The Periodic Table - 2012-05-14

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12:16 AM

@Fx (Was going to post yesterday, but can't message-reply on mobile and you know about the apostrophe) This may be interesting: meta.physics.stackexchange.com/questions/976/… . Similar issue, much larger scale. Gets more and more drama-y as you scroll down. I didn't want to advertise this on the meta.chem.SE meta posts cos I didn't want to attract unwanted attention.

12:45 AM

0

Q: Formatting Sandbox--please test stuff here

What the title says. Use this for testing stuff instead of bumping random posts to the mainspace a million times.

7 hours later…

7:37 AM

@StackExchange @NickT I'm not sure about posting meta Q inside the chat as messages…

@Manishearth well, let's hope Chem.SE will have less drama… after all, chemistry doesn't include such topics as string theory :)

3 hours later…

10:43 AM

0

Q: Who should our beta moderators be?

Chemistry StackExchange has been in public beta for a week now, and soon it will be time for us to get our first crop of moderators, as explained in the “Moderator Pro Tempore” blog post: About a week into the public beta, we will seek out members who are deeply engaged in the community’s dev...

discussion 7-questions moderation

Richard Terrett

10:57 AM

@Fx Evening F'x

Richard Terrett

11:17 AM

Argh, these calculations are driving me nuts.

no molecule should have four metals in superexchange contact

@RichardTerrett metal atoms should be banned altogether

unless they are oxidized into a reasonable state (read s0 d10, e.g. Zn2+)

I started work this morning on a system with only C, N and H atoms… should be good!

Richard Terrett

@Fx no such luck. one of these species has three JT active centres

@RichardTerrett life is short, find a subcontractor :)

Richard Terrett

11:33 AM

i agree that legislative action should be taken against these metal atoms

I like your Stone-Wales question, I even tried a model PAH calculation (larger than the one you show in the Q)… but SCF no converging, my friend

then I got sucked into this thing called work :(

Richard Terrett

@Fx Thanks! I didn't even try. The structures there are simply UFF preoptims, purely qualitative

@RichardTerrett well, my probme was that the starting bond lengths were crazy

and I don't have the setup for a UFF calc at hand

if you have an XYZ file, I can try again

Richard Terrett

@Fx TBH I'm not sure that the rings are regular hexagons, because there's no 1.5 bond type in avogadro that I know of

@Fx I can put an unaligned xyz on pastebin if you'd like to try it

@RichardTerrett yes, that works for me

Richard Terrett

11:44 AM

pastebin.com/raw.php?i=DD8gQYx5

@Fx see above, sorry

I'll be interested to see if you can get a decent SCF

I've been picking up a lot of recherche books recently. got a book on CUDA today

@RichardTerrett that's the one without the defect

this one I already have (sort of), what I didn't manage is to get a good guess at the defective structure

Richard Terrett

@Fx Oh, sorry :S

@Fx pastebin.com/raw.php?i=3dcBFdhe

now this is a great question :D

1

Q: Stiffness of chewing gum

My Sister asked me this: "Why is it that when we chew gum, it is soft and mushy to begin with , but slowly gets firmer and firmer like after 20 mins of chewing?" I think it is because when we initially chew gum it has plenty of sugar causing rapid salivation and hence mushiness and the r...

polymers synthesis polymer-chemistry

best question so far on the site IMHO

Richard Terrett

12:06 PM

@Fx Do you think questions on artificial chemistry are suitable for chem.se or more math.se?

@RichardTerrett what do you call "artifical chemistry"?

oh, I see… well, there's "computational science", for one thing

Richard Terrett

@Fx good point

@RichardTerrett well, no SCF convergence, and won't have time to look into it further

Richard Terrett

@Fx That's okay, it's very nice of you to offer to have a go at it!

sorry about that, see you later!

Richard Terrett

12:15 PM

@Fx See you

1 hour later…

1:36 PM

@RichardTerrett Yeah, it is! It's probably not an easy question--yet it's something that the general public will like. :D

Richard Terrett

@Manishearth - hey there

@RichardTerrett 'ello!

Thinking of self-nomming for pro-tem. Doubt I'll make it (not a chemist, blah). Thoughts?

Richard Terrett

@Manishearth - I think you'd be great for it

@RichardTerrett Really? Thanks :)

@RichardTerrett Are you planning on self-nomming?

Richard Terrett

@Manishearth - Don't know. I'd probably go mad with power.

1:40 PM

@RichardTerrett :P

Richard Terrett

@Manishearth - Think you and F'x are the driving force behind this beta

*I think

@RichardTerrett You seem to be enthusiastic about this site, which is a plus. But, you're also not as experienced with the SE engine :/ So, while the community may like you, the SE overlords may not (you can wait for graduation, though)

@RichardTerrett Really? (Or are you just counting my meta participation)

Richard Terrett

@Manishearth - you've asked a ton of pertinent questions on the main site too

@RichardTerrett Re: power, I really wish SE was open source. Then I'd download it, install it, and spend the day blowing stuff up. (I used to do some mediawiki developing so I did this to WIkipedia quite often)

Richard Terrett

@Manishearth - interesting

I used tiddlywiki for a short time for keeping notes

1:44 PM

@RichardTerrett I sort of thought them beginner-level (and stupid on my behalf--especially my latest brown ring one--that one was a big whoopsies on my behalf). I guess beginner-level questions are OK, but I dunno if we need a lot

@RichardTerrett I use paper :P

(alright, Google Docs as well)

Richard Terrett

@Manishearth - the iron ring question is not stupid at all

@RichardTerrett Uhh, how? Wrong premise?

(I guess my issue is no self-confidence then :/ )

Richard Terrett

NO can be anionic or cationic

Yeah, I know, but my question had to do with the wrong premise that Fe was in +1

Richard Terrett

@Manishearth - which is a fair assumption if you're only familiar with NO+

@Manishearth - this is an interesting one

1:52 PM

@RichardTerrett Alright, I see--good question in general is what you mean. On my side, I did know that NO is both + and - (and also 0, I think--not sure). I thought that Fe was +1 due to something I'd read in my notes somewhere. Can't remember why I'd written that, though

Richard Terrett

Sodium nitroprusside

| Section2 = | Section3 = | Section4 = | Section7 = | Section8 = }} Sodium nitroprusside is the inorganic compound with the formula Na2[Fe(CN)5NO]·2H2O. This red-coloured salt, which is often abbreviated SNP, is a potent vasodilator. The sodium salt dissolves in water and to a lesser extent in ethanol to give solutions containing the dianion [Fe(CN)5NO]2−. Structure and properties Nitroprusside is a complex anion that features an octahedral ferrous centre surrounded by five tightly bound cyanide ligands and one linear nitric oxide ligand. The molecular symmetry is C4v. Linear nitros...

@RichardTerrett Ooh, nitrosyl can be bent. Interesting...

This is why chemistry is fun! All sorts of new stuff wherever you look. Of course, that must make it a headache for theorists ;-)

Richard Terrett

@Manishearth - given coordinative saturation of the iron in the ring test compound, that bent bond has interesting geometric implications

i.e. sterics

Aah

Sounds interesting.. have any links?

Richard Terrett

no

i could try a quick calculation on it

2:04 PM

@RichardTerrett Sure, thanks! :D

Richard Terrett

@Manishearth - actually it doesn't look too crowded...

@RichardTerrett Aah.. Probably because we can't easily imagine the available space in 3D and think its crowded?

@RichardTerrett because other ligands aren't so large, are they?

hi @Manishearth

@Fx 'ello

Richard Terrett

@Fx I underestimate those long dative bonds

2:07 PM

@Manishearth I wouldn't assume anything about the SE overlords :)

@Fx ;-)

You think I stand a good chance if I self-nom?

(Have half a meta post written, not sure if I ought to nom)

okay, it will sound stupid, so it will stay in chat: once you have the inertia tensor of a molecule, and its eigenvalues/vectors, how do you calculate the rotation matrix to puts the molecule's principal axes back into (x,y,z)?

@Fx The overlords do stuff like this when you're not looking

@Fx Sounds like a question for Physics.SE

I assumed it was directly the inverse of the matrix formed by the eigenvectors, but it's not

I'm not too familiar with I tensors, but don't you choose the axes beforehand?

2:10 PM

@Manishearth well, it would be math if anything

but I really should be able to write it, damnit

@Fx Hmm, that as well

@Fx Alright, I decided to nom. Sort of rambled on while writing my post, though :/

@Fx You could head off to math.SE chat and ask them--their chat is always active

/me peers at the phase space question

I've read the paper, and the Wikipedia page, and I still can't work out what the actual use of the method would be...

@Aesin I haven't read in much detail, but it looked like it didn't allow anything that you coulnd't already do with another representation or method

Richard Terrett

2:32 PM

@Manishearth - the calculation is going

@Manishearth - it's not actually coordinatively saturated in the strict sense, my bad

@RichardTerrett I've written an answer to your question

@Fx I'd like input from you on that one, too

@All, Hi.

@CHM Protip: you can make an image smaller by appending "s,m,l" to the url. Eg, i.stack.imgur.com/o2bDc.png-->http://i.stack.imgur.com/…

Richard Terrett

@CHM - whoa cool

(dunno if you want it smaller, though)

@Manishearth I wanted to do that, yes.

Thanks

2:39 PM

Actually, I'm currently writing a script that adds this option to the image upload window... As well as an option for linking the image to the full-res version.

@Manishearth wait, doesn't seem to work

Richard Terrett

@CHM - that's an astonishingly high quality answer, thankyou so much for your time!

Maybe it's the cache that's not updating.

@RichardTerrett This has taken me 5 whole minutes to draft

There's surprisingly not much calculation (couple of seconds, really) involved

Richard Terrett

how did you do those figures? they're awesome

Glad you like it, though. I'd like input from others, to check if my interpretation is right, though.

@RichardTerrett The calculations and graphing are done in Mathematica

Richard Terrett

2:42 PM

@CHM - as I suspected :D

@mannishearth it worked, thanks.

@CHM I was halfway through the process of editing it when you stepped it (I was linking the images as well to the full-res)

@Manishearth Oh, my bad.

No prob :)

/me will be back in an hour

Sure

Richard Terrett

2:46 PM

@CHM - did you code the calculation for that specific question or did you have a pre-existing notebook?

Really evinces the power of mathematica

@RichardTerrett some of both.

I had to modify my existing code to graph each eigenstate. I normally plot time evolution of my system. Was just a couple lines to change

Here's the core of it:

edgeMol =
  ImportString[
   "C1(C=CC2=CC=C3)=CC=CC4=C1C2=C3C=C4", {"SMILES", "EdgeRules", 1}];

From edgeMol, get hamiltMol with some code, then:

evalMol = N[Eigenvalues[hamiltMol]];
evecMol =
 Orthogonalize[N[Eigenvectors[hamiltMol]]];
AdjacencyGraph[adjMol, GraphStyle -> "SpringEmbedding",
 EdgeShapeFunction -> (Line[#1] &),
 VertexShapeFunction -> ({{Opacity[0], Disk[#1, #3]}, {Orange,
      Disk[#1, Abs[evecMol[[1, #2]]]^2]}} &), VertexSize -> 4/3,
 ImageSize -> Full]

Richard Terrett

@CHM - does mathematica have built in smiles parsing?

The code works for any SMILES, but results are only significant when dealing with PAHs, since I haven't coded a way to account for different atoms in my hamiltonian matrix

Will do that, someday.

@RichardTerrett Yes

Richard Terrett

That's really cool

how does mathematica's graph drawing compare to say, graphviz?

@RichardTerrett Never used graphviz

Richard Terrett

2:58 PM

oh ok

I find Mathematica excellent.

Richard Terrett

i have access to a license at school but i've not really taken the time to learn how to use it properly

Have you programmed before?

Richard Terrett

which is funny because i was recently using Processing to write a program to plot band structures

yeah

@RichardTerrett Processing, bleh.

Richard Terrett

3:00 PM

not a fan?

Well, then you'll have no problem learning Mathematica.

@RichardTerrett Actually, I like it. I just wouldn't use it for work.

Richard Terrett

to be clear, the band structures were calculated in another program, i was just visualising them

Especially when I can use MMA.

@RichardTerrett Ok. Even for visualization, wouldn't do it. You need to give a shot at MMA, since you have a license.

Richard Terrett

yeah, problem is i can only use it at school

It's easier (I think) to write a Mathematica program than a Processing one.

Richard Terrett

3:02 PM

but i will dabble some more

Ah, I see.

Richard Terrett

well, processing is just java with easier graphics

Yeah. Anyway, I'm hungry. Time for lunch.

Bye

Richard Terrett

@CHM - see you

@Manishearth - do you know how to centre-align an image on SE?

@Manishearth - the calculation is getting there - 26 geom cycles so far, NO has lots of room to bend

slightly distorted octahedral geometry

the waters are being bent away from the NO group

@RichardTerrett Not via a clean method. You can use <pre> or  , though

Richard Terrett

3:14 PM

@Manishearth - ah ok

@RichardTerrett MSO is your one-stop show for all things related to general SE policies/tipsntricks

Richard Terrett

@Manishearth - the calculation is basically done, the waters are just floppy

it could take some time for the waters to fully flop and it's 1am here

Aah

Richard Terrett

so I'll give you the summary later

@RichardTerrett no problem :)

Cool, got two upvotes on the pro tem nom. People, do you want to see this site in shambles? ;-)

Richard Terrett

3:20 PM

oh, it's actually doing something interesting now

@RichardTerrett What are you exactly doing in the sim?

Richard Terrett

@Manishearth - unrestricted BP86/6-311G* on [Fe(H2O)5NO]2+, spin doublet

O_0

Richard Terrett

it should give a ballpark geometry

DFT

Aah

with animation it seems?

Richard Terrett

3:22 PM

hopefully I haven't flubbed the electronic configuration

@RichardTerrett :P

Richard Terrett

it's a geometry optimisation starting from an asymmetric geometry built in avogadro

pretty arbitrary

the only real objective is to see if the NO group is bent or linear

actually I suspect this calculation will be converged within 10 minutes

Oh, the software does that for itself?

I thought you'd have to plug it in

Richard Terrett

plug in what?

Pretty neat :)

@RichardTerrett All the parameters--which NO ligand, which shape, etc

Richard Terrett

3:26 PM

Oh, i'm just feeding it a rough geometry, and allowing the structure to converge to a local minimum on the potential energy landscape

Oh, I see-- wow, software is so sophisticated these days

Richard Terrett

this software is called orca, and it's free for academic use

@RichardTerrett Which means I'd need to be enrolled in a uni, right?

Richard Terrett

no

@RichardTerrett Alright, I'll download it and play with it when I get time, thanks! :)

Richard Terrett

3:29 PM

you need to sign up with the site to get a license which may take a day or so

@RichardTerrett Alright, will do

Richard Terrett

3:41 PM

I'm kinda glad it's so cold here

computer isn't making a lot of noise

@Manishearth - damn, sorry, calculation didn't converge within 50 cycles

i'll continue it later

No problem :)

Richard Terrett

suffice to say that the waters are doing something interesting and that the NO group is consistently bent

@Manishearth - anyhow, night, or I suppose it's afternoon for you?

@RichardTerrett No, evening :)

Richard Terrett

ah ok

I think a "what timezone/time is this guy in" would be a nice SE feature

/writes a userscript

Richard Terrett

3:50 PM

@Manishearth - good luck with the mod nomination

Thanks!

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Transcript for

May '1214

The Periodic Table

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