Rotational barriers of 1,3-substitute pyridines and benzenes as models for the NAD+/NADH coenzyme

The NAD+/NADH coenzyme is involved in many enzyme-catalysed oxidation-reduction reactions. In order to obtain better insight in the catalytic mechanism of NAD+/NADH dependent dehydrogenases, conformational studies of 1,3-substituted pyridines and benzenes were carried out, using ab initio, semiempirical (AM1 and PM3) and force-field (AMBER 4.0, CVFF and CHARMm21.3) methods. From a comparison with the few known experimental gas-phase data it was found that both force field and ab initio calculated rotational barriers around the C3-C7 bond were too high, whereas AM1 and PM3 calculated barriers were always too low. After introducing appropriate scaling factors, the results of the computational methods could be brought into line with the experimental values. The rotational barriers thus calculated (lower than 5.5 kcal mol-1 allow sufficient flexibility at ambient conditions to permit the necessary adjustment of NAD+/NADH to the enzyme pocket. The AMBER 4.0 force field parameters were accordingly adjusted in such a way as to enable force field simulations on (co)enzymes.