2020-05-15 Chemical Perception meeting notes

Date

May 15, 2020

Participants

• @Hyesu Jang

• @Christopher Bayly

• @David Mobley

• @Lee-Ping Wang

• Caitlin Bannan

• @Josh Fass (Deactivated)

• @Jeffry Setiadi

Discussion topics

(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.