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Topic: Length of limonene  (Read 6255 times)

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Offline Corribus

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Length of limonene
« on: June 07, 2013, 02:30:00 PM »
I know this is kind of a random question - and I wasn't sure where to put it - but if anyone out there has access to a simple computational package (maybe in chem draw or something): I need an estimated length of limonene

http://en.wikipedia.org/wiki/Limonene

I can do a back-of-the-envelope calculation based on some rough bond angles and bond lengths, but I'd like to have a little more accuracy than that.  Anyone want to help a fellow chemist out?
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Offline Archer

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Re: Length of limonene
« Reply #1 on: June 07, 2013, 03:52:39 PM »
ACD Chemsketch freeware, you can draw the molecule and 3D optimise it, the view it in 3D viewer. This allows you to measure between 2 atoms quite easily.
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Offline Corribus

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Re: Length of limonene
« Reply #2 on: June 07, 2013, 07:01:57 PM »
Awesome I will check it out, thanks.
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Offline curiouscat

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Re: Length of limonene
« Reply #3 on: June 08, 2013, 02:53:58 AM »
I used GAMESS via ChemDraw3D and it gets me these coordinates:

COORDINATES OF ALL ATOMS ARE (ANGS)
   ATOM   CHARGE       X              Y              Z
 ------------------------------------------------------------
 C1          6.0   2.1392932433   0.0574292195   0.0303517254
 C2          6.0   1.4819367045   1.1960925503   0.1396276463
 C3          6.0  -0.0320559840   1.3162971227   0.0970603737
 C4          6.0  -0.7045784052  -0.0550451914   0.3147212531
 C5          6.0  -0.0332301413  -1.0704144306  -0.6334810247
 C6          6.0   1.4302872530  -1.2662017078  -0.1997720367
 C7          6.0  -2.2177564126  -0.0195710521   0.1736660547
 C8          6.0  -2.9873905225  -0.3695954992   1.1871083831
 C9          6.0  -2.8165834388   0.4018943750  -1.1567010357
 C10         6.0   3.6452273746  -0.0400362297   0.1456042575
 H11         1.0   2.0242860617   2.1142187606   0.2809326934
 H12         1.0  -0.3351867642   1.7361626253  -0.8574709311
 H13         1.0  -0.3607459756   2.0060748548   0.8682043594
 H14         1.0  -0.4843671396  -0.3672330701   1.3296536356
 H15         1.0  -0.5591337369  -2.0178224267  -0.6057576236
 H16         1.0  -0.0650474273  -0.6999225158  -1.6518432150
 H17         1.0   1.9700485086  -1.8306433467  -0.9547562423
 H18         1.0   1.4640578363  -1.8494340307   0.7183789792
 H19         1.0  -2.5709550276  -0.6723845965   2.1292238378
 H20         1.0  -4.0590218639  -0.3687527698   1.1187169368
 H21         1.0  -3.8980656424   0.3579676853  -1.1127048788
 H22         1.0  -2.4867505029  -0.2477279479  -1.9609439813
 H23         1.0  -2.5343650273   1.4172086178  -1.4132806037
 H24         1.0   4.0998916386   0.9294382619   0.3082887456
 H25         1.0   4.0690849205  -0.4745354762  -0.7555957339
 H26         1.0   3.9144037108  -0.6875092029   0.9767317530

Used Hartree Fock with default geometric optimization parameters. Took 12 steps to converge on to its lowest energy geometry.
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Offline curiouscat

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Re: Length of limonene
« Reply #4 on: June 08, 2013, 02:56:12 AM »
Largest internuclear C-C distance seems ~6.3 7.8  8.3 Å

Would that be your "length"?

What was your ballpark estimate?
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Offline Corribus

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Re: Length of limonene
« Reply #5 on: June 08, 2013, 10:25:16 AM »
What I want is the distance from one tip of the molecule to another.  Basically what I want to get is the rotational diameter.

My ballpark was 0.5 nm, but that was really, really rough.
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Offline curiouscat

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Re: Length of limonene
« Reply #6 on: June 08, 2013, 10:27:55 AM »
Quote from: Corribus on June 08, 2013, 10:25:16 AM
What I want is the distance from one tip of the molecule to another.  Basically what I want to get is the rotational diameter.

My ballpark was 0.5 nm, but that was really, really rough.

My calculation seems more than 50% larger then. Dunno. I could be wrong.
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Offline Corribus

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Re: Length of limonene
« Reply #7 on: June 08, 2013, 10:43:19 AM »
Well not necessarily.  I got my estimate by assuming 150 pm per C-C bond, multiplying by 70% due to the "angle", and multiplying by 70% again for the second angle if necessary.  Then adding.

Not very scientific. :)
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What men are poets who can speak of Jupiter if he were like a man, but if he is an immense spinning sphere of methane and ammonia must be silent?  - Richard P. Feynman

Offline Nonpolar Bear

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Re: Length of limonene
« Reply #8 on: June 12, 2013, 11:13:26 PM »
Dreiding energy = 34.20 kcal/mol
Volume = 154.76 Å3
Minimal projection area = 33.08 Å2
Min z length = 10.10 Å
Maximal projection area = 46.95 Å2
Max z length = 6.84 Å

Dreiding energy: the energy value of the most stable conformer predicted by Dreiding force field. Dreiding force field is the simplest generic force field suitable for providing accurate geometries of organic, biological, and main-group inorganic molecules.
Volume: The van der Waals volume of the conformer. Learn more on wikipedia.org
Minimal projection radius: the radius of the circumscribed circle (green) of the minimal projection of the current conformer.
Maximal projection radius: the radius of the circumscribed circle (yellow) of the maximal projection of the current conformer.
Min z length: the extent (green arrow) of the conformer perpendicular to its minimal projection area.
Max z length: the extent (yellow arrow) of the conformer perpendicular to its maximal projection area.

http://www.chemicalize.org/structure/#!mol=CC1%3DCCC%28CC1%29C%28%3DC%29C&source=fp

I am pretty sure the 10.10 Å would be what you want.
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Offline curiouscat

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Re: Length of limonene
« Reply #9 on: June 13, 2013, 12:55:25 AM »
Does the absolute value of that energy have any inherent meaning? Or only differences matter.
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