6.03 Shapes of Molecules

Transcription

1 6.03 Shapes of Molecules Predicting hemical Structures a riteria for Molecular Polarity Dr. Fred mega Garces hemistry 100 Miramar ollege Shapes of Molecules

2 Shapes and Sense of Smell At the chemical level, a biological cell is a membrane bound sack filled with molecular shapes interacting in an aqueous fluid. omplex processes in an organism often begin when a molecular Key fits into a correspondingly shaped molecular lock. The key can be a relatively small molecule circulating in a body fluid, whereas the lock is usually a large molecule, known as a biological receptor, that is often found embedded in a cell membrane. The surface of the receptor contains a precisely shaped cavity, or receptor site, that is exposed to the passing fluid. Thousands of molecules collide with the site, but when a molecule with the correct shape (that is, the molecular key) lands on it, the receptor grabs it though intermolecular attractions, and the biological response-begins. Let s see how this fitting together of molecular shapes operates in the sense of smell (olfaction). A substance must have certain properties to have an odor. An odorous molecule travels through the air, so it must come form a gas or a volatile liquid or solid. To reach the receptors, it must be soluble, at least to a small extent, in the thin film of aqueous solution that lines the nasal passages. Most importantly, the odorous molecule, or a portion of it, must have a shape that fits into one of the olfactory receptors sites that cover the nerve ending deep within the nasal passage. When this happens, the resulting nerve impulses travel from these needling to the brain, which interprets the impulses as a specific odor. A The location of olfactory receptors within the nose. A. The olfactory area lies at the at the top of the nasal passage very close to the brain. Air containing the odorous molecules is sniffed in, warmed, moistened, and channeled toward this region.. A blowup of the region shows olfactory nerve cells and their hair like endings protruding into the liquid-coated nasal passage.. A further blowup shows a receptor on one of the endings containing at odorous molecule that matches its shape. This particular molecule has a peppermint odor. Link: ow we smell Shapes of Molecules

3 Shapes of Molecules Lewis Structure representation give no indication of how atoms are arranged in 3-dimensional space. ow can the 3D shape of the molecule be determined from its chemical formula or its Lewis Structure? Importance of 3D chemical Structure: Shape of molecule give rise to the unique property of the molecule. i.e., Sense of smell, taste, the potency of drugs - all depend on the shape of the compounds 3 erione odeine Morphine odeine Morphine eroine Methamphetamine Shapes of Molecules

4 ocaine eurotransmitters are block by cocaine up take in the receptor site Shapes of Molecules

5 VSEPR- Valence Shell Electron-Pair Repulsion Theory An extension of Lewis Structure. Main premise of model- Valence electron pair repel each other Molecule assumes Geometry that minimizes electrostatic repulsion: ccurs when electron pair are far apart as possible. Driving force is the Pauli exclusion principle: 2 electrons with same spin, can't occupy the same space. Electronic Geometry is geometry around central atom in which e- e- repulsion is minimize. AE n (system) Molecular Geometry is geometry around central atom when electron pairs are replace by bonding atoms. A m E n (system) Shapes of Molecules

6 Shapes for Energy Minimization Molecules assumes a geometry that minimize electrostatic repulsion g occurs when e- pair are as far apart as possible Shapes of Molecules

7 VSEPR- Procedural Steps 1) Determine the Lewis Structure. a) Valence electrons for each atom in the structure. b) Determine the number of bonds in molecule and identification the central atom 2) Determine electronic geometry (AE n system) from Lewis structure. a) ount the electron domain (region) around the central atom. b) Arrange electron domain to minimize electron-electron repulsion. ccurs when electron pair are far apart as possible. c) 2-domain g linear, 3-domain g trigonal, 4-domaingtetrahedral 3) Determine molecule geometry (A m E n system) from electronic geometry. a) The geometry is based on the position of the atoms. b) The lone pair electrons are ignored for the molecular geometry. i) ElecGeo-Linear AE 2. MolcGeo-Linear A 2 ii) ElecGeo- Trigonal AE 3. MolcGeo- Trig A 3 or ent A 2 E ii) ElecGeo-Tetrahedral AE 4. MolcGeo-tetr A 4, pyramid A 3 E or ent A 2 E Shapes of Molecules

8 ubs, spokes and Wheels What does a wheel have in common with molecular geometry? A Shapes of Molecules

9 Electron Regions and Spokes Ȯ. : Shapes of Molecules

10 Electron Regions (Spokes?) Ȯ. : Shapes of Molecules

11 VSEPR Table Molecular Geometry Determination Guide Valence Shell Electron-Pair Repulsion Theory (VSEPR) : # e- pr AE n Electronic Geometry ond Pair [oord #] 2 AE 2 E A E 3 AE 3 E Linear E A E Trigonal non-bond AE n m Molecular Geometry 2 0 A 2 A Linear 3 0 A A 2 E 4 0 A 4 A Trigonal A ent 4 AE 4 A E E E E 3 1 A 3 E Tetrahedral 2 2 A 2 E 2 A A Tetrahedral Pyramidal A ent Shapes of Molecules

12 oordination 2: AE 2 ¾ A 2 Two electron dense region around a central atom : # e- pr AE n Electronic Geometry ond Pair nonbond AE n m Molecular Geometry ond angle [oord #] ybrid pair 2 AE 2 Linear E A E A 2 0 A 2 Linear 180 sp Examples e 2 2 Examples: 2 or e 2 Lewis Structure Two Regions AEn An Molecular Geometry of e- density Ȯ. AE 2 A 2 all Stick Space filling Shapes of Molecules

13 oordination 3: AE 3 ¾ A 2 E, A 2 Three electron dense region around a central atom : # e- pr AE n Electronic Geometry ond Pair [oord #] nonbond pair AE n m Molecular Geometry ond angle ybrid 3 AE E A 3 A 120 A E E Trigonal Trigonal sp A 2 E A < 120 ent sp 2 Examples F 3 l 3 2 Examples: Lewis Structure Two Regions AEn An Molc Geometry Space 3 of e- density all Stick filling AE 3 A AE 3 A 2 E Shapes of Molecules

14 oordination 4: AE 4 ¾ A 4, A 3 E, A 2 E 2 Four electron dense region around a central atom : # e- pr AE n Electronic Geometry ond Pair 4 AE 4 E E A E E Tetrahedral [oord #] nonbond pair 4 0 A A 3 E 2 2 A 2 E 2 AE n m Molecular Geometry ond angle A A Tetrahedral Pyramidal ybrid sp 3 < sp 3 < Examples A ent sp 3 Examples: Shapes of Molecules

15 VSEPR Table Shapes of Molecules

16 Examples Shapes of Molecules

17 Examples Shapes of Molecules

18 Examples sp 3 sp 2 sp 3 affeine Shapes of Molecules

19 Shapes of Molecules Examples 3 AZT 3 AZT

20 Example: Ibuprofen Shapes of Molecules

21 Summary Key to determine molecular Geometry Lewis Structure Determine electron domain in structure. Electronic Geometry Establish the AE n system. Molecular Geometry Establish the A m E n system. Determine the molecular geometry Remember that lone pairs in the central atom shapes the geometry but do not take part molecular geometry, i.e. bent shape of water Shapes of Molecules