The Periodic Table - 2018-02-15

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1:30 AM

@ApoorvPotnis yep, same problem, I think probably the ores are not just as simple in their actual composition as they are served to us in high school; and the original ore industry might have made advances earlier than organic chemistry did, so the former might not have had the facility to standardize its names (due to lack of comm systems, etc.)

hmm...

14

Q: Synthesis Golf VII: (+)-Clopidogrel

(+)-Clopidogrel (sold as Plavix) is a common pharmaceutical used to help combat the risk of heart disease. The World Health Organisation lists Plavix on its list of 'essential medicines' due to its broad efficacy, low toxicity and low cost (less than 1USD/month in the developing world). Many i...

@Zhe this drug just appeared in our group problems

so I finally got around to devising a synthesis. After realising that I can't selectively ortho-chlorinate phenylalanine methyl ester, I stole your idea for the asymmetric Strecker (I'm guessing we could hydrolyse the aminonitrile, then TMSCl + MeOH to get the methyl ester). I used 3-(hydroxymethyl)thiophene as a starting material, though. Maybe one day I'll post it as an answer, even though it technically doesn't obey the stated rules, since I'm buying the heterocycle.

@ApoorvPotnis "most of the students have no interest in obtaining correct information but only score high." make that "most" to "many/several", using absolute terms like "most" might not always be a good idea

1:50 AM

@AnyChemSoftwareSpecialist do there exist software to generate resonating structures of elementary organic molecules? checked out this list but its extremely out-dated chemistry.meta.stackexchange.com/questions/291/…

chemsketch can generate the iupac name of elementary molecules, so why not the reso structures? :/

2:43 AM

@GaurangTandon I agree, was going to say that

Martin - マーチン

2:55 AM

@ApoorvPotnis That is a very sad truth. However, if you don't seek to learn, those people should not come here and expect that we confirm whatever wrong things they have in these textbooks. If things are wrong, they must be addressed as that, otherwise there would never be any progress.

@ApoorvPotnis You should be completely aware that the blue book for organic nomenclature is about 1300 pages long. I would not call that a handful of rules. The red book for inorganic nomenclature is only about 400 pages. It is similarly as systematic as organic nomenclature.

@M.A.R. nom nom nom...

@GaurangTandon My canned comment links to the tutorials... I have updated your post with chemistry markup. If you want to know more, please have a look here and here. We prefer to not use MathJax in the title field, see here for details.

@Gaurang Also have a look at the hidden points of editing

@GaurangTandon because resonance structures are very difficult to address... see my question: chemistry.stackexchange.com/q/49440/4945

And going a bit further, resonance in itself is not as straight forward as you might think. There are programs, like NBO, which performs natural resonance theory (example), but it is based on MO theory and localising these orbitals. In any case, to address resonance, you need to know the structure and the electronic structure, a Lewis sketch most of the time is insufficient to do this adequately.

It is unlikely that any simple program can come up with a good set of resonance structures, if even the more complicated ones start to fail. Your brain and your intuition is your most powerful tool here. (Natural resonance theory fails for BF3 to name just one example.)

3:25 AM

@Martin-マーチン this page was quite basic and mostly contained formatting overlapping with math expressions; the second one's good though, bookmarked :)

Martin - マーチン

IIRC there was an effort to combine the extensive MathJax knowledge into one post. But I guess that is just a huge effort...

@Martin-マーチン i'm not asking the software to "name" the reso hybrids, just to draw it, won't that be easier? And no, no natural resonance theory, just simple high school reso theory :(

Martin - マーチン

In high school your brain should be your most powerful tool. Honestly though, resonance is complicated for computers, a human mind is more likely to pick these things up via intuition...

@Martin-マーチン but the red book probably doesn't name the ores, does it? here are some example names "sphalerite, argentite, cerussite, casseterite, chalcoite, chalopyrite, anglessite, galena, matlockite" hardly systematic to me :(

Martin - マーチン

@GaurangTandon -ite ;)

3:31 AM

@Martin-マーチン yes but I had to just draw all eight reso structures for paraterphenyl manually in chemsketch :(

@Martin-マーチン ha that's reasonable xD

Martin - マーチン

Mineralogy and its findings probably predates modern nomenclature and therefore a lot of names were common in the literature before that time. They were retained (old habits are hard to kill). We don't question the use of ammonia, acetic acid, toluene, etc. - organic chemistry does the same thing. The compound space of new stuff just is so big, that trivial names can become more complicated than the systematic stuff

noob question but this post states electronic configurations as $(1s)^2(2s)^2$ I always only saw $1s^22s^2$. Are both notations accepted?

mathjax doesn't work in comments :'(

@Martin-マーチン "old habits are hard to kill" reasonable, it's still hard for me to get rid of ridiculous high school notions :(

Martin - マーチン

@GaurangTandon mathjax should work in comments, at least on the main page, not the app though

@Martin-マーチン $2^2=4$ doesn't work on pc, i never use mobile apps

Martin - マーチン

for chat you have to enable it...

3:39 AM

@Martin-マーチン where's the button?

Martin - マーチン

27

Q: Main Chatroom Etiquette Guidelines

When I was walking through some of the chatrooms on the network, I found that mathematics.se has some rules for their chat. I thought this might be a good idea for us as well, hence I propose these guidelines: Have fun! Our chatroom is intended for casual conversations. There is almost nothing ...

discussion faq chat

it's hidden in there how to do it somewhere..

@Martin-マーチン RE "organic chemistry does the same thing." well imho the names like "ammonia, acetic acid,etc." are reasonably distinct from one another to be memorized separately; the same cannot be said for metallurgy though, see "casseterite" and "cerrusite" they're sooo distinct yet names are sooo similar :(

Martin - マーチン

@GaurangTandon I think both are accepted, but the orbital denominators should be upright... the easiest to type (and I think supported by now) is \ce{1s^2 2s^2 2p^2}

@Martin-マーチン this is the method; there's a one time use below, will use that

Martin - マーチン

@GaurangTandon I understand what you're saying; and I hate that some schools put so much focus on nomenclature. If you don't know what the chemistry is, why would you need to know how to name it? I think that are wasted opportunities...

@GaurangTandon i use this... stackapps.com/q/4370/27677

3:46 AM

@Martin-マーチン we are indeed taught the metallurgy of ores, but those are very few (alumina, sphalerite, chalcopyrite, galena, haematite, argentite; basically one for each metal) important ores. The real problem is that we are supposed to know the nomenclature of many more confusing ores, because you never know which one they may ask in the exams! :(

Martin - マーチン

yeah, bulls****

If anyone ever said in school "I'm never going to use that anyway!" {S..}he is completely right about that, given the very few exceptions who go into that field.

@Martin-マーチン exactly

@Martin-マーチン that's better

Martin - マーチン

It doesn't use the correct MathJax version though, so sometimes stuff fails... not sure if $\pu{1 bar}$ works...

nah, it doesn't...

the more you edit, the less you need it...

I don't even see the code

hehe

4:38 AM

i was hoping to set it up such that there's a message in my stackexchange inbox at the top right every time a new question got posted on the chem.SE site

is it possible to do this?

given there are so few questions every day, I wouldn't mind checking them all out

Martin - マーチン

no i don't think this is possible, and not adviseable

right now I have the Newest Questions pgae open all but it isn't the most efficient way to keep track of everything

Martin - マーチン

do you use rss feeds?

i did set up a filter stackexchange.com/filters/122668/new-question but am not sure if it does send a msg in my SE inbox

@Martin-マーチン i can, is there a way through that?

Martin - マーチン

there should be a way

4:46 AM

lol that way easy

chemistry.stackexchange.com/feeds

I'm using RSS Feed Reader Chrome - it setup instantly

let's hope it catches new questions just as well

if you want to filter it by tags just do feeds/tags/tag1+tag2+...

Martin - マーチン

@GaurangTandon yes, sorry i was busy... anyway... new messages get dropped in a feed in chat all the time

+ some maths, physics, bio questions

yes that's ok :)

@Martin-マーチン when did we have these questions on Chem.SE?

Martin - マーチン

feeds has a delay though

@GaurangTandon i don't understand the question

@Martin-マーチン you can change the "feed update interval" to 1 minute (minimum) in rss feed reader; though I think 10minutes is reasonable

@Martin-マーチン I didn't understand why you said "maths, physics, bio questions" would drop in a feed for recent questions list on chem.se

Martin - マーチン

you can't change what se is not pushing ;) you can only update how often your reader checks

4:59 AM

@Martin-マーチン oh yeah, lazy backend, that's reasonable :P

Martin - マーチン

in the chat window, not on the main site...

oh ok

Martin - マーチン

whenever there is a new question in one of the feeds, it'll get posted to the top drop down, that includes a few questions on maths, bio, phys

@Martin-マーチン never seen it before for maths/bio/phys though, will keep an eye out

Martin - マーチン

@GaurangTandon chat.stackexchange.com/rooms/info/3229/…

5:03 AM

oh interesting

i've only seen recent questions from chemistry only

5:33 AM

@GaurangTandon Agreed. 'Most' should be changed to 'many/several'.

@Martin-マーチン Yes. The actual rules for nomenclature may be numerous in number but at an introductory level, they are really a handful.

@GaurangTandon @ApoorvPotnis @AvatarShiny are you all giving JEE too?

Yep

are you in 12th or a dropper?

Dropper

@Rick that's a nice group ;)

5:39 AM

@GaurangTandon Given the state of research in India, I thought 'most' would be correct.

@ApoorvPotnis well, I would tend to refrain from using absolute terms like "most" as long as I am not in a position to accurately justify the claim; the same claim if made by a professor in the teaching field with +10yo experience would be better; hope you understand :)

Yes

11th

me in 12th though

@Rick you in which class?

Even I'm a dropper

@GaurangTandon Agreed

5:44 AM

@GaurangTandon so you have boards too coming soon right?

@Rick i'm in ISC; boards are going on :P

they started 12th feb

6:37 AM

@Martin-マーチン I had set my feeder to check the recent questions feed every 10mins, and it has just now caught a question that was posted just 4mins ago, i'd say that's pretty excellent

Martin - マーチン

well, there is a new feed item in chat, too

damnit, why do people put tags in titles

7:09 AM

What exactly is the mechanism of hydration by "nascent hydrogen"? According to the wikipedia page, it's an outdated theory, but I don't get the actual mechanism from that page. Like what exactly happens when we convert Nitrobenzne to aniline using Sn with conc HCl?

it looks like even Na/ethanol generates this so called "nascent H", I guess having a metal is important then?

@Rick i'll say it probably doesn't matter, at least at our stage :P

@Rick the complete mechanism might not fit into the chat here, so consider asking a new question on the main site ;) (spoilers: i'll upvote and star it immediately)

7:50 AM

alright done.

8:20 AM

@GaurangTandon if you remove the hydrogens on the ghost atom (circled in pink) I'll accept your edit. in that specific case there are no hydrogens there. chemistry.stackexchange.com/review/suggested-edits/73086

Otherwise it looks great

chemsketch won't let me remove the hydrogens

will a note at the end of the image be ok?

chemsketch limitation; no hydrogens should be there at the end of the image

^^^^ that'll work?

@Martin-マーチン it's also pinging me when latest questions get edited even though I've read them, that's bad :(

@GaurangTandon A cursory glance over the question and someone will be stuck with an incorrect concept.

user image

@AvatarShiny is that ok?

(will add the circles)

8:36 AM

Yes that's perfect

@AvatarShiny suggested; please approve

8:56 AM

Approved

9:14 AM

@AvatarShiny regarding this chat.stackexchange.com/transcript/3229?m=42728627#42728627 I checked my lecture notes, my prof has also said that red P+HI will reduce -COOH

But do you have MS Chouhan book? Because in it, it is given that -COOH isn't reduced by RedP+HI

this is a dead end now

Check chapter Aromatic compounds Q 28 synthesis of ibuprofen

9:41 AM

I've been checking industrial methods but none mentions red P +HI except ms chouhan :(
https://en.wikibooks.org/wiki/Structural_Biochemistry/Ibuprofen
http://khakiimonstarr.blogspot.in/2013/06/synthesis-of-ibuprofen.html
http://jacr.kiau.ac.ir/article_516129_239923d1582447450a36d280e0dd4be6.pdf
everyone says the same thing, none mentions RedP+HI :(

still checking

this paper mentions it (indexed by Google) but I don't have access :'(

accessed! (long live sci-hub)

user image

see this, @AvatarShiny clearly shows that redP+HI didn't reduce carboxylic acid

10:07 AM

had to post the question on main site to validate my things, did chemistry.stackexchange.com/q/90696/5026

1 hour later…

11:29 AM

@GaurangTandon we we're taught that

2 hours later…

1:13 PM

@Martin-マーチン In this post from 2014 you happen to use `\mathcal`for formatting the Faraday's constant which gives it a really curvy look
https://chemistry.stackexchange.com/q/20066/5026
Any specific reason for that?
The [wiki post](https://chemistry.meta.stackexchange.com/q/443/5026) doesn't mention it anywhere... _<markdown fails -_->_

Martin - マーチン

I used to type constants with that to distinguish them from variables, but that's just style. I don't do it anymore.

alright I fixed that

and there's one thing that's confusing me for quite a long time now...what is wrong with "number of moles"? :P (honestly serious question though)
I mean, an innocent google search for "number of moles" yields many sites still use that phrase but apparently it's wrong.

I think that's because the mole already refers to a number of some things

so prepending "number of" to it is redundant

like the RAS syndrome?

2:01 PM

@orthocresol O.o

2:41 PM

Hi, would it be ok to have a "pdb" tag on chemistry.SE? I watch this tag on bioinformatics.SE and biology.SE (through email notifications), and now I just realized that there are many similar questions on chemistry: chemistry.stackexchange.com/search?q=pdb but it's harder to monitor them without a tag. I don't have enough points on chemistry to create a tag myself.

2:53 PM

@marcin Could be justified. To be sure you might want to ask on meta.

3:29 PM

@Loong OK, I just asked it on meta

3:54 PM

1

Q: How about [pdb] tag?

Would it be ok to have a [pdb] tag on chemistry.SE? I watch this tag on bioinformatics.SE and biology.SE (through email notifications), and now I just realized that there are many similar questions on chemistry: https://chemistry.stackexchange.com/search?q=pdb but it's harder to monitor them with...

discussion tags

4:46 PM

0

Q: How does reactions like these proceed?

I encountered this question in the chapter Amines and trust me I've gone through many textbooks but couldn't find the functioning of those reagents, well some of them. Firstly could you explain what does the 3 reagents under the same arrow signify? Also, can you explain the mechanism step by s...

organic-chemistry reaction-mechanism amines

Is this question wrong? I thought Gabriel phthalimide reactions cannot make aromatic amines?

@Rick Yes, probably wrong. If there was dinitrochlorobenzene, it should work though.

Klaus was a softie for poor homework, very rarely see him these days

5:02 PM

Alright, thanks

agree with mithoron, i too was taught that SN2 doesn't take place on aromatic rings until EWG groups are placed at ortho/para positions (SN2Ar)

at the crucial part of his answer, Klaus has linked to en.wikipedia.org/wiki/Nucleophilic_aromatic_substitution which also depicts a EWG group

or was he thinking of the benzyne mechanism (given on that wikipedia page under third bullet point)?

that seems to work without EWGs, i haven't been taught that type of substitution though, so I can't comment if Klaus got that part of his answer exactly wrong

@GaurangTandon It woudn't work in this case I think

@Mithoron probably, but I am not at all sure about the benzyne mechanism

Conc. NaOH can make sodium phenolate from PhCl, but I don't think it's compatible

maybe, though I gotta get some sleep now, cya in the morning tomo, or rather my morning tomorrow, timezones differ, lol

2 hours later…

pentavalentcarbon

6:48 PM

I think I'm going to hide a link to chem SE in my dissertation

need to validate my use of this site as a massive time sink

validate to yourself?

pentavalentcarbon

...

maybe I should say "easter egg"

7:01 PM

@pentavalentcarbon :)

pentavalentcarbon

an (edited) answer to at least one post is going in as a section, so hyperlinks need to be hidden somewhere

pentavalentcarbon

7:16 PM

also realized I only have one picture of a molecule

7:32 PM

I put it in my cv.

"have 32,196 reputation on Stack Exchange"

(I didn't write that exactly, but I did put a line about it, especially because there was some kind of recognition:

pentavalentcarbon

publish correction: on <insert date>, rep grew to 33,000

...wait...seriously?

yeah

obviously it wasn't my major selling point

it was under "other activities" which included rubbish such as playing in orchestra

@pentavalentcarbon You can totally put it up front. Just do it in a language that no one understands, and it'll be fine

pentavalentcarbon

well if that's rubbish then my two fun/valuable hobbies are worthless :(

oh, well, it's rubbish in the sense that it doesn't really tip the balance.

pentavalentcarbon

7:37 PM

agreed

It should give you a "well rounded" look.

I can't really tell what impression it gives

it could be "this guy doesn't have a life, in his free time he's still doing chemistry" which may or may not be bad

but because of this I eventually decided to include one line on it

pentavalentcarbon

I remember that

Without that tweet I would probably have left it out.

but yeah, it was a really minor point

You're famous

well, internet famous

Also, I've magically made it to the top 30 for all time reputation

Though I'm not sure if that's good or bad... :/

pentavalentcarbon

7:57 PM

organic chemists get all the rep

where's my communism???

@Zhe You're gonna get 10k soon-ish

Seeing deleted posts and stuff...

@pentavalentcarbon I got +105 for answering a question about the shape of d-orbitals...

In a way that I'm sure will make a real chemist cringe

o.0 Oh not even mention it ;D

pentavalentcarbon

I want to say I'd rather fall on a sword, but one of my most upvoted answers was "what does F10.8 mean in F77"

terrible

most of the good stuff...not so much

@pentavalentcarbon I don't even know the words in that question

pentavalentcarbon

8:02 PM

format specifier in Fortran

tch shame on you

If it was at least F95... :D

I'm not touching fortran

pentavalentcarbon

actually didn't need to say f77, it is valid in all versions, and frankly no different from %10.8f

anyway, back to molecules

@pentavalentcarbon Ehh, learning fortran is some waste of time these days

pentavalentcarbon

since none of my good stuff gets upvoted, I created my own ~/Dropbox/stack_exchange/chemistry/completed/hall_of_fame for my own amusement

8:06 PM

@Mithoron It's OK, he knows python

@Zhe Of course :D

pentavalentcarbon

@Mithoron like all things, it depends...it's more about maintaining old code than anything else...note that I can read but cannot write it

It just doesn't do much good to learn it additionally

@pentavalentcarbon No, it's not. I just delete the old files.

pentavalentcarbon

ok snark master, you know what I mean

8:09 PM

But some software and old-timer scientists still use it ;)

pentavalentcarbon

if you've used quantum chemistry software you've used something written in Fortran

I wonder if there's any fortran in the codebase at work

what's the standard fortran extension?

pentavalentcarbon

.F or .f for 77, .f90 for 90, .f95, .f03, .f08

oh, we have some 3rd party R packages checked in

pentavalentcarbon

unsurprising, they probably call very old stats stuff

8:23 PM

There's certainly no qchem or gaussian

I lied

O.M.F.G.

pentavalentcarbon

...

There's some random library that will read a qchem checkpoint file

Not sure if that's an overinclude or what

pentavalentcarbon

fchk?

But wow

I dunno

I'm not reading it that closely

it's in pymatgen?

pentavalentcarbon

oh, makes sense

fchk is like xyz, it's "standardized" but not, and abused in all sorts of ways

can hold all sorts of...goodies...

I won't ask why pymatgen is in there

8:29 PM

And I wouldn't be able to answer

And if I found out I probably couldn't tell you

8:50 PM

@M.A.R. o/

Hey

I was busy teasing the other Mith in another chat

Oh no! ;)

waves a leek at @M.A.R.

:D

@Mithrandir you're far from home

I have the home advantage

9:00 PM

You triggered my self-stalker system.

Which stalks . . . yourself?

Besides, I figured it might be a good thing if I periodically dropped in here.

@M.A.R. Naturally.

@Mithrandir I think I should call NatGeo

pentavalentcarbon

too many punners in here rn

You are truly a unique species

You too penta, but you already know

pentavalentcarbon

9:03 PM

you don't know the half of it

I know most of it

@pentavalentcarbon I take it that people do periodically make puns on the name of the room?

Except the simulations and the nerdy chemistry

pentavalentcarbon

@Mithrandir no, just this other one cough says weird stuff sometimes

@Mithrandir but they're much better quality puns

Objectively measured

@pentavalentcarbon hey who you calling cough?

Hey Eva. Sorry, @NotEva

pentavalentcarbon

9:06 PM

@M.A.R. you've outed yourself, they aren't "simulations"

@pentavalentcarbon portrayals?

pentavalentcarbon

@M.A.R. more like "wishful thinking"

That funny looking lady is Mona Lisa, not pentavalentcarbon

pentavalentcarbon

sorry, I look nothing like a funny-looking lady, IMO

@pentavalentcarbon shame

@pentavalentcarbon idea: What if, to, say, a lemur, a redneck with 300 kilograms of beard is like a beautiful lady?

pentavalentcarbon

9:12 PM

no comment

Let's change the subject

Talk about hating Google and facebutt for recoding everything we think

And everything we think we think

Or the recent scandals

Or the not so recent scandal

Goddammit, is there anything joyful in the society?

pentavalentcarbon

you think you think?

@pentavalentcarbon I think I think I think I can't decipher that message

I think

pentavalentcarbon

I would google image search for "head exploding" but I have safe search turned off and I don't want to be scarred for life

"Head exploding cartoon gif"?

FWIW, a chest exploding would look uglier

pentavalentcarbon

9:18 PM

I'd rather think about neither

@pentavalentcarbon think about ice cream

pentavalentcarbon

I had some rum raisin the other night

it was good

@pentavalentcarbon the only real flavor is pure vanilla

pentavalentcarbon

with no thoughts of exploding body parts in mind

@M.A.R. I'll pretend you didn't say that

@pentavalentcarbon such a loss. Not too late though. Next time you eat ice cream, think about exploding body parts

@pentavalentcarbon well, I hate real chocolate too

pentavalentcarbon

9:22 PM

@M.A.R. what, are there only 2 flavors over there?

@pentavalentcarbon wat

No, well, I meant I hate that dark chocolate they call real chocolate too

pentavalentcarbon

I am so confused right now

what is the definition of "real flavor"?

are we talking about canonical ice cream flavors?

@pentavalentcarbon real flavor argument is something you use when you have some sort of enjoyable thing that you don't enjoy because of the flavor

pentavalentcarbon

that's almost as confusing to me as most of the questions on this site

@pentavalentcarbon are we talking about anything?

pentavalentcarbon

9:27 PM

@M.A.R. AAAARRRRRGHHHHHHHHHH

wheres @chemobot, I need a !!beer

@pentavalentcarbon etsy.com/market/funny_beer_shirts

pentavalentcarbon

I'll pass

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Transcript for

Feb '1815

The Periodic Table

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

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