Organic Chemistry Introduction PDF

Greetings! Carbon-based bipeds! Arthur Clarke, British Sci-Fi Writer  PHARMACEUTICAL ORGANIC CHEMISTRY UNIT 1. INTRODUCTION Prepared by Romuelle B. Barbado, RPh Faculty, College of Pharmacy Prepared by Romuelle B. Barbado, RPh - for UCU-COP student...

Greetings! Carbon-based bipeds! Arthur Clarke, British Sci-Fi Writer  PHARMACEUTICAL ORGANIC CHEMISTRY UNIT 1. INTRODUCTION Prepared by Romuelle B. Barbado, RPh Faculty, College of Pharmacy Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. OUTLINE  Introduction to Organic Chemistry  Inorganic compounds vs. Organic compounds  Uniqueness of Carbon  Structure and Bonding  Periodic Table  Bonding  Lewis Structures  Resonance  Determining Molecular Shape  Drawing Organic Structures  Bond length and Bond Strength  Electronegativity and bond Polarity  Formal charge  Polarity of Molecules Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. ORGANIC CHEMISTRY  Organic chemistry is the study of the structure, properties, composition, reactions, and preparation of carbon-containing compounds (organic compounds).  Organic compounds are defined as compounds containing carbon  Except for CO2, CO, CO32-, CN, and HCO3  These substances are considered inorganic because they do not contain both carbon and hydrogen in their structure, or their carbon does not have the ability to show catenation, or they are isolated from non-living systems  Most organic compounds contain carbon and hydrogen, but they may also include any number of other elements (e.g., nitrogen, oxygen, halogens, phosphorus, silicon, sulfur).  In contrast, an inorganic compound is defined as a compound Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. ORGANIC CHEMISTRY Organic Compound Inorganic Compound Organic compounds are composed Inorganic compounds are of carbon, hydrogen and oxygen composed of atoms usually other primarily than carbon The nature of inorganic compounds The nature of organic compounds can be electrovalent, ionic, or is covalent due to C-H bonding covalent Melting and boiling points of Melting and boiling points of organic compounds are low inorganic compounds are higher Their solubility in water is low Their solubility in water is high They are bad conductors of heat Inorganic compounds are usually (but usually flammable) and good conductors *because most electricity contain metals  Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. ORGANIC CHEMISTRY Organic Compound Inorganic Compound They have catenation property due Only some inorganic compounds to C have catenation properties Most of these compounds are Inorganic compounds generally colorless have colors Their rate of reactions is generally Their rate of reaction is fast slow These compounds are mostly These compounds are mostly found in living things found in non-living things Most organic compounds are Inorganic compounds are generally biodegradable environment un-friendly Examples of organic compounds Examples of inorganic compounds Reference: Psiberg (2022). Organic vs. Inorganic Compounds: The Main Differences. Retrieved from https://psiberg.com/organic-vs- Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. ORGANIC CHEMISTRY: HISTORY Jöns Jacob Berzelius  First coined the term “organic chemistry” in 1806 for the study of compounds derived from biological sources.  During the 19th century (1800s), chemists noted that there seemed to be an essential yet inexplicable difference between the properties of the two different types of compounds (inorganic vs organic). Baron Jöns Jacob  The vital force theory, sometimes called Berzelius, Swedish Chemist “vitalism” (vital means “life force”), was proposed, and widely accepted, as a way to explain these differences, that a “vital force” existed within organic material but did not exist in any inorganic Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. ORGANIC CHEMISTRY: HISTORY Vital Force Theory  The vital force theory stated that organic compounds could not be made in a lab, but needed a mysterious, God-given power that was found only in living organisms.  Simply, it states that an organic compound is formed and synthesized only within living species( plants and animals ). Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. ORGANIC CHEMISTRY: HISTORY Friedrich Wöhler  In 1828, the “Vital Force Theory” was discredited by Friedrich Wöhler  In that year, Wöhler heated an inorganic salt called ammonium cyanate and was able to produce urea, a compound commonly found in blood and urine. Friedrich Wöhler, German Chemist  Wöhler’s urea synthesis proved that organic compounds can also be produced in laboratories. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. UNIQUENESS OF CARBON Carbon  The 6th element in the periodic table  One of the most common elements found in living organisms  In Octet rule, carbon shares 4 electron via covalent bonding  Carbon can form a combination of single, double, and triple covalent bonds with other atoms.  Catenation: ability of carbon to bond successively with other carbon atoms to form chains or even rings of various sizes, making carbon the “King of all Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. UNIQUENESS OF CARBON Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. TOPIC QUIZ A. Classify each of the following compounds as organic or inorganic: 1. NaCl 2. CH4 3. C6H6 4. NaOH 5. CH3OH 6. Mg(NO3)2 7. Glucose B. Decide whether each of the following characteristics most likely describe an organic or inorganic compound: 8. Flammable 9. Low boiling point 10. Soluble in water Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS  Chemical bonds hold molecules together as a result of interaction between electrons located in the atomic orbitals (region of atom where electrons are can be found)  Also termed as forces of attraction  Two types of chemical bonds:  Intramolecular Bonds: bonds that hold a molecule together. Simply, it is the bond ‘within’ the molecule itself.  Intermolecular Bonds: bonds that hold 2 or more molecules together. Simply, it is the bond ‘between’ numerous molecules. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intramolecular Bonds IONIC BOND: There is a transfer of electrons between a metallic (cations) and a non-metallic element (anions) - An example can be seen between the interaction of Na+ and Cl- to form NaCl. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intramolecular Bonds COVALENT BOND: There is a sharing of elections between two non- metallic elements. An example is water. There are two types of covalent bond: polar and non-polar covalent bonds. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intramolecular Bonds DEFINITION OF TERMS:  POLAR: molecules CONTAINING a positive and a negative end  NON-POLAR: molecules NOT CONTAINING a positive and a negative end Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intramolecular Bonds POLAR COVALENT BOND: Electrons are shared unequally, as in HCl. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intramolecular Bonds NON-POLAR COVALENT BOND: Electrons are shared equally, as in Cl2. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intermolecular Bonds HYDROGEN BOND: the bond formed between a hydrogen atom and an electronegative atom such as F, O, N, S, or an electronegative atom in another molecule.  This is the strongest of the dipole-dipole (polar-polar) interactions  This bond can be seen in water. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intermolecular Bonds ION-DIPOLE BOND: a bond between an ion and a polar molecule.  Ion: An atom with unequal numbers of proton and electron causing it to have a charge either positive or negative.  Dipole/ Polar molecule: a molecule containing two charges due to unequal distribution of electrons.  Ion-dipole bond can be seen in the interaction between Na and water. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intermolecular Bonds ION-INDUCED DIPOLE BOND: a bond between an ion and a non- polar molecule.  Induced Dipole/ Non-Polar molecule: a molecule containing no charges due to equal distribution of electrons. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intermolecular Bonds VAN DER WAALS FORCES London Dispersion: Bond between two non-polar molecules  Also known as: Induced Dipole-Induced Dipole interaction  Proposed by Fritz London Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intermolecular Bonds VAN DER WAALS FORCES Debye Induction Force: Bond between a polar and a non-polar molecule  Also known as: Dipole- Induced Dipole interaction  Proposed by Peter Debye Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. CHEMICAL BONDS: Types of Intermolecular Bonds VAN DER WAALS FORCES Keesom Orientation Force: Bond between 2 polar molecules  Also known as: Dipole-Dipole Interaction  Proposed by Willem Hendrik Keesom Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. VALENCE BOND THEORY Valence bond theory  States that bonds are formed by sharing of electron from overlapping atomic orbitals (covalent)  Atomic orbitals are the region of atom where electrons can be found  When a covalent bond is formed, the atomic orbitals overlap to form a combined orbital containing two electrons  This new orbital is called the molecular orbital  The shape of the molecular orbital is dependent on the shape of the atomic orbitals that combined  The greater the atomic orbital overlap, the stronger the bond  There are two main types of molecular orbital: a sigma (σ) bond Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. TYPES OF MOLECULAR ORBITALS Sigma Bonds (σ) Pi (π) Bonds The bond in single bonds Forms after sigma bonds The first bond to form Only found within double and Stronger and longer bond triple bonds compared to pi bonds Weaker than sigma bonds and are Forms when atomic orbitals are easier to break hybridized (combined) Forms when orbitals are  Formed from the head-on / end- unhybridized (not combined) to-end combination or overlap of Formed from the lateral atomic orbitals (sideways) combination or overlap of adjacent p orbitals Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. TYPES OF MOLECULAR ORBITALS Unhybridized/ not combined Hybridized/ combined Unhybridized/ not combined Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. TYPES OF MOLECULAR ORBITALS Hydrogen Molecule (H2) H + H H-H Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. TYPES OF MOLECULAR ORBITALS Ethene Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. TYPES OF MOLECULAR ORBITALS Ethyne Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. HYBRIDIZATION Hybridization is the idea that atomic orbitals fuse to form newly hybridized orbitals, which in turn, influences molecular geometry (shape of molecule) and bonding properties.  There are three types of hybridization:  Sp3: 4 hybridized orbitals and 0 unhybridized orbitals  4 sigma bonds & 0 pi bond  Sp2: 3 hybridized orbitals and 1 unhybridized orbital  3 sigma bonds & 1 pi bond  Sp: 2 hybridized orbitals and 2 unhybridized orbitals  2 sigma bonds & 2 pi bonds Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. HYBRIDIZATION Sp3: 4 hybridized orbitals and 0 unhybridized orbitals  4 sigma bonds & 0 pi bond Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. HYBRIDIZATION Sp2: 3 hybridized orbitals and 1 unhybridized orbital  3 sigma bonds & 1 pi bond Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. HYBRIDIZATION Sp: 2 hybridized orbitals and 2 unhybridized orbitals  2 sigma bonds & 2 pi bonds Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. HYBRIDIZATION Activity: Determine the hybridization of each carbon atom in the molecule. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. HYBRIDIZATION Activity: Determine the hybridization of each carbon atom in the molecule. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. PERIODIC TABLE Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. PERIODIC TABLE (Concept Recall) Valence Electrons: are the electrons located at the outermost shell of an atom.  When two atoms interact, the electrons in the outermost shells are the first ones to come into contact with each other and are the ones that determine how an atom will react in a chemical reaction.  The valence electrons are involved in bonding one atom to another.  Each group of elements have their own valence electrons:  Group IA: 1 Tends to give their valence  Group IIA: 2 electrons  Group IIIA: 3 Tend to share  Group IVA: 4  Group VA: 5 Tends to accept their valence  Group VIA: 6 electrons  Group VIIA: 7 Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. LEWIS STRUCTURE Lewis Dot Structure/Diagram: used to show how the electrons are arranged around individual atoms in a molecule.  Electrons are shown as "dots" or for bonding electrons as a line between the two atoms. H He Li Be B C N Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. LEWIS STRUCTURE Draw the Lewis structure of nitrate ion (NO3-): 1. First determine the total number of valence electrons in the molecule. This will be the sum of the group number a of all atoms plus the charge. N = 5 Ox3 = 18 Charge =1 24 2. Draw a skeletal structure for the molecule which connects all atoms using only single bonds. The central atom will be the one that can form the greatest number of bonds and/or expand its octet. This usually means the atom lower and/or to the right in the Periodic Table, N in this case Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. LEWIS STRUCTURE Electrons move from an area of high electrons to an area of low Draw the Lewis structure of nitrate ion (NO3electrons, - ): or simply from negative to positive. 3. Now we need to add lone pairs of electrons. Of the 24 valence electrons available in NO3-, 6 were used to make the skeletal structure. Add lone pairs of electrons on the terminal atoms until their octet is complete or you run out of electrons. 3. 4. 4. If there are remaining electrons they can be used to complete the octet of the central atom. If you have run out of electrons you are required to use lone pairs of electrons from a terminal atom to complete the octet on the central atom by forming multiple bond(s). In this case the N is short 2 electrons so we can use a lone pair from the left most O Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. LEWIS STRUCTURE Draw the Lewis structure of nitrate ion (NO3-): 5. Now you need to determine the FORMAL CHARGES for all of the atoms. The formal charge is calculated by: (group number of atom) - (½ number of bonding electrons) - (number of lone pair electrons), i.e. see the figure below. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. FORMAL CHARGE Formal Charge: A formal charge (FC) is the charge assigned to an atom in a molecule, assuming that electrons in all chemical bonds are shared equally between atoms, regardless of relative electronegativity.  No Lewis structure is complete without the formal charges.  In general  the fewest number of formal charges possible, i.e. formal charges of 0 for as many of the atoms in a structure as possible.  the formal charges should match the electronegativity of the atom, that is negative charges should be on the more electronegative atoms (e.g. Oxygen should be more negative than Nitrogen) and positive charges on the least electronegative atoms if possible. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. QUESTION Is this the only possible structure of the nitrate ion? NO Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. RESONANCE Resonance is a way of describing delocalized electrons within certain molecules or polyatomic ions where the bonding cannot be expressed by a single Lewis formula.  Equivalent Lewis dot structures, such as those of above, are called resonance structures.  The position of the atoms is the same in the various resonance structures of a compound, but the position of the electrons is different. Double-headed arrows link the different resonance structures of a compound: Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. RESONANCE Rules of Resonance Forms: 1. Individual resonance forms are imaginary, not real. -The real structure is the hybrid of the structural forms. 2. Resonance forms differ only in the placement of the pi bonds or non- bonding electrons. 3. Different resonance forms of a substance don’t have to be equivalent (e.g. different in charges on the same atom) 4. Resonace forms obey normal rules of valency 5. The resonance hybrid is more stable than any individual resonance form. Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. LEWIS STRUCTURE Draw the Lewis structure of water: Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. LEWIS STRUCTURE Draw the Lewis structure of carbon dioxide: Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. LEWIS STRUCTURE Draw the Lewis structure of acetate ion (CH3COO-): Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. DRAWING ORGANIC STRUCTURES Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. MOLECULAR GEOMETRY Prepared by Romuelle B. Barbado, RPh - for UCU-COP students use only. Reproduction without permission is strictly prohibited. POLARITY OF MOLECULES