Chemdraw Orbitals

[Jon Followell]

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.

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.

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.

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!

Generating 3D representations of molecular orbitals (MOs) is much trickier than simply obtaining the atomic coordinates, but nevertheless, there are a few commercial (and therefore expensive) programs which can do this. Desktop computer packages, such as ChemDraw 3d and HyperChem can both calculate the MOs corresponding to different energies for simple molecules using semi-empirical (such as Extended Hckel theory) methods. More sophisticated mainframe programs, such as Gaussian, MolPro and GAMESS can also do so. The iso-surfaces of these orbitals can then be displayed and manipulated in 3D in the window. However, the MO data from these programs cannot be saved out into a format that can be read by any of the existing web browser plug-ins, which means that displaying interactive MOs on a web page is still not straightforward. However, static gif or jpg images can be captured from the screen, as shown in Fig.15.

Fig.15. The lowest unoccupied MO (LUMO) of acetone, calculated using the HyperChem program. This MO was created very simply in the program - only 4 mouse clicks were required, and no knowledge of the theory behind the calculation was needed! Within the program window, the structure and MOs can be rotated in 3D, different iso-surfaces can be chosen, and the degree of transparency can also be changed, but unfortunately these data cannot be saved into formats readable by other viewing programs. As well as orbitals, HyperChem can also calculate and plot iso-surfaces for total spin density, total charge density and the electrostatic potential around the atoms.

Apple QuickDraw 3d viewer is available both as a stand-alone package and as a browser plug-in, and will display interactive structures of molecules with orbitals. However, it will not load standard 3D coordinate files (such as pdb or mol), and accepts only the QuickDraw 3D Metafile format (3dmf). But, if you have a suitable computer package that can calculate orbitals, such as Gaussian, GAMESS or CACHE, and have the facility to save these data as 3dmf files, then it a compact method of storing and representing 3D orbital data on the web.

Perhaps the best and easiest method of generating 3D orbitals is available as an online java applet located at the University of Erlangen in Germany, as part of their chemical VRML services [10]. The applet is called OrbVis, and produces VRML output which can be displayed and manipulated on-line in a suitable VRML plug-in. The reader must first draw the molecule using a java chemical drawing applet (see Fig.17). The MOs are then calculated, and the reader selects one of the available MOs, which is then displayed in the window of a VRML plug-in, such as Cosmoplayer or Cortona (see Fig.18). Again, the molecule and orbitals can be manipulated in real-time in the window, but unfortunately, the data cannot be saved for subsequent analysis or re-displaying off-line.

Fig.17. Screenshot of the molecule editor applet window from the VRML services page at the University of Erlangen [10], which was originally developed by Peter Ertl at Novartis [11].Fig.18. Screenshot of an orbital for the nitrobenzene molecule, calculated by the OrbVis applet and then displayed in a VRML viewer.

Sometimes we need to display atomic type orbitals in a schematic way to visualize simple concepts. The molecular orbitals or even localized orbitals are then overly complex. Simple examples are the ChemDraw-style orbitals, which are used to rationalize reactions in organic chemistry. Now, is it possible to obtain similar orbitals, but in 3D?

We will now use PySCF to calculate the NAOs. As we are only interested in the schematic form of the orbitals, the small STO-3G basis set will be sufficient. First we construct the PySCF Mole object from the RDKit Mol object.

We can now compute the NAOs from the 1-st order reduced density matrix. Note that we are here actually calculating the pre-orthogonal NAOs (PNAOs) that are even more local that the NAOs. We the write the PNAOs to cube files - these files can be quite large, ca 3 MB each.

I am a results-oriented biochemist with over a decade of experience performing research and process development spanning microbiology, protein chemistry, and formulation development. My background includes extensive work in high-throughput assays, analytical chemistry, microbiology, project coordination, and lab management.

Have you ever wondered how to make professional, easy-to-understand figures of molecules for presentations or publications? While several programs exist for this purpose, ChemDraw is like the Swiss Army knife of chemical sketching programs that most chemists and journals use to prepare figures.

ChemDraw is quite intuitive for new users. If you understand skeletal formulas, you can use ChemDraw! The program includes a plethora of customizable options, like setting bond lengths and widths, changing the font and size of individual atoms, and changing the colors of atoms and bonds. You can include stereochemistry and rotate molecules in all axes. Molecular charges, atomic orbitals, and individual electrons are also included.

Speaking of mass spectrometry, the Mass Fragmentation tool shows the fragment molecular weights as you select possible fragmentation points. Simply drag the fragmenting tool over the bond you want to break to get exact masses of each fragment.

Newer versions of ChemDraw have a direct link to SciFinder, which is a powerful addition to this already versatile software. Simply select a structure or reaction and click the SciFinder button. From there, you can explore experimental properties, published literature and patents, and synthesis routes.

Through many trials, and lots of error, I learned that there are many considerations for mass spectrometry that might not be obvious to you as a molecular biologist. Common contaminants, even in small quantities, can mask important peaks in your mass spec data and have a huge impact on the final results.

Resonance is the movement of electrons from one atom to another via the pi system. It is also the single most stabilizing feature in an organic molecule because it delocalizes charge. Delocalization of charge means spreading charge out over multiple atoms so that each atom has a partial charge (or no charge) instead of a full charge.

Resonance structures represent alternate electron configurations of a single molecule. Resonance structures differ from each other in the placement of electrons, but not in the position of the atoms. Resonance structures are shown with double headed arrows in between each resonance contributor, and then surrounding these structures with brackets. Multiple resonance contributors represent added molecular stability.

These are the 2 resonance structures of ethanoate. They can also be called resonance contributors because they both contribute to the resonance hybrid. A resonance hybrid is a combination of the different resonance structures in a molecule.

If you could observe this molecule in real life, you wouldn't be able to see a shorter C-O double bond and a longer C-O single bond whose O has more electrons than the other. Ethanoate is resonating too fast for us to be able to tell the C-O bonds apart. What we would see is a hybrid of the 2 resonance structures, and we can represent that by drawing a dashed line along the path that the electrons resonate, bracketing the entire molecule, and indicating that the molecule has a full formal charge. Both of resonance structures contribute equally to the resonance hybrid because they are isoenergetic, meaning they are the same energy (and therefore have the same stability), so each oxygen will have an equal partial negative charge.

In order to resonate, the atoms in question must be sp2 hybridized. If an atom with lone pairs is in a situation where it can resonate, it will choose to be sp2 instead of sp3 in order to resonate. sp3 orbitals on adjacent atoms cannot resonate. While they can share electron density to some extent through hyperconjugation, the complete transfer of an electron from one atom to another cannot happen between sp3 orbitals. There are 4 sp3 orbitals that have bond angles of about 110. sp3 orbitals on adjacent atoms are too far away from each other due to their bond angles. But when 2 adjacent molecules are both sp2, their 3 sp2 orbitals are planar, and the p orbital is perpendicular ot the plane of the bonds. This means the 2 p orbitals on adjacent sp2 hybridized atoms can be parallel, and communicate electrically (share electrons).

Aromatic Compounds are extremely stable because of their enhanced resonance. As you can see from the rest of this page, Delocalization of electrons is a stabilizing feature. Molecules that fit into the requirements of huckel's rule can delocalize their electrons so well that it is even more stabilizing than regular resonance. Huckel's rule states that planar, cyclic, conjugated systems containing 4n+2 electrons in the pi system exhibit aromatic stabilization.

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