The Periodic Table

pentavalentcarbon

02:05

@CowperKettle The article is a bit confusing. In a classical molecular dynamics simulation, there are no electrons, only explicitly-specified bonds. There is no distinction between an ionic bond and a covalent bond either. There's either a bond defined, or there isn't.

Secret

03:54

If I have some medium sized molecule (e.g. 50 atoms) and one of them is period 6 (e.g. Bi) and I am using ECP on the period 6 element, do I still need to account for relativistic effects by doing relativistic DFT calculations on it?

Berry Holmes

09:07

@Secret I'm afraid I don't know any of the aforementioned topics

Anonymous

09:21

Could someone please answer this? (In case you happen to know the answer)

Anonymous

2

Q: In the mechanism of Cannizzaro reaction why does the hydride migrate rather than the benzene ring?

The hydride ion is not very stable. On the contrary a negative charge on a $sp^2$ on the benzene ring would be much more stable. So why doesn't the benzene ring migrate instead of the hydride, as the benzene ring with a negative charge would be a better leaving group (as we know that less basic...

hBy2Py

11:20

@Secret Unequivocally NO, do NOT use a relativistic Hamiltonian with ECPs.

Secret

so I can just use the ordinay hamiltonian with ECP and it will suffice even if the element is quite heavy?

hBy2Py

Yep. I don't know the actual theoretical/mechanical reasons, but from my time on the ORCA forum it's an ironclad rule: use EITHER ECPs on all heavy elements and a nonrelativistic Hamiltonian OR a relativistic Hamiltonian PLUS all-electron bases optimized for the relativistic Hamiltonian.

The relativistic effects really only come into play in the core electrons of the heavies.

Secret

Ah I see

hBy2Py

Which is counterintuitive from the classical perspective, where electrons farther out would be expected to have greater velocities.

But, for electrons around a nucleus, kinetic energy increases as the variations in the wavefunction get "tighter"

(The kinetic energy is a function of the second spatial derivatives of the wavefunction.)

And, so, that's the core electrons.

ECPs are calculated using relativistic methods, so the relativity gets "baked into the cake", so to speak.

Secret

Another question: I have a complex and I am trying to do some benchmarking calculations using PBE-D3 and PBE-D2. Suppose it was found that PBE-D2 has better agreement than PBE-D3. However since Gimme dispersion D2 only go up to Xe. Suppose my next calculation Bi is contained in the complex, does it mean I have to use PBE-D3 even though it is found to be less agreement for my system?

hBy2Py

14:12

@Secret Probably, yes, you would need to use the -D3.

You could try to parameterize -D2 yourself, if the software allows custom entry of parameters. That would potentially be a nightmare, though.

Berry Holmes

Hello

Fawad

Hello

Berry Holmes

14:38

What's up?

hBy2Py

15:15

@ortho Do you think adding SMILES w/3D view links to posts with chemical structures, as I did in this answer, is a good idea?

(This was in response to Curt's comment here)

On the one hand, it's more info

On the other, it takes up room in the post, it's more MathJax to render, it would be awkward to do for posts with a large number of structures depicted....

Curt's original idea of just including SMILESes in the alt-text might be better

Less work, less obtrusive, less rendering

Less "vandalismish"

orthocresol

@hBy2Py I saw that comment when he posted it. I thought it would be a good idea if there was a simple way to do it. However this really cannot be a high priority thing

hBy2Py

<nod>

orthocresol

It just takes up too much time. For the posts I write here, I already waste enough time formatting references properly.

And it has to be a non-intrusive way, as you mentioned

Is alt-text searchable?

hBy2Py

Is a fluffy add-on, when there's already more than too-much general maintenance work to do.

Oooh, good question

It is in SEDE.

Not sure about site search goes to test

orthocresol

My own tests indicate that it's not possible.

hBy2Py

15:24

Concur.

orthocresol

I guess it's a nice idea, but just not high priority.

hBy2Py

A site search for "image referred to" does not return this post, which currently contains that string in its image alt text

<nod>

Image links don't return in site search either, looks like.

orthocresol

Alt-text shows up in google, though.

hBy2Py

Searching "uGdr7", the stack.imgur ID, doesn't show in site search

ahh, huh, well that's something at least.

orthocresol

try googling 100-58-3 site:chemistry.stackexchange.com ;D

hBy2Py

15:28

hehehe

I think I can guess which CAS that is...

orthocresol

Of course, CAS numbers won't cover every molecule that has been put on this site.

hBy2Py

Oh

no.

I was expecting that to be o-cresol's CAS

orthocresol

Oh, no. It's something I put in a couple days ago to test out other possibilities.

hBy2Py

disappointment

orthocresol

Hahaha

Well, it was an old version of @M.A.R.

Anonymous

16:54

@orthocresol Sorry for disturbing. But, do you have any idea or suggestions about this question (chemistry.stackexchange.com/questions/74380/…) ?

orthocresol

@blue Nope, I don't know the answer. In fact, I've never heard of it behaving differently with a NO2 group.

Anonymous

@orthocresol Okay no probs. I found some such examples (like the dinitro case) in my institute's textbook.

Anonymous

They were listed as exceptions

orthocresol

The migrating group in the Cannizzaro reaction would essentially be negatively charged, so it makes sense that having electron-withdrawing groups on the arene makes it more likely to migrate.

Anonymous

@orthocresol Yep, but by that logic even a benzene with a negative charge would be more likely to migrate than a H- as the negative charge is much more stable on an sp2 carbon that on H (as electronegativity of sp2 carbon is greater than H)

Anonymous

17:01

I was thinking in terms of steric effects...but that doesn't explain it too

orthocresol

I don't really think there's a huge difference between stability of phenyl and hydride

Hydrogens are always difficult to place when ranking migratory aptitude, though, so I don't think it's a simple answer. It might just be the size, or it might be something else (idk).

Anonymous

@orthocresol What is the approximate value of electronegativity of sp2 carbon? I think it's greater than H if I remember correctly. I guess it is a combined effect of size+ sterics + electron holding capacity. Anyhow, thanks :) Let's wait for an answer

Bounty Hunter

19:18

8

Q: Theoretical basis behind orbital correlation diagram for pericyclic reactions

When discussing pericyclic reactions, the Woodward Hoffman rules allow one to predict whether a reaction will be thermally/photochemically allowed. This has been discussed in many questions on chem.SE, but essentially boils down to the following statement: What the Woodward Hoffman rules fail...

organic-chemistry reference-request symmetry pericyclic

Melanie Shebel

20:32

Sometimes I get downvoted and I'm cool with that -- sometimes my questions are awful and I'm sure that perhaps some of my answers could either be more concise or maybe more thorough (to put things on the other side of the spectrum) or just straight up better.

However, I logged in today to see downvotes on multiple older answers of mine to questions that are unrelated. It wasn't "user has been removed," which is a common causative factor in negative rep.

Perhaps someone is unhappy with me? Whatever the reason, what are some ways to prevent downvotes for reasons other than the quality of th…

Mithoron

@MelanieShebel o/

Melanie Shebel

hey hey

Mithoron

@MelanieShebel Serial downvoting?

Melanie Shebel

Yeah

Mithoron

If someone made it quickly then it will be automagically undone

If not, then oh well, sh*t happens :(

Melanie Shebel

20:37

No worries.

It's only a few rep, no biggie.

Mithoron

indeed

orthocresol

21:41

@MelanieShebel no way of stopping it - people can downvote as they wish (within limits). Maybe they just thought your answers were bad, or maybe they don't like you, we'll never know.

Melanie Shebel

Shock

How could someone think either of those things?!

jk hehe

orthocresol

Serial voting will only be undone if there's a certain number of votes within a certain period of time - in this case, I doubt it will happen, probably too few downvotes.

Haha

I get downvotes sometimes too and I always wonder what I did wrong (or whether I did anything wrong).

I guess at the end of the day, it's best to look at it statistically - if 90% of people think your answer is good, and 10% think it's bad, then it's probably pretty good.

Not always, but generally, I suppose.

Melanie Shebel

True true

Mithoron

22:24

@orthocresol What to do with this:

10

Q: Why can't antiaromatic compounds just escape planarity and become non-aromatic to avoid destabilization?

Why can't just all anti-aromatic systems loose planarity (and hence conjugation) and be non-aromatic like cyclooctatetraene ? Would not they be more stable that way? Because anti-aromatic systems tend to be highl...

organic-chemistry aromatic-compounds

It's based on false premise...

orthocresol

hmm..

Well, it's possible to answer it, say that it's based on a false premise. It's not the best example of how a Q+A should look like but there's also no real reason to get rid of it.

IMO the ideal scenario is someone makes another Q + A, with a better premise, and then you can close this as a dupe of that

Mithoron

@orthocresol I find that possibility attractive :)

orthocresol

Well, what are you waiting for?

:D

Mithoron

Ech it's quite probable that a dupe is already waiting to be found ;D

@orthocresol Hmm, this premise may not be entirely false

13

Q: Is compound aromatic if it has also "anti-aromatic" ring?

Is 5,6,11,12-tetradehydrodibenzo[a,e][8]annulene aromatic: If I use Hückel's rule for the whole molecule, I get the answer as anti-aromatic. But the compound has aromatic rings like anthracene/naphthalene).

organic-chemistry aromatic-compounds

Melanie Shebel

22:52

Todd's comment here has me dying

-2

Q: What happen I drink Francium?

I drink francium and worried about happen. What happens? Do I die or awesome happens in belly? I really need help because it happened 1 hour and I don't what to do.

water

2

orthocresol

23:04

LOL

so tempted to leave a sarky comment

Mithoron

xD

orthocresol

jonsca took it so seriously hahaha

Hazinga

23:52

Say I have a sentence as follows:

trans oxidative addition begins with.

Should it be :

trans-Oxidative
Trans oxidative

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