(JM will link slides here)
JM: I started working on the Openff aniline para, plan is to download the dataset and run geo opt with Openff-1.3.0, and compute their improper angles
CB: And the valence angles also for the same structures?
JM: You mean summing up the valence angles?
CB: Yeah, for checking the pyramidalization
DLM: JM and I were talking about this few days back where Nitrogen cases go either planar or tetrahedral not in between.
CB: I have the same issue for a long time
DLM: So, adding a few more molecules to scan that are squishy would allow us
CB: Looking at the minima for different substituents on the spectrum of pyramidalization would inform us
JM: I was comparing the improper angle and wbo correlation based off the assigned parameter, analyzed the grid opt nitrogens nad created the scatter plots, the overall thing is that there isn’t any correlation
CB: So from the smarts pattern any Nitrogen bound to the sulfur/phosphorus
DLM: Let’s make these plots interactive
JM: Yeah, I am gonna do that
CB: So, the wiberg bond orders are double bonds?
JM: They’re the sum of wbos here
CB: Aniline set?
JM: No, this is an old one from Nitrogen grid optimization with phosphonamides, sulfonamides
CB: I would want to see the improper angle is more planar when the nitrogen is more conjugated, and the relevant bondorder is between the nitrogen and the phenyl
DLM: How do you know without looking at the molecule the bond order of a molecule that is conjugating?
CB: If I can use smarts then nothing Nitrogen/Carbon cannot conjugate, and Sulfur/Phosphorus, anything with #X4 with a hydrogen cannot conjugate
DLM: What if there are two conjugated bonds like n case of a Nitrogen
CB: In case of two phenyls attached to a nitrogen then it would prefer to be planar
DLM: So, we bin the bonds coming out of nitrogen and check how many conjugated bondorders are present
CB: Put the avg bondorder from the conjugated bonds and the improper angle, when you stick a nitrogen in between two phenyls I know it must be planar but I don’t know how much the conjugation is and how planar it would be?
As we look at these relationships with WBO, we have to look at the QM optimized geometries I mean how well the QM WBOs will match to the AM1 WBOs
DLM: So, we want to come out with the conjugated bonds from the Nitrogen, in this process we can exclude bonds to Hydrogen and #X4
CB: I would guess the wbo of N-H wbo would be a good threshold value beyond which we will see the conjugation effects kick in
We may place a sigmoid curve and that would weigh the larger wbos higher
The main purpose of WBOs is to answer the questions on planarity, conjugation, etc., and in this process I would encourage to include impropers, torsions, valence angles, simultaneously.
Let’s look at what the structures tell us
The sum of wbos on this plot shows that it can be anywhere from 2.1 to 2.6 and still be pyramidal
DLM: Yeah, we can improve this plot by picking the conjugated bonds
CB: If we got a phenyl that conjugates the nitrogen, then it is somewhat pyramidal, but if we place another phenyl then we may have two conjugated bonds and averaging it we may get the singly conjugated bond but yet this would be planar, so that would be a misrepresentation
DLM: Let’s separate out the singly conjugated and doubly conjugated into bins
CB: May be we use a geometric mean instead of normal average
TG: One thing I want to point out is that these plots are symmetric around zero
DLM: Some molecules have handedness due to chirality and may pucker in a different direction but for the purposes of FF yeah we can fold the graph
TG: Even when you average?
DLM: Yeah, that should work.
CB: All this physical chemistry conjugation, bondorder, etc., when you place a methyl in place of Nitrogen you will see a drastic difference in the chemical environment, and the 1-4 sterics effect would push the p-orbitals and the nitrogen would be pyramidal, when we put that methyl on aniline and the confounding sterics going to drive the nitrogen planar, I would suggest some poking around by placing a methyl substituent when you have time
DLM: To avoid the supercomplicated cases, we are looking at the cases where MM is definitively better or bad
CB: We are trying to rule out the sterics mixing with our wbo work and looking at NH2 instead of NH(CH3), I agree with the science here, I also hope to look at the other side too since wbo would drop when we have a methyl substituent, valence angles and impropers are not gonna look at the rotation of NH2 so let’s keep looking at the torsions too, and the larger picture is how to capture the pyramidalization in our FF, at the design level we should be prepared to handle the torsions too.
DLM: JM will be out on an OE internship at the start of June, I hope we will get some chemistries out of her analysis work before that.
SB: Yeah, I agree