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Computational Chemistry Tutorial: 3. Building Molecules with MOLDEN

Building Molecules with MOLDEN

Ability to build molecular models with computers in an important skill for chemists who use computer-aided drug design. This tutorial illustrates how to edit and build molecular structures with MOLDEN. The last part of this tutorial illustrates how MOLDEN can be used to optimize molecular structures and prepare molecules for more advanced calculations.

MOLDEN allows building molecules using the connectivity description known as the Z-matrix. In the Z-matrix notation, the atoms in the molecule are defined by bond a length to one of the preceding atoms, by a bond angle made to two preceding atoms and by a dihedral angle made to three preceding atoms. MOLDEN's Z-matrix editor is explained in more detail at http://www.cmbi.ru.nl/molden/zmat/zmat.html.

Start MOLDEN by typing molden ethanol.pdb into Unix shell on the workstation. Two windows, the graphical area and the Molden Control appear. Turn on StickColor and try if the molecule looks better with Shade on or off.

Hit the ZMAT Editor button to open the Z-Matrix editor. Answer Yes if prompted to create a new Z-matrix. Inspect the Z-Matrix by clicking on each atom and observe how the selected atom is highlighted in the graphical window. It also works in reverse: clicking on an atom in the 3D structure will highlight this atom in the Z-matrix. Now click on the bond distances fields in the Z-Matrix editor and notice how the two connected atoms are highlighted. You can measure arbitrary distances easily using the Distance tool in the Molden Control panel. The Zmatrix editor in Molden is pretty simple to learn. The few rules that you should keep in mind when working with Z-matrixes are:

Oftentimes you have a structure that you want to modify slightly. For example, you may notice that more hydrophobic analogs of a drug are more potent and wish to create a higher homolog of your lead compound by extending or branching the alkyl chain. MOLDEN is well suited for such task. Please note that it is recommended to assign a SYBYL force field to the modified molecule every time before writing out a new structure as MOL2 file even if you are not planning to optimize the molecule. Follow the instructions below to create isopropanol (2-propanol) by modifying the structure of ethanol.


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Tutorial by Dr. Kalju Kahn, Department of Chemistry and Biochemistry, UC Santa Barbara. ©2006-2007