ch1 - Chemistry 140A Fall 2009 (K. Albizati) What is...

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Chemistry 140A Fall 2009 (K. Albizati) 1 What is Organic Chemistry and why is it important? Old definition – chemistry of compounds from living organisms New definition – chemistry of compounds which contain carbon Nature has selected this element as the base element of life processes because it is able to form very strong covalent bonds to itself and to other elements. This enables highly complicated compounds, chemical reactions and chemical reaction pathways. Our bodies are just walking bags of chemicals inter-reacting which allow complex events, like locomotion, vision, speech and thought. If you want to understand the field of medicine, you must understand Biochemistry and Molecular Biology. To understand Biochemistry and Molecular Biology, you must have a firm understanding of Organic Chemistry. Chapter 1 – Structure and Bonding Review – Atoms Most of the mass resides in the nucleus which contains protons and neutrons. The nucleus is surrounded by a cloud of electrons populating orbitals which describe the probability of where an electron may be found. This cloud is about 2Å in diameter which means atoms are about 2Å in diameter. A Molecule is made up of atoms held together by chemical bonds. Why do bonds form? Two atoms will form a bond only if it is energetically favorable --- that is if energy is released when the bond is formed. Everything in life tends toward lower energy states in the long run. So, it makes sense that to break a chemical bond you must put energy into the system. Two main causes of bonding are related to Coulomb’s Law: Opposite charges attract (electrons to protons) Like charges repel (protons repel protons but more importantly electrons repel electrons)
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Chemistry 140A Fall 2009 (K. Albizati) 2 Recall that atoms can be viewed as a positively charged nucleus surrounded by a negatively charged electron cloud e - p + e - p + e - p + p + e - e - e - two atoms approach each other from a distance When two atoms that can favorably form a bond approach one another from a distance the energy starts to decrease due to the favorable attraction of one nucleus to the other atoms electrons and vice versa. At some point an optimum distance is reached with respect to the energy of the system, i.e., the low energy point. This attraction/repulsion follows a familiar curve……. \ 0 Energy Absorbed Energy Released Interatomic distance bond length As 2 atoms approach one another from a long distance, attractive forces start to lower the energy of the system until the atoms get to an energetically optimal distance. If they start to get any closer, the repulsive forces between the 2 nuclei starts to become significant and the energy starts to rise quickly. The bottom of this energy well corresponds to the “bond length”. The energy content of the system is at a minimum, its most favorable state.
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Chemistry 140A Fall 2009 (K. Albizati) 3 The Two Extremes of Chemical Bonding The picture shown earlier is a diagram of a covalent bond – one in which the electrons are shared equally between the two nuclei. At the other
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ch1 - Chemistry 140A Fall 2009 (K. Albizati) What is...

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