Conformers of (-)- and (+)-limonene

User 5fe8796231

27-11-2012 07:26:53

Dear developers,


 


cxcalc conformers 'CC(=C)[C@H]1CCC(C)=CC1' -m 50 | cxcalc dihedral -a 2-4-5-6


All genarated conformers of (-)-limonene have axial isopropenyl group.


 


cxcalc conformers 'CC(=C)[C@@H]1CCC(C)=CC1' -m 50 | cxcalc dihedral -a 2-4-5-6


All genarated conformers of (+)-limonene have equatorial isopropenyl group.


 


Is it true behavior? (version 5.10.3)


 


Alexander

ChemAxon e08c317633

27-11-2012 08:30:21

There is an option called "diversity limit".  Increase it and the conformers will be more diverse.


-d, --diversity       <diversity limit> (default: 0.1)

Example:


$ cxcalc conformers 'CC(=C)[C@H]1CCC(C)=CC1' -m 50 -d 0.5 | cxcalc dihedral -a 2-4-5-6
id Dihedral
1 -175,45
2 -175,41
3 -176,84
4 -175,18
5 -174,21
6 -176,17
7 -173,93
8 81,64
9 74,84
10 76,31
11 -170,27
12 176,24
13 -176,90
14 173,00
15 82,91
16 81,18
17 84,92
18 -173,88
19 81,05
20 -173,45
21 83,87
22 132,46
23 123,87
24 153,36
25 88,14
26 -169,32
27 81,61
28 69,06
29 81,57
30 -177,60
31 144,48
....

User 5fe8796231

27-11-2012 09:34:17

Dear Zsolt,



Thanks!


"-d 0.5" is useful workaround. But even with this option we get different sets of conformers for (+)- and (-)-limonenes.


And the most stable conformers are different:



cxcalc leconformer 'CC(=C)[C@H]1CCC(C)=CC1' 'CC(=C)[C@@H]1CCC(C)=CC1' -e -O 3 | cxcalc dihedral -a 2-4-5-6

ChemAxon e08c317633

04-02-2013 11:52:46










genaev wrote:

"-d 0.5" is useful workaround. But even with this option we get different sets of conformers for (+)- and (-)-limonenes.



 Diversity limit is considered after the conformational analysis as parameter for duplicate filtering. (However the conformational analysis is run until the desired number of filtered conformers produced) Since the conformational analysis is not exhaustive, difference in the two set can be expected.











genaev wrote:

 And the most stable conformers are different:



cxcalc leconformer 'CC(=C)[C@H]1CCC(C)=CC1' 'CC(=C)[C@@H]1CCC(C)=CC1' -e -O 3 | cxcalc dihedral -a 2-4-5-6



The "lowest energy conformer" name is missleading. It returns the lowest energy conformer from a generated conformer set. We will clarify that in the future.