[gmx-users] Force Fields Keeping sp3 Nitrogen Groups Planar?

[Mark Abraham]

Hi,

Amide nitrogen atoms are trigonal planar because the group is planar.
There's no free rotation about the n-c bond, and the lone pair forms a
hybrid orbital with the carbonyl.

Mark

On Tue, 4 Apr 2017 18:05 Phillip Rauscher <pmrauscher at uchicago.edu> wrote:

> It occurs to me that an example would be helpful.  Here is an excerpt from
> the OPLS aminoacids.rtp file detailing alanine:
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> *[ ALA ] [ atoms ]      N    opls_238   -0.500     1     H    opls_241
> 0.300     1     CA    opls_224B   0.140     1     HA    opls_140
> 0.060     1     CB    opls_135   -0.180     2    HB1    opls_140
> 0.060     2    HB2    opls_140    0.060     2    HB3    opls_140
> 0.060     2      C    opls_235    0.500     3     O    opls_236
> -0.500     3 [ bonds ]     N     H     N    CA    CA    HA    CA    CB
> CA     C    CB   HB1    CB   HB2    CB   HB3     C     O    -C     N [
> impropers ]    -C    CA     N     H    improper_Z_N_X_Y     CA    +N
> C     O    improper_O_C_X_Y *
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> We can see that the Nitrogen is bound to atoms H, CA, and -C (on the
> previous residue).  In the [impropers] section, an improper dihedral is
> defined for these four atoms (with the nitrogen in both of the dihedral
> planes).  If we look at the definition of that improper in the OPLS
> ffbonded.itp file, we see the following:
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> *[ dihedraltypes ]; Improper OPLS dihedrals to keep groups planar.; (OPLS
> doesnt use impropers for chiral atoms).; Since these functions are periodic
> of the form 1-cos(2*x), they are actually; implemented as proper dihedrals
> [1+cos(2*x+180)] for the moment, ; to keep things compatible.; The defines
> are used in ffoplsaa.rtp or directly in your .top file....; Z -N?-X -Y
> improper torsion#define improper_Z_N_X_Y        180.0      4.18400   2*
> Given the functional form and the parameters used, this potential has
> minima at 0 and 180 degrees, thus keeping all four atoms (centered at the
> nitrogen) in the same plane.
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> On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher <pmrauscher at uchicago.edu
> >
> wrote:
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> > Hello all,
> >
> > I've noticed that in some of the force fields (in the aminoacid.rtp
> > files), an improper dihedral is applied to the nitrogens in the peptide
> > bond (and sometimes other amine groups as well), which are all sp3
> > hybridized with one lone pair.  Interestingly, the dihedral potential
> > parameters serve to keep the groups trigonal planar, rather than
> > tetrahedral.  More specifically, I've seen this in OPLS, Amber03, and
> > Charmm27 - enough to indicate that it's not a mistake (besides the fact
> > that it's applied to ALL amino acids!)  The functional form of the
> improper
> > potential varies between force fields, but the lowest energy angle is
> > always 0 or 180 indicating planar structure.
> >
> > Why is this done?  I've done some digging through the GROMACS
> publications
> > as well as those for the force fields and can't seem to find any
> reference
> > to this practice?  Is it an attempt to "average out" nitrogen inversions?
> > Is it just to eliminate a chiral center?
> >
> > Thanks for your help!
> >
> > -Phil Rauscher
> >
> > --
> > Phil Rauscher
> > Graduate Student
> > de Pablo and Rowan Research Groups
> > Institute for Molecular Engineering
> > University of Chicago
> >
>
>
>
> --
> Phil Rauscher
> Graduate Student
> de Pablo and Rowan Research Groups
> Institute for Molecular Engineering
> University of Chicago
> --
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