The CFF91 Forcefield

Contents

• Functional Form
• CFF91 Atom Types

Functional Form

The CFF91 forcefield employs a quartic polynomial for bond stretching (Term 1) and angle bending (Term 2) and a three-term Fourier expansion for torsions (Term 3). The out-of-plane coordinate (Term 4) is defined according to Wilson et al. (1980). All the cross terms up through third order that have been found to be important (Terms 5-11) are also included--this gives a forcefield equivalent to the best used in a formate anion test case (Maple et al. 1990). Term 12 is the Coulombic interaction between the atomic charges, and Term 13 represents the van der Waals interactions, using an inverse 9th-power term for the repulsive part rather than the more customary 12th-power term. Note that some first-generation forcefields use forms with quadratic diagonals and a few use some cross terms--perhaps with Morse potentials for bonds.

Eq. 3-2:

CFF91 Atom Types

The bond increment sections of the .frc files for both CFF91 and CVFF have been expanded so that partial charges can be determined whenever the Discover program is able to assign automatic atom types.

Table 3-2. Atom Types--CFF91

atom type

description

• hydrogen
• carbon
• nitrogen
• oxygen
• sulfur
• phosphorus
• halogens
• ions
• argon
• silicon
• other

hydrogen types

dw

deuterium in heavy water (equiv. to h*)

h

hydrogen bonded to C or S

hc

hydrogen bonded to C (equiv. to h)

hi

hydrogen in charged imidazole ring

hn

hydrogen bonded to N (equiv. to h*)

ho

hydrogen bonded to O (equiv. to h*)

hp

hydrogen bonded to P (equiv. to h)

hs

hydrogen bonded to S (equiv. to h)

hw

hydrogen in water (equiv. to h*)

h*

polar hydrogen bonded to N or O

h+

charged hydrogen (in cation)

carbon types

c

generic sp³ carbon

ca

general amino acid alpha carbon (sp³) (equiv. to c)

cg

sp³ alpha carbon in glycine (equiv. to c)

ci

sp² aromatic carbon in charged imidazole ring (his⁺) (equiv. to cp)

co

sp³ carbon in acetal (equiv. to c)

coh

sp³ carbon in acetal with hydrogen (equiv. to c)

cp

sp² aromatic carbon

cr

carbon in guanidinium group (HN=C(NH₂)₂) (arg)

cs

sp² carbon in 5-membered ring next to S (equiv. to cp)

ct

sp carbon involved in triple bond

c1

sp³ carbon bonded to 1 H, 3 heavy atoms (equiv. to c)

c2

sp³ carbon bonded to 2 H's, 2 heavy atoms (equiv. to c)

c3

sp³ carbon in methyl (CH₃) group (equiv. to c)

c5

sp² aromatic carbon in 5-membered ring (equiv. to cp)

c3h

sp³ carbon in 3-membered ring with hydrogens (equiv. to c)

c3m

sp³ carbon in 3-membered ring (equiv. to c)

c4h

sp³ carbon in 4-membered ring with hydrogens (equiv. to c)

c4m

sp³ carbon in 4-membered ring (equiv. to c)

c

sp² carbon in carbonyl (C=O) group in amide

c"

carbon in carbonyl group, not amide (equiv. to c*)

c*

carbon in carbonyl group, not amide

c-

carbon in carboxylate (COO^-) group

c+

carbon in guanidinium group

c=

nonaromatic end doubly bonded carbon

c=1

nonaromatic, next-to-end doubly bonded carbon

c=2

nonaromatic doubly bonded carbon

nitrogen types

n

sp² amide nitrogen

na

sp³ amine nitrogen

nb

sp² nitrogen in aromatic amine (equiv. to nn)

nh

sp² nitrogen in 5- or 6-membered ring, bonded to hydrogen

nho

sp² nitrogen in 6-membered ring, next to a carbonyl group and with a hydrogen (equiv. to nh)

nh+

protonated nitrogen in 6-membered ring

ni

sp² nitrogen in charged imidazole ring (his⁺) (equiv. to nh)

nn

sp² nitrogen in aromatic amine

np

sp² nitrogen in 5- or 6-membered ring, not bonded to hydrogen

npc

sp² nitrogen in 5- or 6-membered ring, bonded to a heavy atom (equiv. to nh)

nr

sp² nitrogen in guanidinium group (HN=C(NH₂)₂)

nt

sp nitrogen involved in triple bond

nz

sp nitrogen in N2

n1

sp² nitrogen in charged arginine (equiv. to nr)

n2

sp² nitrogen in guanidinium group (HN=C(NH₂)₂) (equiv. to nr)

n4

sp³ nitrogen in protonated amine (equiv. to n+)

n3m

sp³ nitrogen in 3-membered ring (equiv. to na)

n3n

sp² nitrogen in 3-membered ring (equiv. to n)

n4m

sp³ nitrogen in 4-membered ring (equiv. to na)

n4n

sp² nitrogen in 4-membered ring (equiv. to n)

n+

protonated amine nitrogen

n=

nonaromatic end doubly bonded nitrogen

n=1

nonaromatic, next-to-end doubly bonded nitrogen

n=2

nonaromatic doubly bonded nitrogen

oxygen types

o

sp³ oxygen in alcohol, ether, acid, or ester group

oc

sp³ oxygen in ether or acetal (equiv. to o)

oe

sp³ oxygen in ester (equiv. to o)

oh

oxygen bonded to H (equiv. to o)

op

oxygen in aromatic ring (e.g., furan)

o3e

sp³ oxygen in 3-membered ring (equiv. to o)

o4e

sp³ oxygen in 4-membered ring (equiv. to o)

o

oxygen in carbonyl (C=O) group

o*

oxygen in water molecule

o-

oxygen in carboxylate (COO^- ) group

sulfur types

s

sp³ sulfur in sulfide, disulfide, or thiol group

sc

sp³ sulfur in methionine (C-S-C) group (equiv. to s)

sh

sulfur in sulfhydryl (SH) group (equiv. to s)

sp

sulfur in aromatic ring (e.g., thiophene)

s1

sulfur involved in S-S disulfide bond (equiv. to s)

s3e

sulfur in 3-membered ring (equiv. to s)

s4e

sulfur in 4-membered ring (equiv. to s)

s

sulfur in thioketone (>C=S) group

s-

partial-double sulfur bonded to something that is bonded to another partial-double oxygen or sulfur

phosphorus

p

general phosphorous atom

halogen types

br

bromine bonded to a carbon

cl

chlorine bonded to a carbon

f

fluorine bonded to a carbon

i

covalently bound iodine

ion types

Br

bromide ion

ca+

calcium ion (Ca²⁺ )

Cl

chloride ion

Na

sodium ion

argon

ar

argon atom

silicon

si

silicon atom

other

lp

lone pair

nu

null atom for relative free energy

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