Quaccs: Molecular Mechanics Worshop

The Universal Force Field

The total energy is broken in to 2-, 3- and 4-body terms, along with non-bonding vdW and
electronic interactions:
E = E
bond
+E
bend
+ (E
torson
+E
inversion
) +E
vdW
+E
electronic
(1)
E
bond
(r) =
1
2
k
AB
(r r
AB
)
2
(2)
k
AB
= G
Z

A
Z

B
r
3
AB
(3)
r
AB
= r
A
+r
B
+r
BO
+r
EN
(4)
r
BO
= (r
A
+r
B
) ln(n) (5)
r
EN
= r
A
r
B
(

B
)
2

A
r
A
+
B
r
B
(6)
G = 664.12, = 0.1332, and Z

A
, r
A
and
A
are parameters determined by the atom type.
E
bend
() = K
ABC

C
0
+C
1
cos +C
2
cos 2

(7)
C
2
= (2 sin
B
)
2
(8)
C
1
= 4C
2
cos
B
(9)
C
0
= C
2
(2 cos
2

B
+ 1) (10)
K
ABC
= G
Z

A
Z

C
r
5
AC

3r
AB
r
BC
(1 cos
2

B
) r
2
AC
cos
B

(11)
r
2
AC
= r
2
AB
+r
2
BC
2r
AB
r
BC
cos (12)
where
B
is a characteristic angle for the central atom type.
E
torsion
() =
1
2
V

1 cos n
0
cos n

(13)
V
sp
3 =

V
B
V
C
(14)
V
sp
2 = 5

U
B
U
C
(1 + 4.18 ln(BO
BC
)) (15)
where BO
BC
is the bond order.
For B(sp
3
) and C(sp
3
), V

= V
sp
3, n = 3 and
0
= .
For B(sp
3
) and C(sp
2
), V

= 1, n = 6 and
0
= 0.
For B(sp
2
) and C(sp
2
), V

= V
sp
2, n = 2 and
0
= 0.
Expressions for E
inversion
, E
vdW
and E
electronic
can be found in the original paper:
Rappe et. al., J. Am. Chem. Soc. 1992, 114, 10024. (Just watch out for the typos!)
UFF Parameters
In the following table, the number in the atom type determines geometry: 1 = linear, 2 =
trigonal, R = resonant, 3 = tetrahedral.
Atom r
A

A
Z

A
V
A
U
A

A
H 0.354 180.00 0.712 0.000 0 4.528
C 3 0.757 109.47 1.912 2.119 2 5.343
C R 0.729 120.00 1.912 0.000 2 5.343
C 2 0.732 120.00 1.912 0.000 2 5.343
C 1 0.706 180.00 1.912 0.000 2 5.343
N 3 0.700 106.70 2.544 0.450 2 6.899
N R 0.699 120.00 2.544 0.000 2 6.899
N 2 0.685 111.20 2.544 0.000 2 6.899
N 1 0.656 180.00 2.544 0.000 2 6.899
O 3 0.658 104.51 2.300 0.018 2 8.741
O R 0.680 110.00 2.300 0.000 2 8.741
O 2 0.634 120.00 2.300 0.000 2 8.741
O 1 0.639 180.00 2.300 0.000 2 8.741
F 0.668 180.00 1.735 0.000 2 10.874
Using libmin
The le libmin.f90 contains several algorithms that can be used to minimize a function.
The simplex and brent algorithms require only function evaluations, whereas the bfgs
(Broyden-Fletcher-Goldfarb-Shanno) algorithm requires function derivatives as well (but
converges faster). All three algorithms have a common interface, e.g. simplex(x,n,tol)
where x is an n-dimensional vector and tol is the convergence threshold. All three algo-
rithms rely on the global function func(x,n) which is where you should dene your energy
function. Additionally, if you use the bfgs algorithm you should ensure the dfunc(g,x,n)
returns the gradient of your energy in the g(n) array. The le main.f90 demonstrates how
these functions can be used.
Tasks
1. Implement an energy function that computes the energy of the HF molecule.
2. Use one of the minimization algorithms to determine the equilibrium bond length.
3. Generalize your energy function for other diatomics, e.g. CO.
4. Incorporate bond-angle terms so that you can obtain the structure of water.
If you still have time, try computing the derivative of your energy functional and use the
bfgs algorithm. Does this improve convergence signicantly? Try adding torsion terms so
that you can optimize the structure of hydrogen peroxide.