Conformation, molecular dihedral angle

You can often use experimental data, such as Nuclear Overhauser Effect (NOE) signals from 2D NMR studies, as restraints. NOE signals give distances between pairs of hydrogens in a molecule. Use these distances to limit distances during a molecular mechanics geometry optimization or molecular dynamics calculation. Information on dihedral angles, deduced from NMR, can also limit a conformational search. 

Molecular mechanics (MM) calculations have been employed for determining dihedral angles and to establish a comparison with values calculated from coupling constants, during conformational studies of tricyclic and tetracyclic quinolizidine alkaloids. The MM results had to be treated with care, as they sometimes predicted ring conformations different to those supported by experimental data <1999JST215>. 

The only known complex with a (RSb)5 ligand is cyclo-[ i-(Me3SiCH2Sb)5-Sb1,Sb3- W(CO)5 2].125 The molecular structure is depicted in Fig. 25. The antimony ring adopts a slightly distorted envelope conformation with a Sb4/Sb3 dihedral angle of 129.1°. The metalcarbonyl units are in 1-3 positions trans to each other. 

The idea that the most stable conformation of 42 and 43 may be helical is supported by a molecular mechanics calculation using Discover III with a PCFF force held (MSI, ver. 3.00). Figure 4.31a shows the total energy of a 42 oligomer with 21 Si repeat units as a function of the Si-Si-Si-Si dihedral angle. The respective P- and M-helical conformations of 42 near dihedral angles of 160° and 200° are more stable than a trans planar conformation of... 

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