Restraints orientational

The first step of the structure refinement is the appHcation of distance geometry (DG) calculations which do not use an energy function but only experimentally derived distances and restraints which follow directly from the constitution, the so-caUed holonomic constraints. Those constraints are, for example, distances between geminal protons, which normally are in the range between 1.7 and 1.8 A, or the distance between vicinal protons, which can not exceed 3.1 A when protons are in anti-periplanar orientation. 

The starting point of each structure elucidation is the collection of experimental data like NOE/ROE-derived distances, angular restraints from J-couphngs or CCRs and RDCs as orientational restraints (1). 

Our strategy is to incorporate a prolate redox molecule into the hydrocarbon phase of the organized monolayer. Steric restraints imposed by a dose-packed monolayer would presumably force the redox molecule to adopt an orientation parallel to the hydrocarbon tails. Spacing can then be controlled by a short hydrocarbon chain between the redox center and the metal. A class of molecules fitting these requirements are the assymetric 4,4 -bipyridiniums ... 

Dipolar couplings are very powerful restraints for structure determination of biomolecules and the determination of protein-protein or protein-ligand interactions [16]. They depend on the orientation of an internuclear vector, and its distance and the angular dependence is given by the following formula ... 

Since the energy landscape of a simulated annealing procedure in which only dipolar couplings are included tends to have many local minima, these orientational restraints are usually introduced once a preliminary structure has been calculated from NOE data. This procedure has also the advantage of identifying misassigned NOEs and possible conflicts among the various types of input data. 

---