0303
- Hyesu Jang
1. Issue with amide cic-trans preference
Cis-trans preference is expressed as a one-fold cosine function in torsion term. To properly describe cis-trans preference of N-methyl acetamide, the k2 value(spring constant of one-fold cosine function. f(theta)= k1*(1+cos(2*theta-180)) + k2*(1+cos(1*theta))) of t70c([#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]) seems to be around 1.5 kcal/mol.
Initial guess of the k2 is 2.0kcal/mol, which seems a pretty reasonable value, but it decreases during the fitting to QM amide torsional energy profiles. (in fitting v1.3.0)
2. test fitting (individually)
| SMILES | cis E - trans E (kcal/mol) | t70c k2 | AM1 WBO |
|---|---|---|---|---|
scan1 | CC(=O)NC1=CNC=C1 | 2.0252 | 1.9056 | 1.0329 |
scan2 | CC(=O)NC1=CC=CN1 | 3.8560 | 1.8408 | 1.0087 |
scan3 | CC(=O)NC1=COC=C1 | 1.6432 | 1.8122 | 1.0185 |
scan4 | CC(=O)NC1=CC=CO1 | 0.8685 | 1.2958 | 0.9979 |
scan5 | CC(=O)NC1=CSC=C1 | 1.8339 | 1.7347 | 1.0224 |
scan6 | CC(=O)NC1=CC=CS1 | -0.2350 | 1.5908 | 1.0053 |
N-methyl acetamide | CC(=O)NC | 1.9518 | 1.6562 | 1.0830 |
#95 | CC(=O)Nc1[nH]ccn1 | 7.9196 | 1.9979 | 0.9788 |
#461 | CC(=O)Nc1ccccn1 | 1.9692 | 2.0716 | 1.0355 |
#711 | CC(=O)Nc1ccccn1 | 4.4138 | 1.8254 | 1.0015 |