Dihedral angles conformational search

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. 

To overcome the inefficiency of Metropolis Monte Carlo, which searches all of the conformational space but does so very slowly, a procedure to move rapidly through the space of local minima has been devised.177 The energy of a random starting conformation is minimized. Then, a random change (selected in the range 0 to 2ir) is made in a randomly chosen dihedral angle, and the... 

Fattorusso and co-workers identified a component of wormwood called artar-borol. Correlation spectroscopy (COSY) and rotating frame nuclear overhauser effect spectroscopy (ROESY) experiments allowed for deduction of four possible diastereomeric structures of artarborol, 2-5. Low energy conformers of 11-14 were obtained through a molecular mechanics (MM) search. These conformers were screened to identify those having a dihedral angle of around 90 for the C-8 and C-9 protons due to a low coupling constant between these protons. Only conformers of 11 and 13 satisfied this criterion. Next, five low energy conformers, two... 

Exhaustive conformational search is a simple and practical way to explore the entire conformational space available to a peptide (or molecular segment) with fewer than a dozen rotatable bonds. A search is performed by systematically varying each rotatable bond in the peptide. Rotations are made about backbone dihedrals (<]) and v) and/or side chain torsions (%). In our work, bond lengths and angles are held rigid. After each rotation, the molecule is checked for steric overlap. If overlap occurs, the conformer is discarded otherwise it is... 

Considering only the conformations with a total energy less than 10 kJ mol" above the lowest energy conformations, the same ensemble of conformations as detected in the structural database searches was found. With this systematic backbone and side chain rotamer search approach, we analysed only 144 structures instead of the 10 structures for a conventional grid search with 36° intervals for 6 dihedral angles. 

In examining the conformational space of models Im, 20m and 21m, we considered only AX or AY isomers, which should be more stable than the other types (see Table 2). The conformational space was searched at the PM3 level using two parameters for the dihedral angles [C(2 )C(1 )C(6 )C(5 )] and [C(3 )C(4 )C(5 )C(6 )]. The structures obtained for the minimum-energy and transition geometries were optimized at the B3LYP/6-3 lG(d) level. 

Optimal filtering was proposed by Altman and Jardetzky (1989) as a heuristic refinement method of structure determination and has also been applied to the dihedral angle space (KoeU et al., 1992). Optimal filtering uses the exclusion paradigm, and during the search aU possible conformations are retained except where they are incompatible with the data. This allows a more systematic search of the allowed conformational space. As in the case of distance geometry, it is a ptire geometric method, and it calculates the mean positions and standard deviations of each atom. The output also needs to be refined to add information fi om the empirical force field. 

As in the previous sub-section, we search for a chair conformation in which there is a dihedral angle of 0° or 180°. Conformation 15, with... 

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