Pharm. Organic Chemistry I PDF

Pharm. Organic Chemistry I By Dr/ Ola Abdelaziz Lecturer in Organice Chemistry Faculty of Pharmacy-Mansoura university Dr Ola Abdelaziz Dr Ola Abdelaziz Dr Ola Abdelaziz  Ilentended Learninig Outcaomes (iLOs) This course enables the students to: 1. Gain an...

Pharm. Organic Chemistry I By Dr/ Ola Abdelaziz Lecturer in Organice Chemistry Faculty of Pharmacy-Mansoura university Dr Ola Abdelaziz Dr Ola Abdelaziz Dr Ola Abdelaziz  Ilentended Learninig Outcaomes (iLOs) This course enables the students to: 1. Gain an understanding of the basic principles of atomic structure. 2. Have a good idea about the Types of chemical bond and the concept of electronegativity 3. Enable the student to understand the different theories of covalent bonding 4. Recognize the methods of Drawing chemical structure organic compounds. 5. Have a good idea about the Concept of chemical reactions Teams link : Pharm. Organic Chemistry I Teams code: rdx54vf Dr Ola Abdelaziz  1. Atomic structure: 1.1 Atomic Structure: (The Nucleus) 1.2 Atomic Structure: (Orbitals ) 1.3 Atomic Structure: Electron Configuration Dr Ola Abdelaziz  Atomic structure 1. The Nucleus An atom consists of a positively charged nucleus surrounded by negatively charged electrons. The nucleus consists of Neutrons and Protons Mass number (A) indicates the total number of protons and neutrons in the nucleus. Atomic number (Z) indicates the number of protons (or electrons) in an atom Dr Ola Abdelaziz  Atomic structure 2. The Orbitals ✓ Electrons exist around the nucleus of an atom in specific orbits called levels (shells) ✓ The electron shells (levels) are labelled K, L, M, N, O, P and Q or 1,2,3,4,5,6 and 7. ✓ Each electron shell has a different energy level, shells closest to the nucleus being lower in energy than others farther from the nucleus. ✓ Shells are made up of sub-shells (sub level). These subshells are s, p, d and f Dr Ola Abdelaziz  1.2. The Orbitals 1) Level one has one sublevel s. 2) Level two has 2 sublevels s and p. 3) Level three has 3 sublevels s, p, and d 4) Level four has 4 sublevels s, p, d, and f. ✓ Sub-shells are made up of orbitals, and an orbital is a volume of space in which an electron is most likely to be found. Dr Ola Abdelaziz  Atomic structure 3. Electron Configuration The configuration that corresponds to the lowest electronic energy is called the ground-state electron configuration We can predict this arrangement by following three rules: 1. RULE 1 (Aufbau principle) 2. RULE 2 (Pauli exclusion principle) 3. RULE 3 (Hund’s principle) Dr Ola Abdelaziz  3. Electron Configuration RULE 1 (Aufbau principle) ✓ Electrons fill the lowest energy orbitals first, and then move up to higher energy orbitals. RULE 2 (Pauli exclusion principle) ✓ Electrons act as if they were spinning around an axis. ✓ Only two electrons can occupy an orbital, and they must have opposite spins Dr Ola Abdelaziz  3. Electron Configuration RULE 3 (Hund’s principle) ✓ An electron first singly fills all the orbitals with similar energy before pairing with another electron in a half-filled orbital. ✓ The negatively charged electrons firstly try to get as far as possible from each other before having to pair up. Dr Ola Abdelaziz  2. Development of Chemical Bonding Theory 2.1. The Octet rule 2.2. Types of chemical bond 2.3. Theories of covalent bonding Dr Ola Abdelaziz  The periodic table The periodic table is organized by atomic number. Elements are arranged in rows and columns: 1. A group is a column of elements with similar reactivity in the periodic table. 2. Horizontal rows are called periods of the periodic table. Dr Ola Abdelaziz  Valence electrons The term "valence electrons" is the number of electrons in the outer most energy shell. The outer shell is called the "valence shell" Every group in the periodic table has a "group valence". Group valence is used because the number of valence electrons is equal for all elements in the same group. Dr Ola Abdelaziz  Development of Chemical Bonding Theory Kekulé proposed that, in all organic compounds Carbon is tetravalent, it always forms four bonds when it joins other elements to form stable compounds. Dr Ola Abdelaziz  The Octet rule The octet rule is a chemical rule that states that atoms are most stable when their outer (valence) shells are filled with 8 electrons (8 e–). Dr Ola Abdelaziz  The Octet rule Noble gases in group 8 have a full outer, or valence shell of 8 electrons. A full valence shell is the most stable electron configuration Elements in other groups have partially filled valence shells and gain or lose or share electrons to achieve a stable electron configuration of noble gases (8 e–). Getting filled shells is also the driving force behind bonding. Dr Ola Abdelaziz  Types of chemical bond 1. Ionic bond It is formed by the transfer of one or more electrons from one atom to another to create ions: The alkali metals such as sodium in group 1 achieve a noble-gas configuration (8e-) by losing the single valence electron to form a cation (Na+) The halogens such as chlorine in group 7 achieve a noble-gas configuration (8e-) by gaining a electron to fill their valence shell and form a anion (Cl-) Dr Ola Abdelaziz  Ionic bond The (Na+) and (Cl-) , oppositely charged ions, are held together in compounds like (NaCl) by the electrostatic attraction of opposite charges that we call an ionic bond Dr Ola Abdelaziz  2. Covalent bond Covalent bond is a chemical bond formed when electrons are shared between two atoms. The bonding in methane molecule, is not ionic because it would take too much energy for carbon (2,4) to gain or lose four electrons. Herein, the carbon atom reaches noble gas configuration by sharing four electrons with four hydrogen atoms. The shared electron bond is called a covalent bond. The collection of atoms held together by covalent bonds is called a molecule Dr Ola Abdelaziz  Covalent bond The number of covalent bonds an atom can form depends on how many additional valence electrons it needs to reach a noble-gas configuration: ✓ Carbon has four valence electrons (2, 4) and needs four more electrons to reach the nobel gas configuration (2,8), so it forms four bonds. ✓ Nitrogen has five valence electrons (2,5). It needs three more electrons forming three bonds. Dr Ola Abdelaziz  Valence Bond Theory ▪ According to VB theory, a covalent bond results when two atoms approach each other then, a singly occupied orbital on one atom overlaps a singly occupied orbital on the other atom. The electrons are now paired in the overlapped molecular orbitals. ▪ For example, In the H2 molecule, the H–H Sigma bond results from the overlap of two half-filled s-orbitals. Dr Ola Abdelaziz  Valence Bond Theory Sigma and pi bonds are types of covalent bonds that differ in the overlapping of atomic orbitals: ▪ Sigma bonds are a result of direct head-on overlap of the atomic orbitals. ▪ Pi (π) bond is formed by the lateral overlap of atomic orbitals. Sigma bonds is the strongest covalent bonds, owing to the direct head-on overlapping of the atomic orbitals Dr Ola Abdelaziz  Valence Bond and Hybridization theories ▪ The VB theory would predict that C forms 2 covalent bonds. However, CH2, is a very reactive molecule, can’t exist alone Findings that lead to Hybridization theory: ▪ Modern x-ray methods proved that all C–H bonds are identical. ▪ Carbon should have 4 similar orbitals to bond equally to the four hydrogen atoms. Dr Ola Abdelaziz  2-Orbital Hybridization Theory Definition: Mixing of two or more non- equivalent atomic orbitals (e.g. s and p) to form a new set of hybrid orbitals. Number of hybrid orbitals: is equal to number of atomic orbitals used in hybridization process Dr Ola Abdelaziz  2-Orbital Hybridization Theory How? 1. The first step in hybridization is the excitation of one of the (two 2s electrons) is promoted into a vacant (2 p) orbital. 2. Then, mixing of the three atomic orbitals (2s and 2p) to form a new three hybrid orbitals Dr Ola Abdelaziz Types of hybridization: Dr Ola Abdelaziz  sp3 Hybridization It occurs when s-orbital and three p orbitals combine to form four equivalent hybrid orbitals (sp3). In methane (CH4), the 4 sp3 orbitals of C-atom overlap with 1s orbitals on 4 H-atoms. Dr Ola Abdelaziz  sp2 Hybridization It occurs when s-orbital and two p orbitals combine to form: ✓ Three hybrid orbitals (sp2) ✓ One p orbital remains unchanged. This results in a double bond. Dr Ola Abdelaziz  sp2 Hybridization In the ethylene (CH2=CH2) molecule: Two carbons with sp2 hybridization form a strong sigma (σ) bond by sp2–sp2 head-on Sigma bond overlap with each other. Each carbon forms two sigma bonds with two hydrogens by head-on overlap of the remaining sp2 orbitals with the 1s orbital Two carbons with the non-hybridized p orbitals form pi (π) bond by lateral overlap of the remaining non-hybridized p orbitals Dr Ola Abdelaziz  sp Hybridization It occurs when s-orbital and single p orbitals combine to form: ✓ two hybrid orbitals (sp) ✓ Two p orbital remains unchanged. This results in a a triple bond. Dr Ola Abdelaziz  sp Hybridization In acetylene, (CH≡CH): Two sp-hybrid orbitals on each carbon overlap head-on to form a strong sigma bond between each other. Each carbon forms a sigma bond to one hydrogen by head-on overlap of the two remaining sp hybrid orbitals with the 1s orbitals of the hydrogen Meanwhile, the two carbons form triple bond (C≡C) by lateral overlap of two unhybridized p orbitals. Dr Ola Abdelaziz  Electronegativity and Bond Polarity ❖ The C–C bond in ethane is covalent. However, the two bonding electrons are shared equally, resulting in a symmetrical electron distribution in the bond ❖ Most bonds, however, are neither fully ionic nor fully covalent but are between the two extremes. ❖ When the bonding electrons are attracted more strongly by one atom than the other, electron distribution between atoms becomes not symmetrical Dr Ola Abdelaziz  Electronegativity Electronegativity (EN) is the measure of the ability of an atom to attract the shared electrons in a covalent bond. ✓ Differences in EN produce bond polarity. ✓ Electronegativity increase a cross the period and decrease down the column. ✓ Halogens on right side of periodic table attract electrons strongly, having higher EN Dr Ola Abdelaziz  Electronegativityand Types of bond ❖ The difference in electronegativity determine the type of bond as follows 1. Nonpolar Covalent Bonds between atoms whose EN differ by < 0.5. 2. Polar Covalent Bonds between atoms EN differ by 0.5 to 2. 3. Ionic Bonds between atoms with Difference in EN > 2 Dr Ola Abdelaziz  Drawing chemical structure: 1-Kekulé (Lewis Structures) Kekulé (Lewis Structures) displays all atom and all lone pairs. Covalent bonds are shown using lines. The number of dashes indicate whether the bond is a single, double, or triple covalent bond. Dr Ola Abdelaziz  2-Condensed structure ▪ Condensed structure is the structure where single bonds aren’t shown. If a carbon has three hydrogens bonded to it, we write CH3 ▪ The compound called 2-methylbutane, for example, is written as follows Dr Ola Abdelaziz  3- skeletal structures The rules for drawing skeletal structures are: 1. RULE 1: Carbon atoms aren’t usually shown. RULE 2: Hydrogen atoms bonded to carbon aren’t shown. RULE 3: ▪ Atoms other than carbon and hydrogen are shown. ▪ Open-chain molecules are drawn out in a ‘zig-zig’ shape. Dr Ola Abdelaziz  Concept of Chemical reactions Parts of a chemical reaction In a chemical reaction: 1. The elements that interact are referred to as reactants, listed on the left side 2. The compounds formed as a result of the reaction are referred to as products, listed on the right side 3. Chemists employ chemical equation to express the reactants and products. Dr Ola Abdelaziz  Concept of Chemical reactions Example of chemical reactions In the chemical reaction between methane and oxygen, there are methane and oxygen as reactants and carbon dioxide and water as products. Dr Ola Abdelaziz  Concept of Chemical reactions The balance shows the mass of methane and oxygen on one side exactly equals the mass of carbon dioxide and water on the other. When an equation of a chemical reaction is written, it is “balanced” Dr Ola Abdelaziz Dr Ola Abdelaziz