The Periodic Table - 2012-04-27

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Chemistry Feeds

12:39 AM

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Q: Why is PEG important for efficient yeast transformation?

One way to do an yeast transformation is by using lithium acetate, a single-stranded carrier DNA, and PEG (1). I was wondering why is the polyethylene glycol important for the efficient transformation. How does it affect the take-up of the foreign DNA? Yamakawa et al (2) showed that PEG is essent...

biochemistry molecular-biology yeast transformation

Nick T has made a change to the feeds posted into this room

3 hours later…

3:30 AM

1

Q: During the development of aspartame, why was the methyl ester chosen?

One frequent argument against the safety of the synthetic sweetener aspartame is that it can be hydrolyzed, with one of the hydrolysis products being methanol, which is known to be toxic. Of course, usually not much aspartame is added in food anyway to yield a sufficient amount of methanol or its...

organic-chemistry

3 hours later…

6:24 AM

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Q: How large is the energy difference between keto- and enol-form of guanine and uracil?

The nucleobases in DNA and RNA are generally present in the keto-form, and not in the enol-form. As an interesting historical note, James Watson and Francis Crick did initially believe them to adopt the enol-form, which isn't compatible with the correct model of the DNA they later proposed. But ...

organic-chemistry keto-enol-tautomerism nucleobases

3 hours later…

9:51 AM

0

Q: How to differentiate Metal from its ion?

I am working on metal and its ion. The problem is, i would like to know whether the metal has been converted to its ionic form or not. The hypothesis for the analysis is: Metals are good conductors and ions possess redox potential. Therefore, by measuring the conductance and red-ox potential is ...

ions redox metal conductance

0

Q: Why are arenes with conjoined benzene rings drawn as they are?

Whilst we are taught to represent benzene as below (A) due to its delocalised electrons, however when two benzene rings share carbons (e.g. naphtalene) it seems to be more commonly represented in textbooks as two conjugated rings (B). Whilst I realise that the result is the same, what is the adv...

organic-chemistry arenes benzene structural-diagrams

2 hours later…

11:35 AM

@Fx Well for H2O with an STO-3G basis, it matches Gaussian's SCF energy to at least 8 decimal places. :D

12:26 PM

@LordStryker congrats!

Now i'm building a quote module to tack a quote on at the end of every job XD

@LordStryker :)

my own code says things like You are lucky! Full moon tonight. or Watch out! Bad things can happen on Friday the 13th.

:P

I like to make my error messages being with things like ID 10 T Error, PC Load Letter or Feed me a cat

@Fx Acutally I hacked our HP Laserjet in our lab to have it display the cat one.

It scared everyone for a while :P

The other one I did was Insert Coin(s) to Begin

It was great :P

hum, what do we say about questions that could be answer by a careful bibliographic search?

I'm thinking of this one:

1

Q: How large is the energy difference between keto- and enol-form of guanine and uracil?

The nucleobases in DNA and RNA are generally present in the keto-form, and not in the enol-form. As an interesting historical note, James Watson and Francis Crick did initially believe them to adopt the enol-form, which isn't compatible with the correct model of the DNA they later proposed. But ...

organic-chemistry nucleobases tautomerism

Hmmm

12:30 PM

I suppose it's okay to do the search, find a few relevant papers and write an answer…

Its tricky. Some things are easier to find than others.

I think we should be able to ask questions like that if the question is built around a focused context perhaps?

Not everyone can access the same lit databases.

@LordStryker well, on the other hand, we don't want to spend our time doing others' searches for them, right?

actually, I believe that question is okay, but it brought up the question in my mind

This is very true. Again, I think if the context is very focused and well-defined it should stay. But to ask "what is the value of....?" or whatever should not be here.

Its too early in the morning for me to think up an example. :P

12:45 PM

okay, well, I answered, we'll see how that goes

are there any copyright ramifications to posting tables and stuff from published sources on SE? just out of curiosity

@LordStryker thought about that, have no idea

publishers are such dicks that I'm not going to worry about them

with all I give them for free, I've stopped thinking about their rights :)

0

Q: How to differentiate Metal from its ion?

I am working on metal and its ion. The problem is, I would like to know whether the metal has been converted to its ionic form or not. The hypothesis for the analysis is: Metals are good conductors and ions possess redox potential. Therefore, by measuring the conductance and red-ox potential is ...

ions redox metal conductance

on the above, there's something that I don't like about Georg's tone… I've tried to ask the same question in a nicer way, but is his comment a bit rude to a new user, or is it me not having had enough coffee yet?

1:14 PM

George was unprofessional in another post. I'm not too happy about it.

I flagged his comment as off-topic/non-constructive

1:33 PM

@F'x, I would like to clarify all my queries here.

Reg Red-ox, i have started with the powder form of the metallic compound, say ZnCl2. After the chemical process, i am expecting Zn(0). How do you conclude reaction has yielded Zn(0) or Zn+2?

@Anil you have it as a dry solid?

Yes dry solid powder

this reaction was carried out in aqueous medium and finally i get solid powder

well, the classical test for zinc is hydrochloric acid

it will make a vigorous foaming reaction when it encouters zinc

beware: it's not a nice product to work with, so read safety notices first

I understand this particular reaction. but the question is broader for other metals.

well, it depends on the metal…

1:42 PM

I have done my masters in chemistry and i can understand most of the reactions.

I know it depends on the metal. That is why i had the hypothesis.

@Anil do you known cyclic voltammetry?

Cyclic voltammetry

Cyclic voltammetry or CV is a type of potentiodynamic electrochemical measurement. In a cyclic voltammetry experiment the working electrode potential is ramped linearly versus time like linear sweep voltammetry. Cyclic voltammetry takes the experiment a step further than linear sweep voltammetry which ends when it reaches a set potential. When cyclic voltammetry reaches a set potential, the working electrode's potential ramp is inverted. This inversion can happen multiple times during a single experiment. The current at the working electrode is plotted versus the applied voltage to give th...

Oh yes. I forgot that. Thanks F'x

okay, I've added that answer to the site

@Fx I had this doubt reg potentiometer vis-a-vis conductometer (metal ion and metal)

@Anil I'm not sure, it's not my area of expertise…

anyway, gotta go… see you later!

1:49 PM

Its alright. I was thinking of low end equipment (potentiometer and conductometer) but CV is litle bit higher end.

Thank you bye

how to insert images / web clips like F'x has done?

2:30 PM

@Anil just paste links… if they belong to recognized sites (wikipedia, youtube, etc.) their content (or an extract) will be inlined in the chat

hum, for some reason I had a copy of the IUPAC Graphical representation standards for chemical structure diagrams report on my harddrive.

that should give me bonus points… you hear me, I'm quoting The Holy IUPAC! please hand over points now!

0

A: Why are arenes with conjoined benzene rings drawn as they are?

This is not a complete answer, but I wanted to state the position of the IUPAC on this matter. The relevant publication on this are the IUPAC 2008 Recommandations, titled Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008) [1]. Section GR-6 of the repo...

@Fx *showers Fx with pointsssss!

upvotes for you sir

2:52 PM

@LordStryker let the points rain down on me!

@Fx How about a star? :P

Richard Terrett

Well this sucks - just got ORCA up and running on a very fresh ubuntu install (feeding it the guanine keto-enol problem, just for fun) and now my net connection is throttled :S

1 hour later…

4:08 PM

@Andrew Bah my MP2 energy is off by a little bit... but the SCF code is fine :P

@LordStryker haha that's always how it goes...

I may have not have sorted my E matrix properly or something

Its always something small and stupid that keeps you busy for hours.

@LordStryker in case of some commercial codes, the authors are being kept busy for decades… beware!

I suspect the hardest thing for me on this site will be people talking all the time about energy…

and my thinking all the time “ free energy, please ”

haha I haven't dealt with energy calculations in years now

duly noted :P

@Andrew its all about the energy for us here!

4:17 PM

yes, i feel a bit left out, haha

:P

My coworker and boss recently published a paper where they did coupled-cluster stuff pushed all the way out to full Ts and Qs

CCSDTQ energy points, they were massive

Richard Terrett

@LordStryker - What species?

Small dimer systems such as acetylene and cyanogen stuff

Richard Terrett

were the Ts and Qs nonperturbative?

yup. full on Ts and Qs

Richard Terrett

4:19 PM

good grief

I saw something recently using a sextuple zeta basis

I think he did a paper a while back on water clusters with the massive K-- basis

gah, c'mon MP2. Work alread!

Its the last thing I need to do to finish this awful thing.

Richard Terrett

bad memories of G3MP2rad

what's a K-- basis?

it has k-functions built in

I'd have to go look at the paper to tell ya definitively

@RichardTerrett Its in the MPQC library

@RichardTerrett pentuple zeta, not as big as the one you just mentioned

Richard Terrett

ah

@RichardTerrett recently, a student was defending a small research project and I ask: what's your basis set? — Her: It's 6 zeta. — Me: duh… on a student's computer lab Windows machine? — Her: yes. — Me, after a few seconds: I think you mean to say your basis function had 6 Gaussians, right?

Richard Terrett

4:35 PM

Excellent

@RichardTerrett so what's your type of computational chem?

Richard Terrett

mostly dft on transition metals

@RichardTerrett what code?

Richard Terrett

ADF

mainly

well, anything but VASP, as they say, right? :)

Richard Terrett

4:38 PM

vasp is insanely expensive

I have no idea… I recently bought a CRYSTAL09 license, which I quite like

I do ab initio dynamics the rest of the time… CPMD and CP2K

Richard Terrett

cool

i take it you study periodic systems?

@RichardTerrett yeah

mostly liquid-solid interfaces, nanoporous materials, that kind of stuff

Richard Terrett

interesting

i will probably be looking at 2D materials soonish

@RichardTerrett well, I find it vastly simpler than metals :)

4:41 PM

metals scare me

Complicated beasts

@LordStryker starred; same here

everything that has bands instead of energy levels scares me

and if it's conductive, I try to run fast

@Fx We were doing some work related to metals in the lab. I looked at my boss and said, "soooo how do we define the electronic state of Gold?" he just shrugged and we both never revisited that again.

Richard Terrett

I need to work out how to make GGA+U work for me

and yeah said 2D material is a semiconductor

@LordStryker - Now's a good time to spring the perennial 'why is gold gold?' question!

I have an excellent question for Chemistry.SE that I asked on Physics and got no answer…

but they can't migrate it until we are in public beta :(

Richard Terrett

which one?

4:45 PM

8

Q: Striking examples where Kohn-Sham orbitals clearly have no physical meaning

In Density Functional Theory courses, one is often reminded that Kohn-Sham orbitals are often said to bear no any physical meaning. They only represent a noninteracting reference system which has the same electron density as the real interacting system. That being said, there are plenty of studi...

quantum-chemistry density-functional-theory didactics

@Fx In reality isn't DFT just a 'working fluke' so to speak? @RichardTerrett No offense or anything :P

btw that's a good question I'd love to see an answer to.

@LordStryker aren't post-HF methods just nice shiny toys that are too expensive for any practical use? ;-)

@Fx ahhh you got me

But with DFT, it seems as though it boils down to... "parameterize, parameterize, paramaterize!"

no, DFT has some justification… and more importantly, the effort spent in development of parameterless functionals is increasing (was at a seminar on the topic the other day)

I mean look at Truhlar's new functionals, M08, was essentially just tweaking coefficients given in M06

Richard Terrett

4:48 PM

i think i saw M11 recently

Yeah. he keeps them to himself and his group.

Richard Terrett

M06 is great on paper but too expensive to use for my stuff

there's that great M06 buckycatcher paper...

@LordStryker - my favourite parameterisation is 'B3LYP*' - specify any % of HF you want!

@RichardTerrett :D Great way to get pubs!

Richard Terrett

no functional should have a wildcard in its name :D

@RichardTerrett So any progress on finding the golden functional yet? :P

Richard Terrett

5:04 PM

not my area. one of my acquaintances has a sobering line to the effect of 'there's no reason the exact functional couldn't just be a giant lookup table'

well, it's well and truly waaay past my bedtime

@RichardTerrett Where at?

Richard Terrett

australia

@RichardTerrett It is now lunchtime here :)

@RichardTerrett O.o yeah you better get some

Richard Terrett

good day!

@RichardTerrett Take care

5:07 PM

out of curiosity, what are your chem backgrounds? (schooling, jobs, etc etc)

@Andrew BS in Chemistry, 1 year left for PhD in Physical Chemistry (comp. chem. stuff)

not sure if thats what you were looking for :-\

yup pretty much

I'm a noob around here. :P

I did chemistry undergrad, but now I'm working in software, so I'm really a noob

(although to be fair, I'm only 2 years out of college)

@Andrew What type of software

5:16 PM

business intelligence software, some CRM stuff too, but mostly BI

@Andrew Very cool. I wish my programming skills were up to par but they are seriously lacking

5:53 PM

@Andrew @Fx Ahhh my MP2 number is off by a couple at the 4th decimal place! So close! :D

code issue or data issue?

@Andrew I'm not quite sure. My brain is kind of frazzled at the moment.

bummer, sorry, Friday afternoons are always my least productive debugging time >.<

Haha indeed. If its 6AM i'm on my game. When people start rolling in to work , I tend to slow down.

yes exactly! or I stay late and productivity goes through the roof at like 5:02pm

5:57 PM

@Andrew And when its empty, you can play whatever music you want as loud as you want (for me that helps for sure)

I love my headphones, but can't really use those in lab...

My home system. i.imgur.com/SuptG.jpg

:P

*jealous

closest I ever got to a nice sound system was decking out my dorm suite. We all chipped in for nice surround sound and a tv, but that didn't exactly help me with work :P

@Andrew I've spent a good 6 years putting this rig together. Buy used all the time. Saves money and the equipment is better. Here's the TT i.imgur.com/iDHiB.jpg

@Andrew And this little guy puts out 125 watts per channel i.imgur.com/06scA.jpg

Over 4 simultaneous channels might I add.

the whole thing is incredible

6:02 PM

Unfortunately I dont get to keep this in my lab at work :P

haha or fortunately depending on your labmates

Very true.

we had more "accidents" involving dropped computers, spilled coffee, etc. than anything chemistry related

@Andrew haha that is how it goes

@Andrew We have a running joke. The only chemistry my lab does is make coffee.

My boss actually roasts his own beans. He's pretty gung-ho about it.

haha I somehow missed out on all the computational chem in undergrad

if I had gotten started on that, I probably wouldn't have gone into software

6:07 PM

Should look into doing some GPU programming for quantum software packages! We need that!

There's TeraChem, and I think people are trying to put work into GPU usage for Gaussian and GAMESS-US.

(PS: Hi!)

hey how's it going?

(I'm not really familiar with the chem software, sorry)

6:30 PM

It all tends towards either vast swathes of "advanced" Fortran or ludicrously overengineered C++. You're probably better off in BI. :)

I used matlab for almost everything in college, with some of the archaic spec software thrown in for grins

So I'll stick to the newer stuff if at all possible

:)

My MP2 energy is off at the 4th decimal place now. :( Cannot figure this sucker out.

@Aesin you shouldn't diss Fortran, just like you shouldn't roll you eyes at your mother :)

grand-grand-father, of course, might be more appropriate for Fortran

@Fx it was Fortran that guided me through this SCF code I wrote in Python :)

7:11 PM

@Fx: The triple goto if statement makes me sad. And, often, confused.

7:29 PM

@Aesin ah, the arithmetic IF… obsolescent since the 2003 standard, though, proof that your confusion was shared!

8:22 PM

Hello

I'm wondering why this answer got accepted. It doesn't really answer the question too well, imo. But whatever...

There are some nice questions.

Not sure, up to the ask-er, so...
Hello by the way

@Andrew Hi.

That one also bugs me.

Actually, the answer is good.

But the question is so vague that it puzzles me it was accepted.

I'm not complaining because I want the rep, don't worry.

haha

you can edit the question

It's just that "working on a metal and its ion" is overwhelmingly vague

yeah, that's definitely something that could be edited

8:28 PM

@Andrew I would only edit to clear up obvious mistakes, or formatting, not reformulate the question.

He needs to do it.

Maybe a metal in its "elemental form" and in an "ionized form"

i don't think that's changing the question, just clarifying the meaning

seems like a useful thing to do IMO, not everyone has the chem background to know what the correct terminology should be

Even so, what is he seeking to do? I mean, clearly, elemental iron is solid and doesn't dissolve in water, but Fe2+/3+ does

@Andrew True.

He could also be in the presence of oxides, elemental and chelated metal species.

Anyway, I've commented on his question.

Hopefully he comes back to answer your comment, looks good

@CHM Also, out of curiosity, what's your chemistry background?\

@Andrew Second year undergrad.

Currently working(studying, really) in a theoretical chemistry group.

What's yours?

cool, sounds like fun

I did a chemistry BS at MIT from 2006-2010, now I work in software...

so this is a fun way to stay kinda current on my chemistry knowledge

8:37 PM

Oh. So you're more interested in physical/theoretical chemistry as well?

orgo was my favorite class, took all sorts of organic and organometallic classes

so i'm closer to the orgo/biochem side of things

which I'm clearly putting to good use with my current job :P

Ok.

@Andrew Haha.

Why are you not working in the chemical industry?

Is it by choice?

yes by choice

i have some of the story on careers.stackoverflow.com/ahoy

basically I didn't want to do more school to get a PhD, and I didn't really want to do research

@Andrew @Fx I FINALLY GOT MY SCF/MP2 CODE WORKING! :D :D :D

yay!

8:40 PM

I was comparing my numbers to a frozen-core MP2 energy from Gaussian

what did you do to get it to work?

Had to do an MP2(FULL)

so my numbers were right

just compared them to the wrong numbers :P

haha

so no bugs in your code!

I even coded up a stupid "print random quote to end of job" routine to boot :P

No bugs as far as I know!

haha that's pretty funny

8:42 PM

@Andrew Totally understandable.

Alright! Going home to celebrate!

See you guys!

later!

have a great weekend!

bye

@LordStryker do you know what you want to do post-grad?

@Andrew Reading it atm.

Interesting.

I guess you never know where you'll end up

8:49 PM

haha exactly

I've got to go study org. chem.

:(

Have fun.

lol have a good time

don't forget to post questions about it :P

9:08 PM

Wait wait

This also got accepted

I must appear to be whining

I don't have a problem with the answer per se, but the cited "authority" is wrong.

nice comment

I guess the shortest possible answer would have been "Laziness"

Not at all!

There's an information gain in drawing Clar structures.

Think of Diels-Alder reactions - where will it attack on a PAH?

Drawing the Clar structures clears things up.

Obviously the IUPAC guy has never heard of them

Otherwise he would at least have mentioned it ;)

haha

Generally I prefer to draw out the double bonds for mechanisms

unless it's a starting reagent or a product

@Andrew Ditto

so the reason i draw a circle is just "laziness"

9:13 PM

Clar structures have their use, so have Kekulé's.

Oh, haha.

but anyways, I do like your answer

thanks.

I got lucky - I've had to use Clar structure theory in some work

Anyway, I'll close the computer now. Bye

cya

10:08 PM

Obviously you should look at the physics. Calculate how many electrons are being exchanged between atom A and B, divide by 2, and draw that many bonds.

/me attempts to draw 1.4 bonds between two atoms.

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Transcript for

Apr '1227

The Periodic Table

Haikus are awesome / Chemistry's even better / So pull up a chair

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