( R )dyn ( R )geom

tf

(m + m2 )m3 = 1

R
ti

J tot dt + mr 2

m1 + m2 + m3

mr 2 d = R 2 + mr 2

which leads to a differential equation for the angle R of rotation of a generalized Eckart frame. Integration of the angular velocity of rotation yields the net rotation of a generalized Eckart frame.

where (a) the first term vanishes when the total angular momentum vanishes and (b) the second counter-rotary term is in the opposite direction to the rotation of the diatomic molecule in the rotating frame.

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The Hamiltonian for three-body dynamics in Jacobi coordinates (Lin, 2007)

The Hamiltonian in the lab frame is
H (r1 , r2 , r3 , p1 , p 2 , p 3 ) = 1 1 1 2 2 2 p1 + p2 + p 3 + V r2 r1 , , r3 rcm,12 2m1 2m2 2m3
1 1 2 pr + p R + Vp lin (r , , R ) 2m 2

The reduced Hamiltonian in the center-of-mass frame is

H p lin (r, R, p r , p R ) =

with amended potential given by

V p lin (r , , R ) = V (r , , R ) +

with

2 (m 1 + m 2 + m 3 )

p lin

r R The reduced Hamiltonian in terms of internal coordinates and R is

H plin r , r , R, R , pr , p r , pR , p R

2 p2r p2R pr2 pR = + + + + Vplin (r , , R ) 2m 2 2mr 2 2R 2 2

2 p2 p ( J p ) (J tot p ) pr2 pR H plin (r , , R, pr , p , pR ) = + Vplin (r , , R ) + + + + 2tot 2 2m 2 2mr R + mr 2 2 R 2 + mr 2

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The coupling of overall rotation and internal motions in Hamiltons equations is given by dR/dt (Lin, 2007)
The twice-reduced Hamiltonian is
2 2 pr2 pR p p (Jtot p ) Hplin,J p (r,, R, pr , p , pR ) = + + + tot 2m 2 2mr2 R2 + mr2 + Vplin,Jtotp (r,, R)

The twice-reduced Hamiltons equations for internal motions on a reduced phase space are
pr m p & = 2 mr & p R= R p 2 V ) & (r , , R ) (J tot2 p )(J tot+ p 2 pr = 3 2 mr r R + mr 2 / mr & r=

The twice-amended potential is

Vp lin , J tot p (r , , R ) = V (r , , R ) + + 2(m1 + m2 + m3 ) p lin
2

[(

2 R 2 + mr 2

(J tot p )2

V (r , , R ) ) V & (r , , R ) (J tot2 p )(J tot+ p 2 pR = 2 2 R R + mr / mr & p =

[(

The net overall rotation R is coupled to the internal motions & J mr 2 & R = tot 2 by R + mr 2
& p R = V (r , , R )

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Applications: (a) Net rotation of recoil angle, R, in triatomic

photodissociation and (b) scattering angle in atom-diatomic molecule collisions
(a) Net rotation R of the recoil angle in triatomic photodissociation with internal motions The magnitude |R| of the net rotation of the recoil angle for zero total angular momentum with internal motions (Demyanenko, Dribinski, Reisler, et al.,1999) is
R =
C

mr2 d R2 + mr2 i

The net rotation of the recoil angle for arbitrary total angular momentum including internal motions (Lin, 2007) is
C Jtot mr2 dt 2 d R = 2 R + mr2 R + mr2 ti i

tC

(Demyanenko, Dribinski, Reisler, et al., 1999)

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

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Applications: (a) Net rotation of recoil angle, R, in triatomic

photodissociation and (b) scattering angle in atom-diatomic molecule collisions
(b) Scattering angle in atom-diatomic molecule collisions The atom-diatomic molecule scattering angle omitting internal motions (Cross and Herschbach, 1965) is
= 2 ( R )min

= 2

t min

J tot dt R 2

The scattering angle including internal motions in atom-diatomic molecule scattering (Lin, 2007) is
(Weston and Schwarz, 1972)

Jtot mr2 dt + 2 = 2 2 d R + mr2 R2 + mr2 tmin (tmin )

( )

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Applications in N-body dynamics in Eckart generalized coordinates: Net overall rotation of a three-helix bundle protein
(Zhou, Cook, and Karplus, 2000; Lin, 2007)
Examples of net rotation at zero total angular momentum : (i) Overall rotation of a triatomic molecule in a differenti al geometric study =

The total rotational angular momentum is

J
tot

& = A +

& Bq

a
k =1

The net overall rotation due to internal motions is

()dyn + ()geom
tf

dq k

(ii) Rotation of the recoil angle of the departing O atom due to the rotation of the NO fragment in the dissociati on of NO 2
C

( )dyn ( )geom

ti

J tot dt A

NO r
2 NO

2 2

r + R

d 20 degrees

B dq A

The molecular connection is

A mol = d +

(iii) Overall rotation of a flexible three - helix bundle protein due to internal motions =

B dq A

B dq = 42 degrees A

The molecular gauge potential B A = is

15

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

Geometric formulation: The net overall rotation R in terms

of a geometric phase (Marsden, Montgomery, and Ratiu, 1990; Lin, 2007)
The coordinates of the internal reduced phase space are expressed in Jacobi coordinates by r, , R. For a closed loop in configuration space, the contributions to the net overall rotation are the dynamic phase ( R)dyn the geometric phase (R)geom For a closed loop in configuration space, the geometric contribution to the net rotation of a generalized Eckart frame mr 2 ( R )geom = 2 d = A d 2 R + mr is expressible in terms of a molecular gauge potential (a ratio of moments of inertia, in this case) mr 2 A = R 2 + mr 2 and as the holonomy of a molecular connection mr 2 Amol = d R + 2 d = d R + A d R + mr 2
F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin 16

(Marsden, Montgomery, and, Ratiu, 1990)

Summary: Net rotation in the N-body dynamics in Eckart generalized coordinates and in Jacobi coordinates (Lin, 2007)
General case: In Eckart generalized coordinates, the net rotation of a generalized Eckart frame in the center-of-mass frame due to internal motions is
()dyn + ()geom

Special case: In Jacobi coordinates, the net rotation R of a generalized Eckart frame in the center-of-mass frame due to internal motions is
R ( R )dyn + ( R )geom

( )dyn ( )geom

tf

ti

J tot dt A

( R )dyn =
ti

tf

J tot dt R + mr 2
2

B dq A

( R )geom =

mr 2 d R 2 + mr 2

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Summary: Physical explanation and examples

Physical explanation: Net rotation is due to nonzero orbital or internal angular momentum, respectively:
2 N 3 t f & J tot B q / Adt , J tot 0 =1 = ti t f 2 N 3 & B q / Adt , J tot = 0 t i =1

Examples (contd.): Net rotation of the recoil angle of a departing atom in photodissociation (including nonzero total rotational angular momentum): 20 degrees
C J tot mr 2 dt 2 d R = 2 R 2 + mr 2 ti i R + mr

tC

Examples: Net overall rotation in a three-helix bundle protein (including nonzero total angular momentum and internal motions):t 42 degrees
=

Deflection angle of an atom scattering off a diatomic molecule (including internal motions)
= 2
t min

mr 2 J tot d dt + 2 2 2 R 2 + mr 2 (t min ) R + mr

( )

ti

J tot dt A

B dq A

Acknowledgement WiSE Program, Office of the Provost, University of Southern California

F. J. Lin, California APS 2007, LBNL, Berkeley, CA, October 27, 2007; Copyright 2007 F. J. Lin

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7. 8. 9. 10. 11. 12. 13. 14. 15. 16.

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