Lecture 1_Introduction to Organic Chemistry (1) PDF

Pharmaceutical Organic Chemistry PHARM202 Fall Semester 2024-2025 Level-3 PHARMD Introduction to Organic Chemistry Presented by: Dr. Majidah Alsaeedi Structure and Bonding An atom consists of a small, dense nucleus containing positively charged protons and neutral...

Pharmaceutical Organic Chemistry PHARM202 Fall Semester 2024-2025 Level-3 PHARMD Introduction to Organic Chemistry Presented by: Dr. Majidah Alsaeedi Structure and Bonding An atom consists of a small, dense nucleus containing positively charged protons and neutral neutrons and surrounded by negatively charged electrons. Different types of atom have different numbers of protons, neutrons, and electrons. For example, carbon atoms have 6 protons, 6 neutrons, and 6 electrons.  Structure and Bonding The atomic number of an element equals the number of protons in its nucleus; its mass number is the sum of the number of protons and neutrons in its nucleus. Electrons are located in orbitals. Orbitals are grouped in shells (s, p, d, f).  The first shell (n = 1) has only an s orbital, 1s The second shell (n = 2) has s and p orbitals 2s and 2p The third shell (n = 3) has s, p, and d orbitals, 3s, 3p, and 3d Electronegativity Electronegativity is the power of an atom to attract electron density in a covalent bond The higher the value, the ✔ Fluorine is the most electronegative more electronegative element element. ✔ It has an electronegativity value of 4.0 Pauling’s Electronegativity Scale Electronegativity Increases Electronegativity Increases  Ionic Bonds The reaction between Na and Cl atoms to form NaCl (table salt) is a typical electron-transfer reaction Cation Anion Ionic bonds involve a cation & an anion. The bond is formed when an atom, typically a metal e.g. Na, give up an electron or electrons, and becomes a positive ion, or cation. Another atom, typically a nonmetal e.g. Cl, is able to accept the electron(s) to become a negative ion, or anion. Ionic and Covalent Bonding Ionic bonds are formed by the transfer of one or more valence electrons from one atom to another. The atom that gives The atom that up electrons receives electrons becomes positively becomes negatively charged, a cation. charged, an anion  Covalent bonds Nonpolar A pair of electrons is shared between two atoms. Each atom donates one electron, and a single line represents the two-electron bond. Very strong bonds require large energy to break Important in biology e.g. O2 and peptide bond (chains of amino acid)  Covalent bonds Polar The electron pair is not shared equally between the two atoms. The atoms that are linked carry a partial negative and a partial positive charge. Your life actually depends on polar covalent bonding, e.g. H2O Summary Hydrogen Bonding Attraction between the slightly negative oxygen of one molecule & the slightly positive hydrogen of another. Because of their partial positive & negative charges, polar molecules such as water can attract each other. H- Bonds are weak. Covalent bond  Hybridization ❖ Hybridization is defined as the intermixing of atomic orbitals with the same energy levels to give the same number of a new type of hybrid orbitals. ❖ This intermixing usually results in the formation of hybrid orbitals having entirely different energies, shapes, etc. Types of Hybridization: sp³ hybridization: When one s orbital and three p orbitals from the same shell of an atom mix together to form a new equivalent orbital then this is called sp³ hybridization. Example: CH4 sp² hybridization: When one s orbital and two p orbitals from the same shell of an atom mix2 together to form a new equivalent orbital then this is called sp hybridization. Example: C2H4 sp hybridization: When one s and one p orbital from the same shell of an atom mix together to form a new equivalent orbital then this is called sp hybridization. Example: C2H2 In the molecule CH4, what type of hybridization occurs in carbon? Summary of covalent bonding and hybridization https://www.youtube.com/watch?v=_OZQbemzx_c  Hydrocarbons Aliphatic Aromatic Unsaturated Saturated Unsaturated Cyclic Alkane Alkene Alkayne Single bond Double bond Triple bond Acyclic Cycloalkane ❖ Acyclic compounds contain chains of carbon atoms and no rings. ❖ Carbocyclic compounds contain rings of carbon atoms.  INTRODUCTION AND STRUCTURE OF ALKANES Alkanes are hydrocarbons in which all bonds are single covalent bonds (σ-bonds). Alkanes are called saturated hydrocarbons. Alkanes have the general molecular formula CnH2n+2. sp3 hybridization is found in the carbon atom of all alkanes Example: Methane, Ethane, Propane and Butane etc.  Nomenclature Suffix is -ane The substituent are those group Number of Parent Number of Parent which bonded to parent chain may Carbons Carbons be halogen atom or any alkyl 1 meth 12 dodec group etc. 2 eth 13 tridec 3 prop 14 tetradec 4 but 15 pentadec 5 pent 16 hexadec 6 hex 17 heptadec 7 hept 18 octadec 8 oct 19 nonadec 9 non 20 eicos 10 dec 21 unicos 28 11 undec 22 doicos Substituents: It can be represented as R (Alkyl group) According to IUPAC : Find the longest continuous chain of carbon atoms. Use a parent corresponding to the number of carbons in the longest chain of carbons. Follow the parent with the suffix of “ane” for alkanes Write the name of substituents before the parent name. Number the carbons, starting closest to the first branch. Name the substituent's attached to the chain, in alphabetical order. Use di-, tri-, etc., for multiples of same substituent. If there are two possible chains with the same number of carbons, use the chain with the most substituent's. IUPAC Nomenclature of Unbranched Alkanes IUPAC Names of Unbranched Alkanes  Physical Properties of Alkane Alkanes are almost totally insoluble in water because of their very low polarity and their inability to form hydrogen bonds. The alkanes are the least dense of all groups of organic compounds. The boiling points of the unbranched alkanes show a regular increase with increasing molecular weight. Melting points increase with increasing carbons. INTRODUCTION AND STRUCTURE OF CYCLOALKANES Cycloalkanes are hydrocarbons in which all Carbon atoms form the cycle and are in the state of sp3-hybridization. Cycloalkanes are saturated hydrocarbons. Cycloalkanes have the general molecular formula CnH2n. Example : Cyclopropane, Cyclobutane and cyclopentane etc.  NOMENCLATURE OF CYCLOALKANES Are named by using the prefix cyclo- before the name of the alkane chain with the same number of carbon atoms.  Physical properties of Cycloalkane Cyclopropane and cyclobutane are gases at room temperature while cyclopentane is already liquid at this temperature. Because of symmetry and hindered rotation, the melting and boiling points of cycloalkanes are higher when compared to the corresponding n-alkanes. They are Nonpolar and insoluble in water.  Introduction to Alkenes They are unsaturated hydrocarbons – made up of C and H atoms and contain one or more C=C double bond somewhere in their structures. Their general formula is CnH2n - for non-cyclic alkenes. Example: Ethene-C2H4 Their general formula is CnH2n-2 - for cyclic alkenes. Example: Cyclohexene- Alkenes are also called olefins, meaning “oil-forming gas”. The functional group of alkenes is the carbon-carbon double bond, which is reactive. Benzenes are aromatic compounds and they do not considered as an alkene because they react differently than alkenes 36  IUPAC Nomenclature of Alkenes Find the longest continuous carbon chain that includes the double-bonded carbons. -ane changes to -ene. Number the chain so that the double bond has the lowest possible number. In a ring, the double bond is assumed to be between Carbon 1 and Carbon 2. Example:  Physical Properties of Alkenes Boiling point increases as mass increases. Branched alkenes have lower boiling points. They are less dense than water. Slightly polar: Pi bond is polarizable. Cis alkenes have a greater dipole moment than trans alkenes, so they will be slightly polar. So the boiling point of cis alkenes will be higher than the trans alkenes.  Introduction to Alkynes An alkyne is an unsaturated hydrocarbon containing at least one carbon—carbon triple bond between two carbon atoms. The General chemical Formula of alkyne is CnH2n-2. Acetylene (Ethalyne) (H—C ≡ C—H ) is the simplest alkyne. “Terminal” alkynes have the triple bond at the end of the chain. Example: An internal alkyne is an alkyne in whose molecule there are no hydrogen atoms bonded to triply bonded carbon atoms. Example:  Electronic Structure of Alkynes Each carbon of Carbon-carbon triple bond is sp hybridized and have linear shapes. sp hybridized orbital on each C forming a sigma bond at 180º. The formed C-C triple bond is shorter and stronger than single or double.  Nomenclature General hydrocarbon rules apply with “-yne” as a suffix indicating an alkyne. Numbering of chain with triple bond is set so that the smallest number possible include the triple bond. CH3CH2C≡CCH3 2-pentyne CH3CH2C≡CH - 1-butyne HC≡CCH(CH3)CH2CH3 3-methyl-1-pentyne 3-Nonyne  Physical properties Alkynes have physical properties similar to those of corresponding alkanes. Alkynes up to four carbons (except 2-butyne will be liquid ) are gases at room temperature. Being relatively nonpolar themselves, alkynes dissolve in nonpolar solvents (such as alkane and aromatic) or in solvents of low polarity. Alkynes are very slightly soluble in water. The densities of alkenes and alkynes are lower than that of water. Regarding the 3 following structures answer the questions below alkane alkene alkayne 1.What is the difference you observe between the three compounds? 2.How can you define unsaturated hydrocarbons? contains more the bond one 43  Introduction to Arenes or Aromatic Compounds An aromatic hydrocarbon or arene (or sometimes aryl hydrocarbon) is a hydrocarbon with alternating double and single bonds between carbon atoms forming rings. Example:  Nomenclature of Arenes 1. Monosubstituted benzenes (a) For certain compounds, benzene is the parent name and the substituent is simply indicated by a prefix. (b) For other compounds, the substituent and the benzene ring taken together may form a new parent name. 2. Polysubstituted benzenes (a) If more than one substituent are present and the substituents are identical, their relative positions are indicated by the use of numbers assigned on the ring. The prefixes ‘di-’, ‘tri-’, ‘tetra-’, and so on are used. (b)When more than one substituent are present and the substituents are different, they are listed in alphabetical order. (c) When a substituent is one that when taken together with the benzene ring gives a new parent name, that substituent is assumed to be in position 1 and the new parent name is used.  Ortho, meta and para position Relative positions on a disubstituted benzene ring: ortho- (o) on adjacent carbons (1,2 or 1,6 disubstituted). meta- (m) separated by one carbon (1,3 or 1,5 disubstituted). ortho- meta- para- 1,2- 1,3- 1,4- para- (p) separated by two carbons (1,4 disubstituted).