Dr. Mohammad Nahid Siddiqui

Dr. Mohammad Nahid Siddiqui
Instructor Details Dr. Mohammad Nahid Siddiqui Room: # 4 / 114 Tel: office; Mobile: Personal Homepage: 5/27/2018 Dr. Mohammad Nahid Siddiqui

Office Hours Sat, Mon, and Wed 09:30-11:00 AM also by appointment 5/27/2018 Dr. Mohammad Nahid Siddiqui

COURSE OUTLINE: CHEM 201 (112) : Organic Chemistry I
Textbook: “ORGANIC CHEMISTRY” by R. J. Fessenden & J. S. Fessenden, 6th Edition. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Grading System 5/27/2018 Dr. Mohammad Nahid Siddiqui

Exams Maj Exam 1: Sunday, 04 March; Chap: 1, 2, 3 & 4 at 6:30 PM Maj Exam 2: Sunday, 15 April; Chap: 5, 6 & 7 at 6:45 PM Final Exam: Saturday, 26 May, 2012 at 7:00 PM Note: Make sure both major exams are NOT in conflict with your other exams, if any inform me by next week. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Chapter 1. Atoms and molecules
5/27/2018 Dr. Mohammad Nahid Siddiqui

The Evolution of Organic Chemistry
Organic Chemistry was originally the chemistry of compounds which had been obtained from living things, plants and animals. Now Organic Chemistry is the chemistry of the compounds of carbon. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Why Carbon? Carbon has the ability to bond covalently to other carbon atoms as well to many other elements in a variety of ways. It forms simple compounds such as methane (CH4) as well as very complex compounds containing thousands of atoms, such as proteins and the genetic code. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Who Needs Organic Chemistry?
Organic chemistry is indispensable to many scientists and engineers. Living systems contain primary water and organic compounds. Areas that require organic chemistry include medicine biochemistry, microbiology, agriculture and petrochemistry. Most importantly, Engineering used in the chemical and petroleum industry. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Section 1.1 Electronic Structure of the Atom
A. Atomic Orbitals Most important type of atomic orbitals in organic chemistry are s & p. The first three rows of the atoms in the periodic table are made up primarily of s and p orbitals. 5/27/2018 Dr. Mohammad Nahid Siddiqui

s Atomic Orbitals The s atomic orbital is a symmetric spherically shaped cloud of electrons around the nucleus of the atom. 5/27/2018 Dr. Mohammad Nahid Siddiqui

p Atomic Orbitals The p orbital has two symmetric lobe shaped clouds of electrons on either side are of the nucleus of the atom. Each pair of p orbitals is separated by a nodal plane. 5/27/2018 Dr. Mohammad Nahid Siddiqui

The Degeneracy of the p Atomic Orbitals
There are three possible p orbitals. Each one is aligned along one of the axis of the Cartesian coordinates, namely px, py, and pz. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Filling the Orbitals Electrons have spin. Since they have a charge they also have a magnetic moment. The opposing magnetic moments minimize the repulsion between the negative charges. Each atomic orbital band has two paired electrons. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Aufbau Principle (building up)
The lowest energy orbitals are filled first with two paired electrons in each orbital period (1s, 2s, 2px, 2py, 2pz, 3s, 3p…. The electronic structure of an atom is called the electronic configuration. An example of a configuration is 1s2 2s1, which is the electronic configuration for lithium. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Hund’s Rule Degenerate orbitals receive one electron at a time until they are all filled, then a second electron is added to each orbital. For example carbon has an electronic configuration 1s22s22px12py1 Please see the table on the following slide. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Electronic Configuration of Elements in Periods 1 and 2
Atomic Numbers Electronic Configuration H 1 1s1 He 2 1s2 Li 3 1s22s1 Be 4 1s22s2 B 5 1s22s22p1 C 6 1s22s22p2 N 7 1s22s22p3 O 8 1s22s22p4 F 9 1s22s22p5 Ne 10 1s22s22p6 5/27/2018 Dr. Mohammad Nahid Siddiqui

1.2 Atomic Radius The radius of an atom is the distance from the center of the nucleus to the outermost electrons. The position of these electrons are not clear so the bond length is used. 5/27/2018 Dr. Mohammad Nahid Siddiqui

decreasing atomic radius
B e L i C N O F 3 4 5 6 7 8 9 decreasing atomic radius atomic number 5/27/2018 Dr. Mohammad Nahid Siddiqui

As we proceed from Top to bottom, within a group in the periodic table, the number of electron shells increases. Therefore, the atomic radius also increases. H (1 SHELL) Li (2 SHELLS) Na (3 SHELLS) K (4 SHELLS) INCREASING ATOMIC RADIUS 5/27/2018 Dr. Mohammad Nahid Siddiqui

Atomic Radii of Some Elements in Angstroms
B r C l A S P i M g N a e F O L H 0.37 1.225 0.889 0.80 0.771 0.74 0.72 1.572 1.364 1.248 1.173 1.10 1.04 0.994 1.142 1.334 5/27/2018 Dr. Mohammad Nahid Siddiqui

1.3 Electronegativity Electronegativity is a measure of the atoms attraction for its outer bonding electrons. Electronegativity is affected by a number of protons in the nucleus and by the number of shells containing electrons. Electronegativity increases as we go from left to right in a given period of the periodic table. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Increasing electronegativity
B e L i C N O F 3 4 5 6 7 8 9 Increasing electronegativity 4.0 5/27/2018 Dr. Mohammad Nahid Siddiqui

Electronegativity of Some Elements (Pauling Scale)
2.1 1.0 1.5 2.0 2.5 3.0 3.5 4.0 0.9 1.2 1.8 2.8 I B r C l A S P i M g N a e F O L H 5/27/2018 Dr. Mohammad Nahid Siddiqui

1.4 The Chemical Bond An ionic bond results from the transfer of electrons from one atom to another. A covalent bond results from the sharing of two or more electrons by two atoms. Atoms transfer or share electrons so as to gain a noble-gas electronic configuration. This configuration has eight electrons in the outer shell and called the octet rule. Hydrogen shares only Two electrons to attain electronic configuration of He. 5/27/2018 Dr. Mohammad Nahid Siddiqui

An ionic bond forms from atoms:
Lose electrons and form positive ions called cations, Na+, Ca++ Gain electrons to give negative ions called anions, Cl-, O-- 5/27/2018 Dr. Mohammad Nahid Siddiqui

Formation of Ions 5/27/2018 Dr. Mohammad Nahid Siddiqui

In the covalent bond the shared electrons form new orbitals called molecular orbitals. The structures below are called Lewis Structures. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Sharing of one pair of electron gives a single bond (-), two pairs gives a double (=) and three pairs gives a triple bond 5/27/2018 Dr. Mohammad Nahid Siddiqui

Ionic or Covalent? When the electronegativity difference is greater than 1.7 then bond is Ionic. Carbon has an electronegativity of 2.5, which is an intermediate between the extremes of high and low of electronegativity. Therefore, carbon almost never forms ionic bonds. It usually forms 4 covalent bonds. 5/27/2018 Dr. Mohammad Nahid Siddiqui

The number of covalent bonds (between nonmetal-nonmetal) are related to the Group number in the Periodic Table for completing Octet. 5/27/2018 Dr. Mohammad Nahid Siddiqui

B. Formal Charge In order to draw a completely correct Lewis formula, we must assign static charges, called formal charges, to some of the atoms in the structure. 5/27/2018 Dr. Mohammad Nahid Siddiqui

The formula for nitric acid shows three oxygen atoms bonded to one nitrogen atom. Each oxygen and nitrogen atom has a complete octet, but one oxygen atom is bonded by only one covalent bond instead of by the usual two. If the two electrons in the N-O single bond were divided between the N and O, the O would have seven valence electrons one more electron than a neutral O atom has. Therefore, this oxygen is assigned an electrostatic charge, formal charge, of –1. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Similarly, the N atom has only four valence electrons one fewer electron than a neutral N atom has. This electron-deficient nitrogen atom has a formal charge of +1. The other atoms in nitric acid all have the same number of electrons as would their neutral atoms; their formal charges are all Zero. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Formal Charge (Freshman Chemistry)
An atom’s formal charge is the difference between the number of valence electrons in an isolated atom and the number of electrons assigned to that atom in a Lewis structure. formal charge on an atom in a Lewis structure = 1 2 total number of bonding electrons ( ) total number of valence electrons in the free atom - total number of nonbonding electrons The sum of the formal charges of the atoms in a molecule or ion must equal the charge on the molecule or ion. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Polar Covalent Bonds Atoms with equal or nearly equal electronegativity form covalent bonds which are called nonpolar bonds. Good examples of this are the carbon-carbon bonds and carbon-hydrogen bonds. Some times bonds are polar but molecule is non-polar because of its geometry or shape. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Polar Covalent Bonds In covalent compounds like H2O, HCl, CH3OH or H2C=O, one atom has a substantially greater electronegativity than the other. The more electronegativity atom has a greater attraction for the bonding electrons, but not enough to form an ion and the result is a polar covalent bond, a bond with an uneven distribution of electron density. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Polar Covalent Bonds Besides electronegativity, polarizability of an atom affects the polarity of the bonds. The electron clouds is distorted by the introduced polarity. This usually happens in large atoms where attraction between nucleus and outer electrons decreases with increasing size of the atom. An example of this is a C-I bond, which is polar even though the electronegativity difference between Carbon (2.5) and Iodine (2.5) is Zero. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Partial Charge Symbols
Distribution of electron density in the polar bonds may be symbolized by partial charges; partial positive d+ and partial negative d-. or by crossed arrows  or  5/27/2018 Dr. Mohammad Nahid Siddiqui

B. Polar Covalent Bonds Ionic Character or Polarity of the bonds Increases with Increasing Electronegativity Difference between atoms 5/27/2018 Dr. Mohammad Nahid Siddiqui

C. Bond Lengths and Bond Angles
, 1 . 8 A 9 6 a g 4 5 7 3 H Drawing 3-D structures 5/27/2018 Dr. Mohammad Nahid Siddiqui

D. Bond Dissociation Energy
There are two ways a bond can dissociate, or break apart. One way is by heterolytic cleavage. Both bonding electrons are retained by one of the atoms. In heterolytic cleavage, -ve charge always goes to more electronegative atom e.g. Cl or O than H. 5/27/2018 Dr. Mohammad Nahid Siddiqui

.H and .CH3 are also called Radical or Free Radical
In homolytic cleavage: each atom of a covalent bond gets one electron on dissociation. .H and .CH3 are also called Radical or Free Radical 5/27/2018 Dr. Mohammad Nahid Siddiqui

Enthalpy ∆H The change in enthalpy ∆H (change in heat content or energy) has been calculated for a large number of bond dissociations. 5/27/2018 Dr. Mohammad Nahid Siddiqui

TABLE 1.4 Selected bond dissociation energies (in kcal/mol)

Structure and Dissociation Energy

Section 1.5 Chemical Formulas in Organic Chemistry

Line-bond formulas Complete structural formulas
A. Structural Formulas Line-bond formulas Complete structural formulas 5/27/2018 Dr. Mohammad Nahid Siddiqui

B. Condensed Structural Formulas

Double or Triple Bonds are usually shown in a condensed structural formula. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Line Structures 5/27/2018 Dr. Mohammad Nahid Siddiqui

C. Cyclic Compounds and Polygon Formulas

Rings containing other atoms

Section 1.6 Attractions between Molecules A. Dipole-Dipole Interactions 5/27/2018 Dr. Mohammad Nahid Siddiqui

London/Dispersion Forces London forces arise from dipoles induced in one molecule by another. London forces Increases with Increasing MW or chain length 5/27/2018 Dr. Mohammad Nahid Siddiqui

B. Hydrogen Bonding An especially strong type of dipole–dipole interaction occurs between molecules containing a hydrogen atom bonded to nitrogen, oxygen, or fluorine. N, O and F elements are highly electronegative and have unshared valence electrons. Atomic Size of N, O, F and H also plays important role. We will focus mostly N and O hydrogen bonding. 5/27/2018 Dr. Mohammad Nahid Siddiqui

This interaction of partially +ve H with unshared pair of electrons of the electronegative atom is called a hydrogen bond. Compounds containing only C and H can not form a Hydrogen Bonding. C has no unshared electrons. 5/27/2018 Dr. Mohammad Nahid Siddiqui

The Dissociation energy of a hydrogen bond is much lower than ordinary covalent bonds but stronger than mostly dipole-dipole attractions. The O---H-O is stronger than a H---N-H. Hydrogen bonds may form between two different compounds: CH3NH2 and H2O. There is more than one possibility for hydrogen bonding. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Approximate Dissociation energies of some hydrogen bonds 5/27/2018 Dr. Mohammad Nahid Siddiqui

Effects of Hydrogen Bonding on Boiling points and Solubilities
Boiling Points of compounds having same Molecular Formula but different structures Hydrogen bonded molecules have Higher Boiling Points than Non-hydrogen bonded molecules 5/27/2018 Dr. Mohammad Nahid Siddiqui

SOLUBILITY Solubility of a covalent compounds and water is another property affected by hydrogen bonding. Sugar contains many hydroxyl groups and is quite soluble in water. Cyclohexane cannot form hydrogen bonds and is therefore insoluble in water. Many biological molecules are held together by hydrogen bonding. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Section 1.7 Acids and Bases
A. Bronsted-Lowry Theory of Acidity An acid is a substance that can donate a hydrogen ion (H+) to a base. A base is defined as a substance that can accept a hydrogen ion (H+) from acid 5/27/2018 Dr. Mohammad Nahid Siddiqui

B. Strong and Weak Acids and Bases
Remember a strong acid is a acid that undergoes almost complete ionization in water such as HCl HNO3 H2SO4 Ionization of these strong acids are a typical acid-base reaction. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Weak Acids A weak acid has only a small portion of its molecules broken into ions in water. Carbonic acid is a typical weak acid. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Bases Recall that bases are classified as strong (OH-) or weak (NH3), depending on their affinity (liking) for H+ Amines are a class of organic compounds similar to ammonia: 5/27/2018 Dr. Mohammad Nahid Siddiqui

Reversible and Non-reversible Reactions
Weak Base Weak Acid Strong Acid Weak Base 5/27/2018 Dr. Mohammad Nahid Siddiqui

Carboxylic Acids are Weak Acids
Organic compounds containing a carboxyl group (-COOH) is a Weak acid. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Reactions with Weak and Strong Bases
Weak Base Strong Base Weak Acid 5/27/2018 Dr. Mohammad Nahid Siddiqui

C. Conjugate Acids and Bases
The conjugate base of an acid is the ion or molecule that is formed when an acid loses its H+. If an acid is a strong acid, its conjugate base will be a weak base and vice-versa. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Conjugate Base of Weak Acid
An weak acid gives moderately strong conjugate base. A very weak acid gives very strong conjugate base, depending on the affinity of the conjugate base for H. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Acid Strengths and their Conjugate Bases

D. Some Factors Affecting Acidity
Two Important Factors: The Size and the Electronegativity of atoms. Acidity and Equilibrium 5/27/2018 Dr. Mohammad Nahid Siddiqui

Size In the same Group of the periodic table, the size of an atom bonded to H atom affects the acid strength of a compound. A larger atom can disperse the negative charge over a larger region and thus add stability to the conjugate base. As the stability of the conjugate base increases, the greater is the acid strength of the acid. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Electronegativity In the same (period) row of the periodic table, the electronegativity of the atom bonded to H atom also affects the acidity. A more electronegative atom can carry a negative charge more readily than can a less electronegative atom. A proton is more easily removed from the more electronegative atom thus most acidic in nature. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Effect of Electronegative Atoms
The proximity (closeness) of an electronegative atom to an acidic hydrogen can have a major influence (effect) on the acidity of a compound. 5/27/2018 Dr. Mohammad Nahid Siddiqui

E. Lewis Acids and Base A Lewis Acid is a substance that can accept a pair of electrons. A Lewis Base is a substance that can donate a pair of electrons. H+ and anhydrous metal salts such as ZnCl2, FeCl3, AlCl3 and BF3 are Lewis acids. 5/27/2018 Dr. Mohammad Nahid Siddiqui

Lewis Acid-Base Reactions

F. Acidity Constants Acidity Constant Ka is a Chemical Equilbrium Constant of an acid in water. Ka reflects how far reaction proceeds toward completion. 5/27/2018 Dr. Mohammad Nahid Siddiqui

A stronger acid has a larger Ka values. Ka > 10 is considered as a strong acid. HCl, Ka  107 CH3CO2H, Ka = 1.75 X 10-5 pH and pKa 5/27/2018 Dr. Mohammad Nahid Siddiqui

G. Basicity Constants Basicity Constants Kb is a Chemical Equilbrium Constant of a base in water. A stronger Base has a larger Kb. 5/27/2018 Dr. Mohammad Nahid Siddiqui

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