Z-matrix (chemistry)

In chemistry, the Z-matrix is a way to represent a system built of atoms. A Z-matrix is also known as an internal coordinate representation. It provides a description of each atom in a molecule in terms of its atomic number, bond length, bond angle, and dihedral angle, the so-called internal coordinates, although, it is not always the case that a Z-matrix will give information regarding bonding since the matrix itself is based on a series of vectors describing atomic orientations in space. However, it is convenient to write a Z-matrix in terms of bond lengths, angles, and dihedrals since this will preserve the actual bonding characteristics. The name arises because the Z-matrix assigns the second atom along the Z-axis from the first atom, which is at the origin.

Z-matrices can be converted to cartesian coordinates and back, the information content is identical. They are used for creating input geometries for molecular systems in many molecular modelling and computational chemistry programs. A skillful choice of internal coordinates can make the interpretation of results straightforward. Also, since Z-matrices can contain molecular connectivity information (but do not always contain this information), quantum chemical calculations such as geometry optimization may be performed faster, because an educated guess is available for an initial Hessian matrix, and more natural internal coordinates are used rather than Cartesian coordinates.

Example

The methane molecule can be described by the following cartesian coordinates (in Ångströms):

C 0.000000 0.000000 0.000000 H 0.000000 0.000000 1.089000 H 1.026719 0.000000 -0.363000 H -0.513360 -0.889165 -0.363000 H -0.513360 0.889165 -0.363000

The corresponding Z-matrix, which starts from the carbon atom, could look like this:

C H 1 1.089000 H 1 1.089000 2 109.4710 H 1 1.089000 2 109.4710 3 120.0000 H 1 1.089000 2 109.4710 3 -120.0000

External links

* [http://www.shodor.org/chemviz/zmatrices/babel.html Z-Matrix to Cartesian Coordinate Conversion Page]
* [http://search.cpan.org/~itub/PerlMol-0.35_00.ppm/lib/Chemistry/InternalCoords/Builder.pm Chemistry::InternalCoords::Builder] — Perl module to build a Z-matrix from cartesian coordinates.