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Pictures of the Day CH320M/CH328M Fall 2012

8-31-12
 Atoms are surrounded by electrons and we use the computer to plot molecules to reflect where the electrons are. Above are three different computer images of the methane molecule CH4. The image on the upper left shows the C and H atoms as small balls connected by sticks, i.e. the bonds. This is a nice picture, but does not really show where the electrons are, since they are found farther away from the atomic nuclei. Shown in the middle above is a mesh surface under which the electrons can be found. On the upper right is shown a solid surface, color coded by atom type. This type of representation is referred to as a space filling model. The space filling models are a better way to think about molecules, since they give a realistic picture of molecular size, electrons and all. Refer to the atom type chart to remind yourself which atoms have which colors.
 The most important concept in chemistry is that some atoms are more electronegative than others, in other words, they “hog” more of the electrons in a covalent bond. Thus, electronegativity answers the most important question in chemistry. Electron density distribution in a molecule can be quantitatively displayed in color coding using so-called electrostatic potential surfaces calculated by computer. Shown above are three simple diatomic molecules. On the left is H2, with a single bond between the H atoms. Since two H atoms have the same electronegativity, they share the electrons evenly. This is depicted as a green color on the electrostatic potential surface plot. In the middle is the F2 molecule. Again, since both the F atoms of the bond have the same electronegativity, the electron density is shared evenly between the two atoms and the electrostatic potential plot is green. On the right is the H-F molecule. Fluorine is much more electronegative than hydrogen, so the majority of electron density resides on the fluorine atom. High electron density around the F atom is depicted as the red color on the electrostatic potential surface above. The hydrogen atom has less electron density, depicted as blue color to indicate the absence of electron density. This type of covalent bond, with the electrons shared unevenly is called a polar covalent bond (difference in electronegativities of bonded atoms is greater than 0.5). The polarity of the bond is quantified by using the vector quantity of dipole moment, represented by the arrow symbol above the bond. Note that since electron density has negative charge, the fluorine atom has a partial negative charge (d-) leaving a partial positive charge (d+) on hydrogen.
The polarity of bonds in molecules predicts the properties and reactions of molecules. For example, methane, CH4, has only non-polar bonds. As a result, there are no significant partial charges in the molecule, so molecules in a sample of methane interact only weakly. With only very weak interactions, not very much energy is required to dissociate the molecules (turn the sample into a gas), so the boiling point of methane is very low, -166°C. On the other hand, water has very polar O-H bonds, with the majority of bonding electron density residing on the O atom. This electron distibution puts a partial negative charge on the O atom, and partial positive charges on the H atoms. The result is that the molecules are attracted to each other (opposite charges attract) with the H and O atoms from different molecules in contact with each other as shown above. This interaction, referred to as hydrogen bonding, means that the molecules in a sample of water stick together relatively well, so a great deal of energy is required to dissociate the molecules (turn to steam). At 100°C, the boiling point of water is 266°C higher than that of methane! This huge difference in properties for these two molecules of the same size can only be understood in the context of bond polarity, namely the presence of partial positive and negative charges, which itself is simply knowing where the electrons are! You will learn how reactions of molecules will also be predictable by knowing which bonds are polar, since these are usually the reactive bonds in organic molecules.

BOND ANGLES AND SHAPES OF MOLECULES
The Valence-Shell Electron-Pair Repulsion (VSEPR) model of molecular structure assumes that areas of valence electron density around an atom are distributed to be as far apart as possible in three-dimensional space.


- When using the VSEPR model, lone pairs of electrons, the two electrons in a single bond, the four electrons in a double bond, and the six electrons in a triple bond are each counted as only a single area of electron density.
- Four areas of electron density around an atom adopt a tetrahedral shape with bond angles near 109.5°, such as in methane, CH4.

- Three areas of electron density around an atom adopt a trigonal planar shape with bond angles near 120°, such as in formaldehyde, H2C=O.

- Two areas of electron density around an atom adopt a linear shape with bond angles near 180°, such as in acetylene or CO2.

- The VSEPR model predicts shape but does not explain why the electrons are located where they are.
Thus, it is only a useful model and not a theory.

Click on each category to see animated GIFs of examples of molecules with the indicated geomtry. The final category is of a hybrid molecular containing different atomic geometries. You must be able to simply look at a molecular structure, and be able to predict the geometry around each atom using the VSEPR ideas. Later, you will learn to think of this in terms of hybridized atomic orbitals. Note that we have broken up the different categories onto different pages to avoid a very long download for a single page.

Tetrahedral Geometry (4 Areas of electron density)

Trigonal Planar Geometry (3 Areas of electron density)

Linear Geometry (2 Areas of electron density)

Hybrid Geometry (Different atom types)

Shown above are the Molecular Dipole Moments for some common molecules. Molecular dipole moments are the vector sums of the individual bond dipole moments in a molecule. Being able to predict in a qualitative way what a molecular dipole moment looks like is important for this class because it is requires the synthesis of all the ideas about electronegativity and molecular three-dimensional shapes that we have discussed thus far.