Pharmaceutical Organic Chemistry (1) PHC111 PDF

Pharmaceutical Organic Chemistry (1) PHC111  Course Assessment Written Practical Total Midterm 25 15 40 Final 35 10 45 Attendance 5 Classwork...

Pharmaceutical Organic Chemistry (1) PHC111  Course Assessment Written Practical Total Midterm 25 15 40 Final 35 10 45 Attendance 5 Classwork 5 Participation 5  Pharmaceutical Organic Chemistry (1) Objectives: What is Organic Chemistry? Structure and Electronic Configuration of atoms. Why atoms react with each other? What happen when atoms react with each other? Chemical bonding and their occurrence. Electronegativity. Polar and non-polar compounds. Hybridization in Carbon.  Why Carbon? Carbon is one of the most common elements in the periodic table. Carbon can form many diverse structures (proteins, carbohydrates, DNA, fats,vitamins….) possessing chemical and biological activities. Charcoal Diamond  Structure of Atom An atom consists of Nucleus surrounded by Electrons. Nucleus: Contains protons and neutrons. Protons are positively charged (+) while neutrons are electrically neutral (±). Total charge of nucleus is positive. Total number of protons and neutrons represent the mass number of the atom.  Electrons: Arranged in Seven Energy levels (Shells) denoted by principle quantum numbers (n) (1/2/3/4/5/6/7) or Letters (K/L/M/N/O/P/Q). Electrons are negatively charged (-). The number of electrons is equal to the number of protons, and this represents the atomic number of the atom. Each level can contain up to 2n2 electrons [n = quantum number], and is occupied by maximum number of electrons. K Level: occupies only two electrons. i.e 2n2 = 2(1 2) L Level: occupies only eight electrons. i.e 2n2 = 2(2 2) M Level: occupies only eighteen electrons. i.e 2n2 = 2(3 2) Atomic number and Mass number Each atom is characterized by two numbers: Atomic number and Mass number. Example: 12C6 and 13C6 (6 is the atomic number while 12 or 13 is the mass number) 12C and 13C are known as ISOTOPES. 6 6 Isotopes have same atomic number but different mass number. They differ in number of neutrons. What is the relationship between 1H1 and 2H1? (1H1 is Hydrogen while 2H1 is Deuterium) Select the correct answer/s Isotopes 1- have same atomic number but differs in mass no 2- have same mass number but differs in atomic no 3- have different no of neutrons 4- 12C and 13C are examples  Video showing atomic structure https://youtu.be/TYEYEIuTmGQ?si=hmnF2BVWs9iazrx_  Electronic Distribution Each Level is divided into number orbitals: s orbital can accommodate 2 electrons s2. p orbital can accommodate 6 electrons p6. d orbital can accommodate 10 electrons d10. f orbital can accommodate 14 electrons f14. The K level has one orbital (s) [1s2]. The L level has two orbitals (s and p) [2s2 2p6] or [2s2 2px2 2py2 2pz2]. *RULES The orbital fill order is from lowest energy to highest energy level Since each orbital cannot accommodate more than two electrons of antiparallel spin (paired electrons), therefore p orbital is subdivided into 3 orbitals px , py , pz. If orbitals having same energy level like px, py, pz but not enough electrons are present , the one electron is added to each orbital before a second one is added to pair anyone of them. Shapes of atomic orbitals  Electronic Configurations Electron Configurations in the Periodic Table: Atoms are arranged in the periodic table according to the increase in atomic number. 1A 2A 3A 4A 5A 6A 7A 8A 1 2 H He 1s1 1s2 3 4 5 6 7 8 9 10 Li Be B C N O F Ne 1s2 1s2 1s2 1s2 1s2 1s2 1s2 1s2 2s1 2s2 2s22p1 2s22p2 2s22p3 2s22p4 2s22p5 2s22p6 11 12 13 14 15 16 17 18 Na Mg Al Si P S Cl Ar [Ne] [Ne] [Ne] [Ne] [Ne] [Ne] [Ne] [Ne] 3s1 3s2 3s23p1 3s23p2 3s23p3 3s23p4 3s23p5 3s23p6 Electronic Configuration: This configuration represents the atom in the ground state (i.e. before entering in the chemical reaction).  Why atoms react with each other? They react with each other to attain the stable electronic configuration. Notice that: 1) Helium has K level completely filled with 2 electrons i.e. has Doublet stable configuration. There is no need to gain or lose electrons, so it is inert. 2) Neon has K (2 electrons) & L (8 electrons) levels completely filled with electrons i.e. has Octet stable configuration. There is no need to gain or lose electrons, so it is inert. How they react? The highest occupied electron shell is called the valence shell, and the electrons occupying this shell are called valence electrons. Atoms can attain the stable electronic configuration by either Gain or Loss or sharing of electrons of the outer level. [octet rule and doublet rule] A) Atoms that lose of electrons of the outer level: 3Li: 1s2 2s1 Loses one electron and becomes Li+ cation (1s2) 4Be: 1s2 2s2 Loses two electrons and becomes Be2+ cation (1s2) 5B: 1s2 2s2 2px1 Loses three electrons and becomes B3+ cation (1s2) B) Atoms that gain electrons in the outer level: N: 1s2 2s2 2px1 2py1 2pz1 Gains 3 electrons and becomes N3- anion (1s2 2s2 2p6) 7 O: 1s 2 2s2 2px2 2py1 2pz1 Gains 2 electrons and becomes O2- anion (1s2 2s2 2p6) 8 F: 1s 2 2s2 2px2 2py2 2pz1 Gains one electron and becomes F1- anion (1s2 2s2 2p6) 9 C) Carbon and Sharing of electrons In carbon both possibilities of gain or loss of electrons are equal; therefore, it can attain the stable electronic configuration by sharing of electrons with other atoms. Hydrogen has the ability to share or gain or lose one electron: H 1 : Hydrogen atom (H) 1 H2 : Hydrogen molecule (H – H) H+ : Proton (Loss of 1 electron) :H- : Hydride (Gain of 1 electron).H : Hydrogen Free Radical (equal breaking of H – H) What happen when atoms react with each other? They form Chemical Bonds. What are the types of Chemical Bonds? 1- Ionic bonds. 2- Covalent bonds. A- Non-polar covalent bonds. B- Polar Covalent bonds. 3- Hydrogen bonds. 4- Co-ordinate bonds.  1- Ionic Bond Manifested by electron transfer between two atoms according to their valencies. Occurs between two atoms with different electronegativity > 1.7 Takes place between cation and anion. Ex: Formation of Lithium Fluoride Li+F- N.B: Valency (gain, lose, share) Monovalent: Divalent, tetravalent, pentavalent  Ionic Bond Test Yourself: Stepwise the formation of ionic bond in NaCl Electronegativity of sodium is 0.9 and of Cl is 3, the difference is >1.7 , therefor ionic bond is formed  2- Covalent Bond Involves sharing of electron pairs between atoms of equal or similar electronegativity. A covalent bond may be: Single bond: sigma bond (σ- bond) C – C. Double bond: one sigma bond (σ- bond) and one Pi bond (π- bond) C = C. Triple bond: one sigma bond (σ- bond) and two Pi bonds (2 π- bond) C ≡ C. It happens by overlap of atomic orbitals (hybridization)[sigma overlap (2 s orbitals, 1s and 1 p, or 2 p orbitals head to head), pi overlap is between two p orbitals side to side. A covalent bond may be: A] Non-polar covalent bond: sharing of electron pairs equally between two atoms of equal electronegativity(EN);or