A GLANCE

with ORGANIC CHEMISTRY

Sherwin N. Reyes, MT, MSc, PSM, PSMAP, ISID
FACULTY FEU- Nicanor Reyes Medical Foundation Institute of Medicine School of Medical Technology Departmetn of Microbiology and Parasitology

 ORGANIC CHEMISTRY

ORGANIC CHEMISTRY
Is the chemistry that deals with carbon and its compund.

Carbon
An element that belongs to
Period 2 Group IV of the Periodic Table of Elements

ATOMIC STRUCTURE OF CARBON

Electronic Configuration
Ground State:
1s2, 2s2, 2p2

Excited State:
1s2, 2s1,2px1,2py1,2pz1

COVALENT BONDING and HYBRIDIZATION

When two hydrogen atoms approach each other, their 1s

atomic orbitals interact to form a bonding

H.

.H H:H

H:H

SIGMA BONDING
The bonding molecular orbitals of hydrogen is an example of a sigma bond Strong interactions Formed by head-on overlap of two atomic orbitals

METHANOL
Methanol bonds are example of covalent where there is an uneaqual sharing of electrons Making oxygen more electronegative Electronegative:
C= 2.5 O= 3.5 H= 2.1

3 Types of Carbon Hybrid

sp3,sp2, and sp
Sp3 results from the blending of 1 s orbital and 3p orbitals to form 4 sp3 hybrid orbitals Sp2 results when 1 s orbital and 2 p orbitals blend and form 3 sp2 hydrids leaving 1 of the orbitals unhydridized
Sp results from the combination of 1 s and 1 p orbital forming 2 sp hybrid orbitals with 2 p orbitals left unhybridized.

Sp2
results when 1 s orbital and 2 p orbitals blend and form 3 sp2 hydrids leaving 1 of the orbitals unhydridized

Sp3
Sp3 results from the blending of 1 s orbital and 3p orbitals to form 4 sp3 hybrid orbitals

sp
results from the combination of 1 s and 1 p orbital forming 2 sp hybrid orbitals with 2 p orbitals left unhybridized.

Bonds and Hybridized Centers

Sigma and Pi bonds
All bonds in organic structures are either sigma or pi bonds All single bonds are sigma bonds All double bonds are made up of one sigma and one pi bond All triple bonds are made up of one sigma and two pi bonds

Bonds and Hybridized Centers

Sp, sp2, and sp3 centers
All atoms linked by a single bond are sp3 hybridized except hydrogen Both carbon atoms involved in the double bond of an alkene (C=C) must be sp2 hybridized Both the carbon and the oxygen of a carbonyl group (C=O) must be sp2 hybridized. All aromatic carbons must be sp2 hybridized Both atoms involved in a triple bond must be sp hybridized Hydrogen uses 1s orbital for bonding and is not hybridized

Shapes
The shape of organic molecules and functional groups within them is determined by the hybridization of the atoms present. Examples:
Functional groups containing trigonal planar sp2 centers are planar while functional groups containing sp centers are linear.
Planar functional groups aldehyde, ketone, alkene, carboxylic acid, acid chloride, acid anhydride, ester, amide, aromatic
Linear Functional groups alkyne, nitrile Functional groups with tetrahedral carbons alcohol, ether, alkyl halide

Reactivity
Functional groups which contain bonds are reactive since bonds is weaker than a bond and can easily broken.

Common functional groups which contain bonds are aromatic rings, alkenes, alkynes, aldehydes, ketones, carboxylic acids, esters, amides, acid chlorides, acid anhydrides and nitriles.

Functional Groups

Functional Group

Nomenclature of Simple Alkene

Straight Chain Alkanes # CarbonNameMolecular FormulaStructural Formula 1 Methane CH4 CH4 2 Ethane C2H6 CH3CH3 3 Propane C3H8 CH3CH2CH3 4 Butane C4H10 CH3CH2CH2CH3 5 Pentane C5H12 CH3CH2CH2CH2CH3 6 Hexane C6H14 CH3(CH2)4CH3 7 Heptane C7H16 CH3(CH2)5CH3 8 Octane C8H18 CH3(CH2)6CH3 9 Nonane C9H20 CH3(CH2)7CH3 10 Decane C10H22 CH3(CH2)8CH3

The IUPAC system requires first that we have names for simple unbranched chains, as noted above, and second that we have names for simple alkyl groups that may be attached to the chains. Examples of some common alkyl groups are given in the following table. Note that the "ane" suffix is replaced by "yl" in naming groups. The symbol R is used to designate a generic (unspecified) alkyl group.

Group

CH3 C2H5 CH3CH2CH2 (CH3)2CH CH3CH2CH2CH2 (CH3)2CHCH2 CH3CH2CH(CH3) (CH3)3C R

Methyl Ethyl Propyl sopropyl Butyl Isobutyl sec-Butyl tert-Butyl Alkyl

 IUPAC Rules for Alkane Nomenclature 1. Find and name the longest continuous carbon chain. 2. Identify and name groups attached to this chain. 3. Number the chain consecutively, starting at the end nearest a substituent group. 4. Designate the location of each substituent group by an appropriate number and name. 5. Assemble the name, listing groups in alphabetical order using the full name (e.g. cyclopropyl before isobutyl). The prefixes di, tri, tetra etc., used to designate several groups of the same kind, are not considered when alphabetizing.

Name the following

For the above isomers of hexane the IUPAC names are: B 2-methylpentane C 3-methylpentane D 2,2-dimethylbutane E 2,3-dimethylbutane

Alkenes and Alkynes

Alkene and alkynes are defined by adding the suffixes ene and yne.

Alcohols
Alcohols (or alkanols) are given the suffix anol

Ether and Alkyl halides

Ethers and alkyl halides are not identified by suffixes. Instead, these functional groups are considered substituent of the main alkene chain.

Aldehydes and Ketones

Aldehydes (alkanals) are identified by the suffix anal. Ketones (alkalones) are identified by the suffix anone. Aldehyde must always be at position 1 of the main chain and do not need to be numbered.

Carboxylic acids and Acid chlorides

Carboxylic acids and acid chlorides are identifiedby adding the suffix anoic acid and anoyl chloride. Both these functional groups are always at the end of the main chain and do not need to be numbered.

Esters
Esters are named from the parent carboxylic acid and alcohol. The alkanoic acid is renamed alkanoate and the alkanol is treated as an alkyl substituent. The combined name is alkyl alkanoate. There must be a space between both parts of the name.

Amides
Are termed as alkanamides based on the parent carboxylic acid. If the amide nitrogen has alkyl groups, then are considered as alkyl substituent. The symbol N is used to show that the substituents are on the nitrogen and not some other part of alkanamide skeleton.

Amines
Has a suffix ylamine after the root name.

General Classification of Organic Compounds

1. Hydrocarbons made up exclusively of carbon and hydrogen. 2. Hydrocarbon derivatives one of the subtituents of carbon has been replaced by a non carbon or non hydrogen atom. 3. Biomolecules biologically active macromolecules.

Hydrocarbons
A. Open Chain/Aliphatic Linear
Alkanes Alkenes Alkynes Alkadienes
Conjugated dienes possess alternating double bonds Cumulative dienes possess consecutive double bonds Isolated dienes possess double bonds separated by more than 1 carbon atom intervals.

Hydrocarbons
B. Cyclic possess ring structures
Aromatic benzene ring Cycloalkanes

Hydrocarbon derivatives
One of the subtituent of carbon has been replaced by a non carbon or non hydrogen atoms
Alcohols Ethers Aldehydes Esters Ketones Amines Carboxylic acids Halides

Biomolecules
Biologically active macro molecules
Nucleic acids Proteins Carbohydrates Lipids

Nucleic Acid
are biological molecules essential for life, and include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information. Nucleic acids were first discovered by Friedrich Miescher in 1871.

Nucleic Acids
Deoxyribonucleic acid
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms. The main role of DNA molecules is the long-term storage of information and DNA is often compared to a set of blueprints, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules.

Nucleic Acids
Ribonucleic acid
Ribonucleic acid (RNA) functions in converting genetic information from genes into the amino acid sequences of proteins. The three universal types of RNA include transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). Messenger RNA acts to carry genetic sequence information between DNA and ribosomes, directing protein synthesis. Ribosomal RNA is a major component of the ribosome, and catalyzes peptide bond formation. Transfer RNA serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA. In addition, many other classes of RNA are now known.

Proteins
are biochemical compounds consisting of one or more polypeptides typically folded into a globular orfibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bondsbetween the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequenceof a gene, which is encoded in the genetic code.

Carbohydrates
is an organic compound with the empirical formula Cm(H2O)n (where m could be different from n); that is, consists only of carbon, hydrogen, and oxygen, with a hydrogen:oxygen atom ratio of 2:1 (as inwater). However, there are exceptions to this. One common example would be deoxyribose, a component of DNA, which has the empirical formula C5H10O4. Carbohydrates can be viewed as hydrates of carbon, hence their name. Structurally however, it is more accurate to view them as polyhydroxy aldehydes and ketones

Carbohydrates
The carbohydrates (saccharides) are divided into four chemical groupings: monosaccharides, disaccharides, oligosacch arides, and polysaccharides. In general, the monosaccharides and disaccharides, which are smaller (lower molecular weight) carbohydrates, are commonly referred to assugars. The word saccharide comes from the Greek word (skkharon), meaning "sugar". While the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix -ose. For example, blood sugar is the monosaccharide glucose, table sugar is the disaccharide sucrose, and milk sugar is the disaccharide lactose

Lipids
lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids calledtriglycerides. Lipids also encompass molecules such as fatty acids and their derivatives (including tri-,di, monoglycerides, and phospholipids), as well as other sterol-containing metabolites such ascholesterol. Although humans and other mammals use various biosynthetic pathways to both break down and synthesize lipids, some essential lipids cannot be made this way and must be obtained from the diet.

Lipids
constitute a broad group of naturally occurring molecules that include fats, waxes, sterols, fatsoluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides,p hospholipids, and others. The main biological functions of lipids include energy storage, as structural components of cell membranes, and as important signaling molecules.[4]

Types of Organic Chemical Reactions

1. Addition this is characteristics of unsaturated compounds and usually results to distruption of multiple bonds.
e.g. Hydration of ethene to form ethanol
Uses H2SO4 as catalyst
H2SO4 HSO4 H C=C H + H2O

H H
H2SO4

H-C-C-H
H +

H2O

Addition
In this type of reaction, the site for initiation is the double bond. One of the H atoms of H2SO4 being an electrophile would seek electrons from the electron rich pi cloud of the double bond. As a result, a carbocation intermediate is created.
H2SO4 HSO4 H C=C H H H + H2O H H H2SO4 H-C-C-H H + + H2O

Addition
Because reaction intermediates are ustable, the carbocations reacts with an OH- this time coming from water. The hydrogen from water then goes to the H2SO4 restoring the H2SO4 molecule. Therefore the end product is:
H H H-C-C-H HSO4 H2SO4 H2O H+ H H H-C-C-H H OH w/ H2SO4 regenerated

H OH

Elimination
This is the reverse of addition and usually results to the creation of multiple bonds.

E.g. Dehydration of Ethanol

Also uses H2SO4 as catalyst and dehydrating agent

Elimination
The potential site here is not only the presence of polar C-O and O-H bonds also the Lewis base characteristic of oxygen, which possess lone pairs of electrons that can potentially be shared or donated. This reaction begins when one of the H of H2SO4 reacts with the OH of ethanol.
H H H2SO4 H H H-C-C-H H OH H+ H

H-C-C-H
H OH

H2O

Elimination
A water molecule is then removed and a carbocation is formed.

H+
H H H2SO4

H-C-C-H
H OH

HSO4 H2SO4

Elimination
Because of the instability of the carbocation, one of the H of the neighboring C atom is lost and goes to HSO4 to restore the H2SO4 catalyst. Therefore, the end product is:

H
C=C

H
+ H2O w/ H2SO4 regenerated

Substitution
This simply involves the replacement of one substituent by another.
E.g. The formation of ethanol and sodium bromide from bromoethane and sodium hydroxide.

C2H5Br+NaOH

C2H5OH+NaBr

ISOMERISM
Isomers are defined as compounds possesing the same molecular formula but different structural formula. is the phenomenon whereby certain compounds, with the same molecular formula, exist in different forms owing to their different organisations of atoms. The concept of isomerism illustrates the fundamental importance of molecular structure and shape in organic chemistry.

ISOMERISM CONCEPTUAL CHART

Structural Isomerism
Structural Isomers have different structural formulae because their atoms are linked together in different ways. It arises owing to: arrangement of Carbon skeleton e.g. The formula C4H10 represents two possible structural formulae, butane and methylpropane:

Structural Isomerism
position of Functional group e.g. propan-1-ol and propan-2-ol

Structural Isomerism
different Functional groups e.g. the molecular formula C2H60 represents both ethanol and methoxymethane.

Stereoisomerism
This involves no variation in the bonding arrangement of atoms or groups, only in their orientation in space. Stereoisomers have the same structure and bond order but their atoms and groups of atoms are arranged differently in space. They have different spatial arrangements and their molecules are notsuperimposable. There are Three types:
Geometric or Cis/Trans Optical/Enantiomerism Conformational

Geometric or Cis/Trans
The terms cis and trans are from Latin, in which cis means "on the same side" and trans means "on the other side" or "across". Involves a double bond, usually C=C, that does not allow free rotation about the double bond (unlike a C-C single bond). They are not superimposable. e.g. cis-but-2-ene and trans-but-2-ene

Stereoisomers may possess quite different physical properties, such as melting point, density and solubility in water (look up those of maleic acid and fumaric acid). Ring structures and other steric factors also result in geometric isomerism.

Optical/Enantiomerism
Optical isomerism Involves an atom, usually carbon, bonded to four different atoms or groups of atoms. They exist in pairs, in which one isomer is the mirror image of the other. e.g. butan-2-ol

These isomers are referred to as enantiomers. The central carbon atom to which four different atoms or groups are attached, is called an asymmetrical carbon atom. Enantiomers have identical physical constants, such as melting points and boiling points, but are said to be optically active since they can be distinguished from each other by their ability to rotate the plane of polarised light in opposite directions. A mixture of enantiomers in equal proportions is optically inactive, and is called a racemic mixture. Use an organic chemistry textbook to find out more about optical isomerism.

STRUCTURAL EFFECTS
These structural concepts give us ideas on the electron distribution within atom, and thus also its chemical behavior.
Hybridization Hydrogen bonding Steric Effect - the presence of bulky groups Inductive Effect - distortion of electron cloud Resonance pi electron delocalization CH Hyperconjugation sigma electron delocalization

Thank You for Listening

END OF LECTURE