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

Thu Apr 6 12:17:35 CEST 2017

On 05/04/17 16:09, Phillip Rauscher wrote:
> Thanks so much for the reply Mark!  For my own curiosity, is there a way
> that people generally deal with neutral sp3 Nitogens?  They're chiral
> centers on simulation time scales, but on macroscopic scales pyramidal
> inversion eliminates that.
If we take ammonia NH3 as the simplest example, there is no reason why 
it could not invert. You would model this without any dihedral, just 
bond and angle potentials. If the three HNH angles are less than 120 the 
structure will be pyrimidal. Whether this yields a faithful 
representation of the inversion energy barrier is another matter, most 
likely the simulated barrier will be too high.
>
> On Wed, Apr 5, 2017 at 1:16 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> 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:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *[ 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 *
>>>
>>> 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:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *[ 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.
>>>
>>> On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher <
>> pmrauscher at uchicago.edu
>>>>
>>> wrote:
>>>
>>>> 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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>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
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