Chemistry Fundamentals

• Pharmaceutical Organic Chemistry is the study of carbon compounds.
• Taibah University's class attendance and attendance recording is mandatory.
• 75% attendance is required to take the final exam.
• Attendance will be recorded 10 minutes after class or lab starts.
• Students missing a class, lab, quiz, or exam must file a petition to the Vice-Dean for Academic Affairs for a possible make-up.

Assessment, Evaluation, and Grading Breakdown:

• Quizzes and homework every two weeks account for 5% of the final grade.
• Essay/Report/Lab performance/Practical test accounts for 5% of the final grade.
• Written Test (1) accounts for 15% of the final grade and will be in week(s) 5 and 6.
• Written Test (2) accounts for 15% of the final grade and will be in week(s) 11 and 12.
• The practical final exam accounts for 20%.
• Final Exam (theoretical) accounts for 40% of the final grade and will be during Week(s) 18 and 19.

Course Objectives

• Explain the molecular properties of organic compounds.
• Describe organic compounds' nomenclature (IUPAC and common) and drawing structure.
• Clarify the principal aspects of stereochemistry in organic reactions and their mechanisms.
• Identify practically organic compounds.
• Define the fundamentals of organic chemistry required for related courses in the Pharmacy curriculum.

What is Organic Chemistry?

• A subject that studies structures, properties, and reactions of organic compounds and materials containing carbon atoms.
• Organic compounds also contain hydrocarbons or carbon bonded to hydrogen (C-H).
• Organic compounds can be obtained from living organisms or through synthesis.

Classification of Organic Compounds According to Molecular Framework:

• Organic compounds can be classified into acyclic, carbocyclic, and heterocyclic compounds.
• Acyclic compounds have chains of carbon atoms without rings.
• Carbocyclic compounds contain rings of carbon atoms with a minimum of three carbon atoms.
• Heterocyclic compounds have at least one atom in the ring is a heteroatom (not carbon), commonly oxygen, nitrogen, or sulfur.
• Functional groups are groups of atoms that dictate the chemical properties of a molecule.
• The hydroxyl group (-OH) is the functional group of alcohols.

Atomic Structure:

• Atoms consist of a dense nucleus of positively charged protons and neutral neutrons surrounded by negatively charged electrons.
• The atomic number is the count of protons in the nucleus.
• Atomic weight is the sum of protons and neutrons in the nucleus.

Electron Arrangement

• Electrons are arranged in orbitals (s, p, d, f).
• Each orbital can hold two electrons.
• Orbitals form shells (numbered 1, 2, 3, etc.).
• Valence electrons are in the outermost shell.
• The kernel includes the nucleus and inner electrons.
• Valence determines the number of bonds an element can form.
• The number of electrons to fill valence shells corresponds to Valence.

The Octet Rule:

• Some atoms react to achieve stable arrangements.
• Elements gain or lose electrons to achieve noble gas configuration.
• Atoms transfer or share electrons to reach a filled electron shell, called an octet.
• Atoms will gain or lose electrons in such a way that filled shell of electrons.

Electronegativity (EN):

• The measure of an atom's ability to attract electrons.
• Electronegativity increases from left to right and bottom to top on the periodic table.
• An EN difference less than 0.5 results in nonpolar covalent bonds.
• A difference between 0.5 and 1.9 results in polar covalent bonds.
• A ditference of 2.0 or above results in Ionic bonds.
• Shared electrons are more attracted to atoms with higher electronegativity.

Ionic Bonds:

• Formed by the electrostatic attraction between positively charged cations and negatively charged anions.
• Complete transfer of valence electrons from an electropositive atom to an electronegative atom.
• Electropositive atoms give up electron to form cations.
• Electronegative atoms accept electrons to form anions.

Covalent Bonds

• Results from the sharing of electrons between atoms.

Bond Polarity

• A useful concept to describe the sharing of electrons between atoms.
• Bond polarity arises from electronegativity differences.
• Atoms with more carbon tend to have partial negative charges, while atoms such as hydrogen tent to be neutral with a partial positive charge.
• Equal sharing leads to nonpolar covalent bonds; unequal sharing leads to polar covalent bonds.
• Bond polarity is quantized by dipole moment (μ), measured in Debyes (D).
• Dipole moment measures bond polarity.
• Nonpolar covalent bonds share electrons equally.
• Polar covalent bonds have electrons attracted more strongly, creating partially charged atoms.
• Bond polarization is indicated by an arrow pointing to the negative with a plus sign.
• Double bond, refers to multiple covalent bonds refers to the atoms share electrons.
• Atoms share more than one pair.

Types of Covalent Bonds:

• Double bonds share two electron pairs.
• Triple bonds share three electron pairs.
• Nonbinding electrons are unshared pairs of electron reside on one atom.
• Coordinate covalent bonds form when one atom supplies both electrons to another.

Carbon-Carbon Single Bonds

• They can form between carbon atoms.

Catenation

• The term referring to the ability of carbon atoms to other carbon atoms.
• Breaking a carbon-carbon bond yields methyl radicals, which are very reactive due to unpaired electrons.
• Less heat is needed to break the carbon-carbon bond, which is longer than the H-H bond.
• Bond energy is inversely proportional to bond length.

The Orbital View of Bonding

• Atomic orbitals (s, p, d, f) have define shapes.
• Two atoms approach each other for their orbitals to overlap
• A molecular orbital includes the space occupied by the electrons in the molecule and contains no more than two electrons.
• Sigma (σ) bonds may also be formed head-to-head overlapping of two atomic orbitals
• Pi bonds created when correctly aligned p orbitals can overlap

Hybridization

• It's the concept of mixing 2 atomic orbital to give rise to a new hybridized orbitals.
• Essential for understanding bonding and molecular geometry.
• Hybrid orbitals are made from merging two 's' orbitals or two or mixing of an 's' orbital with a 'd' orbital, they involve equal energies,

Types of Hybridization:

• sp³ hybridization results in a tetrahedral geometry. 4 (1s + 3p) .
• sp² hybridization results in a trigonal planar geometry. 3 (1s + 2p).
• sp hybridization features a linear geometry.2 (1s + 1p).

Carbon Hybridization

• Carbon can form bonds by overlapping of any hybrid and nonhybridized atoms to form ionic compounds.
• In Methyl there is a sp³ hybridization with 109.5 degree angle
• In Ethene there is a sp² hybridization with 120 degree angle
• In Ethyne there is a sp Hybridization with 180 degree angle

Molecular Geometry Depictions

• Carbon can be represented in various structural forms such as slid lines, Ball-and-Stick and Space-filling
• Geometry of carbon is commonly represented as with slid lines showing the atoms or elements in C-H.
• Ball and stick model is showing bonds that connect the atoms for instance represent by the stick.
• Space filling will show the space occupied by the atom.
• Electrostatic potential map will define the molecules whether an electron distribution with a red indicating the negative partial charge, while blue indicates positive partial charge.

Intermolecular Interactions

• Physical properties are determined by intermolecular forces.
• Attraction between molecules without forming bonds.
• Interactions increase with increasing weight and polarity.
• Intermolecular forces are weaker than intramolecular ones.
• Types of Interactions: Dipole-dipole interactions, Van der Waals forces, Hydrogen bonding.

Dipole-Dipole Interactions:

• Between the negative end of one dipole and the positive end of another.
• Polar molecules are held together strongly, and therefore these dipole-dipole interactions.

Nonbonding Van Der Waal's Forces:

• A general terms sued to define attraction of intermolecular forces between molecules and weak interactions.
• Exists between nonpolar molecule that at one point has electron move continuously within bonds and molecule.

Hydrogen Bonding

• A strong kind of attraction between dipole atoms bonded to an electronegative atom.
• Atoms such as atoms covalent bonded with oxygen, fluorine or hydrogen produce this bonding.

Isomerism:

• The same number and kinds of atoms will have different arrangements and formula, this is known as the term of formula that tell the atoms those molecule.

Structural Isomers:

• Have same molecular formula and different arrangement of atoms in their formula.
• Use continuous chain or branch when using written structural formula when using the same molecular formula
• There can be formulas which are abbreviated while the main structural formulas are tire some.
• Structures are combined form smaller chains, the structures can be expressed on a signal in the following ways of using lines.

Resonance:

• Represents 2 or more structure with those identity arrangements to atoms while they different electrons.
• To have these structures, the substance will present the structure of resonance.
• They are all arranged to isomer which have these structure between its elements.
• Arrows used and seen the electrons move in actions, is commonly used to indicate structure in resonance with a single half of a head.

Questions cover topics from VSEPR theory and hybridization to intermolecular forces and basic bonding principles. Explore molecular geometry, electron density, and compound classification. Test your basics of fundamental chemistry.