Molecular Modeling 1

Molecular Modeling 1 - Molecular Modeling 1 Classic...

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Molecular Modeling 1: Classic Molecular Modeling Author: J. M. McCormick* Last Update: August 18, 2005 Introduction Dalton’s Atomic Theory revolutionized chemistry by explaining chemical properties in terms of small, indivisible pieces of matter called atoms that are linked together to form polyatomic species (both ions and molecules). As chemists explored the properties of the polyatomic species, it became clear that they have size and shape and that shape is particularly important in explaining their physical properties and why and how chemical reactions occur. A summary of some of the commonly observed polyatomic shapes (also known as structures or geometries) are shown in Table 1 arranged by the number of atoms around the "central atom." These are idealized structures; real molecules seldom exhibit these idealized shapes. However, the ideal shapes are good starting points toward understanding how the spatial arrangement of atoms in polyatomic species affect their properties and chemistry. Number of Atoms Around “Central Atom” Shape 1 Linear 2 Linear Bent
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Trigonal planar 3 Trigonal pyramidal T-shape Tetrahedral
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4 Square planar Bisphenoid (see-saw) 5 Trigonal bipyramidal Square pyramidal
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6 Octahedral Table 1. Summary of idealized common structures of molecules and polyatomic ions. Chemists often find it convenient to build a model of a molecule or polyatomic ion to help them visualize its actual shape, much in the same as an architect will build a model of a building to help him or her see its structure. The complexity of the model a chemist will use is dictated by the answer sought. And the explanation as to why a molecule or polyatomic ion has a certain structure depends on the theory used. The simplest model is a Lewis dot structure which gives us an approximate picture of the bonding interactions that hold the polyatomic species together. It does not, however, give an accurate picture of structure or the electrons' energies. Because Lewis dot structures assume that all valence electrons are paired and a chemical bond requires two electrons, it is limited to simple compounds of the main group elements (s and p blocks) and some transition metal ions (those with d 0 and d 10 configurations). A Lewis dot structure can be used to obtain a rough picture of structure by using Valence Shell Electron Pair Repulsion (VSEPR) theory.
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