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2: Introduction to Organic Structure and Bonding II

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  • While organic and biological chemistry is a very diverse field of study, one fundamental question that interests all organic chemists is how the structure of an organic molecule determines its physical properties. We will look more closely at the nature of single and double covalent bonds, using the concepts of 'hybrid orbitals' and 'resonance' to attempt to explain how orbital overlap results in characteristic geometries and rotational behavior for single and double bonds, as well as bonds that have characteristics of somewhere in between single and double. Then we will move on to a review of the noncovalent interactions between molecules - Van der Waals, ion-ion, dipole-dipole and ion-dipole interactions, and hydrogen bonds - and how they are manifested in the observable physical properties of all organic substances.

    • 2.1: Prelude to Organic Structure and Bonding II
      To understand why sperm oil has properties that made it both a useful industrial lubricant for humans and an effective buoyancy control and/or sonic lens for a hunting sperm whale, we first have to understand the nature of both the forces holding each wax molecule together and also the forces governing the noncovalent interactions between one wax molecule and all the others around it which determine physical properties such as viscosity, melting point, and density.
    • 2.2: Valence Bond Theory
      Valence bond theory is most often used to describe bonding in organic molecules. In this model, bonds are considered to form from the overlap of two atomic orbitals on different atoms, each orbital containing a single electron. In looking at simple inorganic molecules such as molecular hydrogen (H2) or hydrogen fluoride (HF), our present understanding of s and p atomic orbitals will suffice. In order to explain the bonding in organic molecules, however, we will need to introduce hybrid orbitals
    • 2.3: Molecular orbital theory- conjugation and aromaticity
      Valence bond theory does a remarkably good job at explaining the bonding geometry of many of the functional groups in organic compounds. There are some areas, however, where the valence bond theory falls short. It fails to adequately account, for example, for some interesting properties of compounds that contain alternating double and single bonds. In order to understand these properties, we need to think about chemical bonding in a new way, using the ideas of molecular orbital (MO) theory.
    • 2.4: Resonance
      These two drawings are an example of what is referred to in organic chemistry as resonance contributors: two or more different Lewis structures depicting the same molecule or ion that, when considered together, do a better job of approximating delocalized pi-bonding than any single structure. By convention, resonance contributors are linked by a double-headed arrow, and are sometimes enclosed by brackets:
    • 2.5: Non-covalent interactions
      To understand the nature of noncovalent interactions, we first must return to covalent bonds and delve into the subject of dipoles. Many of the covalent bonds that we have seen – between two carbons, for example, or between a carbon and a hydrogen –involve the approximately equal sharing of electrons between the two atoms in the bond. In these examples, the two atoms have approximately the same electronegativity.
    • 2.6: Physical properties of organic compounds
      Virtually all of the organic chemistry that you will see in this course takes place in the solution phase. In the organic laboratory, reactions are often run in nonpolar or slightly polar solvents such as toluene (methylbenzene), dichloromethane, or diethylether.
    • 2.7: Solutions to Chapter 2 exercises
    • 2.P: Problems for Chapter 2