Molecular Visualization
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1 Molecular Visualization Visualize Molecular Dipoles Even if a molecule contains bond dipoles, it might not have a molecular dipole due to symmetry. Spartan can demonstrates the separation of charges in a molecule and make it easier to decide whether a molecule has a molecular dipole. Procedure pen PCSpartan from the Desktop Choose File>ew Build the molecule CCl 3 using the atomic pieces on the palate to the right Choose Setup>Calculations o Ensure that the charge on the molecule is neutral Choose Setup>Surfaces o Click Add o Choose Surface: Density o Choose Property: Potential Close the Surfaces window Choose Setup>Submit to start the modeling calculation Wait for the calculation to finish Choose Display>Surfaces o Click the yellow box to display the surface The surface shows two properties of the molecule. First, the shape of the surface maps out the shape of the electron distribution around the nuclei. It shows the true shape of the molecule. The colors on the surface are related to the patterns of charge in the molecule. Regions of partial positive charge (δ+) show up as blue. Click on the colored surface and make the surface transparent using the 1
2 menu on the bottom right of the screen to prove that the hydrogen in CCl 3 has a partial positive charge. Areas of partial negative charge (δ-) show up red, as around the chlorine atoms. ne side of the CCl 3 molecule has a net positive charge and the opposite side has a net negative charge. This type of charge separation indicates a bond dipole. The positive end of the molecular dipole corresponds to the location of the hydrogen atom, the negative end of the dipole is between the three chlorine atoms. ow build the molecule CCl 4 and contrast it with CCl 3. Choose Build>Add Fragment Change the molecule to CCl 4 Check the Setup>Calculations and Setup>Surfaces options to ensure that they are the same as you had set in the calculation for CCl 3. Choose Setup>Submit View the surface once the calculation is complete There is no way to find a side of the CCl 4 molecule that has a net charge relative to the opposite side. The CCl 4 molecule therefore has no molecular dipole. ow draw three-dimensional sketches of the Lewis structures for the following molecules and ions in your notebook. 1 C 2 4 S 2 7 C CS 2 5 C C-CCl 3 3 CS 6 C 2 Cl 2 9 S 3 Using the Lewis structures as a guide, build each molecule or ion in Spartan and perform a calculation as you did for CCl 3. Don t forget to minimize the energy after building each molecule. Be sure to indicate the proper charges in the Setup>Calculations window. View the potential surfaces and decide whether a molecular dipole exists. In your notebook, indicate the direction of the dipole, if it exists, on the sketch of the molecule. 2
3 To build some of these molecules, you may need to use the Expert menu in the builder to place single-bonded oxygen atoms onto open bonds on a central atom. Visualize Lewis Bases Visualizing a Lewis base uses many of the same skills you used to discern molecular dipoles. A Lewis base is likely to provide one of its pairs of electrons to a Lewis acid. In another way of looking at Lewis basicity, a Lewis base attacks a Lewis acid with a particularly active pair of electrons. The location of a very active pair of electrons can be visualized on the electron density surface as a particularly negatively charged area, which shows up as red in our version of the software. Procedure pen PCSpartan from the Desktop Choose File>ew Build the molecule C 2 using the atomic pieces on the palate to the right Choose Setup>Calculations o Choose Calculate>Single Point Energy o Ensure that the charge on the molecule is neutral Choose Setup>Surfaces o Click Add o Choose Surface: Density o Choose Property: Potential Close the Surfaces window Choose Setup>Submit to start the modeling calculation Wait for the calculation to finish Choose Display>Surfaces o Click the yellow box to display the surface 3
4 Locate the area on the density surface with the greatest negative charge. The atom which this region surrounds (the oxygen atom) is the most basic atom in the molecule. ow build the following molecules and ions. Be sure to indicate the proper charges in the Setup>Calculations window. View the potential surfaces and locate the most basic atom in the molecule. In your notebook, sketch the molecule and label the most basic atoms. 1 C 3-5 C 3 C C - 7 S 3 4 acetyl chloride C 3 Cl 8 indigo Visualize Lewis Acids Visualizing a Lewis acid is somewhat different from visualizing a Lewis base. Think about itthe Lewis acid has a place on the molecule that can accept more electrons, an opening for new electrons to come in. Chemists have a term for the next place on a molecule that can fit a new electron: the LUM (Lowest Unoccupied Molecular rbital). The location of Lewis acid site in a molecule can be visualized as the atom that is surrounded by the greatest amount of the LUM. Try this procedure to see what this means. Procedure pen PCSpartan from the Desktop Choose File>ew Build the molecule C 2 using the atomic pieces on the palate to the right 4
5 Choose Setup>Calculations o Choose Calculate>Single Point Energy o Ensure that the charge on the molecule is neutral Choose Setup>Surfaces o Click Add o Choose Surface: LUM Close the Surfaces window Choose Setup>Submit to start the modeling calculation Wait for the calculation to finish Choose Display>Surfaces o Click the yellow box to display the surface Locate the atom that is surrounded by the largest amount of the LUM. It should be the carbon atom. The carbon atom in formaldehyde (C 2 ) is the most Lewis acidic atom in the molecule. ow build the following molecules and ions. Be sure to indicate the proper charges in the Setup>Calculations window. View the potential surfaces and locate the most acidic atom in the molecule. In your notebook, sketch the molecule and label the most acidic atoms. 5
6 1 C 3 -CCl 3 4 CS 2 C 3 -B 2 5 S 3 3 acetyl chloride C 3 Cl 6 indigo Question: In your notebook, sketch the molecule 2 -C 2 -=C- 2. Use Spartan to find the most Lewisacidic carbon atom, the most Lewis-basic nitrogen atom, and determine if the molecule has a molecular dipole. Indicate your answers on the sketch. Show your Spartan evidence to the instructor. 6
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