I honestly do not know why you brought up the atomic structure of lithium as I cannot see any resemblance of it in Sasuke’s EMS. You can say the pupil represents the nucleus but where are the orbital levels/states that surround it? Perhaps you are talking about the three triangle-shaped structures that comes off from the pupil but even that does not portray a nice representation of the schematic model of lithium you posted above.
The design of Sasuke's original mangekyo sharingan made me think, "Dude, it's Lithium!" from the first moment I gazed upon his newfound countenance. Treating the nucleus as a singular point mass provides a pupil and eliminating the electrons gives vacant orbitals which form three concentric ellipses:
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The design of Sasuke's eternal mangekyo sharingan retained all of the aspects exhibited by the original mangekyo sharingan except for the blackened pupil, which is inverted to red for the sake of the inclusion of Itachi's contribution to the EMS:
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If any one individual doesn't see the resemblance of Sasuke's MS or EMS to Lithium, then that's merely a matter of perspective; there's nothing I can do to change that.
Individual viewpoints notwithstanding, it can still be surmised that the atomic model for lithium serves as a decent basis for visually constructing the major components of his EMS.
If you prefer, I can include a manner by which you could construct the major components by graphing them in a graphing calculator, plotting them via math software (like MATLAB or OCTAVE), or plugging the following equations into
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simultaneously:
x^2/2+y^2+xy=1; x^2/2+y^2-xy=1; y^2/5+x^2=1; x^2+y^2=1/25
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But I digress.
The bottom line is that Sasuke's EMS is designed to have three intersecting concentric ellipses with slightly pointed tips about the semi-major axes. In the recent episode, the lines that trace out the ellipses were nearly left out altogether with only the intersecting portions (the triangular-ish bits) maintaining a presence.
In essence, the image of Sasuke's EMS in episode 326 left out what I consider to be the greatest defining trait of the intended design.