The connectivity definitions will also change. The atoms will be resorted in numerical order. Simply change the numbering in the Order column on the far left, and click the ReOrder button. Use the following procedure to edit the Z-matrix: The Opt columns specify whether each coordinate is to be optimized (O), fixed (F), or scanned (S, S2). The Z-Matrix entry for each atom is defined by the length, angle, and dihedral with respect to previously defined atoms under the Na/Length, Nb/Angle, and Nc/Dihedral angles, respectively. In the Z-matrix editor, the atoms are listed by element and atom index under the Atom column. This is useful for visualizing the index associated with each atom, which is used in specifying the Z-matrix. When the Z-matrix editor is invoked, the index of each atom is displayed in the editor, and the View tool is activated. Z-Matrix Editor Dialog Box Editing the Z-Matrix The Z-matrix editor is invoked with Tools:Edit Z-Matrix.
The WebMO Z-matrix editor allows complete control over the Z-matrix for the current molecule. It is sometimes necessary to edit the default Z-matrix to specify a particular coordinate for scanning or to minimize numerical sensitivity in an optimization. WebMO creates a Z-matrix every time atoms are added or deleted. Z-matrices are not unique (the same geometry can be specified by different Z-matrices), the geometry can be highly sensitive or insensitive to the underlying coordinates (e.g., rings or nearly linear systems), and sometimes they are ill-defined (e.g., a dihedral angle including three linear atoms). While Z-matrices are a very intuitive coordinate system for chemists, they can occasionally cause numerical complications. A Z-matrix specifies molecular geometry relative to other atoms using bond lengths, bond angles, and dihedral angles.
0 kommentar(er)
