Friday, February 15, 2013

LECTURE NOTE: Introduction to Organic Molecules and Functional Group



CH3: Introduction to Organic Molecules and Functional Group
-        Functional Group
o   Heteroatoms—atoms other than carbon or hydrogen. Common heteroatoms are nitrogen, oxygen, sulfur, phosphorous, and the halogens
o   Π Bonds. The most common Π bonds occur in C—C and C—O double bonds
o   Functional group is an atom or a group of atoms with characteristic chemical and physical properties. It is the reactive part of the molecule
o   Why do heteroatoms and Π bonds confer reactivity on a particular molecule?
§  Heteroatoms have lone pairs and create electron-deficient sites on carbon
§  Π bonds are easily broken in chemical reactions. A Π bond makes a molecule a base and a nucleophile (donate electrons)
o   C—C and C—H σ bonds form the carbon backbone or skeleton to which the functional groups are bonded (R). R—Functional Group
o   Ethane has only C—C and C—H σ bonds, so it has no functional group. Ethane has non polar bonds, no lone pairs, and no Π bonds, so it has no reactive sites (alkane)
o   Ethanol has two carbons and five hydrogens in its carbon backbone, as well as an OH group (hydroxyl functional group). Ethanol has lone pairs and polar bond that make it reactive with a variety of reagents, including acids and bases (Alcohol)
-        An Overview of Functional Groups
o   We can subdivide the most common functional groups into 3 types
§  Hydrocarbons
§  Compounds containing a C—Z σ bond where Z = an electronegative elements
§  Compounds containing a C=O group
o   Hydrocarbons are compounds made up of only the elements carbon and hydrogen. They maybe aliphatic or aromatic
§  Aliphatic hydrocarbons can be divided into three subgroups
·        Alkanes have only C—C σ bonds and no functional group. Ex. Ethane (CH3CH3)
·        Alkenes have a C—C double bond as a functional group. Ex. Ethylene (CH2=CH2)
·        Alkynes have a C—C triple bond as a functional group. Ex. Acetylene (HC triple bond CH)
§  Aromatic hydrocarbons (named after the strong and characteristic odors). Ex. Benzene, the sixed membered ring and three Π bonds of benzene comprise a single functional group
·        When benzene is bonded to another group, it is called phenyl group (phenylcyclohexane)
§  Polyethylene is a synthetic plastic and high molecular weight alkane, consisting of chains of CH2 groups bonded together (no reactive site, so stable compound and not readily degrade)
o   Compound containing C—Z σ bond. The electronegative heteroatom Z creates a polar bond, making carbon electron deficient. (lone pairs on Z are available for reaction with protons and other electrophiles, especially Z=N or O)
§  Halo group (R—X) X= F, Cl, Br, I
§  Hydroxyl group (R—OH)
§  Alkoxy group (R—O—R)
§  Amino group (R—NH2, R2NH, or R3N)
§  Mercapto group (R—SH)
§  Alkylthio group (R—S—R)
o   Compounds containing a C=O group (carbonyl group)
§  The polar C—O bond makes the carbonyl carbon an electrophile, while the lone pairs on O allow it to react as a nucleophile and base. The carbonyl group also contains a pie bond that is more easily broken than a C—Z σ bond
§  Atenolol is a βblocker, a group of drugs used to treat hypertension
§  Carbonyl group (R—(CH=O)) or (R—(CR=O))
§  Carboxy group (R—(C(OH)=O))
§  COOR (R—(C(OR)=O))
§  CONH2, CONHR or CONR2
§  COCl (R—(CCl=O))
o   The importance of a functional group cannot be overstated. A functional group determines all the following properties of a molecule:
§  Bonding and shape
§  Type and strength of intermolecular forces
§  Physical properties
§  Nomenclature
§  Chemical reactivity
-        Intermolecular forces – are the interactions that exist between molecules. Functional group determines the type and strength of these interactions
o   Ionic compound (extremely strong electrostatic interactions)
o   Covalent compounds (in order of increasing strength)
§  Van der Waals forces (London forces)
·        Caused by momentary changes in electron density in a molecule (the only attractive forces present in nonpolar compound)
·        When compound is not completely symmetrical, creating temporary dipole
·        The weak interaction of these temporary dipoles constitutes van der Waals forces
·        The larger the surface area, the larger the attractive force between two molecules, and the stronger the intermolecular forces
·        Polarizability is a measure of how the electron cloud around an atom responds to changes in its electronic environment
·        Larger atoms like iodine, which have more loosely held valence electrons, are more polarizable than smaller atoms like fluorine, which have more tightly held electrons.
o   More loosely, so easily induced by temporary dipoles
§  Dipole-dipole interactions – are the attractive forces between the permanent dipoles of two polar molecules
§  Hydrogen bonding – typically occurs when a hydrogen atom bonded to O, N, or F, is electro statistically attracted to a lone pair of electrons on an O, N, or F atom in another molecule
-        Physical Properties (Compound’s intermolecular forces determines many of its physical properties)
o   Boiling point (bp) – is the temperature at which a liquid is converted to gas
§  Stronger the intermolecular forces, the higher the boiling point
·        Ionic compounds have very high boiling points
·        Covalent molecules, the boiling point depends on the identity of the functional group
·        The larger the surface area, the higher the boiling point
·        The more polarizable the atoms, the higher the boiling point
·        Liquid having different boiling point can be separated in the laboratory using a distillation apparatus
o   The more volatile component (lower boiling point compound) distills first, followed by the less volatile, higher component
o   Melting point (mp) – is the temperature at which a solid is converted to its liquid phase
§  The stronger the intermolecular forces, the higher the melting point
§  Given the same functional group, the more symmetrical the compound, the higher the melting point
·        Ionic compounds have very high melting points
§  Symmetry also plays a role in determining the melting points of compounds having the same functional group and similar molecular weight, but very different shapes
o   Solubility – is the extent to which compound, called the solute, dissolves in a liquid called the solvent
§  Compounds dissolve in solvents having similar kinds of intermolecular forces
·        “Like dissolves like” (structurally similar)
·        Polar compounds dissolve in polar solvents. Nonpolar or weakly polar compounds dissolve in nonpolar or weakly polar solvent
§  Water and organic liquids are two different kinds of solvents (water is polar, organic solvents are either nonpolar or weakly polar
§  Most ionic compounds are soluble in water, but insoluble in organic solvents. To dissolve an ionic compound, the strong ion-ion interactions must be replaced by many weaker ion-dipole interactions
§  An organic compound is water soluble only if it contains one polar functional group capable of hydrogen bonding with the solvent for every five C atoms it contains
§  Acetone is so soluble in water that acetone and water are miscible—they form solutions in all proportions with each other
§  A low molecular weight alcohol like ethanol is water soluble because it has small carbon skeleton (< five C atoms) compared to the size of its polar OH group
·        Cholesterol is insoluble in water
§  The nonpolar part of a molecule that is not attracted to H2O is said to be hydrophobic
§  The polar part of a molecule that can hydrogen bond to H2O is said to be hydrophilic
§  MTBE soluble in water, 4’-dichlorobiphenyl is not soluble in water, but in organic solvent
-        Application: Vitamins
o   Vitamins are organic compounds needed in small amounts for normal cell function (A, C, D, E,K) (B1, B2, B12)
§  Vitamin A or retinol is an essential component of the vision receptors in the eyes (mucus membrane and skin)
§  Contains 20 carbons and a single OH group, making it water insoluble (soluble in any organic medium (stored in fat cells, particularly in liver)
§  Beta carotene, the orange pigment (carrots)
o   Vitamin C
§  Has six carbon atoms, each bonded to an oxygen atom that is capable of hydrogen bonding, making it water soluble
-        Application of solubility: Soap
o   Soap molecules have two distinct parts:
§  Hydrophilic portion composed of ions called polar head
§  A hydrophobic carbon chain of nonpolar C—C and C—H bonds, called nonpolar tail
§  Dissolving soap in water forms micelles, spherical droplets having the ionic heads on the surface and the nonpolar tails packed together in the interior
-        Application: The Cell Membrane
o   Structure of the cell membrane
§  The cytoplasm is the aqueous medium inside the cell, separated from water outside the cell by cell membrane
§  Phospholipids, contains a hydrophilic ion portion and hydrophobic hydrocarbon portion, in this case two long carbon chains composed on C—C and C—H bonds (a polar head and 2 nonpolar tails)
§  When phospholipids are mixed with water, they assemble in an arrangement called lipid bilayer, with the ionic heads oriented on the outside and the nonpolar tails on the inside
§  Cell membranes are composed of these lipid bilayers
o   Transport across cell membrane
§  Some ions are transported across the membrane with the help of molecules called ionophores
·        Ionophores are organic molecules that complex cations. They have hydrophobic exterior that makes them soluble in nonpolar interior of the cell membrane, and a central cavity with several atoms whose lone pairs complex with a given atom (central cavity to hold cation)
·        Two naturally occurring antibiotics that act as ionophores are
o   Nonactin
o   Valinomycin
·        Several synthetic ionophores have also been prepaed, including one group called crown ethers ( are cyclic ethers containing several oxygen atoms that bind specific cations depending on the size of their cavity)
o   Functional Group and Reactivity
§  Functional group create reactive sites in molecules
§  Electron-rich sites react with electron-poor site
§  All functional groups contain a heteroatom, a pie bond, or both, and these features make electron-deficient (electrophilic) and electron rich (nucleophilic) sites in a molecule
§  An electronegative heteroatom like N, O, or X makes a carbon atom electrophilic
§  A lone pair on a heteroatom makes it basic ad nucleophilic
§  Pie bonds create nucleophilic sites and are more easily broken than sigma bonds
§  An electron-deficient carbon atom reacts with nucleophile, symbolized as :Nu-
§  An electron-rich carbon reacts with an electrophile, symbolized as E+
-        Biomolecules – are organic compounds found in biological systems
o   Sugar, amino acids, lipids and nucleotides



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