International Journal of Nonlinear Analysis and Applications

Calculation of cartesian internal molecular coordinates

Document Type : Research Paper

Authors

1 Department of Statistics, Faculty of Basic Science, University of Kurdistan, Sanandaj, Iran

2 Department of Biophysics, North Tehran Branch, Islamic Azad University, Tehran, Iran

Abstract

For the solution of a variety of problems which concern molecular structures, it is often necessary to calculate the Cartesian coordinates of the atoms from a set of geometric parameters. In order to fully utilize symmetry operations in the calculation of Cartesian coordinates, it is necessary to construct the molecule within a primary coordinate system. This is accomplished by introducing a set of four dummy atoms, by which unit vectors are specified. One atom is placed at the origin and the others at unit distances along each of the three Cartesian axes. in this framework according to the attachment procedures described below. The atoms of a molecule are positioned through the use of a secondary coordinate system. A base coordinate system is defined by the positions of three atoms, numbered 1, 2, and 3. The origin is taken at Atom 1, the negative x-axis passes through Atom 2, and Atom 3 lies in the first or second quadrant of the xy plane. In order to define the angles, the following conventions are adopted: for a general atom j, the atom to which it was attached is called $j^{\prime}$, and the atom to which $j^{\prime}$ was attached is called $j^{\prime \prime}$, and the atom to which $j^{\prime \prime}$ was attached is called $j^{\prime \prime \prime}$. Two special cases where these definitions do not suffice are atoms attached to Atom 1 and to Atom 2. Where j is attached to Atom 2, Atom 1 is taken as $j^{\prime \prime}$ and Atom 3 as $j^{\prime \prime \prime}$. Where j is attached to Atom 1, Atom 2 is taken as $j^{\prime \prime}$ and Atom 3 as $j^{\prime \prime \prime}$. The program described is being used extensively for specifying molecular structures for electron diffraction investigations. Other current uses are in programs for x-ray diffraction of polymers, for estimating magnitudes of energy via postulated force field functions, and in molecular orbital calculations.

Keywords

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International Journal of Nonlinear Analysis and Applications
Volume 15, Issue 4
April 2024
Pages 217-220
  • Receive Date: 17 February 2023
  • Revise Date: 19 May 2023
  • Accept Date: 27 May 2023