7 - Chapter 7 Molecules as objects representing molecular...

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1 Chapter 7 – Molecules as objects: representing molecular structure with models Molecules are a collection of point masses of fixed positive charge; this positive charge creates a field of force that binds the negatively charged electrons. More than 99.9% of the atom’s mass is contained in the nucleus yet the diameter of the nucleus is 10,000 times smaller than the diameter of the space occupied by the electrons. In other words, the vast majority of space assigned to a molecule is virtually empty, occupied only by the tiny mass of the electrons. When describing geometric aspects of molecular structure, we need to know the position of the atoms. The Cartesian x , y , and z coordinates of an atom’s nucleus provide a useful means of pinpointing its location in space since the majority of the atom’s mass can be found there. This ability to quantitatively describe the position of an atom using nuclear coordinates gives precise meaning to van’t Hoff and le Bell’s notion 1 of molecular geometry – the idea that atoms occupy a definite arrangement in three dimensional space, thereby serving as attachment points for structural connections. Organic molecules are three-dimensional (3D) objects, not the 2D line-angle drawings that we write on a piece of paper. The ability to interpret line-angle drawings as 3D objects is a learned skill. Just like any other skill, you will need to practice if you expect to become proficient at the task. To facilitate the development of this skill, students must take an active role in the learning process, by using physical models (i.e., plastic molecular model kits) and / or software that aid 3D visualization. These visualization aids will help you understand the relationship between a molecule's three dimensional structure and its two dimensional projection. Instructions for using your molecular model kit Your molecular modeling kit contains spheres that represent the hydrogen atoms, colored polyhedra that represent the non-hydrogen atoms, cylindrical pegs that represent bonds, and balloon-shaped sheets that represent orbitals. The polyhedra display a series of holes intended to accommodate a varied combination of bonds at angles that mimic atomic geometries. Make sure you use the holes that are angled at the desired geometries for organic chemistry (180 ˚ for linear; 120 ˚ for planar; 109 ˚ for tetrahedral). The cylindrical pegs you choose for bonds should be of the same length. A detailed set of instructions and information regarding interpretation of scale is available online: http://www.hgs-model.com/manual/1000/1000.html 3D Visualization with computer software MarvinSketch is an advanced, Java-based chemical editor for drawing chemical structures, queries and reactions. It has many editing features and is “chemically aware,” meaning that it warns the user of possible drawing errors. The software is free and plugs into nearly all available modern web browsers. You can find MarvinSketch at the URL listed below: ( http://www.chemaxon.com/demosite/marvin/index.html ).
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This note was uploaded on 10/02/2008 for the course CHEM 232 taught by Professor Vanderdonk during the Fall '08 term at University of Illinois at Urbana–Champaign.

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7 - Chapter 7 Molecules as objects representing molecular...

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