Organic and Biological Chemistry Notes

Objective – Brief Review

• Definition of atoms and compounds.

• Configuration and classification of Atoms.

• Trends in Periodic Table.

• Chemical Bonds and polarity.

Elemental Atoms and Compounds

• Atoms make up all matter.

• Atoms of 1 element ${\neq}$ atoms of another element.

• Compounds are a combination of elements.

Compounds

• The specific atom combination determines the properties of a substance.

• Chemical reactions are processes that convert elements to compounds or one compound to another.

Compounds - Chemical Formulas

• Represented using chemical formulas (Symbol of elements + subscript).

• symbols ‐ type of element.

• subscripts ‐ no. of each element.

• eg. Methane $CH_4$ (contains 4 H atoms and 1 C atom).

Sub‐atomic Particles

• An atom is composed of:

  • A positively charged nucleus composed of protons (+ charge) and neutrons (0 charge).

  • Negatively charged electrons orbiting the nucleus; different layers represent different electron energy.

  • Closer layer = higher attraction.

  • Basis for chemical reactions.

Electron Arrangements

• Atoms are neutral particles: positive charge = negative charge.

  • eg. H has 1 proton and 1 electron

Periodic Table

• Arrangement of elements.

Electron Arrangements

• In the center is the nucleus, containing protons and neutrons.

• The nucleus is very small compared to the total atom.

Electron Arrangements: Layers/Orbits

• View the atom as a series of layers/orbits.

• Each layer can hold only a certain number of electrons.

• Layers get larger and can hold more electrons as you move out.

Electron Arrangements

• A new layer of electrons is added for each row of the periodic table.

• Rows in the periodic table represent # of layers.

• Valence electrons are in the outermost layer, that’s where most chemical reactions occur.

Rules for Electron Configuration

• For all representative elements (except Helium) the number of valence electrons = group number.

• Group IA=1 outer-most electron.

• Group IIA= 2 outer-most electrons.

• Energy level of the valence electrons depends on the row the element is in.

• You can use the periodic table to predict the electron configuration of the elements.

Basic Information in Periodic Table

• Number of electrons and protons.

• Mass of atom.

• Properties of atoms.

• “Likes” and “dislikes” of an atom.

• Types of chemical bonds.

General Rules for Trend Prediction

• Going down the period: Increasing number of shells.

• Going across the row: Increasing proton in the atom core.

Ionization

• Process where an $e^−$ is stripped off an atom.

• Ionization Energy (I.E.) ‐ amount of energy to remove an electron completely from atoms.

• Ions are electrically charged atoms – non‐neutrals.

• Examples:

  • $H \rightarrow H^+$

  • $Na \rightarrow Na^+$

  • $O \rightarrow O^{2-}$

Trend of Ionization Energy

• Electrons closer to the atomic core experience increasing attraction due to more positive core.

Ionization - Classes of Atoms

• Metals: (I‐IIA + transition metals).

  • Low ionization energy $\rightarrow$ need only a small amt of energy to remove $e^−$ .

  • Lose $e^−$ to form +ve ions (cations).

• Non‐metals: (III‐VII A).

  • High ionization energy $\rightarrow$ strong attractions for valence $e^−$.

  • Gain $e^−$ to form ‐ve ions (anions).

Electronegativity, EN

• Index that shows the relative attraction an element has for electrons in a bond.

• Electronegativity has the highest value of 4.0 for F, fluorine; lowest is 0.7 for Cs, cesium.

• Generally, EN has the same trend as ionization energy.

Trends in the Periodic Table

• Increasing ionization energy, decreasing atomic radius, increasing electronegativity.

• Decreasing ionization energy, increasing atomic radius, decreasing electronegativity.

Study Points

• Differences of atoms and molecules.

• Composition of an atom.

• Periodic Table of Elements.

• Ionization energy and electronegativity.

• Trend prediction in Periodic Table.

Objectives

• Identifying types of bonds (Ionic, Covalent).

• Octet Rule.

• Understanding differences between non‐polar and polar covalent bonds.

• Identifying polarity in molecules.

Ionic Bond

• Characterized by complete transfer of electrons from one atom to another.

• Crystalline solid structure; held in place by electrostatic forces.

Covalent Bond versus Ionic Bond

• Ionic Bond:

  • Complete transfer of electrons from on to the other element (ions formed).

  • formed between metal and nonmetal atoms.

  • example: salt (NaCl).

• Covalent Bond:

  • elements share electrons.

  • formed between nonmetal atoms.

  • example: sugar ($C<em>6H</em>{12}O_6$).

Prediction of # of Bonds – The Octet Rule

• General rule (except Group I‐IIIA): Non‐metals tend to gain electrons to fully‐fill their valence shell (8 $e^−$ in their outer electron shell)

• # of covalent bonds formed will depend on how many more $e^−$ are needed to complete octet

  • Example: O, Valence election = 6 (group VIA), Electron to be gained = 8 – 6 = 2 $\rightarrow$ It will form 2 bonds, (example $H_2O$)

Types of Covalent Bonds

• Single bond: 2 atoms sharing 1 pair of electrons

• Double bond : 2 atoms sharing 2 pairs of $e^−$

• Triple bond : 2 atoms sharing 3 pairs of $e^−$

• C atom can form total of 4 bonds.

Significance of Type of Bonds

• Salt (NaCl) molecules break into $Na^+$ and $Cl^-$.

• Sugar molecules remain intact.

• Differences in behavior due to differences in molecular bonding!!

Polarity and EN

• Bond Polarity is a chemical property indicating the presence of dipoles in a covalent bond between two atoms.

• Dipoles = permanent partial + or – charges.

• Term applicable only for covalent bonds.

Polarity and EN

• Polarity is directly related to electronegativity (EN) difference between two bonded atoms.

• EN difference = 0 ‐ 0.5 => non‐polar => no permanent dipole.

• EN difference = 0.5 ‐ 2.0 => polar => existence of permanent dipole.

• EN difference >2 => ionic bond, permanent full charges (+ and – charges) are created.

Non‐Polar Bonds

• Non‐polar covalent bond:

  • Both atoms in the bond share electrons equally.

  • Between two atoms that are close in position in the periodic table.

Polar Bonds

• Polar covalent bond: The electrons in polar bonds are not shared equally.

Molecular Polarity

• The vectorial sum of all the individual bond arrows determine molecular polarity or dipole:

  • For symmetric molecules, e.g. carbon dioxide, bond dipoles cancel out resulting in a nonpolar molecule.

  • For assymetric molecules, the arrows generally not cancel out and the molecule will be polar.

Molecular Polarity- Examples

• Polar and Nonpolar molecules are shown.

Polar Bonds - Acetic Acid

• The molecule is asymmetric with a negative end where the oxygen is and the other end of the molecule is slightly positive.

Learning Points

• Definition of ionic bonds.

• Charges of atoms.

• Definition of covalent bonds.

• The octet rule $\rightarrow$ # of possible bonds.

• Bond polarity and EN difference rule of thumb.

• Difference of molecular and bond polarity.

Molecular Formula

• Shows only the type and number of each kind of atoms in the molecule but does not indicate how the atoms are bonded.

• Example: $C<em>3H</em>6O$

Structural Formula

• Shows how all the atoms are bonded to each other.

Condensed Formula

• Method – Horizontal Representation of Chemical Structures.

• All C atoms on the same branch or chain are written on a single line.

IUPAC Nomenclature

• IUPAC ‐ International Union of Pure and Applied Chemistry.

• Nomenclature ‐ system for naming.

• System must be able to tell Number of carbons in the longest chain, Location of any branches, Location of functional groups.

IUPAC - General

• The name consists of prefix, infix and suffix. Number indicates location of the higher order bond.

IUPAC Nomenclature - Prefixes

• Prefix indicates number of carbons:

  • Meth- (1), Eth- (2), Prop- (3), But- (4), Pent- (5), Hex- (6), Hept- (7), Oct- (8), Non- (9), Dec- (10)

IUPAC ‐ Ranking of Functional Groups

• Name the functional group using the “As suffix in parent” column when it is the highest ranked functional group in the molecule.

IUPAC - Functional Groups

• Certain functional groups appear only as prefix: Halogenated, Nitrated, Alkylated, Ethers.

IUPAC Nomenclature – Hydrocarbon with no Functional Groups

1. Find the longest chain (main chain). Use as base name with ‐ane ending

2. Count and number the C atoms in main chain Use correct prefixes

3. Locate any branches on chain Use base name with yl ending

4. For multiple branches of the same type Modify with di, tri, …

5. Show location of each branch with numbers

6. List multiple branches alphabetically; di, tri, … are not taken into consideration

IUPAC Nomenclature - Practice

Name of compound is determined by number of carbons and type of bond.

IUPAC Nomenclature - Practice

When only one branch exists, numbering of carbon on main chains should start with one nearest to the branch.

IUPAC Nomenclature - Practice

If there are multiple branches, add prefix of di-, tri- or tetra- for identical substituents.

IUPAC Nomenclature - Practice

If there are multiple branches with equivalent rank / priorities , e.g. two hydrocarbon branches, with equal total number follow the alphabetical order of the branch name.

IUPAC Nomenclature - Practice

Draw the structure of 3,5,5-trimethylheptane: Start with base name and draw carbon skeleton, then add 3 branches at 3,5,5.

Cycloalkanes - Practice

Just add the word cyclo‐ to the front.

Steps for Complicated Examples

1. Locate and rank all functional groups.

2. Locate unsaturations (double or triple bond)

3. Locate main/parent chain.

Steps for Complicated Examples

Number the main/parent chain: group must have as low number as possible, priority given to alphabetical order.

Steps for Complicated Examples

Start naming the Parent Chain and the various substituents.

Solving Reaction Sequences

• Number of Arrows indicate the number of reactions to be performed

• Solve the sequences one reaction at a time, i.e. one arrow at a time

• Consider only major products to be uses for subsequent steps of reactions

Hydrocarbons ‐ Outline

• Introduction to Hydrocarbons and Their Classifications

• Properties of Hydrocarbon

• Recap of Nomenclature for Hydrocarbons

• Isomerisms of Hydrocarbons

• Reactions of Hydrocarbons

Hydrocarbons

• Hydrocarbons are organic compounds containing carbon C and hydrogen H only.

Classification of Hydrocarbons

• Classification includes:

  • Linear vs Cyclic

  • Saturated vs Unsaturated
    Hydrocarbon Saturated - alkanes, Unsaturated - alkenes, alkynes

Molecular Formula

• Shows number of each kind of atom (C and H). Does not tell anything about the arrangement or structure.

• Alkanes have the general formula $C<em>nH</em>{2n+2}$.

• For alkenes $C<em>nH</em>{2n}$, for alkynes $C<em>nH</em>{2n-2}$.

Hydrocarbon - Linear Chains vs Cyclic

• Linear chain alkanes have the general formula: $C<em>nH</em>{2n+2}$

• Cyclic alkanes general formula: $C<em>nH</em>{2n}$

Unsaturated Hydrocarbons

• Contain carbon-carbon multiple bonds (Alkenes, Alkynes).

Hydrocarbon Properties

• Physical: Non‐polar, Insoluble in water but soluble in non‐polar solvents, Density <1g/ml

• Chemical: Alkanes are chemically unreactive or INERT; Alkenes/Alkynes Source of Reactivity

Alkenes/Alkynes – Nomenclature

• Locate main chain  longest chain of C and must contain the double/triple bond

• Number the main chain with atom of the double/triple bond has the lowest number

• Indicate the position of double/triple bond Change suffix to –ene (double bond)/yne (triple bond)

Alkenes/Alkynes ‐ Nomenclature

Use 'ene' or 'yne' with position number to indicate double or triple bonds respectively.

Alkenes/Alkynes - Nomenclature

• If there are more than one double bonds, location for each of them must be numbered diene (two double bonds), triene (three double bonds) etc.

Alkenes/Alkynes - Nomenclature

If the longest C chain does not contain all existing double bonds, number the main chain such that the branches fall at set of smaller numbers.

Cyclic alkenes - Nomenclature

When naming substituted cycloalkenes number the ring double bond 1 and 2.

Nomenclature - Alkynes

Four carbons – prefix is but: Contains triple bond - use yne, with the position number, name of compound such the 1-butyne.

Study points

• Classification and Molecular Formulas of hydrocarbons

• Nomenclature of alkenes and alkynes

• Dispersion intermolecular‐forces

• Solubility concept: like‐dissolves‐like

• Effect to boiling point

Isomerism in Hydrocarbons

• Structural isomers have same number of atoms, but different arrangement

Structural Isomers

• This also means they have very different properties.

Isomerism in Hydrocarbons Free rotation about a C-C single bond is possible

.

Geometric Isomers

• Rotation around a C=C double bond is not possible.

Geometric Isomers

• Geometric isomers exist when 2 or more isolated arrangements are possible due to type of bonds

• Geometric isomers do not interconvert under normal conditions

Geometric Isomers

• Geometric isomers can follow 'cis' or 'trans' arrangement

Geometric Isomers

• Rules to determine cis or trans isomers of alkenes

  1. Locate double bond

  2. Determine if the compound is unsymmetrical at each C

  3. If compound unsymmetrical: cis if the two large groups are on the same side, trans if the two large groups are on the opposite side

Geometric Isomers

• Rules to determine cis or trans isomers of alkenes

• Ethyl > methyl > single atom else priority of ‘large’ groups according to atomic number.

Geometric Isomers - Examples

Identify the configurations cis and trans.

Reactions of Hydrocarbons

• Chemical equations are a chemist’s shorthand to describe a reaction and contains states of substances and conditions used in the reaction.

• Chemical Reactions ‐ Organics include Substitution reaction, Elimination reaction, Addition reaction.

Substitution of Alkane: Halogenation

• Energy input in the form of heat or light is necessary to initiate these halogenations

• Simple substitution reaction between H and Cl; One $CH_4$ molecule can add up to 4 Cl atoms; Mixture of products always occur

Hydrogen Classification

Connecting number determines degree of the carbon.

Alkane Halogenation

Halogenation are more likely to occur for secondary or tertiary hydrogens.

Alkenes ‐ Preparation

Atoms or functional groups attached to 2 adjacent carbon atoms will be eliminated to create a double bond.

Preparation of Alkenes - Elimination

Use of base to remove acidic H‐X elements (HCl, HBr, HI) from alkyl halide.

Preparation of Alkenes

Water removed from adjacent carbons of alcohol (Dehydration).

Preparation of Alkenes - Elimination

When assymetrical alkanes are the reactants, elimination can result in formation of more than 1 alkene – product mixture; major product will be the one which is most stable which has more no. of substituents or R‐groups attached to the double bond.

Elimination - Orientation

The product with the highest number of substituents is more stable and most favoured.

Alkenes – Addition Reactions

A reaction due to the carbon‐carbon double bond, reagents add to it to form a saturated compound.

Alkenes - Hydrogenation

Addition of a molecule of $H_2$ results in the formation of an alkane, where Reaction condition require increase temperature/pressure and a catalyst like Pt, Pd or Ni.

Alkenes - Hydration

Addition of $H<em>2O$ to an alkene to form an alcohol; requires a small amount of acid to work, e.g. $H</em>2SO_4$.

Alkenes - Hydration & Markovnikov’s Rule

Markovnikov’s rule states The carbon atom with the most hydrogen atoms initially will receive the additional hydrogen atom. Only used if the alkene is unsymmetrical.

Alkenes - Hydrohalogenation

Addition of a molecule of acid halide (HX = HI, HCl, HBr) results in the formation of an alkyl halide; also follows Markonikov’s rule.

Alkenes - Halogenation

Addition of a molecule of halogen gases ($Cl<em>2$ or $Br</em>2$ ) results in the formation of an alkyl halide.

Alkynes - Addition Reaction

Alkynes can add either 1 or 2 equivalents of reagents.

Alkynes - Addition Reaction

The product formed depends on the reagent used.

Alkynes - Hydration

Adds $H_2O$ to alkynes differently than alkenes; reaction products are aldehydes or ketones.

Alkyl Halides

Are alkanes with one or more halogens in place of hydrogen. The general formula is R - X.

Alkyl Halides

The names used for halogens (Group VIIA) are Fluorine, Chlorine, Bromine and Iodine.

Alkyl Halides - Properties

Melting points and boiling points Higher than alkanes – due to its higher polarity, Increase with higher MW and number of halogen atoms and soluble in non-polar solvents.

Alkyl Halides - Preparation (1)

Alkyl halides are produced by halogenation, a reaction where a halogen replaces one or more hydrogen atoms through a free radical substitution process and are produced by free radical chain reaction in 3 steps Initiation, Propagation and Termination.

Alkyl Halides – Preparation (1)

Reaction requires energy in the form of radiation, heat, or peroxides.

Free Radical Substitution

A termination process where two free radicals combine to form unreactive centers, and stops the substitution reaction by consuming the free radicals

Alkyl Halides – Preparation (1)

In the presence of chlorine and long reaction time, more substitution occurs which produces a mixture of chloromethane

Alkyl Halides – Preparation (2)

Follows Markovnikov’s rule: The carbon atom with the most hydrogen atoms initially will receive the additional hydrogen atom

Alkyl Halides – Preparation (3)

A reaction between benzene and halogen gas where a hydrogen on a benzene ring is replaced with X, Required catalyst is Lewis acid (FeX3).

Alkyl Halides – Preparation (4)

Substitution of alcohol to alkyl halides and the reagents react in the order tertiary > secondary > primary alcohols.

Alkyl Halides - Reactions

Nucleophilic substitution is the replacement or substitution of the halide group with nucleophiles, where nucleophiles are electron‐rich species that can donate electrons to electrophiles to form a new bond.

Nucleophilic Substitution.

C-X bond in alkyl halides are polarized and when neutral nucleophiles are used, usually a small amount of base is required, for faster reaction.

Nucleophilic Substitution Examples

The substituted products can be Halogen, Sulphur, Alcohol/Ether or Amino groups.

Nucleophilic Substitution

Substitution products can be further substituted in this order: Halogen, Sulfur, Alcohol/Ether, Amino group.

Alcohols

Alcohols, phenols and ethers can be thought of as derivatives of water where the hydrogen is replaced with hydrocarbon groups (R).

Alcohols - Solubility

Decrease aqueous solubility with longer C chain, where HC CH HC CH $H_2C$ CH $OH$ HO $OH$ $OH$ O HO.

Alcohols - Classification

A product by combination of Alkyl with hydroxyl groups.

Alcohols - Nomenclature

Replace -ane ending with -ol, with the lowest number.

Alcohols - Nomenclature

If the OH group is a side chain (if there is another functional group with higher priority) the OH group becomes a side chain and is called hydroxy.

Alcohols - Nomenclature

Polyhydric alcohols that contain 2 or 3 OH groups use alkanes with modified ending to show the multiple groups.

Alcohols - Common Names

Common names are widely used and it refers to naming carbon chain with yl ending and adding alcohol to the end.

Alcohols – Preparation (1)

Hydration is the addition of water to an alkene while following Markovnikov's rule

Alcohols – Preparation (2)

Reduction of Aldehydes and Ketones produces alcohols.

Alcohols - Reactions

Oxidation happens at C connected to the OH in alcohols: Starting alcohol must have at least 1 C-H bond.

Alcohols - Reactions - Rules of Oxidation

The number of C-H bonds show the number of times the alcohol can be oxidized

Phenol

Benzene with an alcohol group attached to it.

Ether - Thiol

Ethers contain two alkyl or aryl (aromatic ring) groups bound to an oxygen. Thiols - Similar to alcohol but have sulphur instead of an oxygen.

Ether - Nomenclature

IUPAC System - Identify the longest carbon chain and use as base name and identify shorted with the substituent.

Amines* Basic chemical formula of amines: $NR_3$

* Can be seen as derivatives of ammonia (when all 3 R are H).
* Biologically significant: amino acids, proteins, DNA, alkaloids (stimulants, anesthetic)

Classification

Connected number of R group with the nitrogen.

Properties

Nitrogen is electronegative resulting is high boiling point due to potential for Hydrogen bonding.

Nomenclature

Follow position number in the longest chain; use 'amine' suffixes for primary amines; and use prefix 'amino' for group the chains.

Preparation

Reaction with the alkyl or substitution with X groups