Biomedical Engineering: Organic Chemistry (CHE 111)

Biomedical Engineering Course Notes

• Biomedical engineering is a specialized scientific program.
• The course is about organic chemistry (CHE 111).
• Specific course references include texts like "Organic Chemistry" by P.Y. Bruice (2016, Pearson, USA), "Organic Chemistry" by T.W. Graham Solomons (11th Ed., 2014, John Wiley), "Organic Chemistry" by Francis A. Carey (2014, Mc Graw Hill), "Organic Chemistry" by William H. Brown (2018, Cengage Learning), and "Biochemistry, An Organic Chemistry Approach" by Michael B. Smith (2020, Taylor & Francis).
• Team code for the course is Oxh0kgc.

Course Objectives

• Students will gain an understanding of fundamental molecular concepts, including structure, bonding, geometry, resonance, isomerism, and acid-base chemistry.
• Grasp the primary functional groups in organic compounds and study their various properties (physical and chemical).
• Learn about significant chemical reactions and mechanisms associated with each family of compounds.
• Understand significant applications of organic chemistry tailored to biomedical engineering.
• Develop practical skills in handling and identifying organic compounds.

Course Contents

• Organic chemistry course covers topics like carbon compounds and chemical bonds, representative carbon compounds (alkenes, alkynes, etc), aromatic compounds, and alcohols, and phenols.

Evaluation Procedures

• First Midterm Exam is worth 12.5 points.
• Second Midterm Exam is worth 12.5 points.
• Lab work is worth 15 points.
• Lecture attendance and quizzes are worth 10 points.
• Final Exam is worth 50 points.

Chapter 1: Carbon Compounds and Chemical Bonds

• The chapter focuses on organic chemistry, specifically including an introduction to the field, and identifying specific learning objectives

Learning Objectives

• Define organic chemistry and its importance.
• Understand various types of chemical bonds.
• Techniques for representing organic molecules.
• Learn about resonance theory.

Organic Chemistry and Life

• Organic chemistry is essential to many biological systems and processes.
• Examples of organic compounds frequently involved in biological systems include DNA, proteins, enzymes, vitamins.
• Components such as pesticides, paints, adhesives, and plastics are all compounds derived from organic compounds.
• Biomedical uses of organic compounds are significant in technologies such as medicine, bioengineering, and nanotechnology.
• Example: Artificial heart components are synthetic organic compounds like polycarbonate and polyurethane.

Biological Relevance

• Bioorganic compounds are crucial constituents of living systems, encompassing carbohydrates, fats, proteins, nucleic acids, enzymes, and hormones.
• Many bioorganic compounds are significantly more complex compared to simpler organic molecules.
• Bioorganic compounds frequently comprise more than one functional group.

Biomolecules

• Includes carbohydrates, lipids, proteins, and nucleic acids.

Common Examples of Bioorganic Compounds

• Sucrose (C12H22O11)
• Vitamin B2 (C117H120N406)
• Cholesterol (C27H46O)
• DNA

Organic Compounds: Number and Variety

• The number of known organic compounds is about 16 million.
• The prevalence of carbon-containing compounds stems from carbon's unique position in the periodic table.
• Carbon's central position within the second row of elements enables it to readily form bonds with various types of atoms.
• Carbon commonly shares electrons to accommodate the octet rule.

Covalent Bonds

• Carbon atoms usually form covalent bonds, in which electrons are shared between atoms.
• The sharing of electrons is driven by the need for each atom to reach stable electron configurations resembling that of inert noble gases.
• Covalent bonds in organic molecules form when multiple types of atoms, like carbon, H, N, oxygen, etc., share electron pairs, forming bonds and molecules.

Molecular Orbitals Theory (MOT): Sigma Bond

• Atomic orbitals on different atoms combine to create molecular orbitals.
• Two hydrogen atoms can form a covalent bond, by overlapping of their 1s orbitals, forming a sigma bond.
• The sigma bond results from electrons being shared between the two nuclei of two atoms.

Bond Angles and Shapes of Molecules: Hybrid Orbitals Model

• Bond angles in organic compounds are often around 109°, 120°, or 180°.
• The variation of bond angles stems from hybridized orbital models rather than the simplistic model of using only s and p orbitals
• Examples: Methane (CH4), Ethane, Ethene, Ethyne, all have specific and measurable bond angles resulting from hybridization of orbitals on the carbon and other atoms

Hybrid Orbitals and Bonding

• Atomic orbitals can combine to form hybrid atomic orbitals (sp³, sp², sp).
• Hybrid orbitals influence molecular shapes (e.g., methane (sp³), ethene (sp²), ethyne (sp)).
• The ability of hybrid orbitals to form bonds relies on the properties of those orbitals to form more efficient bonds compared to non-hybridized orbitals.
• Hybridized orbitals improve bond formation and bonding strength

Representing Structural Formulas

• Lewis structures, three-dimensional structures, and two-dimensional bond-line formulas exist for depicting structural formulas.
• Lewis structures explicitly show each valence electron and formal charge
• Three-dimensional structures depict spatial arrangements.
• Bond-line structures are useful for compactness and depict carbon atoms and their bonds implicitly.

Formal Charge

• Formal charge on an atom is determined using its group number, number of bonds, and number of unshared electrons in a Lewis structure.

Resonance

• The concept of resonance is used to represent actual structures of molecules or ions.
• More stable resonance forms are better representations of the real molecule.
• Resonance can result in bonding with partial double bonds which have bond orders intermediate in length, that are equivalent to single or double bonds.
• This gives a more accurate picture of the real structure than any of the contributed resonance structures.

This quiz covers essential concepts in organic chemistry as part of the Biomedical Engineering course (CHE 111). Students will explore molecular structure, bonding, functional groups, and key reactions. References include major textbooks by Bruice, Solomons, Carey, and others, integral to understanding organic chemistry in a biomedical context.