BIOCHEMISTRY - BASICS OF ORGANIC CHEMISTRY - BSN 1G.pdf

BASICS OF ORGANIC CHEMISTRY CHEMICAL BONDS Chemical Bonds - are formed when 2 or more are usually gases, liquids, or solids with low melting atoms are held strongly together. Atoms form points. M...

BASICS OF ORGANIC CHEMISTRY CHEMICAL BONDS Chemical Bonds - are formed when 2 or more are usually gases, liquids, or solids with low melting atoms are held strongly together. Atoms form points. Many, such as gasoline, vaporize readily. Many chemical bonds to achieve stability. are pliable in their solid forms—for example, plastic bags and paraffin. M - Recall that the subatomic particles that are involved in chemical bonds are the electrons, more specifically the electrons present in the DEFINITION & HISTORY OF ORGANIC CHEMISTRY outermost shell of an atom known as the valence electrons. Organic chemistry - the chemistry of carbon - The central concept of bonding, as explained by compounds, except carbon dioxide, carbon monoxide, G.N. Lewis and W. Kossel, is that atoms become carbonates, and cyanates. The compounds studied by stable when they achieve a configuration where organic chemistry also contain the elements hydrogen, its valence shell contains 8 electrons. This is oxygen, nitrogen, sulfur, phosphorus, and halogens. known as the Octet Rule. It originated from the idea that living things contain “vital force” which was necessary to create organic - There are 2 ways that an atom may achieve compounds (Vitalism Theory). In other words, organic Octet, and thus, forming chemical bonds. This is compounds can only be created inside a living thing either by giving off and receiving valence because there is a necessity for a vital force. electrons, or by sharing valence electrons. The Theory of Vital Force was disproven by 2 TYPES OF CHEMICAL BONDS Friedrich Wohler when he was able to synthesize urea, a compound found in human urine, in the laboratory, using ammonium cyanate, an inorganic compound. Ionic Bonds - the interaction of metals (located on the left side of the periodic table) His discovery only means that organic compounds can with nonmetals (located on the right side.) actually be created from inorganic and non-living substances. - In the formation of this bond, the metal atom gives off valence electrons resulting Despite the demise of the demise of vitalism in to an ion with a positive charge, known science, the word organic is still used today by some as cation. people to mean “coming from living organisms” as in the term “organic supplements” and “organic - The electrons given off by the metal will fertilizers”. then be accepted by a non-metal atom resulting to an ion with a negative ORGANIC COMPOUNDS charge, known as anion. - The chemical bond is then formed by the Organic compounds - Organic compounds are electrostatic attraction between the 2 hydrocarbons and hydrocarbon derivatives. These can ions with different charges. be found in living things (biochemical compounds and - They are mostly soluble in water and natural products) or can be synthetic. dissociates into ions. Covalent Bonds - generally results between the interaction of non-metals. - The chemical bond is formed when the 2 - non-metal atoms share their electrons with each other. -Prepared by: Heart Most Galo of substances with covalent bonds 1  BASICS OF ORGANIC CHEMISTRY DIFFERENCE BETWEEN ORGANIC AND BONDING & STRUCTURES OF OGRANIC INORGANIC COMPOUNDS COMPOUNDS INORGANIC The other major elements present in organic ORGANIC COMPOUNDS COMPOUNDS compounds aside from carbon (H, O, N, S and Composed of carbon and halogens) are all non-metals, therefore the bonds Composed of almost all that they form with carbons are all covalent. few other elements (H, O, kinds of elements N, S, P, and halogens) Following Octet Rule, each non-metal should Composed entirely of have 8 bonds around it, and would mean that the Mostly ionic bonds covalent bonds elements C, H, O, N, S and halogens should form May be gases, liquids, or bonds as shown below: Usually solids with high atoms directly attached to it. solids with low melting melting point points DISTRIBUTION Mostly insoluble in water Mostly soluble in water and TOTAL OF TOTAL and soluble in non-polar insoluble in non-polar ELEMENT NUMBER OF NUMBER OF solvents solvents BONDS BONDS When soluble in water, 4 singles Aqueous solutions conduct solutions do not conduct C 4 2 singles, 1 double electricity electricity 1 single, 1 triple Very few are combustible 3 singles Combustible and produces and do not form carbon N 3 1 single, 1 double carbon (soot) when burned when burned 1 triple Chemicals reactions are Chemical reactions are usually very slow often very fast 2 singles O or S 2 1 double IMPORTANT PROPERTIES OF CARBON H or 1 1 single 1. Carbon is tetravalent - it can form 4 strong Halogens covalent bonds with each other and other elements. 2. Carbon can form multiple bonds (up until triple bond) - Carbons with only single bonds are FAMILIES OF ORGANIC COMPOUNDS considered saturated, while carbons with multiple bonds are considered unsaturated Functional Groups - are common and specific 3. Carbon has the ability for catenation (form long arrangement of atoms that impart predictable reactivity chains) into long linear chains, branched chains, and and properties to a molecule rings. Hydrocarbons – these are the simplest form of 4. Carbons in an organic compound can be organic compounds containing only carbon and classified according to their degree of hydrogen substitution: a. Primary (1o) Carbon – has only one carbon o Alkanes - hydrocarbons that do not have atom directly attached to it. multiple bonds between carbon atoms (single b. Secondary (2o) Carbon – has two carbon bonds only), and we can indicate this in the atoms directly attached to it. family name and in names for specific c. Tertiary (3o) Carbon – has only three carbon compounds by the –ane ending. atoms directly attached to it. d.Prepared Quaternary Carbon – has four carbon by: Heart Galo 2  BASICS OF ORGANIC CHEMISTRY carbon triple bond, and this is indicated in the family name and in names for specific compounds by the –yne ending. - Alkanes can also be involved in The carbon-carbon triple bond also has a rings, and in that case, they are specific reactivity; therefore, it is known as cycloalkanes. considered as the functional group of alkynes o Arene - a special class of hydrocarbon containing a special type of ring, the most common example of which is benzene ring - Compounds (hydrocarbons or not) containing such rings are known as - Alkanes are considered to be a aromatic compounds. compound with no functional group due to its relative - The term aromatic is historical in origin, inertness. because earliest known aromatic compounds are derived from aromatic - The principal sources of alkanes substances. There is no special ending for are natural gas and petroleum. the general family of aromatic compounds. o Alkenes -hydrocarbons containing at least one carbon-carbon double bond, and this is indicated in the family name and in names for specific compounds by the –ene ending. - Alkenes are the most abundant hydrocarbons in nature o Alkynes – these are hydrocarbons containing at least one carbon- Prepared by: Heart Galo 3  BASICS OF ORGANIC CHEMISTRY - Although the structure of benzene resembles an alkene, it is not really considered to be part of that subgroup as it has different set of properties. The alternating double bonds in its structure allow for the movement of the carbon- carbon bond electrons around the ring, which is a process known as electron o Alkyl Halides - These are compounds in delocalization. which a halogen (F, Cl, Br or I) replaces a hydrogen from a hydrocarbon. TAKE NOTE! - It has the generic formula R – X where X = - compounds such as the alkanes, whose halogen. molecules contain only single bonds, are referred to as saturated compounds because these compounds contain the maximum number of hydrogen atoms that the carbon compound can possess. - Compound with multiple bonds, such as alkenes and alkynes, are considered unsaturated compounds because they possess fewer that the maximum number of hydrogen atoms, and they are capable of reacting with hydrogen under proper - Chlorofluorocarbons (CFCs), main agent in conditions. damaging the ozone layer, are alkyl halides - Benzene is structurally unsaturated, but o Alcohols - These are compounds containing a has a chemical reactivity different from hydroxyl group (–OH) attached to a saturated common unsaturated hydrocarbons. Thus, carbon. it is strictly not considered unsaturated. We still refer benzene as aromatic. - It has a generic formula of R – OH, Hydrocarbon Derivatives – these are organic compounds containing other elements other than carbon and hydrogen. - The group of atoms containing the other elements usually becomes the functional - Methanol is known as wood alcohol and is group of a hydrocarbon derivative. highly toxic and flammable. Ethanol is the only ingestible alcohol and is present in alcoholic - The group of atoms containing only beverages. carbon and hydrogen atoms that are not part of the functional group is known as an - Alcohols can be classified into 3 groups: This alkyl group. classification is based on the degree of substitution of the carbon to which the In general structural formulas, alkyl groups hydroxyl group is directly attached. are always denoted as R. Prepared by: Heart Galo 4  BASICS OF ORGANIC CHEMISTRY ❖ Primary Alcohol- the –OH o Thiols - known as the sulfur analogs of is attached to a primary alcohols because the structures of thiols carbon. replace the oxygen in the hydroxyl group (– OH) with a sulfur forming a new functional group known as a sulfhydryl group (–SH). - It has the generic formula R–SH. ❖ Secondary Alcohol - the –OH is attached to a o Ethers - compounds containing an oxygen secondary carbon. in between an alkyl group or a phenyl ring. - It has the generic formula R–O– R’, where R and R’ can be the same or different alkyl groups. - A ether with similar alkyl groups beside its oxygen atom is referred as symmetrical ether, while the one that has different alkyl groups ❖ are known as asymmetrical ether. ❖ Tertiary Alcohol - the – o Amines - compounds that are considered OH is attached to a tertiary organic derivatives of ammonia, since carbon. structurally an amine is formed when one of the hydrogens in ammonia is replaced with an alkyl group or phenyl ring. - The nitrogen in an amine is known as the amino group. - Alcohols can be classified into 3 groups: based on the number of organic groups attached to the nitrogen atom. ❖ Primary Amine- the nitrogen is attached - If the hydroxyl group (–OH) is to 1 organic group. attached to a benzene ring, it is not considered an alcohol. It is referred to as a phenol. Prepared by: Heart Galo 5  BASICS OF ORGANIC CHEMISTRY ❖ Secondary Amine - the - The carbonyl group of an aldehyde is nitrogen is attached to 2 bonded to one hydrogen atom and one organic groups. carbon atom (except for formaldehyde, which is the only aldehyde bearing 2 hydrogen atoms.) The carbonyl group of a ketone is bonded to 2 carbon atoms. - The carbonyl group of a ketone is bonded to 2 carbon atoms. Their generic formulas are: ❖ Tertiary Amine - the nitrogen is attached to 3 organic groups. o Carboxylic acids, Esters, and Amides - When a carbonyl group is attached to a hydroxyl group, it becomes a supra-functional group known as carboxyl group. The reason this is considered to be a new functional group is because this combination results to acidic properties. Compounds containing carboxyl groups are known as carboxylic acids. - Amines usually have a foul odor of decaying matter or rotten fish. o Esters and amides are considered derivatives o Aldehydes & Ketones - - Both of of carboxylic acids. The formation of carboxylic these families of compounds acid derivative is usually done by replacing the contain a carbonyl group – a group –OH of the carboxyl with a different group. in which a carbon atom has a - An ester is formed when the –OH of the double bond to an oxygen. carboxyl is replaced with an ether-like group (– O – R’). - - An amide is formed when the –OH of the - carboxyl is replaced with an amino group (– NH2. - Prepared by: Heart Galo 6  BASICS OF ORGANIC CHEMISTRY - Some common examples of carboxylic acids are: - Proteins and plastics, such as Nylon, have amide in their structures. FUNCTIONAL GROUPS AND DRUG DESIGN Knowledge of functional groups is very important in researches for drug design. The different functional groups have different reactions in the cells. Thus, researchers are studying the incorporation or derivation of different functional groups in a drug to ensure that it - Acetic acid is responsible for the tart will be effective, and will have less side effects and high taste of vinegar. Butyric acid is the stability. cause of the characteristic smell of old butter. As an example, let us consider salicylic acid and acetylsalicylic acid (Aspirin), which both have analgesic - Benzoic acid is used in (pain-relieving) effects. pharmaceuticals as antimicrobial agent. Most carboxylic acids often have irritating odor. The illustration of their structure below reveals that they are very much related except for a single - Some common examples of esters are: functional group difference. Let’s discuss how important this change is. - Ethyl acetate has the characteristic smell of plastic balloon and is used as organic solvent. Ethyl butyrate is ester responsible for the smell of pineapples. Most esters have fruity odor and are used in flavorings and fragrances. Prepared by: Heart Galo 7  BASICS OF ORGANIC CHEMISTRY - The Sumerians were noted to have used remedies derived from the willow tree for pain management as far back as 4000 years ago. Hippocrates also used it for managing pain and fever. He even utilized tea brewed from it for pain management during childbirth. - It was 1829, when a crystalline substance from the willow tree was derived by Henri Leroux, and was later called salicylic acid. In the 1800s, the Heyden Chemical Company was the first to mass-produce salicylic acid commercially. - Despite its success in pain management, salicylic acid also offered a lot of disadvantages, such as being too irritating to the oral and gastrointestinal cavities. This is due to the presence of a phenol in its structure. - It was not until 1899 when a modified version named acetylsalicylic acid was registered and marketed by Bayer under the trade name Aspirin. In this derivative, the phenol group was converted into an acetyl ester. - Aspirin still has the same analgesic effect as salicylic acid, but is already mildly irritating due to the conversion of phenol into an ester. - In the example above, we learned how converting even only one functional group in a dug could have an important effect on its properties. Prepared by: Heart Galo 8