Unit 5- Module 1

Unit 5- Module 1 - Module 1 Unit 5 Analyzing Structure John...

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Module 1- Unit 5 Analyzing Structure John Pollard University of Arizona If you consider the current theory of evolution, it is amazing to think that over 4 billion years ago, all that existed on the planet were simple, small molecules. At some point during the first billion years of the existence of earth, these simple molecules began to engage in chemistry that produced the larger molecules which became the building blocks of life. What were the factors that drove the formation of complex molecules like amino acids from simple species such as CO 2 , CH 4 , H 2 , N 2 , O 2 and H 2 O (all thought to be present during this formative era)? In order to begin thinking about these early processes, we need to be able to explain and make predictions about the likelihood of a chemical process. In this analysis, we must consider the directionality and extent of chemical reactions ( thermodynamics ) as well as the rate and mechanism by which they happen ( kinetics ). To express both the thermodynamic and kinetic factors of any chemical process, it is common to draw a “reaction coordinate” diagram. As we will see, these diagrams can be expressed in different ways, but to start we will be using graphs that plot the potential energy of the substances vs. the “reaction coordina te”. The reaction coordinate axis tracks the molecular orientation and structural aspects of a successful reaction. These orientations are plotted against the potential energy of the system as the reaction progresses from reactants to products. The thermodynamic aspects of the reaction are expressed in the relative differences in potential energy of the reactants and products. The kinetic aspects are expressed in the activation energy barrier (E a ) that separates reactants and products. In the beginning of this unit, we will focus on the thermodynamic aspects of reactions. We will start by considering the factors that control the directionality and extent to which chemical processes occur. A
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primary characteristic that must be considered when evaluating the extent to which a reaction happens is the relative stability of the reactants and products. How can we predict the relative stability of reactants and products in a reaction? To do so, there are two primary items that must be considered; energetic and entropic factors. Energetic Factors and Stability The energetic stability of a substance is essentially a measure of its potential energy. To evaluate the potential energy of a substance, we must consider the structural units that make it up (ions, molecules) and the features that define these units such as chemical composition, intra-molecular bond strengths, charge distribution, intermolecular forces and the overall state of matter the structural units exist in.
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