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   maestro - building molecules
Chemical Information Laboratory

Maestro - Building Molecules

The Build panel for Maestro (Menu: Project->Build...) starts with the Fragments option displayed. Clicking on any of the fragments in the list and then clicking in the Workspace will draw the fragment. Clicking on any atom in the workspace will transform it into that fragment. A good way to draw an alkane is to click Methyl in the fragments window, click in the Workspace to draw methane, and then click on hydrogens to transform them into methyl groups.

The next set of options in the Build panel are Atoms & Bonds. These allow you to Draw molecules by clicking on the screen, each new atom being joined to the last. Rings can be created by clicking on existing atoms, and multiple bonds by retracing bonds. Structures drawn this way are flat, but atoms can be moved forward and backwards (along the z-axis) by clicking Move-Z and Move+Z.

The small picture below shows the screen after five atoms have been drawn. The purple box shows the position to which a new bond will be made when there is another mouse left-click in the Workspace. This could be to create a new atom to make hexane, to close the ring to make cyclopentane, or to make a double bond (pentene).

The structure which has just been drawn has no hydrogen atoms. These can be added by going to the Hydrogen Treatment section. The illustration shows that "All-atom" is selected, so clicking on "Apply current treatment to all atoms" will fill all spare valencies with hydrogen. Some force-fields prefer to use united-atoms, and this is another of the options available.

The Adjust section allows distances, bond angles and dihedral angles to be adjusted by first selecting them and then moving the mouse with the middle button held down.

Complicated molecules can be hard to understand because too many atoms are shown on the screen. This problem can be addressed by using the Display section to show only a selection of the atoms available.

The Properties section is used to adjust formal charges, etc. This can be confusing because charges are not automatically displayed in the workspace. In order to see the charges and other atomic labels, it is necessary to select the Atom Labels panel (Menu: Display->Atom Labels...).

The Atom Labels panel allows many properties of each atom to be displayed on the structure in the workspace, including atomic charge, element type, atom number (Maestro automatically numbers all of the atoms in every structure) and so on.

Once a molecule has been built using the Build panel, it can be further manipulated in Maestro, or be used for energy calculations with MacroModel or Jaguar.

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department of chemistry University of Cambridge