Generation and best fitting of molecular models

Abstract

Two programs useful in crystallographic computation are described. The first permits the calculation of cartesian atomic coordinates from molecular interatomic distances and bond angles. The second obtains the best fit between two molecular models as a function of three rotation angles, by searching the smallest weighted sum of the distances between corresponding atoms.

Determination of the molecular packing in the crystal of coumarin by means of potential-energy calculations

“…The atomic coordinates in A of the molecule at p'x=~,2 =~,3=0 ° and tx=ty=0 A were generated (Gavuzzo, Pagliuca, Pavel & Quagliata, 1972) and are reported in Table 1. The coefficients of the van der Waals potentials in the generalized form" a exp ( -br) ...... cr -6 V(r) -ra are listed in Table 2.…”

Some uses of a best molecular fit routine

“…For some years we have been using in this laboratory a least-squares best molecular fit program (BMFIT); apparently at least one other laboratory has independently developed a similar routine (Gavuzzo, Pagliuca, Pavel & Quagliata, 1972). The routine, and some uses to which it has been put, are described here because they do not seem to be widely known.…”

Crystal structure and van der Waals energy study of the 2:1 inclusion compound between deoxycholic acid and norbornadiene

“…The refinement was resumed including NBD as found in the potential-energy calculations, except that very slight adjustments were made to the atomic coordinates of the model by using the 'molecules best fitting' program (Gavuzzo, Pagliuca, Pavel & Quagliata, 1972) to obtain the best overlap with the peaks of the difference synthesis.…”