Pharmaceutical Organic Chemistry-1 Lecture Notes PDF

Pharmaceutical Organic Chemistry-1 PC102- Lec.1 Dr Samar Samir Tawfik [email protected] Dr Selwan Mahmoud [email protected] 1. Objectives of the course: Studying this course enables the students to:  Acquire a complete idea and understanding of...

Pharmaceutical Organic Chemistry-1 PC102- Lec.1 Dr Samar Samir Tawfik [email protected] Dr Selwan Mahmoud [email protected] 1. Objectives of the course: Studying this course enables the students to:  Acquire a complete idea and understanding of atomic structure.  Understanding stereochemistry of the chiral organic compounds.  Enable the student to understand the basics of the chemical reactions and their mechanisms.  Predict the characteristics of organic compounds. 1. Course k. elements: On finishing the course, the student should be able to dominate the following key elements: Domain 1- Fundamental Knowledge  Identify the basics of Pharmaceutical organic chemistry.  Learn how to use pharmaceutical chemical terminology, abbreviations and symbols related to organic chemistry and stereochemistry appropriately.  Utilize the rules of fundamental organic chemistry to handle, identify, prepare and analyze synthetic starting materials and final products.  Analyze and use the 3D techniques that may be applicable to pharmaceutical industry. Domain 2: Professional and Ethical Practice  Identify, prepare and purify pharmaceutical organic materials from different sources.  Identification of simple organic compounds through utilizing lab equipments.  Writing practical chemical reports for identified samples. Domain 4: Personal Practice: Team work ability and mastering management skills.  I. Introduction 1.Atomic Structure and Chemical bonding  I. Introduction 1.Atomic Structure and Chemical bonding  I. Introduction 1.Atomic Structure and Chemical bonding  I. Introduction 1.Atomic Structure and Chemical bonding 1.1 Atoms, electrons and orbitals  I. Introduction 1.Atomic Structure and Chemical bonding 1.1 Atoms, electrons and orbitals Each element has a unique atomic number Z, which is equal to the number of positively charged protons in the nucleus. A neutral atom has equal number of protons and electrons, the negatively charged particles that revolve around the nucleus of the atom in orbitals. Orbitals are the positions surrounding an atom's nucleus where the electrons are most likely to be at any given moment. There are four basic types of orbitals: s, p, d, and f.  The Octet rule: The tendency of atoms to have eight electrons in the valence shell giving it the same configuration as noble gases. The rule is applicable to carbon (C), nitrogen (N), oxygen (O), and the halogens (F, Cl, Br, I) and more generally to s-block and p-block of the periodic table. Atoms tend to reach the electronic configuration of the nearest noble gas through losing electrons, gaining electrons or sharing electrons.  1.2 Types of Chemical bonds in organic molecules: Atoms combine with each other to give compounds with different properties than the atoms they contain. The attractive force between atoms in a compound is a chemical bond. Types of bonds: a) IONIC BOND b) COVALENT BOND a) Ionic bond:  It is the force of attraction between oppositely charged ions (positive cations and negative anions) in which one or more electron is transferred from one atom to another.  Atoms involved widely differ in electronegativity.  Molecules with ionic bonds form ionic compounds.  Example: sodium chloride. b) Covalent bond:  The atoms bond by sharing electrons.  Usually occurs between nonmetals of same or similar electronegativity.  The products are called molecules.  The two atoms approach each other closely so a singly occupied orbital on one atom overlaps a singly occupied orbital on the other one. Types of covalent bonds: i) Sigma (σ) bonds the strongest covalent bonds formed by head-on overlapping of orbitals on two different atoms. A single bond is usually a σ bond. ii) Pi (π) bonds are weaker and are due to side overlap between p (or d) orbitals. A double bond between two given atoms consists of one σ and one π bond, and a triple bond is one σ and two π bonds. Valence: The number of atoms which are typically bonded to a given atom is termed the valence of that atom. A non-bonding electron is an electron not involved in chemical bonding. This can refer to:  Lone pair, with the electron localized on one atom. e.g. Nitrogen atom in ammonia (NH3), shares six valence electrons in three covalent bonds and remaining two valence electrons are nonbonding (lone pair). Theories of covalent bonding: 1. Valence bond theory and orbital hybridization 2. Mode of orbital overlap 3. Molecular Orbital (MO) Theory 1.Valence bond theory (VBT) and orbital hyberidization:  VBT states that the overlap of incompletely filled atomic orbitals leads to the formation of a chemical bond between two atoms.  The unpaired electrons are shared and a hybrid orbital is formed.  Orbital hybridization is mixing atomic orbitals to form new hybrid orbitals  New orbitals have different energies, shapes than the component atomic orbitals  Occurs through excitation of 1 or more electrons.  The number of hybrid orbitals: is equal to number of pure atomic orbitals used in hybridization process. For example, in a carbon atom which forms four single bonds the valence-shell s orbital combines with three valence-shell p orbitals to form four equivalent sp3 mixtures in a tetrahedral arrangement around the carbon to bond to four different atoms.  Types of Hybridization: 1. sp3 Hybridization It occurs when s-orbital and three p orbitals combine to form four equivalent, unsymmetrical, tetrahedral orbitals (sppp = sp3), each consisting of 25% s- character and 75% p-character. - Carbon has 4 valence electrons (2s2 2p2) - In methane (CH4), sp3 Orbitals on C-atom overlap with 1s orbitals on 4 H- atoms to form 4 identical C-H bonds, having tetrahedral shape, with H–C–H angle of 109.5° In ethane (C2H6), two C-atoms bond to each other by σ- overlap of an sp3 orbital from each.  Valence Shell Electron Pair Repulsion (VSEPR) Theory - It is used to predict the bond angles in hybridized compounds. - Outer Shell of valence electrons are present in pairs. - Electron pairs repel each other, so, they are arranged in an orientation that gives minimum repulsion. - Valence electrons may form single, double, or triple bonds or they may be unshared. - Nonbonding pair repulsion > Nonbonding-bonding repulsion > bonding pair repulsion. NH3: bond angle is 107.3° not 109.5° why? The unshared pair of electrons on the nitrogen repels adjacent electron pairs more strongly than do bonding pairs of electrons. H2O: bond angle is 104.5° not 109.5°. Distortion is greater, why? The 2 unshared pair of electrons on the oxygen repels adjacent electron pairs more strongly than do bonding pairs of electrons. H2S: bond angle is 92° not 109.5°. Why? The 2 unshared pair of electrons on the sulfur repels adjacent electron pairs more strongly than do bonding pairs of electrons. But bond angle distortion is greater than H2O, why? Difference in electronegativity between O & S atoms (O > S) makes displacement of electrons towards O in O-H bond, leaving slight +ve charge on H atoms to repel one another, keeping the bond angle maximum.