Lab Manual- Experiment 7

Lab Manual- Experiment 7 - Experiment 7 Molecular Modeling...

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E x p er i m e n t 7: M o l ec ul ar M o d e l i n g BACKGROUND READING: Wade Chapter 3; Solomons Chapter 4. Pay close attention to the definitions of Torsional Strain, Steric Strain, Angle Strain, and 1,3-Diaxial Interactions . INTRODUCTION: The approximate shapes of molecules can be visualized with the aid of molecular models. These might be physical model kits with solid pieces that represent different types of atoms or molecules, or virtual model kits in which computer software is used to calculate and represent the three dimensional shapes of molecules. In this exercise, molecular model kits will be used to build the three-dimensional structures of molecules and illustrate the conformations of acyclic compounds as well as various derivatives of cyclohexane. Figure 1. Proteus Molecular Models Proteus® molecular modeling kits will be used for this exercise. These model kits have pre- formed pieces that represent sp 3 , sp 2 and sp hybridized atoms. They are designed to approximate the bond angles within molecules and to give some indication of spatial relationships between different groups on a molecular structure. Black colored pieces are meant to represent carbon atoms, red pieces are used for oxygen and the blue pieces are designed to represent nitrogen. In addition, there are other colored extensions that are used as framework pieces representing atoms such as hydrogen, fluorine, chlorine and iodine. A unique feature of these Proteus ® model kits is that each of the bonding arms has a locking mechanism that allows you to manipulate and change the conformations of the models that you build without them coming apart. This is especially important when working with the chair conformations of cyclohexane derivatives, allowing you to see the impact that a simple conformational change (ring flip) can have on the relationship between substituents on the cyclohexane ring Figure 2. Some Assembled Molecular Models DEFINITIONS: It will be helpful here to define a few terms related to symmetry since you will have to examine the symmetry properties of the molecular models that you construct. A P l a n e of S y mm e t r y divides a geometric figure or molecule into two equal halves so that one half of the shape is the mirror image of the other. A plane of symmetry is also referred to as a mirror plane and examples of planes of symmetry of a variety of geometric shapes and molecules are illustrated below:
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C l A l Cl Cl A Ce n t e r of S y mm e t r y is a point about which a molecule or three- dimensional structure can be rotated so that all parts of the molecule or structure equidistant from that point become identical. For example, each point on the surface of a sphere is equidistant from its center, which is also a center of symmetry. In another example, there are a variety of ways in which the bipyramidal figure illustrated here might rotated about the point at its center to give an image that cannot be distinguished from the original structure. A
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Lab Manual- Experiment 7 - Experiment 7 Molecular Modeling...

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