Spring Cleaning

Feeds

00:06

cleanup action chemistry.stackexchange.com/questions/72116/… retagged, closed (ortho)

hBy2Py

02:10

@MelanieShebel This will get automatically scrubbed

@MelanieShebel Edit the question to fit the answer, I'd say

Get Klaus a Reversal (I think it is?)

@MelanieShebel This one is too broad, and should be downvoted to the point where it gets automatically deleted

@MelanieShebel This should never have been answered in the first place. The answer would probably be best absorbed into a massive canonical post on acidity trends. It's a tricky case, though.

@MelanieShebel (a) Who said the haloform contains iodine? (b) in a haloform reaction, I wouldn't think a haloform would be one of the products.... This should be downvoted heavily

@MelanieShebel Answer should be downvoted and deleted (no references). Since the question is closed as a duplicate, it will and should probably be kept around.

Martin - マーチン

04:28

> Stack Overflow Team (Stack Overflow)

Apr 6, 14:54 EDT

Don

that was everything I got on the matter

M.A.R.

08:09

@hBy2Py Goodness

This room was placed in timeout for 15 seconds; Testing . . . Markdown

I can still post

All ROs probably can

Good

Markdown works too

@hBy2Py when you mean we still have the list of questions tagged with [reaction], you mean because SEDE hasn't updated yet, right?

I guess there's some benefit to outdated things.

M.A.R.

08:48

Organik FTW

M.A.R.

08:59

BTW @Ortho it would be really really nice if you manage to post the new policy thing to Chem.meta before the next next TRE

hBy2Py

09:51

@Martin-マーチン @M.A.R. I think it's actually indirectly my fault. I posted about that query, showing the drop in deleted questions 1yr ago.

Shog9 answered it, and we went back and forth about the details for a bit.

I linked to Spring Cleaning as part of that post

Martin - マーチン

Nope.

hBy2Py

I think it may have brought the burnination request to his direct attention again

Martin - マーチン

I asked them about a week ago to do it.

hBy2Py

Ah.

@M.A.R. Anyways, yes, SEDE still had all the info we needed

The Google Doc with the [reaction] question links is here.

3

Martin - マーチン

nice

well, I'm glad that the tag is gone. Now it's just reading questions and voting on them and not necessarily editing them...

hBy2Py

10:08

yeah, this could actually make it go a lot faster

Pull up question, look it over - if nothing needs doing, then just move on.

Wish I'd made it to 10k before the event - the inline tag editing would be super-handy

homework is going to be a much more prolonged, painful thing.

@M.A.R. And I completely agree. It may not be perfect, but it's such a dramatic improvement from what we've got

Martin - マーチン

10:21

@hBy2Py It's going to be the last event that you don't have the rep though ;)

hBy2Py

heh, maybe, if I can get some other stuff posted

I'm ][ this close to done with the answer for airhuff's hexamethylbenzene dication question

Not like that's likely to garner huge upvotes, though

Martin - マーチン

i think i got a ton of rep from that one

The covalent-to-ionic character of a bonding orbital is completely independent of whether it is occupied or not. The more I explore bonding with QTAIM and ELF, the more convinced I am that it's erroneous to apply the notion 'covalent' or 'ionic' to specific orbitals, even if they're localized orbitals clearly of, e.g., $\sigma$ or $\pi$ symmetry. Bonding character is a property of the overall electron density, not of any specific orbital(s) making up a subset of a wavefunction. — hBy2Py Mar 26 at 12:11

I didn't see that before...

i need to rework that answer

hBy2Py

10:43

@Martin-マーチン Is that comment coherent? I still stand by it based on my current understanding, but I could well be off-base on it

Martin - マーチン

well... you cannot tell anything about ionic or covalent bonding from an orbital...

so yeah you are right

if you'd apply these labels, a bonding orbital would always be covalent, an anti bonding orbital always ionic, there is no middle ground

hBy2Py

And that's only in traditional cases, with orbitals that localized to two centers

Multicenter localized/natural orbitals break the paradigm completely

Martin - マーチン

no they don't

every orbital is either bonding or anti-bonding with respect to the atoms involved

it's one of the few concepts that are actually black or white

In reality for a multi-centre bond you always have a totally bonding orbital with the highest symmetry

hBy2Py

hunh

Martin - マーチン

all other orbitals are likely anti-bonding towards some atom pairs

hBy2Py

10:52

depending on whether the orbital is odd or even around some central point of the bond?

i.e., bonding orbitals are of even parity, antibonding orbitals of odd?

Loosely related: do you understand how Weinhold defines sane energies for NBOs?

Martin - マーチン

bonding orbitals do not have a nodal surface between the atoms, anti-bonding do

neglecting any inner core sign changes

nope, I don't think that NBOs can have sane energies

but then again, I have not looked extensively at the maths behind it

hBy2Py

I think it relates to some claim the NBOs diagonalizing the 1st-order density operator, which is Hermitian

But even if so I don't see how that leads to energies, since the observable of the density operator is a density (or whatever), not an energy

Martin - マーチン

no idea.

i would really need to look that up

and still... there is an open question about NBO

28

Q: Natural Bond Orbital analysis: Significance of stabilization energy determined by 2nd order perturbation

PREFACE: I am no expert on this topic. My questions at the bottom may be off base. I have some experience with symmetry-adapted perturbation theory (SAPT) when it comes to analyzing intermolecular interactions. The total interaction energy of a system can be quantified in four different energy...

then recently there was this garbage article about NBO and the H-bonds...

claiming some break through science, but was in fact just stating the obvious

let me find that...

hBy2Py

11:07

<nod>, that question is a specific example of the broader unease I have about NBO

Qualitative and useful, sure!

Martin - マーチン

dx.doi.org/10.1021/acs.jpca.6b12930

hBy2Py

Weinhold gets pretty quantitative about it in Discovering Chemistry, and Valency & Bonding is (or at least gives the appearance of being) extremely rigorous.

@Martin-マーチン Oh, yeah, I saw that one - it was discussed 'round these parts, as I recall

Martin - マーチン

i mean... if you use a wave function to describe an intermolecular h-bond, then it's going to fail, and any analysis related to this is based on a failed premise...

hBy2Py

?

Martin - マーチン

we can agree, that a hydrogen bond is at least half electrostatic interaction in the first place?

hBy2Py

11:14

His argument is that H-bonding isn't purely electrostatic

Let's see if there's a preview somewhere...

Martin - マーチン

hmm. I mean his point is valid, and you should not use NBO to analyse hydrogen bonds...

hBy2Py

@Martin-マーチン Oh, sorry - Weinhold's argument is that H-bonding isn't purely electrostatic

Martin - マーチン

yeah, i think he's right with that asumption

hBy2Py

QTAIM supports that it's different

Martin - マーチン

?

hBy2Py

11:26

ELF @ the HF--HF LCP of the HF dimer is much higher than in, e.g., NaF

The ELF topology of (HF)2 is hard to interpret, though, due to the delocalized ELF attractors of the F lone pairs

I have plans to analyze some more mundane H-bonding examples to clarify

H2O H-bonded to pyrimidine, say

Martin - マーチン

isn't that all highly dependent on the level of theory?

hBy2Py

Not sure.

I have some calculations scratched together reaching toward answering that question of yours

Preliminarily, my guess is that the dependence of the QTAIM results on the level of theory is proportional to the amount and type of correlation present in the system.

For the sulfanilic acid zwitterion, HF -> MP2 is a noticeable change

MP2 -> CCSD is pretty minimal

@Martin-マーチン I haven't compared the DFT results much yet

Martin - マーチン

are you talking about the AIM charge question of mine?

hBy2Py

yeah

Martin - マーチン

cool :D

how far are you with writing something?

hBy2Py

11:44

Not far

Still don't have solid conclusions yet

Only have done cursory examination of the sulfanilic zwitterion, no other species; and haven't looked into DFT at all

preliminarily: level of theory can matter

but I think it's system-dependent how much it matters

basically, it should be correlated to the extent to which the density depends on the method

I think, anyways

Multiwfn is going to be really handy... calculating RMSD between density fields & such

seeing how that correlates to the atomic charges, and to other diagnostics of the wavefunction

T1 stats for CCSD, etc.

Feeds

cleanup action chemistry.stackexchange.com/questions/72142/… <-- retagged, edited (ortho)

Martin - マーチン

12:00

that sounds pretty neat, i'm looking forward to it

hBy2Py

Part of me thinks, "I should write a paper"

Another part goes, "Gah, all the work that would take...!"

I actually think QTAIM and ELF can provide a classification scheme for bonds

I already know pretty well how I would distinguish covalent, ionic, charge-shift, and coordinate-covalent

H-bonding is next to tease out

then halogen

then probably metallic

But I'm envisioning a decision flowchart

The "canonical" systems of each bond type I've looked at so far are pretty well delineated

Martin - マーチン

determining whether a bond is ionic or covalent with QTAIM is quite easy

either the laplacian is positive or negative along the bond axis...

hBy2Py

Is the B-N bond of H3B-NH3 covalent or ionic?

orthocresol

12:15

@hBy2Py dative

hBy2Py

@orthocresol Agreed

orthocresol

Does "dative" mean anything to you guys anymore?

hBy2Py

And dative has its own QTAIM/ELF signature

orthocresol

(serious question)

hBy2Py

quite distinct from covalent and ionic

I think we're supposed to call it 'coordinate-covalent' now, btw

Martin - マーチン

12:16

well, a dative bond should be covalent, shouldn't it

hBy2Py

Agreed.

However, the Laplacian at that B-N LCP is +0.397

Is the C-F bond in fluoromethane covalent or ionic?

O-F bond in HOF, same question?

A year or two ago, I'd've said they're both covalent

C-F of CH3F: -0.117 (consistent with expectations)

O-F of HOF: +0.223 (not so much)

ELF at these same LCPs:

N-B: 0.144

C-F: 0.405

O-F: 0.697

for comparison, ethane C-C:

LCP laplacian: -0.617

LCP ELF: 0.956

Martin - マーチン

What's LCP?

hBy2Py

line critical point

less controversial term than Bader's BCP

Martin - マーチン

controversial?

hBy2Py

Massive foofaraw about whether the presence of a critical point between two atoms constitutes a bond or not.

Bader called (3,-1) critical points 'bond critical points'

major mistake

Many people immediately assumed he was arguing 1:1 correspondence between a (3,-1) CP and the presence of a bond between atoms

See, e.g., doi:10.1021/jp906341r

He should have stuck to topological terms: point/line/ring/cage critical point

Martin - マーチン

12:34

meh

all them naysayers

orthocresol

cleanup action: chemistry.stackexchange.com/questions/4583/… <-- deleted

(Sorry to interrupt)

hBy2Py

well, cleanup is the actual topic of the room....

Martin - マーチン

true...

hBy2Py

And I need to go be family-social IRL for a while.

Martin - マーチン

whenever a question starts with the two letters s and o.... i get sad.

@hBy2Py have fun... i'm about to start weekend

meaning: doing laundry :D

@orthocresol meh. I'd say away with it. While I understand the question, and it isn't that bad, it's likely not very helpful for someone who is dealing with a similar analysis... meaning calculating the yield. and the answer is just not helpful O.o

orthocresol

12:41

I find a lot of these stoichiometry questions really limited.

Martin - マーチン

well, they are...

when you are dealing with a set of equations, there is not much diversity possible

and for many of these cases a single... how to balance post would suffice...

orthocresol

Yeah, I think we actually have some of those, we should probably find them and merge (if there are multiple)

Martin - マーチン

I think it's enough to just link them. If I see a question with a gazillion answers I am always intimidated that I might have to read all of that to get the full picture, but if they are identical, then yeah go for it

Feeds

cleanup action chemistry.stackexchange.com/questions/72145/… retagged

M.A.R.

13:08

@hBy2Py OH SO IT WAS YOU

@hBy2Py Where? I don't see anything in the comments

@hBy2Py I just want the overzealous HW closures to stop

It would be most unfortunate to introduce Jan to older posts to get even more overzealous HW closures.

M.A.R.

13:43

-3

Q: Java run with php application without javabridge

if possibility is there php code inside java method or .class or .jar we call without javabridge.jar implementation. If possibility is there tell me ASAP. More urgent. Advance Thanks,

java php java-bridge-method

> Advance Thanks,

hBy2Py

@M.A.R. In the comments to his answer

M.A.R.

18:21

@hBy2Py Could you please link all the queries we need to work with, once again?

I'm typing the stuff I'm gonna say right before the start of the event, and I'm almost done

hBy2Py

@M.A.R. For [reaction], there is only the Google Doc

M.A.R.

@hBy2Py Huh?

hBy2Py

The SEDE queries aren't useful anymore for actually navigating to questions

M.A.R.

I meant SEDE stuff I need to link people to

@hBy2Py Because the questions don't have the tag?

hBy2Py

because the links they generate rely on site search

yep

@ortho numbered the questions in the Google Doc

You'll just have to assign ranges of question indices

We could write SEDE queries to pull up links to questions

M.A.R.

18:28

@hBy2Py But SEDE hasn't updated yet

hBy2Py

but those queries wouldn't update to show what work has been done

All it has is a snapshot from 4/2

As people clear [reaction] questions, they'll need to periodically return to the GDoc and delete the links to the ones they've finished.

It's really klunky, but it's what we've got.

I don't picture us making it all the way through [reaction]

but, if we do... for [homework], the queries will still be usefl.

so, I'll paste links shortly

M.A.R.

So we'll be doing [HW] tomorrow?

hBy2Py

I thought that's what you said in the TRE II post

M.A.R.

Then why didn't you edit to say that in the meta post?

!!flip/hBy2Py

hBy2Py

> This episode will feature the following tags:

> * reaction

> ...

> * homework

I have no problem restricting it to [reaction]

I did name the chat event to focus on [reaction]

M.A.R.

18:32

Well, the episode contains multiple events . . .

hBy2Py

@M.A.R. Ahhh, $N_\mathrm{ev} > N_\mathrm{ep}$, gotcha.

Ok

[reaction] only, then

And Google Doc only

and that link is pinned

M.A.R.

Oh got it

We can leave it pinned

to

hBy2Py

@Mart, be thinking of good criteria for SEDE queries to track down any of this flood of questions lately, to make sure we clean them up & they don't fade into the backfiles.

M.A.R.

19:58

@hBy2Py when you get the time, go evaluate the event's starting messages

Feeds

23:22

cleanup action chemistry.stackexchange.com/questions/72179/… retagged, closed (ortho). I don't know why I bother, since this question sucks and anyway statistically speaking most of these people don't come back to improve their question, and thus these questions are extremely likely to be automatically deleted. I guess I just hope for the best.

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