1. Chemistry XXI Unit 3 How do we predict properties? M1. Analyzing Molecular Structure Predicting properties based on molecular structure. M4. Exploring Electronic Structure Predicting properties based on electron-configurations. M3. Characterizing Ionic Networks Predicting properties based on ion charge and size. M2. Considering Conformations Predicting properties based on spatial conformations. The central goal of this unit is to help you develop ways of thinking that can be used to predict the physical properties of chemical compounds based on their submicroscopic structure.

2. Chemistry XXI Unit 3 How do we predict properties? Module 2: Considering Conformations Central goal: To explain and predict the physical properties of macromolecular compounds based on nature and strength of the interactions between different parts of a molecule, or between different molecules.

3. Chemistry XXI The Challenge Large molecules (macromolecules) have properties that depend on how their different geometric centers orient with respect to each other in space. A small change in this conformation may alter the properties or vital function that the molecule has. How can we explain and predict the conformation that these macromolecules have? Modeling How do I explain it? The specific conformations that molecules adopt depend on intra and intermolecular interactions.

4. Chemistry XXI Dynamic Structures Molecules are dynamic structures that are in constant movement even in solid systems. For molecules with more than one geometric center, this movement may allow them to take different conformations. The most stable conformations are determined by the nature of the interactions within the molecule and between the molecule and its surroundings. Click

5. Chemistry XXI Conformational Analysis Let’s consider the molecule of ethane C 2 H 6. How do you explain the variations in E p ? Which conformation is most stable?

6. Chemistry XXI Steric Effects When atoms in a molecule get too close together as parts of the molecule vibrate or rotate, electric repulsions between electrons may hinder some conformations and favor others (Steric effects). Steric effects lead to conformations in which repulsions are minimized; this lowers the potential energy of the molecule (more stable).

7. Chemistry XXI Let’s Think Draw an schematic representation of the most stable conformation of “isooctane” (C 8 H 18 ). Which of these conformations of “butane” (C 4 H 10 ) is the most stable?

8. Chemistry XXI Macromolecules Conformational analysis is of central importance in explaining and predicting the properties and function of molecules with hundreds of atoms, such as synthetic and natural polymers. For example, the main macromolecules in our body, nucleic acids and proteins, are large molecular chains that adopt very specific structures which determine their function. DNA Myoglobin

9. Chemistry XXI Polymers Polymers, natural or synthetic, are composed of repeating structural units (monomers) connected by covalent bonds. MonomerPolymer

10. Chemistry XXI Synthetic Polymers Length, size (branching), and functionality affect the conformations that polymer chains can adopt and how they interact with themselves and other chains in a given material. PVC Polyethylene Teflon Nylon Cellulose Cl H C F N O

11. Chemistry XXI Chain length and branching in polymer synthesis is used to control properties such as rigidity, elasticity, and thermo-plasticity. Design Let′s think! In which ways could the properties of these types of polymeric materials differ?

12. Chemistry XXI Changing functionality will alter not only how the polymer chains interact with themselves, but also with other materials. Consider three solid surfaces made with the following materials. Which of them are likely to be wetted by water (H 2 O will stick to them), and which ones are likely to be dissolved by water (H 2 O will be able to separate the chains)? What would happen if we use acetone or hexane? Let’s Think

13. Chemistry XXI Mixing the polymer with other substances is also a common way to alter and control its properties. Predict how the properties could change when mixing with a Boric Acid. Consider Polyvinyl alcohol (PVA) Let’s Think

14. Chemistry XXI Proteins Proteins are natural polymers made by the combination of smaller molecules called amino acids (monomers). AmineCarboxyl Peptide bond Amino Acid

15. Chemistry XXI Primary Structure Every protein has a unique sequence of amino acids or “primary structure.” Let’s Think Analyze the “geometry” and “polarity” of the backbone. Assign partial charges (  + and  -) to the different atoms. What types of IMFs can exist within the backbone itself or with another chain? Backbone and side chain polarities determine the 3D structure that proteins adopt. Backbone Side chain

16. Chemistry XXI Hydrogen Bonding The stronger interactions are hydrogen bonding in the same or in different chains. Although hydrogen bonds are not “real” bonds and are weaker than covalent bonds, there are so many of them within a single protein that they determine the 3-D structure of these macromolecules.

17. Chemistry XXI H-bonding between regions in the backbone of the protein chain leads to regions of ordered structures: secondary structure. Helices and Sheets Alpha helixBeta sheet

18. Chemistry XXI Folding Interactions between elements of the side chain (residues) cause the protein to “fold” into its final conformation. Will all the residues interact with each other? Which interactions are stronger? Side chain

19. Chemistry XXI Let’s Think 3 + Consider this “folded” protein. What types of intermolecular forces are present in this system Arrange these interactions from strongest to weakest Why do you think the protein is folded in this particular way?

20. Chemistry XXI Similar with Similar Although there are attractive interactions between all types of residues (or particles), energy is minimized when parts, or particles, with interactions of similar strength are close together. 3 +

21. Chemistry XXI Assess what you know Let′s apply!

22. Chemistry XXI Solvent Effects Proteins do not exist isolated in our body. They are surrounded by water or by lipids in cell membranes. - Discuss how you would expect this protein to fold if you immerse it in a) water; b) lipid (oil). Justify your reasoning. Let′s apply!

23. Chemistry XXI Let’s Apply Let’s explore the validity of your predictions: Explore and explain the effect of changing the solvent and the type of amino acids on protein folding. The simulation allows you to change the nature of the solvent and of each amino acid in the chain: Charged Polar (Hydrophilic) Non-Polar (Hydrophobic) Go to: http://www.chem.arizona.edu/chemt/C21/sim Folding

24. Chemistry XXI Identify one topic of your interest in which the ideas discussed in this module are relevant.

25. Chemistry XXI Summary Molecules are dynamic structures that are in constant movement. This movement may allow them to take different conformations. Considering Conformations The most stable conformations are determined by the nature of the interactions between different parts of the molecule (intramolecular interactions) and between the molecule and its surroundings.

26. Chemistry XXI Summary Conformational analysis is of central importance in explaining and predicting the properties and function of molecules with hundreds of atoms, such as synthetic and natural polymers. Considering Conformations Nylon Myoglobin Polymers are composed of repeating structural units (monomers) connected by covalent bonds. Composition, structure, and functionality affect the conformations that they adopt.

27. Chemistry XXI For next class, Investigate what a polymer is and identify different types of natural and synthetic polymers. In which ways are the properties of very large molecules different from those of smaller molecules?