Organic chemistry for medicine and biology students Chem 2311 Chapter 1 Introduction By Prof. Dr. Adel M. Awadallah Islamic University of Gaza 1

Chapter 1 Bonding and Isomerism Atoms consist mainly from a)Nucleus: (containing Protons and Neutrons) Protons (positive particles, Atomic Number) Neutrons (Neutral particles) Protons + Neutrons (Atomic weight) b) Electrons: negatively charged particles 2

Electronic Configuration (review) 1)Shells (n = 1,2,3,4, ….) 2)(Subshells, s, p, d, f) 3)(orbitals: rgions of space around the nucleus containing electrons) 4)each orbital contains only 2 electrons with different spins Name of orbitalsNumber of orbitals (electrons)Subshell s1 (2)S P x, p y, p z 3 (6)P D xy, d yz, d xz, d z 2, dX 2 -y 2 5 (10)d 3

Examples: Filled Shells Play almost no role in chemical reaction Valence Electrons They are the outermost electrons and they are mainly involved in chemical bonding 4

Ionic Compounds They are formed by the transfer of one or more valence electrons from one atom to another Electropositive atoms: give up electrons and form cations. Electronegative atoms: accept electrons and form anions Ionic compounds: are composed of positively charged cations and negatively charged cations 5

Covalent compounds A covalent bond: is formed when two atoms share one or more electron pairs. A molecule consists of two or more atoms joined by covalent bonds Bond energy: is the energy necessary to break a mole (6.022 x )of covalent bonds. Bond length: is the average distance between two covalently bonded atoms 6

Valence and bonding in organic compounds 7

Polarity of Bonds: depends on the electronegativity difference 8

Examples: 9

Polarity of Molecules: depends on the sum of the polarity of bonds (geometry) 10

Isomers: different compounds having the same molecular formula 11

Abbreviated structural formulas 12

Formal Charges: are the charges that each atom carries, and can be calculated as follows Formal charge = Valence electrons – bonds – electrons Example: Resonance: arises whenever we can write two or more structures for a molecule with different arrangements of electrons but identical arrangement of atoms 13

Arrows: 14

The orbital view of bonding 15

Orbital picture of Methane and ethane The bond formed by end-to-end overlap is called a sigma bond. 16

Bond Angles in Methane 17

Bonding in Ethylene (ethene) 18

A pi bond is one in which the electrons in the p orbitals are held above and below the plane of the molecule. The sigma bond is stronger than the pi bond. A double bond is formed from a sigma bond and a pi bond, and so it is stronger than a single bond. 19

Bonding in acetylene (ethyne) 20

Classification of organic compounds according to functional groups 21