The Periodic Table

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bonCodigo

6:35 AM

Looking for Pritt & JSmol

Pritt Balagopal

@bonCodigo Hello

Welcome to chat

!!greet/bonCodigo

Chemobot

Welcome to The Periodic Table bonCodigo! Here are our chat guidelines and it's recommended that you read them. If you want to turn Mathjax on, follow the instructions in this answer. Happy chatting!

bonCodigo

Hello!

Pritt Balagopal

So, regarding your 3d models

bonCodigo

yes

Pritt Balagopal

6:36 AM

You can do it for any molecule

But you need its SMILES first.

bonCodigo

Easier than Wolfram I guess?

Pritt Balagopal

Well, I never used Wolfram so I can't say

Anyway, the link I showed in my answer is: chemapps.stolaf.edu/jmol/jmol.php?model=C=C(Cl)

In that link, the "C=C(Cl)" is the SMILES of chloroethene.

bonCodigo

I figured, that was just the answer molecule. But I am curious to get edit mode to it for other molecule usage.

Oh... SMILES... I am grinning now.

Pritt Balagopal

Yes yes,

Haha

Anyway, it's easy to get the SMILES, visit this website: cactus.nci.nih.gov/translate

bonCodigo

hmm... helpful again.

Pritt Balagopal

6:39 AM

There's an editor, where you can draw a molecule

Suppose I wanted to get the 3d model for this:

You'd draw this in the editor and submit it.

bonCodigo

I am listening

Pritt Balagopal

In the box below, the smiles will pop up. Copy it, and go to: chemapps.stolaf.edu/jmol/jmol.php?model=

after the = at the end, copy the smiles and click load page

bonCodigo

I tried SMILES link for e.g. Syntax error in SMILES string "C11C3C4C1C5C4C3C25".

Pritt Balagopal

Oh, you haven't submitted it perhaps

bonCodigo

A sub question, it seems I can also use pdb for this jmol

Pritt Balagopal

6:45 AM

Maybe, although I'm not really a cheminformatics expert, heck I just came out of high school.

Alright, let's try another example:

Head to this page:

bonCodigo

Ok I got the USMILE

Unique SMILES: User-supplied SMILES:
CC=CC=CC(C)=C

Pritt Balagopal

Great then, you got the SMILE

SMILES*

Now it's easy, just type chemapps.stolaf.edu/jmol/jmol.php?model=**CC=CC=CC(C)=C**

bonCodigo

Some weird molecule.. but works

chemapps.stolaf.edu/jmol/jmol.php?model=CC=CC=CC(C)=C

Pritt Balagopal

Great, was it the molecule you wanted?

bonCodigo

Is there any other way to use this chemapps.stolaf.edu/jmol/jmol.php? than to manipulate the address/link? lol

Pritt Balagopal

6:48 AM

Actually I discovered this link from Wikipedia,

It's the link Wikipedia gives for showing 3d structures

bonCodigo

Genius.

Pritt Balagopal

Fortunately it uses SMILES, so I was able to exploit it for my personal StackExchange use :P

Yeah, it's a pretty neat site, very helpful to explain structures.

bonCodigo

It was almost like the one we use for SO for coding e.g. sql editor online, sqlfiddle.com

How does it add colour to the molecule though?

Pritt Balagopal

Color? Oh you mean for non carbon atoms, they're colored using the CPK scheme

CPK coloring

In chemistry, the CPK coloring is a popular color convention for distinguishing atoms of different chemical elements in molecular models. The scheme is named after the CPK molecular models designed by chemists Robert Corey and Linus Pauling, and improved by Walter Koltun. == History == In 1952, Corey and Pauling published a description of space-filling models of proteins and other biomolecules that they had been building at Caltech. Their models represented atoms by faceted hardwood balls, painted in different bright colors to indicate the respective chemical elements. Their color schema included...

It's a general color coding to identify molecules by color in molecular models.

bonCodigo

Learnt many things via this question today. I added Cl to above link, and got green ^^

Pritt Balagopal

6:52 AM

For starters: oxygen=red, nitrogen=blue, carbon=grey/black, hydrogen=white

Yup, chlorine is green

Bromine is brown, try that too,

and iodine is purple/violet.

bonCodigo

If we want to know angles and so on, what do you use?

Pritt Balagopal

Ahh, that one I don't know. Angles, well, for famous molecules, you could head to wikipedia.

Though I doubt anyone would need the angles to some crazy "1,3,5-bromophenylnaphthylcyclohexane" or something.

bonCodigo

From your experience, will this specifically show the conformations like chair etc?

Pritt Balagopal

Yes, it shows the most stable conformations.

However you can input geometrical isomers as well

bonCodigo

How so? I am trying it out. Can I input more than one in anyway to see a comparison?

Pritt Balagopal

6:56 AM

for example, "C\C=C\C" is trans-2-butene

and "C\C=C/C" is cis-2-butene

use the slashes to indicate.

bonCodigo

The right click has the most functions... gee!

Pritt Balagopal

My, I never tried right-clicking before. Thanks

bonCodigo

It allows measurements... something to really explore (it..) :D

I am just trying to put two molecules into the same page.

Pritt Balagopal

Oh, I have tried to put two molecules as well, unfortunately it only SMILES'd the bigger one,

ANNOUNCE: This persistent editor: chemistry.stackexchange.com/review/suggested-edits/59344 keeps adding 2Na as anonymous.

@bonCodigo If you're thinking about hanging around here, please check out my guide to draw 2d structures and mechanisms, for explaining organic reactions: chemistry.meta.stackexchange.com/questions/3736/…

bonCodigo

Added to favourites :D watching.

Pritt Balagopal

7:07 AM

I am yet to make a 3d guide, I will probably do so when I'm a bit more free.

@bonCodigo Or if you'd like, you can make a guide too.

bonCodigo

LOL you are offering a hard deal - tempting yet time is...

There are still many doubts I posted as questions here.

Still searching for some answers/reasoning.

@Pritt Thanks heaps for the tips and sharing the knowledge. Will surely catch ya soon!

Pritt Balagopal

Sure thing @bonCodigo

Later, I gotta run. Hope to see you around here,

3 hours later…

Bounty Hunter

10:37 AM

Q: Significance & applications of polarizability

One of the reasons given for the greater nucleophilicity of Iodine ion compared to fluorine ion is the greater polarizability of the large electron cloud of Iodine. The other reason given is that it is less crowded by polar protic solvent molecules. However, when the solvent is changed to a pol...

organic-chemistry

M.A.R.

10:56 AM

@PrittBalagopal not every ping is supposed to be important :)

Like a ping that says not every ping is important

@PrittBalagopal I saw that comma,

Pritt Balagopal

11:24 AM

@M.A.R. Whoops, I keep forgetting english grammar.

repeats in mind "don't forget to put a period at the end of sentence"

M.A.R.

11:40 AM

@PrittBalagopal punctuation doesn't matter much anyway, especially in a chatroom. I sometimes forget to put anything at the end of the sentence. It's just that nitpicking is extremely fun

1 hour later…

Pritt Balagopal

12:53 PM

Ahh, alright then @M.A.R.

3 hours later…

1,3-feeds

4:05 PM

Q: What's the difference between "flagging → duplicate" and "flagging → should be closed → duplicate of..."?

I remember this confusion that I had before I was given the close-vote priviledge. Since I can't show it on this site, let me use BioSE's flagging (where I don't have close vote): and Apart from them being in two different locations, what do the two different duplicate buttons do? Is there ...