Introduction to Organic Chemistry

Chemical Bonding and Reactions

Scientific Method

• A systematic approach to research• Hypothesis: a tentative explanation

for a set of observations and experiments

• Law: a description of a phenomenon that allows for general predictions

• Theory: a well-established explanation for scientific data; not fully tested; can be disproven

• Experiments: systematic observations and measurements performed under controlled conditions

http://catalog.flatworldknowledge.com/bookhub/4309?e=averill_1.0-ch01_s02

Classification of Matter

Matter

Pure matter

Elements Compounds

Mixtures

Homogeneous Mixtures

(solutions)

Heterogeneous Mixtures

• Matter is any physically present substance that has a mass and occupies space• Matter is composed of atoms and molecules

Elements• An element is a single substance in

its simplest form that cannot be split into any more separate substances by chemical means

• Everything around us is comprised of chemical elements

• 112 elements, 90 of them naturally occurring

• Only 25 of these are essential for the human body

• Hydrogen (H), carbon (C), oxygen (O) and nitrogen (N) make up of ~97 % of body weight and 99 % of total atoms

• Elements are made of atoms

Name Symbol

Aluminum Al

Carbon C

Copper Cu

Iron Fe

Oxygen O

Potassium K

http://www.chem.wisc.edu/deptfiles/genchem/sstutorial/Text3/Tx33/tx33.html

Periodic Table

• Periodic table is a chart in which elements with similar physical and chemical properties are grouped in a periodic way

• The elements are arranged according to their atomic number• In a periodic table, horizontal rows are called periods and

vertical groups are called groups• Elements within each group have similar chemical and physical

properties• Groups 1-2 and 13-18 are called main group elements (also

called 1A through 8A groups)• Groups 3-12 are called transition group elements (also called 3B

through 12B group elements)

Periodic Table

Descriptive Names for Groups in the Periodic Table

• 1A – alkali metals: lithium, sodium, potassium are most common, very reactive against air and water, hydrogen (H) is also in this group, but it is not a metal

• 2A – alkaline earth metals: magnesium and calcium are the most abundant in nature among the group, found mainly as minerals

• 7A – halogens: fluorine, chlorine, bromine, iodine are the most common – halogens react readily with metals to form salts (sodium chloride, calcium chloride)

• 8A – noble gases: helium, neon, argon, krypton, xenon, radon – they are very unreactive gases – also called inert gases, they are present in monoatomic form

• Transition metals (B group elements) – contain many of the common metals, such as iron, nickel, copper, cobalt, zinc, platinum, gold, silver

http://en.wikipedia.org/wiki/Composition_of_the_human_body#mediaviewer/File:201_Elements_of_the_Human_Body-01.jpg

Essential Elements for the Body

Classification of Elements

Elements

metals

Good conductors of electricity and heatMalleable

ShinyAll are solids at RT, except Hg

Semimetals (metalloids)

Intermediate properties

between metals and nonmetals

nonmetals

Poor conductors of heat and electricity

Are not shinyMight be gas, liquid and solid

brittle

17 nonmetals8 semimetals

Atoms and Atomic Theory• The smallest unit (particle) of an element is atom• Atom is made up of subatomic particles; protons, neutrons

and electrons – number of these determine the characteristic of an atom

http://physics.taskermilward.org.uk/KS4/additional/html/atomic_structure.htm

Atoms

• Atomic Number (Z): number of protons (or electrons in a neutral atom) in an atom

• Mass Number (A): (number of protons) + (number of neutrons)

http://physicsnet.co.uk/gcse-physics/atomic-structure/

http://commons.wikimedia.org/wiki/File:Atomic_number_depiction.jpg

Atoms and Ions• Ions: gain electron – anion, lose electron –

cation (fluoride, F- ; sodium cation, Na+)• Atoms form ions as part of their reaction

with other atoms to form molecules. • The readiness with which an atom gains or

loses electrons dictates its reactivity

• F + 1e- F-

19

9

19

9

Neutral fluorine atom

Fluorine anion

9 protons, 9 electrons9 protons, 10 electrons

Isotopes of Atoms• Isotopes: atoms with the same number of protons and

electrons, but different number of neutrons 16O, 17O, and 18O• Elements are present in nature as mixtures of their isotopes• Chemical behaviors of isotopes are identical, nuclear

properties might be different; radioactivity • Atomic mass of an element is the weighted average mass of

all the isotopes – not same as mass number• 35Cl (~75.8%) and 37Cl (~24.2%) – atomic mass is 35.45

http://chemistry.tutorcircle.com/inorganic-chemistry/isotopes.html

http://chemistry.tutorcircle.com/inorganic-chemistry/isotopes.html

• Isotopes are important inbiology and medicine

• Radioactive isotopes are usedfor monitoring biochemical activity

Representation of Atoms: Lewis Symbols

• Representing atoms by showing only the valance electrons

• Electrons (valance) are represented as dots around the chemical symbol of the atom

• Dots can be placed on the 4 sides of the chemical symbol – place one electron each side, then start to add remaining electrons

Each unpaired dot is available for bonding with other atoms

https://classes.lt.unt.edu/Fall_2010/CECS_5030_026/mrp0113/Lewis%20Dot%20Project%20Page.htm

Atomic Orbitals and Energy Levels• Electrons of an atom are

found in discrete shells around the nucleus – from closest to the nucleus to the farthest (valance shell)

• These shells also correspond to energy levels;

(n = 1, n = 2 etc.)• The energy level

corresponds to the period number at the periodic table (hydrogen, n = 1, period 1)

(Lithium, n = 2, period 2)http://gcsechemistryhelp.tumblr.com/post/6753442513/periodic-table-electron-shells-part-1

Valance shell

Calcium (Ca) is in the 4th period

Atomic Orbitals and Energy Levels• 1) Principal energy levels: Shown as n = 1, 2, 3 etc. – total electron

capacity of a principal energy level is equal to 2(n)2

(for n=1, capacity 2 e-, for n=1, capacity 8 e-, for n = 3 capacity 18 e-)• 2) Sublevels: Within each principal energy level, there is a set of

equal-energy orbitals – designated as s, p, d, f(Both principal energy level and type of sublevel is specified for describing the location of an electron)• 3) Orbital: Sublevels have atomic orbitals, which is a specific region of

a sublevel where electron is located (probability of finding the electron is high);

• 4) An orbital can have maximum 2 electrons Number of orbitals Electron capacity

s 1 2p 3 6d 5 10f 7 14

Octet Rule• Octet rule; atoms react in such a way that they have eight electrons in their valance

(outermost) shell (more stable configuration)• This configuration of 8 electrons in the valance shell is also known as “noble gas

configuration” • Noble gases (group 8A) are not reactive, since they have their valance shells already

filled with 8 electrons (Helium is an exception and has 2 electrons in its only shell) • Other atoms lose/gain or share electrons to achieve the more stable noble gas

configuration

By using octet rule, we can predict the chemical changes between atoms

http://www.masterorganicchemistry.com/2010/08/14/from-gen-chem-to-org-chem-pt-7-lewis-structures/

Shapes of Orbitals

1 kind of s,3 kind of p,5 kind of d orbitals

http://butane.chem.uiuc.edu/pshapley/GenChem2/Intro/2.html

Electron configuration and Aufbau Principle

• 1st principal energy level (n = 1) - 1s• 2nd principal energy level (n = 2) – 2s 2p• 3rd principal energy level (n = 3) – 3s 3p 3d • 4th principal energy level (n = 4) – 4s 4p 4d 4f

• Aufbau principle: electrons fill the lowest-energy orbital that is available first

How to write the electronic configuration of an atom?

Rules:• 1) Start filling the orbitals from the lowest energy; (1s orbital is the

lowest energy orbital)• 2) Each principle energy level contain n sublevels and each sublevel

contain certain number of orbitals • 3) No more than 2 electrons can be placed in an orbital

For example, 1s < 2s < 2p < 3s < 3p is the order of energy for the first three principal levels

Be: 1s2 2s2

O: 1s2 2s2 2p4

Ne: 1s2 2s2 2p6

Mg: 1s2 2s2 2p6 3s2

http://www.amasci.net/knowledge/oxidation-states.php?lang=eng

Molecular Interactions: How do molecules form?

• Substances that are made of more than one element are called compounds, e.g. water (H2O) and carbon dioxide (CO2)

• Valance electrons ; The valence shell holds the electrons located furthest from the nucleus

• Valance electrons are important because; the rearrangement and redistribution of valence electrons between atoms enable atoms to ‘bond’ to one another

• Full valance shell is the most stable form for an atom

• The principal aim of chemical bond formation is to generate full valence shells

Valance shell

Chemical Bond Formation• There are two types of chemical bonding:1) In a “covalent bond” one or more pairs of

electrons are shared equally between the atoms

2) In an “ionic bond” electrons are totally transferred from one atom to another

Two non-metal atoms will react to form a covalent compound

A non-metal will react with a metal to form an ionic compound

1) Covalent Bond: Sharing of Electrons• In covalent bonding electrons are shared

between atoms

• The two orbitals with the valance electrons should overlap for covalent bond formation

• This way the atoms sharing electrons gain full valance shell – more stable (octet rule)

• Atoms which are linked by covalent bonds form discrete units called molecules; the smallest part of a single element (O2) or a compound (such as glucose, C6H12O6)

• The molecular formula show the composition of one molecule of a covalent compound

C3H8S (1-thiol), odour of onion

C6H12O6 (glucose), sugar

http://hyperphysics.phy-astr.gsu.edu/hbase/chemical/lewis.html

2) Ionic Bond: Transfer of Electrons

• Ionic bonds are formed when one or more electrons are fully transferred from one atom to another – one atom becomes positively charged (cation) another becomes negatively charged (anion)

• The attraction between the oppositely charged cations and anions makes the the ‘ionic bond’ between the ions - electrostatic interaction

• Ionic compounds exist as extended lattices–a network of cations and anions

• Ionic compunds have an overall charge of zero due to equal number of positive and negative charges within the compound http://www.chemguide.co.uk/atoms/structures/ionicstruct.html

Covalent Bonds: Single and Multiple Bonds

• Types of covalent bonds: Sigma (γ) and pi (π) bonds

• Single or multiple bonds can form between two atoms

• Single bonds are always sigma bonds

• Single bond – one sigma bond• Double bond – one sigma bond

+ one pi bond• Triple bond – one sigma bond +

2 pi bonds

http://hyperphysics.phy-astr.gsu.edu/hbase/chemical/lewis.html

Polar Covalent Bonding and Electronegativity• Although there is no electron transfer in

covalent bonding, the atoms making the covalent bond might have partial charges

• In a heteroatomic molecule, the electron distribution around the molecule is not even; electrons are not shared equally – this gives partial charges to atoms

• Electronegativity is the measure of the ability of an atom to attract electrons in a chemical bond

• Electronegativity determines which of the atoms in a molecule will be partially negative and which will be partially positive

http://apbrwww5.apsu.edu/thompsonj/Anatomy%20&%20Physiologyhttp://bio1151b.nicerweb.net/Locked/media/ch02/http://www.f.u-tokyo.ac.jp/~fukuyama/interactive_trial

Chemical Bonding vs. Non-covalent (Intermolecular) Interactions

• Non-covalent interactions are weak interactions between molecules • Non-covalent interactions determine physical properties such as

boiling point, melting point, density etc.• These interactions are very important in biological systems

(assembly of lipid bilayers, packing of genome etc.) • Although they are weak, multiple non-covalent interactions occur at

the same time between two molecules to give a large overall effect

Type of Interaction Energy

Covalent 20-100 kcal/mole

Van der Waals 1-2 kcal/mole

Hydrogen bond 3-5 kcal/mole

Dipole-dipole

Ion-dipole

Type of Non-covalent Interactions

1) Electrostatic Interactions2) Van der Waals Forces3) Hydrogen bonding4) Hydrophobic Interactions

1) Electrostatic Interactions (Coulomb Interaction)

• Opposite charges attract, like charges repel• Due to polar covalent bonds – one part of the

molecule has partial negative and one part has partial positive charge – these molecules are said to have dipole

• Ion-dipole and dipole-dipole interactions are types of electrostatic interactions

• Not all molecules with polar bonds are indeed polar – such as CO2

2) Van der Waals Interactions

• 1) Dispersion forces: Interactions between all molecules due to induced dipole – the only form of non-covalent interaction between nonpolar molecules such as methane,

• These interactions are due to temporary dipoles and short-lived

• 2) Dipole-dipole İnteractions: Non-covalent interactions that occur between polar molecules due to attraction between opposite partial charges on the molecule

• These interactions are due to permanent dipole of molecules and are long-lived

2) Van der Waals Interactions

• 3) Steric Repulsion: Repulsion between two molecules due to close proximity of their electrons

---------------------------------------------------------------------• Van der Waals interactions is the sum of the

dispersion forces, dipole-dipole interactions and steric repulsions

• Distance and medium are two important parameters that determine the magnitude of Van der Waals interactions

3) Hydrogen Bonding• What is hydrogen bonding?: A hydrogen

atom covalently bound to an oxygen (O), nitrogen (N) or fluorine (F) atom can interact with an unshared electron pair on another oxygen, nitrogen or fluorine atom to form a hydrogen bond

1) A hydrogen atom must be bonded to an atom of oxygen, nitrogen or fluorine2) This hydrogen atom must interact with a lone pair on an atom of oxygen, nitrogen or fluorine• Hydrogen bonds are relatively weak

compared to covalent bonds, but stronger than Van der Waals interactions

• Hydrogen bonding is a special type of dipolar interaction

Hydrogen bonding between water molecules

http://commons.wikimedia.org/wiki/File:Hydrogen-bonding-in-water-2D.pnghttp://www.cliffsnotes.com/sciences/biology/biochemistry-i/protein-structure/secondary-structure

Changing of The Three States of the Matter

• The extent of physical (non-covalent) interactions between molecules determines the physical state of a substance; solid, liquid, gas

• Solid > liquid > gas (the order of the strength of non-covalent interactions)

• The physical state of a substance can be changed by altering the number of non-covalent interactions between its molecules; this is achieved by giving or taking energy from the substance – generally by heat energy

http://scienceehs.blogspot.com.tr/2011/09/three-states-of-water.html

Three States of Matter• As we increase the energy of a substance, its molecules

exhibit greater degree of movement and finally overcome the attractive forces holding the molecules together

• Polar molecules have higher melting and boiling points, non-polar molecules have lower melting and boiling points

(water b.p. =100 °C vs. methane b.p.= -161 °C)

http://www.edplace.com/worksheet_preview.php?eId=2914&type=topic

Chemical Reactions• A chemical reaction involves breaking of bonds between atoms (reactants)

and the formation of new bonds to form products• It is the movement of valence electrons that lies at the heart of many

chemical reactions• In formation of molecules, valence electrons are shared between atoms in

such a way that all atoms complete full valence shells (octet rule)

• In a chemical reaction, reactants and products react in precise amounts (stoichiometry)

• Stoichiometry is indicated by numbers in front of the chemical formula in the reaction scheme

6 CO2 + 6 H2O → C6H12O6 + 6 O2 (photosynthesis)

6 : 6 1 : 6 reactants products

Nucleophiles and Electrophiles• A nucleophile (Nu– or Nuδ –), is an electron-rich

species, which has a valence electron pair (which may be a non-bonding pair) that can be donated to form a covalent bond

• An electrophile (E+ or Eδ+), is an electron-poor species, which can accept a complete electron pair and share it with the nucleophile to form a covalent bond

http://science.uvu.edu/ochem/index.php/alphabetical/m-n/nucleophile/

Oxidation and Reduction Reactions• In oxidation and reduction

reactions (also called redox reactions) oxidation of one molecule is couple to the reduction of the other molecule

• A nucleophile can donate an electron(s) to an electrophile such that the nucleophile will lose electrons and the electrophile will gain electrons

• The species that loses electron becomes oxidized and the species that gains electron becomes reduced

http://www.meta-synthesis.com/webbook/15_redox/redox.php

http://www.meta-synthesis.com/webbook/15_redox/redox.php

In many cases; loss of hydrogens is oxidation and gain of hydrogens is reduction; loss of oxygen is reduction, gain of oxygen is oxidation

• There are many examples of redox reactions in biology; for example many oxidation reactions of organic compounds are couple to reduction of cofactors such as NAD+ or FAD

Mechanism of a Reaction

• The reaction mechanism tell us how electrons are redistributed during the change from reactants to products

• A reaction goes through certain stages to form the product

• These stages determine the mechanism of the reaction

• Mechanism is the type of the changes of reactant into products (number of steps, nature of reaction etc.)

Mechanism of a Reaction• A reaction might be one

step or multiple steps• Consider a one step

mechanism: A + B C• Reactants do not go into

products suddenly; instead goes through a transition state

• Transition state is the highest point of energy of a reaction

• In transition state some bonds are partially broken and some bonds are partially formed

http://chemistry.tutorvista.com/organic-chemistry/hammond-postulate.html

Transition States and Intermediates• Consider a multi-step reaction: • Reactants form an

intermediate compound at each step and at the last step the product is formed

• In a multi-step reaction, formation of each intermediate goes through a transition state

• Intermediates are more stable than transition states and have a longer life-time

Types of Reaction Mechanisms

1) Substitution2) Addition3) Elimination4) Condensation

1) Substitution

• In a substitution reaction, an atom on the reactant is replaced by a different atom

• A + B - X ----> B + A - X (A is substituted with B)

• A substitution reaction can be nucleophilic or electrophilic

• Nucleophilic substitution reactions are more common

Nucleophilic Substitution• If a nucleophile attacks the parent molecule

where substitution occurs, this reaction is called nucleophilic substitution reaction

• A nucleophilic substitution reaction can occur in one or two steps

http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis/Chapter_08%3A_Nucleophilic_substitution_reactions_I

2) Addition• In an addition reaction, two

molecules combine to give one single product; the product contains all the atoms of both molecules

• A + B ---> AB• The most common type of addition

reactions is addition of small molecules to the carbon-carbon double bond of alkenes - double bond acts as a nucleophile and the adding molecule acts as an electrophile

• Addition of a nucleophile to the carbon-oxygen double bond (carbonyl bond – a common functional group) is also a common addition reactionhttp://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis

3) Elimination• In an elimination reaction, a molecule loses some of

its part to form a compound with a double bond and the eliminated part becomes a new molecule:

• An elimination reaction is the reverse of an addition reaction

• Elimination reactions result in the formation of a double bond in a molecule

• Elimination reactions can proceed through a one-step or two-step mechanism

4) Condensation• In a condensation reaction, two molecules combine together to give a

large product and a small product:• A-X + B-Y A-B + X-Y (minor small product)• Condensation provides a way of joining two molecules together to form a

larger product• In many cases, the eliminated small product is water (also called

dehydration reactions)• Many examples in biology; amino acids combine to from proteins, nucleic

acids combine to form DNA/RNA – all condensation reactions

http://www.bbc.co.uk/bitesize/higher/chemistry/carbon/reaction_carbon/revision/3/

5) Hydrolysis• The reactions in which large molecules are broken down

into smaller molecules through reaction with water; large molecules react with water and split into two

• Opposite of condensation• Don’t mix hydration and hydrolysis!; in hydration water

adds to a molecule and there is no splitting into smaller molecules

• One of the most important hydrolysis reaction in biology is hydrolysis of ATP molecules