2020-05-15 Chemical Perception meeting notes
- Hyesu Jang
- Diego Nolasco (Deactivated)
Date
May 15, 2020
Participants
@Hyesu Jang
@Christopher Bayly
@David Mobley
@Lee-Ping Wang
Caitlin Bannan
@Josh Fass (Deactivated)
@Jeffry Setiadi
Discussion topics
Item | Presenter | Notes |
|---|---|---|
inspection on t69 | Hyesu Jang |
(1) Torsion parameter for dialkyl amide doesn’t exist.
CIB: for amides with hydrogen on nitrogen, t70 takes the major role while other three torsions don’t contribute with current parameter sets.
CIB, CB: There seems the need of modifying t70 definition so that it assignes to all 4 torsions of amide rotations.
[#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4] → [*:1]-[#7X3:2]-!@[#6X3$(*=[#8,#16,#7:4]):3]~[*:4]
CIB: should check if data indicates whether amide w/ hydrogen on nitrogen and amide w/o hydrogen have different barriers.
(2)
LPW: view of torsion as a central bond with one or more substituent on ether side, or torsion as a combination of independent atom quartets.
parameterizing individual central bonds as a groups of substituents or parameterizing individual atom quartets and letting them being added up?
CIB: each contribution could be asymmetrically split. For the second point of view(consider individual atom quartets separately), need to consider all different cases. CHARM vs AMBER school perspectives.
very generic parameter → assumption that barrier heights are distributed equally among from different bond paths. from looking into different cases, can figure out different contribution from each atom quartets.
DM: one different approach could be averaging over the torsions passing through the central bond rather than adding them.
CIB: it can allow chemical distinctness of each separate four paths while avoiding pathology of having too many torsion contributing to the overall barrier.
DM: put a toggle into the force field format so that we can switch behaviour and do a fit that toggles behaviour and see which one behaves better. (ping @Jeffrey Wagner for implementing the toggle)
LPW: check how many times torsion applies across the central bond and divide parameter by like three or four.
DM: need to draw histograms of, in a particular chemical context, across many molecules “how many total torsion parameters are applied to the central bond”, set the number constant.
LPW: we need to measure of linear dependency of torsions. building matrix.