Definitions
fig16.jpg





























Use of the aufbau principle to arrive at the electronic configurations of the elements

Element Configuration Valence electrons
H  1s1 1
He  1s2 2
Li  1s2 2s1 1
Be  1s2 2s2 2
B  1s2 2s2 2p1x 3
C  1s2 2s2 2p1x 2p1y 4
N  1s2 2s2 2p1x 2p1y 2p1z 5
0  1s2 2s2 2p2x 2p1y 2p1z 6
F  1s2 2s2 2p2x 2p2y 2p1z 7
Ne  1s2 2s2 2p2x 2p2y 2p2z 8

Examples of the most common bonding patterns found in organic compoundsa

Atom Valence Positively charged Neutral Negatively charged
C 4
N 5
O 6
halogen 7
aThe formal charge on the central atom depends on the number of bonds (shared pairs) and the number of nonbonding electrons
















Electronegativities

We often use electronegativities as a guide in predicting whether a given bond will be polar and the direction of its dipole moment. The Pauling scale is the system of electronegativities most commonly used by organic chemists. The Pauling scale is based on bonding properties, and it is useful for predicting the polarity of covalent bonds. Elements with higher electronegativities generally have more attraction for the bonding electrons. The next slide shows the Pauling electronegativities for some of the important elements in organic compounds. Notice that the electronegativities increase from left to right across the periodic table. Nitrogen, oxygen, and the halogens are all more electronegative than carbon; sodium and lithium are less electronegative. Hydrogen's electronegativity is similar to that of carbon, and we usually consider C-H bonds to be nonpolar.

The electronegativities of some of the elements found in organic compounds
















Resonance Hybrid

A molecule or ion for which two or more valid Lewis structures can be drawn, differing only in the placement of the valence electrons. These Lewis structures are called resonance structures.

Major contributors: the more important, lower energy structures
Minor contributors: the less important, higher energy structures

When a charge is spread over two or more atoms by resonance, it is said to be delocalized and the molecule is said to be resonance stabilized.


Covalent binding

  • Bonding that occurs by the sharing of electrons in the region between two nuclei.
  • For a covalent bond to form, two atoms must be located so that an orbital of one overlaps an orbital of the other; each orbital must contain a single electron.
  • The formation of a bond is accompanied by evolution of energy. The amount of energy (per mole)that is given off when a bond is formed (or the amount that must be put in to break the bond) is called the bond dissociation energy.
    • single bond: A covalent bond that involves the sharing of one pair of electrons.
    • double bond: A covalent bond that involves the sharing of two pairs of electrons.
    • triple bond: A covalent bond that involves the sharing of three pairs of electrons.

  • polar bond: A covalent bond involving unequal sharing of electrons.
  • nonpolar bond: A bond with equal sharing of electrons.

    • Main types of weak bonds

    • hydrogen bond
    • the ionic bond
    • van der Waals interaction
    • hydrophobic bond or interaction

    Importance of Multiple Weak Bonds

    The importance of multiple weak bonds in stabilizing an association between two molecules. In the complex on the left, four noncovalent bonds bind the two protein molecules together. Even if two of the bonds are broken, as in the complex on the right, the remaining two bonds will facilitate the re-formation of the broken ones.

















    The water molecule as a dipol



    Black line: The energy (U) required to separate the participating particles versus the distance they are apart (r).
    -- Note: this energy is the sum of the attractive and repulsive forces.

    Red line: attractive force

    Blue line: repulsive force
    -- This changes so rapidly with r that it acts effectively as a barrier.
















    Hydrogen bonding

  • A strong intermolecular attraction between a nonbonding pair of electrons and an electrophilic OH, SH, or NH
    		•
  • donor groups:
    		•  , ,  pair of nonbonding electrons
  • acceptor groups:
    		•  ,
  • typical hydrogen bond lengths
    		•
    Bond Length (nm)
    0.26
    0.27
    0.28
    0.29
    0.30
    0.31
    The values listed are the distances between the nuclei of the donor and the acceptor atom.




































    Hydrogen bonding - cont.

    Example of hydrogen bonding in biological structure
    Major type of hydrogen bonds in biologically important molecules
    Hydrogen bonding of water:































    Types of noncovalent interaction


    summary
































    Hydrophobic and hydrophilic porperties of the phospholipid molecule


    Electrophil and nucleophil molecules

  • Electrophil ("lover of electrons"): accepts a pair of electrons

  • Nucleophil ("lover of nuclei"): donates a pair of electrons to nucleus with an empty orbital
    		•


    Definitions

  • Isomers - Different compounds with the same molecular formula.

  • Stereoisomers (configurational isomers) - Isomers whose atoms are bonded together in the same order but which differ in how the atoms are oriented in space

  • Diastereomers - Stereoisomers that are not mirror images.

  • Geometric isomers (cis-trans isomers) - Isomers that differ in their cis-trans arrangement on a ring or double bond. Geometric isomers are a subclass of diastereomers.

    • Cis - On the same side of a ring or double bond

    		•

    • Trans - On opposite side of a ring or double bond



  • Enantiomers - A pair of nonsuperimposable mirror image molecules; mirror-image isomers.

  • Conformers (conformational isomers) - Structures that differ only by rotations about sigma bonds. In most cases conformers interconvert at room temperature, thus are not different compounds and not true isomers.

  • Structural isomers (constitutional isomers) - Isomers that differ in the order in which their atoms are bonded together.

  • Optical isomers (archaic) - Compounds with identical properties except for the direction in which they rotate polarized light.



    • Levorotatory (L) - Rotating the plane of polarized light counterclockwise.

    • Sinister (S) - Rotating the plane of polarized light counterclockwise.

    • Dextrorotatory(D) - Rotating the plane of polarized light clockwise

    • Rectus(R) - Rotating the plane of polarized light clockwise.

    • Chiral- Different from its mirror image

    • Chiral carbon atom (asymmetric carbon atom)- A carbon atom that is bonded to four different groups.

    • Atoms with higher atomic numbers receive higher priority.
    • Conformational isomers can interchange by simple deformation of the molecule. (ie. rotation around the sigma bond).

    • But configurational isomers (stereoisomers), can interconvert only through the breaking and reformation of covalent bonds.


  • Superimposable - Identical in all respects. The three-dimensional position of all atoms coincide.

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    More to print:
    Overview 1
    Overview 2