Ch7ComputerAssistedMolecularModelingUsingSpartan - Ch 7...

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7-1 Ch. 7 Computer Assisted Molecular Modeling Objectives To use computer calculations to enhance understanding and limitations of VSEPR theory To use computer calculations to find lowest energy conformations of small molecules To use calculations to predict the dipole moments and charge distributions within a molecule To use computer modeling software to visualize the interaction between biologically relevant macromolecules Introduction In this lab, we will extend our discussion of molecular shape using computationally assisted modeling. You will learn to operate a molecular modeling program called Spartan . This program will help you build complicated molecules more easily than you could with a model kit. In addition, Spartan uses a quantitative description of the chemical concepts you have learned, such as Valence Shell Electron Pair Repulsion (VSEPR) and polarity to predict the lowest energy (and therefore most favorable) shape for each molecule. Using Spartan , you will examine trends in bond lengths and bond angles to refine your understanding of molecular geometry. In addition, Spartan will predict the electron density and partial charge of atoms within the molecules you are exploring. As you will see later in your chemistry courses, understanding the charge distribution in a molecule is important for understanding its chemical reactivity and for understanding its non-covalent interactions. Finally, you will discover that molecules can change their shapes by rotating around a single bond! This leads to molecules having many varying geometric conformations in three- dimensional space. As you can imagine, this fact makes it very difficult even for the best chemists in the world working with the best computer programs to predict the shapes of large molecules such as proteins.
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Chapter Seven 7-2 How are computer modeling programs used in chemistry and biochemistry? As you have seen already, the shape of a molecule is particularly important for its biological function. Consider the example of the drug aspirin. Substances similar to aspirin have been used for thousands of years to treat pain and swelling. It was not until the 1970’s that scientists discovered that aspirin binds to a protein called cyclooxygenase (COX). This enzyme normally binds to a molecule found inside your cell membranes called arachidonic acid (Figure 1) and converts it into prostaglandins, which can cause pain and swelling. Scientists determined the three-dimensional structure of COX and found a binding pocket inside. We now know that aspirin also targets this binding pocket, even though it does not look very much like arachidonic acid! OH O O O Aspirin Vioxx Arachidonic Acid O S O O H 3 C O OH Figure 1: Structures of Simple Compounds of Interest to Industry People had a cure for pain many years before we understood the way that aspirin works in our bodies. However, chemistry and biochemistry have helped drug companies to solve a major problem with aspirin: it can cause severe stomach irritation, especially with prolonged use. Patients who are in chronic pain need a medicine they can take every day that will not damage
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Ch7ComputerAssistedMolecularModelingUsingSpartan - Ch 7...

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