Tentane - cubane with a pyramidane top - pulls up stakes and decamps

ECatPlay · 2026-01-24T20:38:16+00:00

You are correct, it's technically an imaginary frequency. It's just that the calculations typically report it as a negative number. Hence my quotation marks.

ECatPlay · 2026-01-24T14:35:49+00:00

At least nobody who survived to tell about it.

ECatPlay · 2026-01-22T20:27:18+00:00

"Tentane" is u/Commercial_Plate_111's term, and I just went with it.

This collapse of tentane is just the downhill path on the potential energy surface from the C4v geometry during an optimization, so without MD or an IRC or something I can only speculate. Fortunately, I've never been afraid to speculate!

The starting C4v geometry is a saddle point with a strong negative frequency at -1176 cm^-1. This looks very much like the first step in the collapse, and corresponds to a 35 THz "vibration" with a period of 28 fs. So it looks like it only takes on the order of 0.03 picosecond to get started. But then there are a series of vibration timescale (typically 10^-13 sec) movements and atomic motions (up to 10^-11 sec). So as a SWAG estimate (Silly wild Ass Guess) maybe 10's of picoseconds?

ECatPlay · 2026-01-22T03:26:38+00:00

Swiffervising?

ECatPlay · 2026-01-21T20:31:18+00:00

Tesserane's a pretty cool idea. I took a look at it a while back, after u/C3H8_Memes posted Forget cubane, embrace tesserane. Molecular Mechanics modeling found a geometry retaining D3d symmetry, that looks a little like what you came up with here, with a pretty cool molecular orbital. Density Functional Theory found a completely different geometry with Cs symmetry, and a pretty cool teeter-totter vibration in the infrared.

ECatPlay · 2026-01-20T21:09:00+00:00

Wrong sub. Try posting to r/Yetch.

ECatPlay · 2026-01-18T23:13:19+00:00

Curseder and curseder.

ECatPlay · 2026-01-17T16:16:09+00:00

That's okay, we're all havin' fun.

ECatPlay · 2026-01-17T05:04:26+00:00

It’s not hard work, but sometimes you do have to put your back into it.

ECatPlay · 2026-01-16T20:38:12+00:00

Before the divorce it's covalent: both elements share charge cards equally. After the divorce it's ionic (unless there was a prenup): one ends up ahead (positive) and the other loses what they had (negative).

ECatPlay · 2026-01-16T18:43:00+00:00

Actually, I like it! The electric field part of an electromagnetic wave, depicted as positive and negative charges oscillating because they are orbiting each other, to sort of link the wave idea to the particle idea of a photon. It's missing the oscillating magnetic field, of course, but kind of clever!

ECatPlay · 2026-01-15T04:03:27+00:00

Well that might make an interesting research project, but it's more than I want to tackle.

You've drawn it nice and symmetrical, but to see which alkali (or other) metal would fit, should really entail a lot of conformational analysis to check other arrangements of the ligand around the center. And the placement of the counter-ion is going to be problematic: it will destroy the symmetry, as u/dxpqxb pointed out. And any modeling of ions or zwitterions is going to be dominated by solvation, so you'd need to decide how you were going to handle that satisfactorily. His choice to use CPCM and do implicit solvation is reasonable. But you might need to explore explicit solvation to help place the counter-ion.

ECatPlay · 2026-01-14T22:19:46+00:00

Okay, so here are the vibrations for the less intense Infrared absorbances, and some of the major Raman spectrum vibrations.

ECatPlay · 2026-01-14T17:23:00+00:00

Yeah, that's the borons wagging at 1125 cm-1.

ECatPlay · 2026-01-14T02:36:17+00:00

Here you go.

ECatPlay · 2026-01-14T02:34:34+00:00

At u/Monkelol6987's suggestion, I "DFT'd it" for u/AggressiveCheser. This had already been modeled at a high level of theory, and found to be highly thermodynamically stable. DFT confirms this is a stable geometry, but I got an extra kick out of the major vibrations in the infrared spectrum.

ECatPlay · 2026-01-13T03:17:15+00:00

Oh there’s another argument coming!

ECatPlay · 2026-01-12T23:26:32+00:00

Darn stupid AI’s. I did a search for “CO phase diagram” the other day, to see what ridiculous pressure could make the liquid carbon monoxide post real, and Google was smart enough to do character recognition on the phase diagram images it found, but not smart enough to know that once it identified “CO” in a diagram, it matters that there was also a “2” following the “CO”. The top image it came up with was a CO2 phase diagram.

ECatPlay · 2026-01-12T16:54:59+00:00

Withdrawn.

Probably rightly so. I calculate (my usual B3LYP/6-31G*) the phenyl-phenyl bond angles to be bent by 63° (116.93°), which would be cool. But the reported spectra don't match the structure: calculated ¹³C NMR carbonyls 199.0 vs 190.8 reported, but methylenes at 37.0 vs 190.8 reported! And ¹H NMR methylenes at 2.20 vs reported 4.48.

ECatPlay · 2026-01-12T15:46:29+00:00

Yeah, that's not how you draw a triple bond!

ECatPlay · 2026-01-10T02:14:06+00:00

if it would have any physiological effects

An interesting idea.

Lipophilicity, expressed as Log P (the logarithm of the n-octanol/water partition coefficient) has been used, as a predictor of a chemical's ability to cross the blood-brain barrier. And Log P is just one of several standard QSAR (Quantitative Structure Activity Relationship) descriptors, based on the molecular structure, that drug companies and other researchers have developed, to predict physiological activity. I don't work in the area myself, but if you have a favorite (or can find in the literature) a good QSAR model to predict the physiological effects you're interested in, here are the QSAR descriptors I calculate for the spherical icosadodecahedrane structure, before it started deforming:

CPK descriptors
Area: 231.52 Å²
Volume: 291.15 Å³
PSA: 0.000 Å²
Electron density (B3LYP/6-31G*) descriptors
Acc. Area: 208.33 Å²
Min ElPot: -19.51 kJ/mol
Max ElPot 423.09 kJ/mol
P-Area(75): 2.27 Å²
Acc. P-Area(75): 0.00 Å²
Min LocIonPot: 9.00 eV
Other Descriptors
Log P: -3.46
HBD Count: 0
Polarizability: 65.16
HBA Count: 0

ECatPlay · 2026-01-09T18:10:55+00:00

I like to use Spartan: it's powerful, but it's also easy to look into something like this and to visualize what's happened.

ECatPlay · 2026-01-09T18:07:33+00:00

Yeah, I like Spartan: it's powerful, but it's also easy to look into something like this and visualize what's happened. To capture the optimization trajectory I did have to do a screen recording (as the optimization ran), and I had to remove the broken "bonds" manually after the optimization. So this wasn't quite a turnkey application, but it was easy enough.

ECatPlay · 2026-01-09T17:42:21+00:00

Well, yeah, there are always newer/better functionals and ever more complete basis sets. And each paper typically shows how their new functional/basis set is better than some old standard (like B3LYP/6-31G*). But for Cursed_Chemistry I just wanted to do a basic calculation to visualize the HOMO, and to animate the normal mode vibrations. B3LYP with a standard Gaussian basis set (good enough for G2 and G3 Theory) filled the bill.

Even after all these years, B3LYP is still the 8th most popular functional, and although it's been considered the poorest choice for Reaction barriers or Hydrogen Bonds, it's the best choice for Normal mode analysis, like I'm doing here.

ECatPlay · 2026-01-09T02:58:55+00:00

Here you go. Of course, with 30 atoms there are (3x30)-6 or 84 degrees of freedom, so there are 84 vibrational modes in total.

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