Molecular Structures

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1 E x p e r i m e n t Molecular Structures Objectives To determine the number of valence electrons in molecules. To determine the Lewis structure of molecules. To determine the electron pair geometry and geometry (shape) of molecules. To determine the hybridization of molecules. To build molecular models. To draw three-dimensional picture of models. In the Lab Students will work in pairs. You do not need to write a full lab report for this experiment. Complete the Chem21 worksheet assignment. Waste None Safety Students need to wear goggles for this experiment. 49

2 E x p e r i m e n t 1 1 Molecular Structures A team of researchers looking into developing new drugs are using molecular modeling to see how the new drugs fit into the cell s receptors for this drug. Molecular modeling uses mathematical models to describe molecular properties and behaviors of molecules and generally displays that information in the form of a picture. Before the researchers can build their mathematical models, they need you to help provide some information about the basic structures of some simple molecules. For each of the molecules in the lists below, use your model kit to construct a model of the compounds and to provide the researchers with the following information: Total number of electrons: 1. Valence electrons 2. electrons 3. Non-bonding electrons Number of bonds single, double, triple Hybridization Number of electron groups Electron geometry Molecular geometry 3-D drawing of molecule All information needs to be provided to your supervisor through the Chem21 website, so that it can easily be converted into the mathematical models. Your TA will tell you which list you should report on. Your supervisor has provided the following instructions in regards to using the molecular model kits available to you. Materials Molecular model set with the following parts 16 sp 3 (black) 10 sp 2 (gray) 2 half double bond (blue) 4 double bond (purple) 4 octahedral (metallic gold) 2 linear (orange) 2 trigonal (copper) 1 triple bond (yellow) 2 bond extenders (silver) marker balls Model Sets 12 white (hydrogen) 6 green (halogens) 6 red (oxygen and nitrogen) 2 hot pink (undesignated atoms) These model sets are from Darling Models ( Sets similar to this one and many others are available at a very reasonable price if you are interested in having your own set or if you will be taking Organic Chemistry. Most Organic Chemistry courses will require or recommend that you have a model set. Assembly and Disassembly of Molecular Visions Atoms Darling Models ; pieces shown in Figure.1. Figure.1. From top to bottom, sp 3 piece, trigonal atoms, octahedral pieces, and linear bond. 50

3 E x p e r i m e n t 1 1 Molecular Structures The Atom The tetrahedron may be taken apart by gently spreading the V shaped bonds on one piece, to unlock the teeth, while pushing it out of its locked position. Figure.2. The U shaped center of the atom piece. Each atom consists of a U shaped center as shown in Figure.2, with two or three bonds. The bonds end in a rod or tube. The small teeth at the opening of the U serve to grip the square at the end of the other piece, locking the two pieces to form an atom with bonds. The procedure for joining two atom pieces is shown in the following paragraphs. The Tetrahedral Atom Figure.3. Assembling the tetrahedral atom with bonds. This may be accomplished in one motion with one hand, by placing two or four fingers across the V of one piece and the ball of the thumb on the opposite side. A gentle squeeze will spread the V slightly and push the two pieces apart. In Figure.5, the left hand stabilizes the piece while the right hand spreads both pieces and separates them. Figure.5. Disassembling the tetrahedral atom. The Trigonal-Bipyramid Atom 1. Slide the U openings together at right angles (see image above). 2. Pinch the two pieces together until they click (see image below). 3. Grasp the two pieces against the central U. Pull sharply with the left hand and push sharply with the right hand until there is a second click as shown in Figure.4. Figure.6. Assembly of a trigonal bipyramid. Figure.4. The final step to assemble the tetrahedral atom with bonds. Figure.7. Disassembly of a trigonal bipyramid. 51

4 E x p e r i m e n t 1 1 Molecular Structures A linear bond is joined at right angles with a trigonal atom using the same push-pull motion as for the tetrahedral atom. The trigonal bipyramid is disassembled by slightly spreading the opening of the trigonal atom with the thumbs while using the two fingers of the right hand to pull the linear bond towards the user. Creating Bonds between Atoms Bonds are formed between atoms by joining the rod of one atom with the tube of another. The pieces should be gripped firmly as shown to prevent bending of the rod. The Octahedral Atom Figure.10. Creating bonds between atoms. Figure.8. Assembly of an octahedral atom. The octahedral atom is assembled by pushing the two octahedral pieces together. The octahedral atom is disassembled by placing two fingers of each hand around the horizontal bonds of each respective piece and gently pulling the pieces apart as shown in Figure.9. Instructions courtesy of Darling Models, P.O. Box 1818, Stow, OH or on the web at Electron Groups Electron groups are any electron cloud that acts to repel another group of electrons. This would include single, double, triple bonds as well as lone pairs. The idea of an electron group or cloud is at the heart of the VSEPR model describing the repulsive interactions that result from coulombic forces within atoms. How much of a repulsive force occurs determines the geometry of the molecule (Table.1). Hybridization When atoms come together to form molecules, the orbitals found within the atom are not the same as they were when they were a single atom. Hybridization is the mathematical way in which the changes in the shapes and energies of orbitals are described and occurs most frequently with atoms in the interior of molecules. The type of hybridization that occurs depends on the number of available orbitals participating in the bonding, such that the number of atomic orbitals that goes in equals the number of degenerate hybrid orbitals that come out. Figure.9. Disassembly of the octahedral atom. 52

5 E x p e r i m e n t 1 1 Molecular Structures Table.1. VSEPR geometry. # of e Groups e Pair Geometry # of Lone Pairs Molecular Geometry Ideal Bond Angles 2 linear 0 linear trigonal planar 0 trigonal planar trigonal planar 1 bent tetrahedral 0 tetrahedral tetrahedral 1 trigonal pyramid tetrahedral 2 bent trigonal bipyramidal 0 trigonal bipyramidal 90, 120, trigonal bipyramidal 1 seesaw 90, 120, trigonal bipyramidal 2 t-shaped 90, trigonal bipyramidal 3 linear octahedral 0 octahedral 90 6 octahedral 1 square pyramidal 90 6 octahedral 2 square planar 90 Drawing Molecules in 3-D Use the model you build to help you draw a 3-D drawing of the molecule. Rotate the molecule so that as many bonds and/or lone pairs as possible are in the same plane. Draw this portion of the molecule. Without moving the model, look for bonds projecting out of the plane. Any bonds projected toward you should be indicated with a solid wedge and bonds projected away from you should be drawn with a dashed triangle. See example for water molecule shown on page 56. The lone pairs are in the plane, while one O H bond projects toward you and the other O H bond is projecting out of the plane away from you. Multiple Central Atoms For molecules with more than one central atom, give the electron pair geometry and geometry (shape) around each central atom. Mark the information for each atom so that it is apparent which information goes with which atom. See the second example for more information. 53

6 E x p e r i m e n t 1 1 Molecular Structures Table.2. List of molecules. List 1 List 2 List 3 List 4 1 CCl 4 NH 4 + PO 4 3 CF 4 2 PCl 5 NO 2 NO 3 CO 2 3 SO 3 2 PBr 5 SbF 5 CH 3 Cl 4 CO 3 2 PCl 6 IF 3 AsI 5 5 ICl 2 ICl 3 ICl 2 + BrF 5 6 CHCH NH 2 NH 2 C 2 O CH 3 OH CH 3 OCH 3 (O is bonded to two carbons) CH 3 CHO CHOCH 3 (O is bonded to two carbons) 8 CH 3 CN CH Cl CH 3 COO CH 3 NH 2 9 SF 6 XeF 2 SeF 4 SF 2 10 XeF 4 ClO 3 PCl 3 PF 3 C 6 H 6 (all carbons in the ring, don t forget resonance structures) O 3 (center O, don t forget resonance structures) C 6 F 6 (all carbons in the ring, don t forget resonance structures) O=CN (don t forget resonance structures) 12 C 7 H 14 (all carbons in the ring) C 4 H 8 (all carbons in the ring) C 5 H 10 (all carbons in the ring) C 6 H 6 (all carbons in the ring) 54

7 E x p e r i m e n t 1 1 Molecular Structures For you and your lab partner to work on the same computer, you will need to have two different browsers open. For example, you would need to log onto Chem21 using Internet Explorer while your lab partner logged onto Chem21 using Chrome or Firefox. You and your lab partner MUST enter the same List Number so that you are working on the same list of molecules. Compound 1: CH 3 CH Valence Number of Non- Number of Bonds Points Single Double Triple Points Hybridization /Geometry Electron Groups Hybridization Electron Geometry Molecular Geometry 3D Drawing 55

8 E x p e r i m e n t 1 1 Molecular Structures Examples Valence Number of Non- Compound 1: H 2 O Number of Bonds Points Single Double Triple Points Hybridization /Geometry Electron Groups Hybridization Electron Geometry Molecular Geometry 4 sp 3 tetrahedral bent 3D Drawing 56

9 E x p e r i m e n t 1 1 Molecular Structures Valence Number of Non- Compound 2: CH 3 CH Number of Bonds Points Single Double Triple Points Hybridization /Geometry Electron Groups Hybridization Electron Geometry Molecular Geometry 3 sp 2 trigonal planar trigonal planar 3D Drawing 57

10 E x p e r i m e n t 1 1 Molecular Structures 58

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