Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Unit 3 How do we predict properties? 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. Chemistry XXI M1. Analyzing Molecular Structure Predicting properties based on molecular structure . M2. Considering Conformations Predicting properties based on spatial conformations. M3. Characterizing Ionic Networks Predicting properties based on ion charge and size. M4. Exploring Electronic Structure Predicting properties based on electron-configurations. Unit 3 How do we predict properties? Chemistry XXI 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. The Challenge Modeling How do I explain it? Chemistry XXI 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. The specific conformations that molecules adopt depend on intra and intermolecular interactions. How can we explain and predict the conformation that these macromolecules have? Dynamic Structures Chemistry XXI 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. Click The most stable conformations are determined by the nature of the interactions within the molecule and between the molecule and its surroundings. Conformational Analysis Let’s consider the molecule of ethane C2H6. Chemistry XXI How do you explain the variations in Ep? Which conformation is most stable? Steric Effects Chemistry XXI 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). Let’s Think Chemistry XXI Which of these conformations of “butane” (C4H10) is the most stable? Draw an schematic representation of the most stable conformation of “isooctane” (C8H18). Macromolecules Chemistry XXI 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 Chemistry XXI Polymers Polymers, natural or synthetic, are composed of repeating structural units (monomers) connected by covalent bonds. Monomer Polymer 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 H C N O Chemistry XXI Nylon Polyethylene Cl F Teflon Cellulose Design Chain length and branching in polymer synthesis is used to control properties such as rigidity, elasticity, and thermo-plasticity. Chemistry XXI Let′s think! In which ways could the properties of these types of polymeric materials differ? Let’s Think 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 (H2O will stick to them), and which ones are likely to be dissolved by water (H2O will be able to separate the chains)? What would happen if we use acetone or hexane? Let’s Think Mixing the polymer with other substances is also a common way to alter and control its properties. Chemistry XXI Consider Polyvinyl alcohol (PVA) Predict how the properties could change when mixing with a Boric Acid. Proteins Proteins are natural polymers made by the combination of smaller molecules called amino acids (monomers). Amino Acid Chemistry XXI Amine Carboxyl Peptide bond Primary Structure Every protein has a unique sequence of amino acids or “primary structure.” Backbone Chemistry XXI Side chain Backbone and side chain polarities determine the 3D structure that proteins adopt. Let’s Think Analyze the “geometry” and “polarity” of the backbone. Assign partial charges (d+ and d-) to the different atoms. What types of IMFs can exist within the backbone itself or with another chain? Hydrogen Bonding Chemistry XXI 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. Helices and Sheets Chemistry XXI H-bonding between regions in the backbone of the protein chain leads to regions of ordered structures: secondary structure. Alpha helix Beta sheet Folding Interactions between elements of the side chain (residues) cause the protein to “fold” into its final conformation. Chemistry XXI Side chain Will all the residues interact with each other? Which interactions are stronger? Let’s Think Consider this “folded” protein. 3 Chemistry XXI 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? Similar with Similar 3 Chemistry XXI 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. Chemistry XXI Let′s apply! Assess what you know Let′s apply! Solvent Effects Chemistry XXI 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 Let’s explore the validity of your predictions: Go to: http://www.chem.arizona.edu/chemt/C21/sim Chemistry XXI Folding 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) Chemistry XXI Identify one topic of your interest in which the ideas discussed in this module are relevant. Considering Conformations Summary Chemistry XXI Molecules are dynamic structures that are in constant movement. This movement may allow them to take different 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. Considering Conformations Summary Chemistry XXI 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. Polymers are composed of repeating structural units (monomers) connected by covalent bonds. Composition, structure, and functionality affect the conformations that they adopt. Nylon Myoglobin 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?