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

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

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
....

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

 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.

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.