Drawing Orbitals

The latest update to ChemDoodle (v3.2) introduces a new toolbar, the Orbital toolbar. In addition to creating figures of structures, reactions and spectra, you can now create images of orbitals. Many different styles are provided and currently, ChemDoodle has the largest selection of orbital types of any chemical drawing tool.

The Orbital Toolbar

The Orbital toolbar provides quick access to the orbital drawing tools. Using the orbital tools is very simple. When selected, just hover over an atom or bond and click to add the orbital. Orbitals will lock to standard angles and lengths, but the shift modifier key will allow you to place an orbital of any size aligned to the axes, while the alt modifier key will allow you to place an orbital at any size and angle. Orbitals can also be placed directly into a document without first hovering an atom or bond.

Each orbital type can be rendered with several different fill styles. They can be empty, solid or gradient filled. Some orbital types have available different variations on the fill patterns.

There are currently 10 different orbital shapes available. They include atomic orbitals, hybrid orbitals and bonding orbitals.

Atomic Orbitals s px|y|z dxz|yz|xy|x2-y2 dz2 fxz2|xy2|x(x2-3y2)|y(3x2-y2) fz3

Hybrid Orbitals sp3 sp lobe

Bonding Orbitals σ π

ChemDraw File Compatibility

All orbital types that are inclusive between ChemDoodle and ChemDraw are both read from and written to ChemDraw files (CDX and CDXML). The following two images are of a complex file containing many orbitals created in ChemDraw. The left image is of the file opened in ChemDraw while the right image is of the file opened in ChemDoodle. All orbital types, orientations, sizes, colors and other properties are also read from and written to ChemDraw files. Note that ChemDoodle displays page margins while ChemDraw does not.

ChemDraw File Containing Orbitals

ChemDoodle Opening the CDX File Containing Orbitals

Orbital Visual Specifications

Apart from the color, border line widths and border line styles, there are a couple visual specifications specific to orbital shapes. They can be set in the Preferences window, under the Visuals tab, in the Shapes subtab.

1. Length Multiplier – This number slider will set the default length from the center of the orbital to the extent, to help maintain standard sizes while placing them. This setting is in bond lengths, and by default it is set to 1 bond length.
2. Stroke Shaded Lobes – This on/off checkbox with set whether shaded filled orbital lobes will also be surrounded with a border.

All together, ChemDoodle is one of the most thorough software tools available for creating chemical graphics and media. ChemDoodle works on Windows, Mac OS X and Linux, and a free trial is provided to anyone. Try it out today!

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