Reduced phase spaces in molecular dynamics: Coupling of overall rotation and

internal motions in a generalized Eckart frame

F. J. Lin University of Southern California Department of Mathematics, KAP 108 3620 S. Vermont Avenue Los Angeles, CA 90089-2532 Classical and Quantum Approaches in Molecular Modeling Institute for Mathematics and Its Applications University of Minnesota, Minneapolis July 26, 2007

Abstract
This presentation describes the internal dynamics of molecular N-body systems in an internal reduced phase space and describes the coupling of the internal motions with the overall rotation in the center-of-mass frame. Traditionally, molecular motions have been separated into translational, rotational, and internal motions [15]. Symplectic reduction [1114] provides a systematic method for obtaining reduced phase spaces and has been applied to describe N-body molecular dynamics [7-9]. This presentation points out three examples of observations of net rotation due to internal motions: (a) a net rotation in a differential geometric study of a triatomic molecule [5], (b) a net rotation of 20 degrees in the recoil angle of a departing O atom in the experimental dissociation of NO2 [3], and (c) a net rotation of 42 degrees in 105 reduced time steps in a computational study of protein dynamics [16]. For the case of Jacobi coordinates [2], the net rotation follows from (a) the conservation of total rotational angular momentum and, equivalently, (b) Hamiltons equations in the center-of-mass frame [9]. For Eckart generalized coordinates [4], the net rotation follows from the conservation of total rotational angular momentum. A phase space associated with the Eckart [4] frame is an example of a reduced phase space. Even after reducing to the internal phase space, the reduced internal dynamics are coupled to the overall rotation in the center-of-mass frame. In terms of the net rotation, the strength of the coupling is mass- and coordinate-dependent. When the total angular momentum vanishes, the coordinates of overall rotation and internal motions are separated when the internal angular momentum vanishes, in agreement with a condition for the separation of energies [6]. Appendix A provides further applications [1, 3] of the derived net rotation. Appendix B provides a differential geometric [10] description of the net rotation.

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 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 coupling of the dynamics of overall rotation in the center-of-mass frame 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-ofmass frame. This coupling can be described in terms of various internal coordinates and is mass-dependent. After describing various observations of this coupling [3, 5, 16] and describing this coupling in terms of Jacobi coordinates, the coupling is described in terms of Eckart generalized coordinates for a generalized Eckart frame as a reduced internal phase space [9]. When the total angular momentum vanishes, the coordinates of overall rotation and internal motions are separated when the internal angular momentum vanishes, in agreement with a condition for the separation of energies [6].

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 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) Summary References Appendix A (further applications) (a) 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. (b) 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. Appendix B (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.
F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

(1) Various internal coordinates can be used to describe the dynamics of three-body to N-body molecular systems:
Guichardet coordinates
m2 (q2,q3)

Internuclear distances

m3

m1 (q1,0)

Jacobi coordinates

Bond angles, bond lengths, dihedral angles,

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

(2) Background: Observations of rotation at zero total angular momentum

(a) 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
=

(b) 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, the magnitude of the rotation of the R vector (i.e., the change in the angle R of the recoil velocity of the departing O atom) during photodissociation is approximately 20 degrees, i.e.,

C i

a dq
k k

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

a1 = m1m2 q3 / D(q)

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

NO r 2 d 20 degrees NO r 2 + R 2

2 2 D(q ) = m1 (m1 + m3 )q12 + m2 (m2 + m3 ) q2 + q3

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

(2) Background: Observations of rotation at zero total angular momentum

(c) 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

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

(3) Jacobi coordinates for three-body systems, e.g., Atomdiatomic molecule complex or NO2

m3 R R m1

m2

r
r

m1 = O, m2 = N, m3 = O
F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin 8

(3) 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

The net rotation of a generalized Eckart frame

R ( R )dyn + ( R )geom

has dynamic and geometric terms

( R )dyn ( R )geom

tf

mm m= 1 2 m1 + m2

(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.

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

(3) 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 ) + 1 p lin 2 (m 1 + m 2 + m 3 )
2

with

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

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

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(3) 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 ) + + 1 p lin 2(m1 + m2 + m3 )
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 )

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

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(4) Examples of coupling in the N-body dynamics in Eckart generalized coordinates: Dynamics of a three-helix
bundle protein
(Zhou, Cook, and Karplus, 2000; Lin, 2007)

The total angular momentum is

J
tot

Examples of net rotation at zero total angular momentum : (i) Overall rotation of a triatomic molecule in a differenti al geometric study =

& = A +

& Bq

The net overall rotation due to internal motions is

()dyn + ()geom
tf

a
k =1

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 i

( )dyn ( )geom

ti

J tot dt A

B dq A

NO r 2 d 20 degrees NO r 2 + R 2

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 is A =

12

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

(5) 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

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

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References
1. 2. 3. 4. 5. 6.

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

R. J. Cross and D. R. Herschbach, Classical scattering of an atom from a diatomic rigid rotor, J. Chem. Phys. 43, 3530 3540 (1965). L. M. Delves, Tertiary and general order collisions, Nucl. Phys. 9, 391 399 (1958/59); 20, 275 308 (1960). A. V. Demyanenko, V. Dribinski, H. Reisler, H. Meyer, and C. X. W. Qian, Quantum-product state-dependent anisotropies in photoinitiated unimolecular decomposition, J. Chem. Phys. 111, 7383 -- 7396 (1999). C. Eckart, Some studies concerning rotating axes and polyatomic molecules, Phys. Rev. 47, 552 558 (1935). A. Guichardet, On rotation and vibration motions of molecules, Ann. Inst. Henri Poincar, Phys. Thor. 40, 329 342 (1984). J. Jellinek and D. H. Li, Separation of the energy of overall rotation in any N-body system, Phys. Rev. Lett. 62, 241 -- 244 (1989). F. J. Lin and J. E. Marsden, Symplectic reduction and topology for applications in classical molecular dynamics, J. Math. Phys. 33, 1281 1294 (1992). F. J. Lin, Symplectic reduction, geometric phase, and internal dynamics in three-body molecular dynamics, Physics Letters A 234, 291 300 (1997). F. J. Lin, Hamiltonian dynamics of atom-diatomic molecule complexes and collisions, Discrete and Continuous Dynamical Systems, Supplement 2007, to appear (2007). J. E. Marsden, R. Montgomery, and T. Ratiu, Reduction, symmetry, and phases in mechanics, Mem. Amer. Math. Soc., Vol. 88, No. 436 (American Mathematical Society, Providence, RI, 1990). J. E. Marsden and T. Ratiu, Introduction to Mechanics and Symmetry, (Springer-Verlag, New York, 1994). J. Marsden and A. Weinstein, Reduction of symplectic manifolds with symmetry, Rep. Math. Phys. 5, 121 130 (1974). K. R. Meyer, Symmetries and integrals in mechanics, in M. M. Peixoto, ed., Dynamical Systems, (Academic, New York, 1973), pp. 259 272. K. R. Meyer and G. R. Hall, Introduction to Hamiltonian Dynamical Systems and the N-body Problem, (Springer-Verlag, New York, 1992). E. B. Wilson, Jr., J. C. Decius, and P. C. Cross, Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectra, (Dover, New York, 1980), republication of McGraw-Hill edition of 1955. Y. Zhou, M. Cook, and M. Karplus, Proteins at zero-total angular momentum: The importance of long-range correlations, Biophys. J. 79, 2902 2908 (2000). F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin 14

Appendix A (Further applications): (a) Scattering angle and

(b) Net rotation of recoil angle, R, in triatomic photodissociation
(a) Scattering angle The atom-diatomic molecule scattering angle omitting internal motions (Cross and Herschbach, 1965) is

(b) Net rotation R of the recoil

= 2 ( R )min = 2

t min

J tot dt 2 R

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
mr2 R = 2 d R + mr2 i
C

The scattering angle including internal motions in atom-diatomic molecule scattering (Lin, 2007) is
Jtot mr2 = 2 2 dt + 2 d R + mr2 R2 + mr2 (tmin ) tmin

()

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

F. J. Lin, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

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Appendix B (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, Classical and Quantum Approaches in Molecular Modeling, Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, July 26, 2007; Copyright 2007 F. J. Lin

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