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Chem 351: Molecular Models

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Chem 351: Molecular Models MOD.1 MOLECULAR STRUCTURES AND MODELS Note: There will be no pre-laboratory quiz for this experiment. However, you should start work on the content. The laboratory period will run more like a tutorial, it’s “open book”, you can work in groups and ask your TA about any concepts you don't understand. This laboratory activity is assessed based on an online Moodle “molecular models” graded activity (30 min. time limit (including 50% technology time)) that is to be completed within 48 hrs of your in-person laboratory session. This activity is essentially the same as one we have successfully used for many years to help students with the visualization of molecules and to learn how to use their model kits. Model kits are a tool that chemists will use to visualize and explain aspects of chemical structure. They are very useful for helping students develop the ability to visualize molecules in 3 dimensions (after all, very few molecules are actually flat). Some students certainly struggle to grasp and manage this stereochemistry without the use of model kits (like the one shown below which it the type we typically recommend). Since we regard model kits as a valuable tool, and a tool a chemist might use, for many years we have allowed model kits to be used during examinations. We also know that many students don’t really know how to use model kits correctly and effectively so this activity tries to show that while also exploring some to the topics related to stereochemistry that many students often struggle with. We always ask UofC Bookstore to stock model kits. While the kits might appear expensive, they are worth the investment to support your studies and can retain most of their resale value. MOD.2 INTRODUCTION This experiment uses a molecular model kit to help address and clarify the theoretical concepts of covalent bonding and molecular structure. Molecular models are designed to reproduce molecular structures in three dimensions, allowing many subtle features concerning shapes of molecules (such as dipole moment, polarity, bond angle, and symmetry) to become clearer. Learning how to use a model kit correctly can help you to realise how they may be able to help you answer questions about molecular structure. Remember that you can use model kits during examinations and assignments to help you answer the questions we might ask. An important fundamental principle is that a molecule tends to position its atoms to give the arrangement with the lowest possible energy. This allows us to predict the shape of a molecule, and the subsequent physical and chemical properties to a very good approximation. In this laboratory period you will learn how to use your model kit to help answer questions and investigate: • the implications of hybridisation on molecular shape • aspects of isomerism • conventions used in 2-D representations of 3-D molecules. • counting types of atoms in a molecule (i.e. looking for equivalent groups, especially H and C) • index of hydrogen deficiency • chirality and chirality centers – R/S nomenclature • Enantiomers and diastereomers – E/Z and cis/trans designation • plane of symmetry, superimposable mirror images, enantiomers • meso compounds In preparation you should review the following concepts and terms from 1st year chemistry, 351 lectures and / or tutorial materials: • hybridisation and atomic orbital shape • alkanes, functional groups, constitutional isomers, conformational isomers • Newman projections; eclipsed/staggered, anti/gauche, potential energy diagrams • cis/trans, E/Z and R/S nomenclature • the implications of hybridisation on shape • structural flexibility • conventions used in the two dimensional representation of molecules and add that all important third dimension. • counting types of atoms in a molecule (i.e. looking for equivalent groups) • index of hydrogen deficiency MOD.3 MOLECULAR MODELS The three dimensional shape of molecules results from the three-dimensional arrangements of their constituent atoms, and as such are often difficult to visualise in terms of a two-dimensional diagram on a page or computer screen. For this reason chemists often make use of molecular structure models (either physical models or computer models). In addition to the qualitative appreciation of molecular structure, scale models can be used to make approximate quantitative measurements. For this experiment you should use your own set of models if you have them. We have a small number of the Molymod Molecular Models that can be borrowed. From the Molymod Models we shall use the following components: ATOMS Colour Atom No. of Holes Bond Angle Black C 4 109 28' White H 1 Blue N 4 109 28' Red O 4 109 28' Green Cl 2 Orange Br 1 Atoms are joined together by inserting the appropriate bond into the holes in the atoms. The single short rigid bond should be used to represent sigma () bond. Two curved pieces should be used to represent a double bond and three curved pieces to represent a triple bond. Sometimes more than one sensible structure may be drawn for a particular molecular formula. In this case the arrangement of atoms must be determined experimentally. The different arrangements are said to be "ISOMERS" of each other. Depending upon the relationship of the structures, the pair of structures can be subcategorised as different types of isomers. This is schematically represented by the isomer tree diagram on the following page and is an important part of the materials covered by this experiment. At each branch in the tree, a “yes/no” question is asked in order to decide what path to follow. The many different possible arrangements of the same set of atoms is the main reason for the enormous number (over a million) of known organic molecules. These different arrangements are possible since carbon has a singular ability to form very strong bonds with itself (as carbon chains or carbon rings), hydrogen atoms, or heteroatoms. MOD.4 Do the compounds have the same molecular formulae ? NO Not isomers YES Isomers Do the compounds have the same connectivity ? NO YES Constitutional Stereoisomers O Can the compounds be OH interconverted by rotation about single bonds ? (skeletal, positional, functional) NO YES Configurational Conformational H C H H H Is the isomerism at a 3 H H H tetrahedral center ? NO H YES H CH3 H3C CH3 Geometric Optical Are the compounds non-superimposable mirror images ? NO YES Diastereomers Enantiomers Cl H Cl Cl H C H C 3 H 3 Cl H H CH3CH2 CH2CH3 H H CH H3C H C H C 3 3 Br 3 Br ISOMER FLOWCHART This figure helps you identify the type of isomer between a pair of structures. Note that some classes are not always mutually exclusive (e.g. technically geometric isomers and conformational isomers are also diastereomers). In general, it is usually best to use the more specific term. Start at the top and ask each the question about the pair of molecules you are trying to define. Based on your YES or NO answer, follow the corresponding path to the next question, or the end point and the isomer answer. MOD.5 EXPERIMENTAL PROCEDURE "Tutorial" work in small groups, open book. Work through the following tutorial questions using your model kit, text book etc. and record your answers, talking to your TA as you work through them. After the end of the laboratory period, you will need to complete an individual online Moodle assessment. CARBON: Tetrahedral - sp3 carbon Since four single bonds are formed, the carbon atom is situated at the centre of a tetrahedron. This is the largest number of -bonds carbon can form and hence the carbon is termed a "saturated carbon". Construct an ethane molecule with the medium straight bonds and confirm that the carbon atoms are both at the centre of a tetrahedron. H H H C C H ethane H H The molecule is flexible; grasp one carbon atom and view the molecule along the C-C axis. Now rotate the front C atom about the C-C bond for a full 360 rotation. The relative positions of the hydrogen atoms on the different carbon atoms are constantly changing, and every different relative arrangement is called a "CONFORMATION" or they can be described as "CONFORMATIONAL ISOMERS" or "CONFORMERS". There are two extreme conformations, and these have important names. staggered conformation eclipsed conformation It is often useful to inspect interactions between groups on adjacent atoms by viewing along the C-C bond. This particular projection, represented above, is known as the "Newman Projection". (Groups attached to the front carbon intersect at the centre of the circle; those attached to the rear carbon project only as far as the edge of the circle). Another convention very frequently used for the diagrammatic representation of three-dimensional molecules is the wedge-hash diagram. bond in the plane of the paper bond projecting behind the plane of the paper bond projecting in front of the plane of the paper Therefore, a staggered conformation of ethane could be represented in a wedge-hash diagram as: MOD.6 H H H C C H H H At room temperature the rotation about C-C bonds takes place many thousands of times per second, however the different conformations do not have identical energies. The staggered and eclipsed conformations are the two extreme energy conformations since the electrostatic repulsion of the pairs of electrons in bonds (or lone pairs) when they are spatially in close proximity destablises the eclipsed conformation (note there are other explanations of the reasons for the difference in the energies of the two conformations). Thus, the staggered conformation is the more stable conformation. This destabilization effect tends to get larger as the groups involved get larger. In real terms, that means that it is at a minimum for two H atoms.
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