Organic Chemistry: Structure and Nomenclature

Intro to Organic Chemistry

• Chemical structures are the words of organic chemistry.
• These structures are usually represented by skeletal formulas.
• These formulas provide a graphical representation of the molecule and omit most hydrogen atoms for clarity.
• Full Lewis structures are used rarely when a complete drawing is needed.
• Drawing molecules includes Lewis-type, condensed, and skeletal formulas.

Drawing the Structure of Organic Molecules

• Lewis-type structures use lines to represent shared electrons instead of electron dots.
• Lone pairs are usually left out.
• Condensed formulas use elemental symbols to suggest connectivity.
• H3C is the same as CH3, although CH3 is more common.
• Atoms in skeletal chains tend to make zig-zag lines in molecules.
• It is difficult to make stick straight molecules unless they contain sp triple bonds.
• Zig-zag molecules and bonds are more feasible.

Basics of Organic Nomenclature

• The International Union of Pure and Applied Chemistry (IUPAC) has a system of nomenclature for alkanes based on two rules.
• Identify the longest carbon atom chain in its structure to identify an alkane.
• Add prefixes to the name of the longest chain indicating substituent positions and names.
• Substituents are branches or functional groups that replace hydrogen atoms on a chain.
• Substituent position identified by the number of the carbon atom to which it is bonded.
• The chain's carbon atoms numbered by counting from the end nearest the substituents.
• Multiple substituents are named individually and placed in alphabetical order.
• When more than one substituent is present, they are listed alphabetically with carbon atom numbering, beginning at the end closest to the substituent.
• The longest carbon atom chain is numbered to produce the lowest number for the substituents.
• The ending -o replaces -ide at the end of the name of an electronegative substituent.
• The number of same-type substituents indicated by prefixes di- (two), tri- (three), tetra- (four), and so on.
• Each of the six equivalent hydrogen atoms of the first type in propane and that type's nine equivalent hydrogen atoms in 2-methylpropane are bonded to a carbon atom bonded to only one other carbon atom.
• Two different alkyl groups can be formed from each, depending on which hydrogen atom is removed.
• The name of an alcohol comes from the hydrocarbon which it was derived and replaced by -ol, and its carbon atom to which the -OH group is bonded is indicated by a number placed before the name.
• When a carboxyl group is added to a ring the suffix -carboxylic acid is added to the name of the cyclic compound.
• The ring carbon attached to the carboxyl group is given the #1 location number.
• Salts of carboxylic acids are writing the name of the cation followed by the acid's name with the -ic acid ending replaced by an -ate ending.
• For dicarboxylic acids, location numbers are omitted for both carboxyl groups because both functional groups occupy the parent chain ends, and the ending -dioic acid is added to the parent chain.
• Esters are named as if the alkyl chain from the alcohol is a substituent, with no number assigned to this alkyl chain.
• This is followed by the parent chain's name from the carboxylic acid part with an -e removed and replaced with the ending -oate.

Amines, Amides, Aldehydes and Ketones

• The word "amine" derived from ammonia.
• The class of compounds known as amines is commonly named as substituted ammonias.
• Primary amines (RNH2) named with the substituent as a prefix.
• More systematic nomenclature appends -amine to the longest chain, as for alcohols.
• N is included to indicate the substituent is on the nitrogen atom unless there is no ambiguity.
• Each of the R groups is named as a separate word, except when the groups are identical.
• Use of the prefix di or bis based on the simple or substituted nature of groups.
• Primary amides are named by changing the name of the acid after dropping the -oic acid or -ic acid endings and adding -amide.
• The carbonyl carbon is given the #1 location number.
• Secondary amides are named by using an upper case N to designate the alkyl group is on the nitrogen atom.
• IUPAC assigns a characteristic suffix -al to aldehydes.
• An aldehyde carbonyl group must always lie at the end of a carbon chain, and is always given the #1 location position in numbering.
• Common parent chain names are used for aldehydes similar to carboxylic acids, and the suffix -aldehyde is added to the end.
• In common aldehyde names, carbon atoms near the carbonyl group are often designated by Greek letters.
• If an aldehyde moiety is attached to a ring, the suffix -carbaldehyde is added.
• The carbon attached to this moiety will get the #1 location number in naming.
• A ketone carbonyl function may be located anywhere within a chain or ring.
• An aldehydic ketone gets an oxo substituent in the nomenclature.
• The IUPAC system assigns a characteristic suffix of one to ketones.
• For dialdehydes, dial is added to the parent chain name ending with omission of location numbers.
• In naming cyclic ketones, the carbonyl group is assigned location position #1, but is not included in the name unless more than one carbonyl group is present.
• With carbonyl and hydroxyl molecules the carbonyl gets the lowest position number along with its suffix.
• In molecules with carbonyls and alkenes, the carbonyl is given priority by the IUPAC system.

Aldehydes and Ketones as Fragments

• Alkanoyl is the common name of the fragment
• Acyl is still widely used.
• Formyl is the common name of the fragment.
• Acetyl is the common name of the CH3-C=O- fragment.

CARBOHYDRATES

• Also called saccharides, they are molecular compounds containing carbon, hydrogen and oxygen.
• Include monosaccharides (e.g. glucose) and disaccharides (e.g. sucrose), which are relatively small molecules.
• Are often called sugars.
• Other carbohydrate molecules are very large (polysaccharides such as starch and cellulose).
• Carbohydrates are a source and stores of energy and building blocks for polysaccharides.
• Monosaccharides -simplest carbohydrates and building blocks for larger carbs.
• General molecular formula (CH2O)n, where n can be 3, 5, or 6.
• Classified by # carbon atoms trioses (n=3) [glyceraldehyde] pentoses (n=5) [ribose & deoxyribose], hexoses (n=6) [fructose, glucose & galactose]
• Molecules that have the same molecular formula but different structural formulae are isomers.
• Glyceraldehyde contains an aldehyde group and two hydroxyl groups and is a reducing sugar.
• Aldehydes and ketones are organic compounds which incorporation a carbonyl functional group.
• At least one of these substituents is hydrogen the compound is an aldehyde hydroxyl group is a functional group in organic chemistry that consists of one oxygen atom bonded to one hydrogen atom.
• Forms of Pentoses and Hexoses can exist in cyclic and non- cyclic forms.
• Aldoses have an aldehyde group and are reducing sugars.
• Ketoses have a ketone groups and are non-reducing sugars reducing sugars can not donate electrons
• Non-cyclic forms of carbohydrates
• Glucose: The most important carbohydrate fuel.
• Consists as a ring structure as alpha + beta glucose.
• Reacts to form disaccharide maltose and polysaccharide like starch and cellulose.
• Alpha/beta glucose have two forms of glucose due to position of hydroxyl group.
• Galactose similar structure to glucose that reacts with glucose to make lactose
• Fructose: A hexose classified as a ketose and fructose reacts with glucose to form sucrose.
• Disaccharides are soluble +broken down in small interest into monosaccharides. Further condense with other reactants for the formation of poly
• Polysaccharides: When mono undergo series of reactions until polymers are formed Amylose forms a helical structure, amylopectin is forms through a set of branching energy storage.
• Glycogen: Acts as carbo storage but shorter branches and high energy inside cells
• Cellulose: Made of a series of glucose molecules forming tight straight chains.
• Provides toughness to the hydrogen, cant be broken down but broken down by others.

Lipids

• Lipids are fats, oils, waxes, and fat- like molecules.
• Lipids include cell membrane components (phospholipids and cholesterol), energy stores, chemical messengers (steroid hormones), protection, waterproofing, insulation, and buoyancy agents.
• Triglycerides are esters of glycerol (an alcohol) and fatty acids (long chain carboxylic acids).
• Each fatty acid has a carboxylic acid (-COOH) group at one end & a methyl group at the other end.
• Contain an even number of carbon atoms, commonly ranging between 10-20 carbon atoms long.
• Hydrocarbon chains can be either saturated or unsaturated (mono or poly)
• Fats are solids, obtained primarily from animals, while oils are liquids obtained primarily from plants.
• Omega number refers to the position of the double bond nearest the methyl (CH3) end of the carbon chain.
• Triglycerides contain hydroxyl groups + alcohol reacts with acids.
• Unsaturated hydrocarbon chains contain one or more double bonds.
• Saturated hydrocarbon chains contain only single bonds appear solid at room temperature. Animal fats (butter, lard) & tropical oils (palm, coconut)
• Hydrogenation is the addition of more "solid" effects stability and protects against oxidization.
• In addition hydrogenation adds hydrogens to the fats making them more stable
• Phospholipids are a diglyceride for one of the glycerol binding sights that contains is substituted that a phosphate groiup is linked
• steriods are a list that continue 17 carbons and are used around membranes
• Cholesterol and hormones are well known

Proteins

• Biological molecules which are made up of biological amino acids found inside cells.
• Contribute to the mechanical structure and rates of the reaction in living things
• Facilitate transport of molecules and is component of immune system
• Proteins made of acids; classified by # of amino acids in chain.
• Acids composed of carbon, hydrogen, oxygen and nitrogen with a general formula
• Composed of carboyxlic acids+ amine chain.
• Peptides,Tripeptides,Polypeptides, and proteins
• Proteins typically have 100-10,000 acids that are linked together.
• 20 diffiernt proteins are used to define proteins Essential Non essential acids used.
• Structure, Secondary,Teritary,Quaternary
• Enzymes are catalicts and reactions in biological setting s/
• Speed up reactions with lower actiavtion and participate to remain in at end Enzymes specificity comes from specific shape inside molecules
• Enzyme activity is sensitive to PH and temp
• cofactors and prosthetic groups,activators
• Collisin theory states reacting mloucles mus trcollide with corect orientation and need good energy.

Enzymes Function

• This site is part of a molecule that contains the rite shape with a group and correct reation
• Enzymes change shape with apporach making complex suctrate
• Hydroen bond increases kinetic energy and collison rates, 37.5 c for humans PH for working and braking range - enzymes change that can break bonds. Alter enzyme shape and efectivnes.
• Enzyem substrate has a high dependece on the rate of reaction.
• Higher the substrate means reaction increase -
• Non cometetive is a structure that has a similar bond to its active sight
• Non Competitive attach elsewhere, not share allifnit and prevent substrat bind _enzymer has protein or supporter structure in cells from vitamns

Vitamins and Nucleic Acids

• Most coensymes are vitamins or dirived that are small in the cell.
• Vitamins are generaly not synthedizised at adequete levels byt the body inside adn obaitned from deit
• Votamin A is used in the vision for epithicla cell
• VitaminD for increasing absiroto[tion Vitamine
• Fat sobulte antiodixt
• k used in blood clot Vitamines has phsopate inside
• Nucule acids: impportant molecules fot continuty of life/ Genetic blueprint from cell to cel. Two main types fo nacids are : rna/dna building blcks
• Sructres Nitrogneus base,pentos sugat and a group: base atahced with surgat inside inside.
• Types of pesntose, deoxy ribose or ribose nad cabon residues in pentnose numbered thruogh fove .Dna and rna for the structure, in dna its the deoxyrbose. Nitrougnus bases and contains that prtential with binder. They reduce the hydroen and make more basic.
• Dna and rna nitrogenus that use the the core to binder and form
• Rna vs dNA with the help structures to combine inside cells. Base sequences complemtbary to rna and dNA Dna double helux with the help odygen to maintain shapes insed to hella and bases.
• Chromsonoms that cnatins proteins for the strcutres nad carry instruction for proteins.
• dna functions ,m rna, r rna , and trana that can be involved .