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Author Topic: Sandbox?  (Read 42324 times)

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Dan

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Re: Sandbox?
« Reply #30 on: February 19, 2013, 12:12:57 AM »

Ok, I think I found a bug:

C[C@H]1CC(=O)[C@H](C)CC1=O

Claims to be chiral, but is in fact a meso compound (achiral).

Same is true for the rendering of ribitol:

OC[C@H](O)[C@H](O)[C@H](O)CO

Same problem here:

C[C@H]1CCCC[C@H]1C
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Borek

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Re: Sandbox?
« Reply #31 on: February 19, 2013, 12:42:31 AM »

« Last Edit: February 20, 2013, 12:37:42 AM by Borek »
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sjb

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Re: Sandbox?
« Reply #32 on: February 19, 2013, 01:46:42 AM »

In some way related to the fact you can't represent a racemic mixture, as at http://www.chemicalforums.com/index.php?topic=65809.msg236734#msg236734 ? Not sure....
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Re: Sandbox?
« Reply #33 on: February 19, 2013, 01:51:13 AM »

C(C)(C)[C@H]1CC[C@@H](C1)O and C(C)(C)[C@@H]1CC[C@H](C1)O

Hm, when chirality doesn't matter isn't it better to just show the molecule as

C(C)(C)C1CCC(C1)O?

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sjb

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Re: Sandbox?
« Reply #34 on: February 19, 2013, 01:58:01 AM »

Hm, when chirality doesn't matter isn't it better to just show the molecule as

C(C)(C)C1CCC(C1)O?

Not really, in this case there are a cis pair and a trans pair of diasteromers.

Your compound also includes C(C)(C)[C@H]1CC[C@H](C1)O and C(C)(C)[C@@H]1CC[C@@H](C1)O to my mind.

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Re: Sandbox?
« Reply #35 on: February 19, 2013, 02:55:24 AM »

OK, I see what you mean - but I have no idea what you mean ;)

I mean - I see why the "flat" representation can be too wide (mean to many things), but I have no idea how the racemic mixture SHOULD be represented?
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sjb

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Re: Sandbox?
« Reply #36 on: February 19, 2013, 03:09:16 AM »

In a previous life I worked indirectly with DAYLIGHT on a few things, a sample presentation (not by me, but by someone who was in effect my boss) is at http://www.daylight.com/meetings/emug04/Lock/index.html

The cases we are discussing are ~ slide 20-23

I seem to recall that in the GSK system (as referenced above) there were "chiral" and "racemic" flags you could put on the molecule when imported from ISIS draw (as was) which helped distinguish these cases. Not sure how it worked on the back-end though :(
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Dan

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Re: Sandbox?
« Reply #37 on: February 19, 2013, 04:24:33 AM »

I have no idea how the racemic mixture SHOULD be represented?

I would draw one enantiomer and indicate that it is racemic with a (±) symbol underneath it.
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Re: Sandbox?
« Reply #38 on: February 20, 2013, 07:47:49 AM »

Another incorrect "chiral" flag today -but more obviously incorrect. It seems as though specifying configuration of even non-stereogenic centres fools it into assuming the molecule is chiral:

C[C@H]1CCCCC1
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billnotgatez

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Re: Sandbox?
« Reply #39 on: March 03, 2013, 11:37:45 AM »

2(H-C≡C-H) + 5(O2:rarrow: 4(CO2) + 2(H2O)
or
2C2H2 + 5O2  :rarrow: 4CO2 + 2H2O

I wrote the above two formulas using the formatting available in the reply box

Question 1 - which one do you like
Question 2 - could I have used LATEX or SMILES


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Borek

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Re: Sandbox?
« Reply #40 on: March 03, 2013, 12:12:49 PM »

Both are OK with me - it really depends on what you are trying to show. The latter is simpler, but if for some reason you want to stress out you are talking about alkyne - teh latter makes sense.

In this particular case I would not use neither SILES nor LaTeX. Call it a personal preference.
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billnotgatez

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Re: Sandbox?
« Reply #41 on: March 03, 2013, 12:20:27 PM »

I am a dolt also an Adult
but
Do we have links to teaching
SMILES and LaTex handy
I think I am being common sensed challenged here, since I am not seeing any
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Borek

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Re: Sandbox?
« Reply #42 on: March 03, 2013, 12:47:37 PM »

There are some basic links in the About post formatting... thread.
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Re: Sandbox?
« Reply #44 on: March 03, 2013, 04:49:43 PM »


In this particular case I would not use neither SILES nor LaTeX. Call it a personal preference.

+1 SMILES only becomes relevant above a certain minimum complexity of molecule. Usually, no one needs to be reminded how, say, ethane is structured internally.
« Last Edit: March 03, 2013, 05:31:19 PM by curiouscat »
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