ORGANIC CHEMISTRY. Naming Saturated Hydrocarbons. The International Union of Pure and Applied Chemistry (IUPAC) names for the first 12 "straight-chain" or "normal" alkanes are:. Alkanes and Cycloalkanes. The simplest saturated hydrocarbons are called alkanes.
n-hexane 2-methylpentane 3-methylpentane
Resonance structures of benzene, C6H6 Abbreviated representation
of resonance structure
π electrons delocalized
m-xylene o-xylene p-xylene
attached to a C atom that has bonds to
2 other C atoms.
1-pentanol 2-pentanol 3-pentanol
1-pentyl alcohol 2-pentyl alcohol 3-pentyl alcohol
• Aldehydes and ketones
The general formula for carboxylic acids is:
R represents an alkyl or an aryl groupCarboxylic Acids
–General overall reaction
R–C + R´OH R–C + H2O
–If an ester is heated with water in the presence of a strong acid or base, the reverse reaction will occur, producing the parent alcohol, R´OH, and either the carboxylic acid, RCO2H (under acidic conditions), or the carboxylate anion, RCO2– (under basic conditions)
– The two substituents on the amide nitrogen can be hydrogen atoms, alkyl groups, aryl groups, or any combination of two of those species O
– Are prepared by the nucleophilic reaction of amines with other, more electrophilic carboxylic acid derivatives, such as esters
– Are unreactive because of bonding interactions between the lone pair of electrons on nitrogen and the carbonyl group, which inhibits free rotation about the C–N bond
– Stability of amide bond is important in biology because they form the backbones of peptides and proteins
When compounds contain more than one functional group, the order of precedence determines which groups are named with prefix or suffix forms. The highest precedence group takes the suffix, with all others taking the prefix form. However, double and triple bonds only take suffix form (-en and -yn) and are used with other suffixes.
– Primary carbon is bonded to only one other carbon and a functional group
– A secondary carbon is bonded to two other carbons and a functional group
– A tertiary carbon is bonded to three other carbons and a functional group
– A carbocation is an electrophile, a species that needs electrons to complete its octet
– A tertiary carbocation is more stable than one that is primary because it increases electron density at the carbocation
CH3Cl + OH– CH3OH + Cl
HCl + CH2CH2 CH3CH2Cl
CH2–CH2 CH2CH2 + A–B
• Differences between the conformations are depicted in drawings called Newman projections
In the conversion of one constitutional isomer to another, at least one bond must be broken and reformed at a different position in the molecule
Geometric isomers can only occur when there is a C=C double bond. Geometric isomers differ in the relative placement of substituents in a rigid molecule; members of an isomeric pair are either cis or trans, with interconversion between the two forms requiring breaking and reforming one or more bonds; their structural differences causes them to have different physical and chemical properties and to exist as two distinct chemical compounds
non-superimposable mirror images.
These molecules are non-superimposable mirror images.
• Interactions of enantiomers with other chiral molecules
• All the functional groups described are found in the organic molecules that constitute and maintain every living organism on Earth
– This carbon is designated by an asterisk in structural drawings and is called a chiral center, chiral carbonatom, asymmetric carbon atom, stereogenic center, or stereocenter
• The most abundant substances found in living systems belong to four major classes:
4. Nucleic acids
Monosaccharides - simple sugars, with multiple hydroxyl groups.
Based on the number of carbons (e.g., 3, 4, 5, or 6) a monosaccharide is a triose, tetrose, pentose, or hexose, etc.
Disaccharides - two monosaccharides covalently linked
Oligosaccharides - a few monosaccharides covalently linked.
Polysaccharides - polymers consisting of chains of monosaccharide or disaccharide units (starches and cellulose)
• Carbohydrates are the most abundant of the organic compounds found in nature; they constitute a substantial portion of food consumed to provide energy.
• Carbohydrates are polyhydric aldehydes or polyhydric ketones
– The simplest carbohydrates consist of unbranched chains of three to eight carbon atoms; one carbon is a carbonyl carbon and the others are bonded to hydroxyl groups
– The structure of a carbohydrate can be drawn either as a hydrocarbon chain, known as a Fisher projection, or as a ring, or cyclic form, called a Haworth projection
– The two cyclic forms in a Haworth projection are called anomers
Sucrose, common table sugar, has a glycosidic bond linking the anomeric hydroxyls of glucose and fructose. Because the configuration at the anomeric carbon of glucose is a (O points down from the ring), the linkage is designated a(1®2). The full name is a-D-glucopyranosyl-(1®2)b-D- fructopyranose.
What is the difference between a and b D-glucose?
Glycosidic bonds: The anomeric hydroxyl group (axial) and a hydroxyl group of another sugar or some other compound can join together, splitting out water in a condensation reaction to form a glycosidic bond.
R-OH + HO-R'-->R-O-R' +H2O
– Form a family of compounds that includes fats, waxes, vitamins, and steroids
– Fatty acidsare the simplest lipids and have a long hydrocarbon chain that ends with a carboxylic acid functional group
1. Saturated fatty acids — the hydrocarbon chains contain only C–C single bonds that stack in a regular array
2.Unsaturated fatty acids — have a single double bond in the hydrocarbon chain (monounsaturated) or more than one double bond (polyunsaturated); double bonds give fatty acid chains a kinked structure, which prevents the molecules from packing tightly
• Waxes are esters produced by nucleophilic attack of an alcohol on the carbonyl carbon of a long-chain carboxylic acid
• Triacylglycerolsare esters that are used by the body to store fats and oils and are formed from one molecule of glycerol and three fatty acid molecules
R = organic group with NO C=C bonds
C12 = Lauric acid
C16 = Palmitic acid
C18 = Stearic acid
What is the functional group in a fat or oil?
R = organic group with C=C bonds
C18 = oleic acid
• Proteins are biologically active polymers formed from amino acids linked together by amide bonds; in addition to an amine group and a carboxylic acid group, each amino acid contains a characteristic R group
• All the amino acids found in proteins are chiral compounds except glycine, which suggests that their interactions with other chiral compounds are selective
• Some proteins are enzymes that catalyze biological reactions
Adding more peptide links ---> PROTEIN
• Nucleic acids are the basic structural components of DNA and RNA, the biochemical substances found in the nuclei of cells that transmit the information needed to direct cellular growth and reproduction
• Structures are derived from nitrogen-containing cyclic compounds called pyrimidines and purines, which can hydrogen-bond through the lone electron pair on nitrogen (in pyrimidine and purine) or through the hydrogen of the amine (in purine)
• When a pyrimidine or purine is linked to a sugar by a bond called a glycosidic bond, a nucleoside is formed; addition of a phosphoric acid group to the sugar produces a nucleotide
Cytosine Thymine Uracil
Connects #9 Nitrogen to #1 carbon of sugar to form a nucleoside
Connects #1 Nitrogen to #1 carbon
of sugar to form a nucleoside
Connects to #5 carbon of a nucleoside to form a nucleotide
Joins to nucleotides at the #3 carbon to make DNA and RNA (nucleic acids)
Rules for Naming Complex Species
Typical Simple Ligands
tris(ethylenediammine) cobalt(III) nitrate
• Structural isomers involve different atom to ligand bonding sequences.
attachment of ligands
• Stereoisomers (identical bonding)
• geometrical isomers
• optical isomers
[Pt(NH3)4][PtCl6] vs [Pt(NH3)4Cl2][PtCl4]
bonding via C cyano-bonding via N isocyano-
bonding via S thiocyanato-bonding via N isothiocyanato-Structural (Constitutional) Isomers
cis- [Pt(NH3)2Cl2] trans-[Pt(NH3)2Cl2]