The shapes of molecules tend to be controlled by the number of electrons in the valence shell of the central atom. The valence-shell electron-pair repulsion (VSEPR) model provides a simple method for predicting the shapes of such species.
The Cambridge Structural Database contains a wealth of diverse molecular geometries, and provides the ability to visualize and manipulate molecules in three-dimensions. This is vitally important in order to study and understand the shapes adopted by particular molecules.
Tables 9.1-9.3 in your textbook will help you with your predictions.
- To investigate shapes of molecules by analyzing experimental crystal structure data.
- To understand the factors that determine the preferred shape adopted by particular molecules.
- To use the valence-shell electron-pair repulsion (VSEPR) model to predict the shapes of given molecules.
Answer the following questions on the answer sheet as you use the CCDC website.
Part 1: Examining the structures of di-, tri-, and tetrachloro mercury
Consider the following series of molecules: HgCl2, HgCl3-,and HgCl4-2. As we move across the series we are successively adding a Cl to the central Hg atom. For each structure how would you expect the Cl atoms to arrange themselves around the Hg atom?
1. Sketch each of the structures in your lab notebook to show the shape of the molecule you predict.
2. For each of the three structurespredictthe Cl-Hg-Cl bond angles in the structure. Predictions should go in Table 1.
3. Check your answers by inspecting the corresponding crystal structures. The following structures are provided: HgCl2(refcode OKAJOZ), HgCl3-(refcode KUSMAM), and HgCl4-2(refcode KEYZUK). Do the shapes of the experimentally determined structures agree with your predictions?
4. For each of the three structuresmeasurethe Cl-Hg-Cl bond angles in the structure. Record these values in Table 1. What do these angles tell you about the observed geometries? Record the shapes for each structure in Table 1.
Part 2: The VSEPR Model
The valence-shell electron pair repulsion (VSEPR) model is used for predicting molecular shape. The primary assumption of the VSEPR model is that regions of enhanced electron density (i.e. bonding pairs, lone pairs and multiple bonds) take up positions as far apart as possible so that the repulsions between them are minimized.
Thus, in a molecule EXn, there is a minimum energy arrangement for a given number of electron pairs. For example, in HgCl2repulsions between the two electron pairs in the valence shell of Hg are minimized if the Cl-Hg-Cl unit is linear. In HgCl3-electron-electron repulsions are minimized if a trigonal planar arrangement of electron pairs (and thus Cl atoms) is adopted.
1. Consider the structure of hexafluorophosphate, PF6-. With 6 atoms off of the central atom, we would predict that it would form an octahedral shape. Thus the angles between F-P-F should be around 90°. Examine this molecule using the website (refcode WINFAA). Was this prediction correct?
2. Fill out Table 2 with your predictions for the angles between the central atom and two external atoms for each structure. There are no lone pairs of electrons on the central atoms in any of these structures.
3. Now check the CCDC website to see what the angles and shapes are for the actual structures as measured in experiment.
- [BrF6]-: refcode ZAQBIC
- [I3]-: refcode RIKTAG
- In(CH3)3: refcode TRMEIN03
- [BeF4]2-: refcode KIPPEE
- [NH4]+: refcode ACARBM01
- Fe(CO)5: refcode FOJBOV01
- [SbF6]-: refcode FUJLAX
Part 3: Modifications to basic shapes: considering the effect of lone pairs
The molecules you have encountered so far include only bonding pairs. How does the presence of lone pairs affect molecular shape? Consider the molecule water (H2O).
The electron domain shape of water is tetrahedral. There are two sets of lone pairs in this ion, and they will get as far from each other as possible. (Repulsion order is lone pair/lone pair > lone pair/bonding pair > bonding pair/bonding pair.) Thus for water (refcode MUSIMO01) the electron domain shape is tetrahedral but the molecular shape is bent.
1. Measure the angle of the H-O-H angle in water. Is it close to 109.5° like other tetrahedral shapes? What is the actual value and why is it different?
2. Di-bromodimethylselenium (refcode RIZMIW) has 5 electron pairs (4 bonding pairs, and 1 lone pair), so the electron domain shape is therefore trigonal-bipyramidal. According to Table 9.3 in the book, with one lone pair, the molecular shape should be “seesaw.” Examine the 3D structure on the CCDC website. Is it a “seesaw” shape as expected?
Part 4: Further Examples
Apply the VSEPR model in order to predict the geometry of the following molecules. Confirm that your answers are correct by examining the corresponding crystal structures.
1. Comment on how closely the observed bond angles agree with the expected ideal values.
2. Can you account for any deviation from the ideal values?
- Sulfur dioxide (draw Lewis structure): refcode DADXOW
- [CeCl6]2-: refcode CLCAME01
- Dichloro-trifluoromethyl)iodine (3 atoms, 2 lone pairs off central atom): refcode COXYIX
- NH3(draw Lewis structure): refcode KATLAT
- [BCl4]-: refcode PETKAB
- trans-bis(Isothiocyanato)-bis(trimethylphosphine)-nickel(ii) (4 atoms, 2 lone pairs off central atom): refcode BAZSUR
- B(OH)3(Boric acid): refcode JAGREP
- [ClF4]-(draw Lewis structure): refcode ROLSEQ
- Pentaphenoxyphosphorane (5 atoms off central atom): refocde PPHOXP
- [SbBr5]2-(5 atoms, 1 lone pair off central atom): refcode CLPYSB
- tris(Acetonitrile)-trichloro-titanium acetonitrile (6 atoms off central atom): refcode DUDKUI10