Introduction to Organic Chemistry - PDF

MARINDUQUE STATE UNIVERSITY COLLEGE OF AGRICULTURE Introduction to Organic Chemistry NATURAL SCIENCES 2 PREPARED BY CLARISSE JESSICA A. MAYORES, RMT INSTRUCTOR Phone | 0960-585-6131 Email | mayores.clarissejessica@mscmarindu...

MARINDUQUE STATE UNIVERSITY COLLEGE OF AGRICULTURE Introduction to Organic Chemistry NATURAL SCIENCES 2 PREPARED BY CLARISSE JESSICA A. MAYORES, RMT INSTRUCTOR Phone | 0960-585-6131 Email | [email protected] Profile Clarisse Jessica A. Mayores, RMT November 9, 2001 | 22 years old Address: Dolores, Santa Cruz, Marinduque Contact No.: 09605856131 Email Address: [email protected] EDUCATION: Bachelor of Science in Medical Technology Faculty of Pharmacy, University of Santo Tomas Magna Cum Laude Year of Graduation: 2024 AUGUST 2024 MEDICAL TECHNOLOGY LICENSURE EXAMINATION (MTLE) BOARD PASSER  Course Orientation MAYORES, CLARISSE JESSICA ARELLANO 2A/B/C Bachelor of Science in Agriculture Recitation Points Signature Recitation Points Signature RECAP  MATTER Table 1. Differences between Mixtures and Compounds 03 https://unacademy.com/content/upsc/study-material/ncert-notes/science-class-9-pure-substance-vs-mixture/ ATOM the smallest unit of matter that can't be divided by chemical means and has unique properties. Table 2. Properties and Location within Atoms of Protons, Neutrons, and Electrons 03 https://www.expii.com/t/electrons-structure-properties-8610 Periodic Table of Elements In 1860s, Russian Scientist Dmitri Mendeleev (1834-1907), then professor of chemistry at the University of St. Petesburg, produced one of the first periodic table. 118 Elements 03 https://www.modelscience.com/PeriodicTable.html  The periodic table is organized into several key parts, each with its own significance: Periods: These are the horizontal rows Groups: These are the vertical columns, in the periodic table. There are seven also known as families. There are 18 periods, and each period indicates the groups, and elements in the same number of electron shells in the atoms group have the same number of of the elements within that row. valence electrons, which gives them similar chemical properties. 03 https://www.modelscience.com/PeriodicTable.html  GROUPS IN THE PERIODIC TABLE OF ELEMENTS Group 1: Alkali Metals Elements: Lithium (Li), Sodium (Na), Potassium (K), Rubidium (Rb), Cesium (Cs), Francium (Fr) Properties: Highly reactive, especially with water; soft metals; low density; form +1 cations. Group 2: Alkaline Earth Metals Elements: Beryllium (Be), Magnesium (Mg), Calcium (Ca), Strontium (Sr), Barium (Ba), Radium (Ra) Properties: Reactive, but less so than alkali metals; harder and denser than Group 1 metals; form +2 cations. Group 3-12: Transition Metals Elements: Includes Scandium (Sc), Titanium (Ti), Vanadium (V), Chromium (Cr), Manganese (Mn), Iron (Fe), Cobalt (Co), Nickel (Ni), Copper (Cu), Zinc (Zn), etc. Properties: Form various oxidation states; often form colored compounds; good 03 conductors of heat and electricity; metals with high melting points and densities.  GROUPS IN THE PERIODIC TABLE OF ELEMENTS Group 13: Boron Group Elements: Boron (B), Aluminum (Al), Gallium (Ga), Indium (In), Thallium (Tl) Properties: Vary from metalloids (Boron) to metals (Aluminum, Gallium, Indium, Thallium); form +3 cations. Group 14: Carbon Group Elements: Carbon (C), Silicon (Si), Germanium (Ge), Tin (Sn), Lead (Pb) Properties: Vary widely from nonmetals (Carbon) to metals (Lead); form +4 or +2 cations. Group 15: Nitrogen Group Elements: Nitrogen (N), Phosphorus (P), Arsenic (As), Antimony (Sb), Bismuth (Bi) Properties: Includes nonmetals (Nitrogen, Phosphorus), metalloids (Arsenic, Antimony), and metals (Bismuth); form -3, +3, and +5 oxidation states. 03  GROUPS IN THE PERIODIC TABLE OF ELEMENTS Group 16: Oxygen Group Elements: Oxygen (O), Sulfur (S), Selenium (Se), Tellurium (Te), Polonium (Po) Properties: Includes nonmetals (Oxygen, Sulfur), metalloids (Selenium, Tellurium), and metals (Polonium); form -2 anions. Group 17: Halogens Elements: Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I), Astatine (At) Properties: Highly reactive nonmetals; form -1 anions; strong oxidizers. Group 18: Noble Gases Elements: Helium (He), Neon (Ne), Argon (Ar), Krypton (Kr), Xenon (Xe), Radon (Rn) Properties: Inert gases; very low reactivity; complete outer electron shells. Lanthanides (f-block) Elements: Lanthanum (La) to Lutetium (Lu) Properties: Lanthanides are f-block elements known for their similar chemical properties and their placement in the 4f block. Actinides (f-block) Elements: Actinium (Ac) to Lawrencium (Lr) 03 Properties: Actinides are f-block elements, many of which are radioactive, and include elements like Uranium and Plutonium. Classifications of Elements METALS Metals are found on the left side and in the center of the periodic table specifically located in s, p, d, and f blocks. They are typically shiny, good conductors of heat and electricity, ductile, and malleable. They also have low electronegativity. These are elements that are solid at room temperature (except for Mercury which is liquid. They form alloys and tend to give up their elections in chemical reactions.). Examples: copper, tin, zinc, lithium, sodium, calcium, magnesium, barium, lead, indium, etc. NON-METALS Nonmetals are located on the right side of the table. They are usually not shiny, poor conductors, and brittle. In their reactions, they tend to accept electrons. Examples: oxygen, carbon, hydrogen, sulfur, phosphorus, nitrogen, iodine, bromine, helium, neon, argon, etc. METALLOIDS Metalloids have properties of both metals and nonmetals and are found along the zigzag line that divides metals and nonmetals. 03 Examples: Boron, Silicon, Germanium, Arsenic, Antimony, Tellurium. Special Blocks: The periodic table can be divided up into several blocks based on their highest energy electron orbital type. There are 4 types of electron orbitals; "s" which can hold 2 electrons and is sperical in shape, "p" which can hold 6 and is shaped like a dumb-bell, "d" which can hold 10 and "f" which can hold 14. s-block: Groups 1 and 2, plus hydrogen and helium. p-block: Groups 13 to 18. d-block: Transition metals, which are groups 3 to 12. 03 f-block: Lanthanides and actinides, which are the two rows placed below the main body of the periodic table3  Mass Number is the sum of the protons and neutrons in the nucleus. Problem: What is the mass number of an atom containing: a. 58 protons, 58 electrons, and 78 neutrons? 03 b. 17 protons, 17 electrons, and 20 neutrons  Atomic number is the number of protons in its nucleus. Neutral atom: no. of protons = no. of electrons Therefore, the number of neutrons = mass number - atomic number Electronegativity is the tendency of an atom to attract electrons. It cannot be measured directly and needs to be computed from other atomic properties. Fluorine has the highest electronegativity and francium the lowest. If the electronegativity difference between two atoms is very large, then the bond type tends to be more ionic, if the difference in electronegativity is small then it is a nonpolar covalent bond. 03 Ionization Energy The first ionization energy is the energy it takes to remove an electron from a neutral atom in gaseous phase. In general, the 1st ionzation energy increases as we go across a period; as the electrons are held closer to the nucleus with the increasing effective nuclear charge. In general, the 1st ionization energy decreases as we go down a group; as the electrons are further from the nucleus with each increasing energy level. The noble gases possess very high ionization energies because their full valence shell makes them highly stable. 03 Valency This is the number of electrons in an atom’s outermost electron shell. Valence Electrons Valence electron is an electron associated with an atom that can form a chemical bond and participate in a chemical reaction. These are outer shell electrons for main group elements. For the transition metals with partially-filed d shells, valence electrons are those electrons outside the noble gas core. The number of valence electrons indicates the maximum number of chemical bonds an atom can form. Valence Shell The valence shell is the outermost energy level of an atom that contains electrons. The electrons in this outermost shell are 03 called valence electrons.  METHODS IN DETERMINING THE NUMBER OF VALENCE ELECTRONS 1. Determining Valence Electrons Using Energy Levels: Identify the Valence Shell: Determine the highest principal quantum number in the electron configuration of the atom. This highest number corresponds to the valence shell. Count the Electrons in the Valence Shell: Count the number of electrons present in this outermost energy level. 03 03 2. Electronic Configuration Determine the Valence Shell: Identify the highest principal quantum number (n) in the electron configuration, which corresponds to the valence shell Count the Electrons in the Valence Shell: Count the number of electrons in this outermost shell. For example: Sodium (Na): Its electron configuration is 1s² 2s² 2p⁶ 3s¹. The valence shell is the third shell (n=3), which has 1 valence electron in the 3s orbital Sulfur (S): Its electron configuration is 1s² 2s² 2p⁶ 3s² 3p⁴. The valence shell is the third shell (n=3), which has 6 valence electrons (2 in the 3s and 4 in the 3p orbitals). 03 3. Periodic Table Position: For Main Group Elements: Groups 1 and 2: The number of valence electrons corresponds to the group number. For example, elements in Group 1 (alkali metals) have 1 valence electron, and elements in Group 2 (alkaline earth metals) have 2 valence electrons. Groups 13 to 18: The number of valence electrons is determined by subtracting 10 from the group number. For instance, elements in Group 14 have 4 valence electrons, and elements in Group 15 have 5 valence electrons. Example: Carbon (Group 14) has 4 valence electrons, and oxygen (Group 16) has 6 valence electrons. 03 The Octet Rule Basic Concept: The octet rule states that atoms are most stable when they have eight electrons in their valence shell. This is analogous to the electron configuration of noble gases, which naturally have full valence shells and are chemically inert. Applying the Octet Rule: Atoms Bond to Achieve an Octet: Atoms will either gain, lose, or share valence electrons in order to achieve a complete octet. Example: Ionic Bonding: Atoms transfer valence electrons to achieve an octet. For example, sodium (Na) has one valence electron and chlorine (Cl) has seven valence electrons. Sodium donates its one valence electron to chlorine, resulting in sodium becoming 03 Na⁺ (with an octet) and chlorine becoming Cl⁻ (also with an octet).  Example: Covalent Bonding: Atoms share valence electrons to complete their octet. In a water molecule (H₂O), oxygen has six valence electrons and shares electrons with two hydrogen atoms, each contributing one electron. This sharing allows oxygen to achieve a full octet and each hydrogen atom to achieve a stable duet (two electrons). Exceptions and Extensions: Hydrogen: Follows the duet rule instead of the octet rule, needing only two valence electrons for stability. Elements Beyond the Second Period: Can expand their valence shells to accommodate more than eight electrons, using available d-orbitals. For example, phosphorus in PCl₅ has ten valence electrons around it. Odd-Electron Molecules: Molecules with an odd number of electrons (e.g., nitric oxide NO) cannot satisfy the octet rule for all atoms. Octet Rule 03 Valence electrons are directly related to the octet rule, as the rule is based on the idea that atoms achieve stability by having a full outer shell of electrons.  Chemical are the forces that hold atoms together in molecules and Bonds compounds. DIFFERENT KINDS OF CHEMICAL BONDS 1. IONIC BOND This bond forms when one atom donates one or more electrons to another atom, resulting in the formation of positively and negatively charged ions. The electrostatic attraction between these oppositely charged ions holds them together. Bond that forms between metals and non-metals. Example: Sodium chloride (NaCl) is a classic example. Sodium (Na) donates an electron to chlorine (Cl), forming Na⁺ and Cl⁻ ions which are held together by ionic bonds. 2. COVALENT BOND This type of bonding occurs when two atoms share one or more pairs of electrons. This sharing allows each atom to attain the electron configuration of a noble gas, achieving stability. This bond forms between two non-metals. Example: Water (H₂O) is an example of covalent bonding. Each hydrogen atom shares one electron with the oxygen atom, resulting in two single covalent bonds. 3. METALLIC BOND Occur when electrons are not shared between individual atoms but are free to move throughout a lattice of metal cations. This "sea of electrons" creates a bond that holds the metal atoms together and imparts properties like electrical conductivity and malleability. Example: In solid copper (Cu), the copper atoms are surrounded by a sea of delocalized electrons, which contribute to the metal's conductivity and strength. 4. HYDROGEN BOND Forms when a hydrogen atom that is covalently bonded to an electronegative atom (such as oxygen, nitrogen, or fluorine) interacts with another electronegative atom nearby). Example: Highly electronegative oxygen atom is connected to a hydrogen atom in the water molecule. The shared pair of electrons are attracted to the oxygen atoms more, and this end of the molecule becomes negative, while the hydrogen atoms become positive. 5. VAN DER WAALS FORCES These are weak, transient interactions between molecules or within molecules that arise from temporary dipoles. They include London dispersion forces and dipole-dipole interactions.  ORGANIC CHEMISTRY a branch of chemistry focused on the study of carbon-containing compounds and their reactions. It plays a crucial role in various fields, including medicine, agriculture, and environmental science. ORGANIC CHEMISTRY I. HISTORICAL PERSPECTIVE In the early days, scientists thought that organic compounds are produced by living organisms and inorganic compounds are produced by non-living organisms. Chemists believe that organic compounds cannot be synthesize only from inorganic compounds. In 1828, Friedwich Wohler (1800-1882) carried out an experiment. He heated an aqueous solution of ammonium chloride and silver cyanate which are both inorganic compounds and obtained urea which is an organic compound found in urine. Few years after, August Kekule defined organic compounds as those containing carbon. II. DISCOVERY Chemists discovered and synthesized more than 10 million organic compounds and estimated 10, 000 new ones are reported each year. II. RELEVANCE Carbohydrates, lipids, proteins, enzymes, nucleic acids (DNA and RNA), hormones, vitamins, and almost all other important chemicals in the living systems are organic compounds.  IMPORTANCE OF ORGANIC CHEMISTRY 1. MEDICINE AND PHARMACEUTICALS Organic chemistry is fundamental in the development of pharmaceuticals. Many drugs are organic compounds, and understanding their chemistry is essential for drug design, synthesis, and optimization. For example, the development of antibiotics, antivirals, and cancer treatments relies heavily on organic chemistry. 2. AGRICULTURE Organic chemistry is vital for the synthesis of pesticides, herbicides, and fertilizers, which help increase agricultural productivity. These compounds are designed to target pests or enhance plant growth while minimizing harm to the environment. 3. ENVIRONMENTAL SCIENCE Organic chemistry is key to understanding and addressing environmental issues. It helps in analyzing pollutants, developing methods for waste management, and studying the impact of chemicals on ecosystems. For instance, organic chemists study the degradation of organic pollutants and the development of green chemistry techniques. 4. MATERIALS SCIENCE The development of new materials, such as polymers, dyes, and advanced materials for electronics, relies on organic chemistry. Polymers, which are long chains of organic molecules, are integral to many everyday products, from clothing to medical devices. 5. ENERGY Organic chemistry is involved in the development of alternative energy sources, such as biofuels and organic solar cells. Research in this area aims to find sustainable and efficient ways to produce and use energy. Table 3. Organic Vs. Inorganic Compounds How do we obtain Organic Compounds? A. Isolation from Nature Living organisms are "chemical factories." Each terrestrial, marine, and freshwater plant (flora) and animal (fauna) even microorganisms such as bacteria makes thousands of organic compounds by a process called biosynthesis One way, then, to get organic compounds is to extract, isolate/ and purify them from biological sources. Examples include vitamin E, penicillin, table sugar, insulin, quinine, and the anticancer drug paclitaxel (Taxol). Nature also supplies us with three other important sources of organic compounds: natural gas, petroleum, and coal. B. Synthesis in the Laboratory Compounds made in the laboratory are identical in both chemical and physical propertjes to those found in nature assuming, of course, that each is 100% pure The majority of the more than 10 million known organic compounds are purely synthetic and do not exist in living organisms. For example, many modern 07 drugs- Valium, albuterol, Prozac, Zantac, Zoloft, Lasix, and Viagra.  Writing Formulas of Organic Compounds Lewis Dot Formula: This shows the bonding between atoms in a molecule and the lone pairs of electrons that may exist. Each dot represents a valence electron, and lines are used to denote bonds between atoms. For example, in a water molecule (H₂O), the Lewis dot formula would show oxygen with two lone pairs and single bonds to two hydrogen atoms.  Writing Formulas of Organic Compounds Structural Formula: This represents the arrangement of atoms within a molecule, showing which atoms are connected to each other. It can be depicted with lines for bonds, and it often includes the spatial arrangement of atoms. For example, the structural formula of ethanol (C₂H₅OH) would show the specific connections between carbon, hydrogen, and oxygen atoms.  Writing Formulas of Organic Compounds Molecular Formula: This indicates the number and types of atoms in a molecule but doesn’t show how they are connected. It gives the overall composition of the molecule. For ethanol, the molecular formula is C₂H₅OH, which tells us there are 2 carbons, 6 hydrogens, and 1 oxygen atom. Condensed Formula: This is a simplified version that groups atoms together in a compact way, without showing all the bonds. It often lists the atoms in a sequence that reflects their connectivity. For ethanol, the condensed formula would be written as CH₃CH₂OH.  Writing Formulas of Organic Compounds Empirical Formula: This shows the simplest whole-number ratio of the elements in a compound. It doesn’t provide information about the actual number of atoms or the structure. For ethanol, the empirical formula is CH₃O, which simplifies to the smallest whole-number ratio of carbon, hydrogen, and oxygen atoms. Skeletal Formula: This is a simplified way of drawing organic molecules that omits hydrogen atoms explicitly and shows only the carbon skeleton and functional groups. It uses lines to represent bonds between carbon atoms, with each vertex representing a carbon atom. For ethanol, the skeletal formula would show a chain of two carbon atoms with an -OH group attached to the end, without showing the hydrogens. Ethanol Butanone Alkanes Alkenes and Alkynes Alcohols Aldehydes and Ketones Carboxylic Acid Amines C 6 H 15 N Propylamine Pentylamine Hexylamine Amides Esters  Overview of Different Functional Groups These are specific groups of atoms within molecules that are responsible for the characteristic chemical Functional Groups reactions of those molecules. Each functional group has a distinct structure and reactivity that defines its behavior and interactions in chemical reactions. 1. Hydroxyl Group (-OH): A hydrogen atom bonded to an oxygen atom, which is then bonded to a carbon atom. It characterizes alcohols and phenols. Example: Ethanol (CH₃CH₂OH) 2. Carbonyl Group (C=O): A carbon atom double- bonded to an oxygen atom. This group is found in aldehydes and ketones. Aldehyde: R-CHO (e.g., formaldehyde, HCHO) Ketone: R-CO-R' (e.g., acetone, (CH₃)₂CO) 3. Carboxyl Group (-COOH): A carbonyl group attached to a hydroxyl group. This defines carboxylic acids. Example: Acetic acid (CH₃COOH) 4. Amino Group (-NH₂): A nitrogen atom bonded to two hydrogen atoms. This is characteristic of amines. Example: Methylamine (CH₃NH₂) 5. Ester Group (-COO-): A carbonyl group adjacent to an ether linkage. Esters are often formed from carboxylic acids and alcohols. Example: Ethyl acetate (CH₃COOCH₂CH₃) 6. Amide Group (-CONH₂): A carbonyl group bonded to a nitrogen atom. This defines amides. Example: Acetamide (CH₃CONH₂) 7. Nitrile Group (-C≡N): A carbon triple-bonded to a nitrogen atom. This group is found in nitriles. Example: Acetonitrile (CH₃CN) 8. Alkene Group (C=C): A carbon-carbon double bond, found in alkenes. Example: Ethene (ethylene) (C₂H₄) 9. Alkyne Group (C≡C): A carbon-carbon triple bond, found in alkynes. Example: Ethyne (acetylene) (C₂H₂) 10. Phenyl Group (C₆H₅-): A benzene ring (a six-carbon ring with alternating double bonds) attached to another group. Example: Phenylalanine (a common amino acid) References Bettelheim, F. A., Brown, W. H., Campbell, M. K., Farrell, S. O., & Torres, O. (2018). Introduction to general, organic, and biochemistry (11th ed.). Cengage. McMurry, J. (2016). Organic chemistry (9th ed.). Cengage Learning. Chemistry Libre Texts. (n.d.). Introduction to the Periodic Table. https://chem.libretexts.org/Bookshelves/General_Chemistry/Book%3A_General_Chemistry%3A_Pr inciples_Patterns_and_Applications_(Averill)/01%3A_Introduction_to_Chemistry/1.08%3A_Introduc tion_to_the_Periodic_Table Model Science Software. (n.d.). Periodic Table. https://www.modelscience.com/PeriodicTable.html Chemistry Libre Texts. (n.d.). Types of Chemical Bonds. https://chem.libretexts.org/Bookshelves/General_Chemistry/Book%3A_General_Chemistry%3A_Pr inciples_Patterns_and_Applications_(Averill)/01%3A_Introduction_to_Chemistry/1.08%3A_Introduc tion_to_the_Periodic_Table Helmenstine, A. (2021). What are valence electrons? Science Notes. https://sciencenotes.org/what-are-valence-electrons-definition-and-periodic-table/ Thank You Phone 09605856131 Email mayores.clarissejessica@ mscmarinduque.edu.ph