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363. CYCORD: Program for Calculating the Coordinates
of Atoms in Mono- and Polycyclic Molecules When the
Dihedral Angles Are Not Known
by D.V.S. Jain, S. Singh and V. K. Gombar, Department of Chemistry, Punjab University, Chandigargh, India The underlying method fixes the reference axes-frame with atom 1 (I-1) at the origin, atom 2 (I) on the x- axis, and atom 3 (I+1) in the X-Y plane. Then the coordinates of the atom I+2 in a new frame of axes in which origin has been shifted to atom I+1 followed by the rotations around z-axis to make y(I) = 0 and x(I) +ve around y-axis to make z(I) = 0 and x(I) +ve around z-axis to make z(I-1) = 0 and Y(I-1) +ve are given by x(I+2) = D(I+1) cos A(I+1) y(I+2) = D(I+1) sin A(I+1) cos TILT(I) z(I+2) = D(I+1) A(I+1) sin TILT(I) whereD(I+1) is the distance between atoms I+1 and I+2 A(I+1) is the angle at atom I+1 subtended by the atoms I and I+2, TILT(I) is the approximate dihedral angle of the lines between I-1, I and atoms I+1, I+2. This set of coordinates is then transferred back to the reference frame of axes. These calculations are carried out for the values of I varying from 2 to N, so that coordinates of atoms 4 to N and 1 and 2 (now named 1' and 2') are known afresh. The present iterative method modifies the dihedral angles in a way that the sum of squares of distances between 1,1' and 2,2' (DIST) minimizes. For a given conformation, the dihedral angles of the substituents are exactly known, hence the calculations of their coordinates are trivial. In the case more than one ring are present, the atoms of the second ring which are directly attached to the first ring are considered as the substituent to the first ring. The rest of the atoms of the second ring are treated like those of the first ring. FORTRAN Lines of Code: 463 Recommended Citation: D.V.S. Jain et al., QCPE 11, 363 (1978). |