The Periodic Table

7:23 AM

16 hours ago, by CowperKettle

Dog-whistle politics

Dog-whistle politics is political messaging employing coded language that appears to mean one thing to the general population but has an additional, different or more specific resonance for a targeted subgroup. The phrase is often used as a pejorative because of the inherently deceptive nature of the practice and because the dog-whistle messages are frequently distasteful to the general populace. The analogy is to a dog whistle, whose high-frequency whistle is heard by dogs but inaudible to humans. The term can be distinguished from "code words" used in some specialist professions, in that dog...

Although dog whistles should not be considered only in the context of politics.

1 hour later…

8:25 AM

Hey guys, I am looking for any software (preferably free) that can read and visualise molecular orbitals from gaussian checkpoint files, cause Gaussivew lags too much on this poor internet connection?

1 hour later…

9:34 AM

@Secret any particular reason why checkpoint files? As far as I know every program has to format them first any way, and you should not keep them as a source for information - they are binary, dependent on the platform they are created with

Well, the main reason is because the calculation is outputted in gaussian, thus the MO info are gaussian checkpoint files

I would have used gaussview, but the internet connection in australia is so bad that the interface lags to unusability

It takes on average 5-10 mins for the windows to load up via the NCI terminal. and I am not aware of any way to gain access to offline versions of gaussview even via academic subscriptions

@Secret always, always format your checkpoint files before you copy them, especially across platforms.

You can probably use the log file instead of a checkpoint file for most things

but how could one visualise the orbitals using just the log files, cause if I recall, the log files only give the eignevectors, orbital energy and population info?

Q: Generating neat orbitals/surfaces from molden/wfn-files

The free stuff is molden, Avogadro, multiwfn, etc... There are plenty for Gaussian

@Secret are you not using #p?

You might want to include gfinput

Also paid stuff: Chemcraft

I usually use Gaussian/GaussView and don't have to bother with other programs as I think that GaussView is capable of producing nice orbital/surface pictures like this one of one of uracil's Kohn-Sham-orbitals. But when it comes that I have to use other programs than Gaussian - such as Turbomole...

Most of what is mentioned there works for Gaussian log files

9:51 AM

no, I only have use #T for my calcualtions so far, I might be able to try them out with #P.

What I need is a orbital visualiser that works offline, because the online ones are all slowed down by the slow internet connection of australia in general. I should check multiwfn, I had some kind of molden like program with a 3x3 red bricks icon, but the interface is discoloered and a lot more weird on a mac for some reason (and I have yet to find the orbital option there, but I will try again)...

Please don't use checkpoint files for anything other than restarting, or continuing calculations

If you need the information contained in them, use formchk to write the appropriate text file

All if the solutions I told you so far work well on a local install. You simply need to transfer all the relevant files beforehand, and that might very well be your bottleneck

Checking things on the fly is only barely possible with a slow connection anyway...

the downloading of MO fchk files is relatively manageable (well within an hour), it's only the visualiser that is slow

and I have everything else in the whole workflow automated, so everything will be on autopilot

I will see how it goes, hopefully it works cause the full library of my project has 11*11*5 molecules to analyse

10:07 AM

@Secret for producing publication quality images, I recommend Chemcraft, which is not free, but it's a small price to pay for the features it offers. But there are tons of free alternatives available. Let the linked post be your guidance

In any case, gv is probably one of the worst interfaces ever

yeah, gv is precisely the thing I typed in the NCI terminal, and the interface is made even more (insert suitable word) by the XQuartz and the (forgot terminal term for displaying graphical interfaces)

10:37 AM

I never used that program, I really can't understand why it is so popular

typo: (insert suitable lag related word)

It's ok whn standalone or in a local computing cluster but it lags like hell online

10:55 AM

Been there, done that, still think it's garbage

DSVA

11:24 AM

I second Chemcraft for looking at gaussian output in general. It's so much better than GV (except for some problems with IRCs)

2 hours later…

1:00 PM

Hello! Can someone explain why $\ce{CH3COONa} + \ce {HCl}$ can act as buffer?

Its sodium acetate and hydrochloric acid.

I think because acetate is a stronger base than chloride so it can abstract H+ ?

Forming CH3COOH and NaCl ?

aannyyoonnee

@samjoe Acetate is indeed the stronger base but it is better to think of acetic acid being the weaker acid. So if you mix sodium acetate and hydrochloric acid in a 2:1 molar ratio, the hydrochloric acid will protonate half of the acetate molecular ions to generate a 1:1 mixture of acetic acid and acetate — a buffer.

@Jan Wow thats a very nice explanation. Thanks a lot! I was also thinking similarly, forgot to include the left over acetate..

@NotEvans. You probably don’t remember this but I had time to reinvestigate that stupid Grignard today. I found out that what I had isolated had never been a Grignard but was in fact just $\ce{[Mg(THF)_n]^2+}$. A third peak from silicon grease had almost the exact same integral so I interpreted it as the magnesium-bound carbon …

Today I did a different method and got the same two peaks as in the old NMR but without the silicon grease. Today was a bad day. For many, many reasons ^^'

1:18 PM

Ok @Jan so one last q. If we had $\ce{NH4Cl }$ and $\ce{NaOH}$, first one is $a+b$ mols, second one is $a$ mols. So it will form $a$ mols of $\ce{NH4OH} + \ce{NaCl}$, and $b$ mols of $\NH4Cl$ So again its a buffer amirite

Pretty much, yeah. The equilibrium is towards NH3 + H2O though.

Oh Treating it as Arrhenius base

Not to NH4OH

So will it be a base

I mean a buffer?

Yeah, it will be.

1:21 PM

Ok thanks alot!

With the general ammonia problem of it diffusing out of solution giving time because it’s a gas ;)

that's not my problem :)