Chemistry of Life - Carbon Compounds: Structure, Properties, Reactivity

Carbon Compounds: Structure, Properties, Reactivity

Week 5A Overview

• Appreciate carbon's suitability as a foundation for complex structures.

• Interpret various representations of organic structures.

• Identify and name saturated, unsaturated, aliphatic, and aromatic hydrocarbons.

• Understand functional groups in organic chemistry.

• Identify and name key functional groups in biological small molecules.

• Describe chemical reactions of functional groups.

• Identify and name types of isomerism in organic molecules.

• Understand physical properties of functionalized organic compounds.

• Identify resonance in organic compounds and its impact on chemical reactivity.

• Recognize small organic compounds as building blocks of biological macromolecules.

Notices and Announcements

• Lecture content from the previous week is available on Moodle.

• Quiz 2 information:

  • Two portfolio quizzes have been completed.

  • Late enrollees should monitor email announcements regarding make-up opportunities for early assessments; mitigating circumstances requests will not be expected by the University.

  • Students who missed quizzes can apply via the SEAtS Mitigating Circumstances portal.

• Week 6: Roehampton Futures Week – Biomedical Science announcements.

  • Special sessions to enhance employability.

  • Attendance may be monitored where timetabled; attendance is encouraged where not timetabled.

  • Dr. Patterson's emails provide details for Biomedical Science students.

  • The Wednesday 9-11 am slot will be available for Biomedical Science students; Neuroscience students are also welcome.

  • The syllabus for Week 6 will change, with Dr. Amande lecturing on nucleic acids.

Biomedical Science Level 4 Arrangements for Next Week (also see Dr. Patterson’s email)

• Monday 4 Nov

  • 9 am, PH.G11 – Dr. Patterson – careers in Science Communication

  • 10 am, PH.G11 – NHS Pathology Practice Educators – careers in NHS diagnostic labs

  • 11 am, PH.G11 – Alumni careers: Katie Birditt and others

  • 1 pm – late enroller clinic on Teams

  • 2 pm, PH.G17 – Dr. Al-Agil – Artificial Intelligence in Medicine

• Tue 5 Nov

  • 11 am, PH.236 – Dr. McDonald – Teamwork between Biomedical Scientists and Histopathologists

  • 3.30 pm, QB.148 – GradCracker session – STEM careers focus

• Wed 6 Nov

  • 9 am, PH.G17 – A look inside biomedical lab equipment (this module)

• Fri 8 Nov

  • 11 am, PH.104 – “Boot Camp” with Dr. Reeves, supporting students to submit their work at the first attempt.

• PLUS Uni-wide offerings via NEST: https://roehamptonprod.sharepoint.com/sites/portal/nest/Pages/roehampton-futures.aspx

Practical Debrief

• In Week 10 (3rd practical), avoid crowding during the 11 am shift.

• Some KOH stock bottles were contaminated with acetic acid in the second shift – avoid contamination and follow instructions.

• Utilize the data analysis guide in the “Practical Information” section.

Sample Titration Data

• Data from a previous year is presented, showing volume added, volume reading, and pH values.

Working out the unknown [KOH] concentration

• Formula: $Va \times Ca = Vb \times Cb$

  • $Va$ = 14 ml (measured, approx.)

  • $Ca$ = 0.1 M (given)

  • $Vb$ = 20 ml (given)

  • $Cb$ = unknown

• Solve for $Cb$

• $14 ml \times 0.1 M = 20 ml \times Cb$

• $Cb = (14 ml \times 0.1 M) / 20 ml = 0.07 M$

Determining KOH Molarity from pH

• The pH reading of the KOH solution without acetic acid was 13.02.

• Determine the molarity of KOH based on this reading and compare it with the titration result to evaluate accuracy.

Calculating Molarity from pH

• Given pH = 13.02, calculate the molarity of KOH.

• $pH + pOH = 14$

• $pOH = 14 – pH = 14 – 13.02 = 0.98$

• $pOH = -log_{10}[OH^-]$

• $[OH^-] = 10^{-0.98} = 0.105 M = 105 mM$ (vs. 70 mM by titration)

• Note: This method is more sensitive to minor calibration errors.

Carbon: The Backbone of Life

• Living organisms are primarily composed of carbon-based compounds.

• Carbon forms large, complex, and varied molecules.

• Proteins, DNA, carbohydrates, and pharmaceuticals are carbon compounds.

Organic Chemistry

• Organic chemistry studies covalent carbon compounds.

• Organic compounds include simple to complex molecules.

• Most contain hydrogen atoms (hydrocarbons) and heteroatoms (O, N, P, S).

Carbon Bonding

• Carbon can form covalent bonds with up to four other atoms or groups, enabling a variety of molecules.

• Carbon also forms covalent compounds with other carbon atoms.

Carbon and sp³ Hybridization

• Carbon undergoes sp³ hybridization, resulting in four tetrahedral sp³ orbitals.

VSEPR Theory

• VSEPR (valence shell electron pair repulsion) theory rationalizes the shapes of common organic molecules.

• Molecular geometry is predicted by the repulsion of electron pairs, achieving maximum separation.

• This applies to both bonding electrons and lone pairs.

• The steric number (SN) is used to determine molecular shape.

• SN=4: Tetrahedral (109.5º)

• SN=3: Trigonal planar (120º)

• SN=2: Linear (180º)

Hybridisation, Bonds Formed, vs. VSEPR Steric Number and Bonding Geometry

• Hybridisation and bond types are related to VSEPR steric number and bonding geometry.

  • sp : s s p p

  • sp2 : s s s p

  • sp3 : s s s s

Representing Chemical Structures

1. Molecular formula:

• Indicates the relative number of atoms in a molecule (elemental composition).

• Does not uniquely define the structure.

1. Structural formula:

• Indicates how atoms are connected in a molecule.

Examples of Molecular and Structural Formulae

• Pentane:

  • Molecular Formula: $C<em>5H</em>{12}$

  • Structural Formula: $CH<em>3CH</em>2CH<em>2CH</em>2CH_3$

• Ethanol:

  • Molecular Formula: $C<em>2H</em>6O$

  • Structural Formula: $CH<em>3CH</em>2OH$

Simplifying Structural Formulae

• Full structural formulae can be complex and cluttered.

• Simplified skeletal formulae represent the carbon framework.

• Shows bonds linking atoms, omitting H atoms and indicating C atoms without writing them out; shows the shape of the molecule.

Drawing Structures

• Example: Pent-2-ene structure representation.

Representing Organic Structures

• C atoms are represented as vertices.

• Only the C skeleton is shown, and H atoms are implied.

• Examples:

  • $C<em>5H</em>{12}$

  • $C<em>3H</em>6$

  • $C<em>6H</em>{12}O$

Hydrocarbons

• Simplest organic compounds containing only carbon and hydrogen.

• Classified as aliphatic or aromatic.

Aliphatic Hydrocarbons

• Include:

  • Alkanes

  • Cycloalkanes

  • Alkenes

  • Alkynes

Alkanes

• Simplest hydrocarbons are unbranched alkanes.

• Longer chains are named by their carbon chain length in Greek (pentane, hexane, heptane, octane).

• Summary formula: $C<em>nH</em>{2n+2}$

• All carbons are sp³ hybridized (tetrahedral).

Types of Alkanes

• Straight-chain: Linear chain of carbon atoms.

• Branched-chain: Chain splits into two at one or more atoms.

• Cyclic: Ends of the chain join to form a sealed ring.

Straight-chain vs. Branched-chain Alkanes

• Structural isomers have the same summary formula but different connectivity.

• Example: n-pentane and isopentane (2-methyl butane) have the same formula ($C<em>nH</em>{2n+2}$).

Prefix Nomenclature

• Alkanes are named with the suffix '-ane'.

• Branched alkanes are named after the longest unbranched carbon chain with the suffix '-ane'.

• Branches are added as prefixes with '-yl'.

Cyclo-alkanes

• Summary formula: $C<em>nH</em>{2n}$

• Cyclopropane, cyclobutane, cyclopentane, cyclohexane etc.

• Cyclohexane adopts a “chair” or “boat” 3D geometry.

• Cycloalkanes are generally stable.

Biological Example

• Steroids contain multiple cyclohexane and one cyclopentane rings.

Alkenes

• Hydrocarbons with at least one double C-C bond.

• Summary formula for one double bond: $C<em>nH</em>{2n}$, (same as cycloalkanes)

• Each additional double bond reduces the number of H atoms by 2.

Nomenclature (Alkenes)

• Follow the same naming system as alkanes.

• The first part indicates the number of C atoms in the longest chain.

• The suffix indicates saturation level.

• '-ene' signifies one double bond.

• '-diene' two double bonds.

• '-triene' three double bonds, etc.

• A number indicates the position of the double bond in the chain.

Stereoisomers

• Stereoisomers have the same atoms and connectivities but different spatial orientations (different configurations).

• Geometric stereoisomerism occurs in C=C double bonds.

Geometric Isomers

• Share the same atoms joined in the same way but have different configurations.

Cis/Trans Isomerism

• Geometric isomers exist in cis (same side) or trans (opposite side) forms.

• Trans isomers are generally more stable.

Cis/Trans Nomenclature

• Cis: Substituent groups are on the same side of the double bond.

• Trans: Substituents are on opposite sides of the double bond.

Alkynes

• Alkynes are hydrocarbons with one or more triple bonds between C atoms.

• The high-energy triple bond gives alkynes lower stability and greater reactivity than alkanes and alkenes.

Alkynes Nomenclature

• Alkynes have the suffix '-yne'.

• The simplest alkyne is ethyne ($C<em>2H</em>2$).

Saturation

• A saturated compound has absorbed the maximum number of H atoms.

• An unsaturated compound can have more H atoms added at double or triple bonds.

• Double/triple bonds are functional groups that impart novel chemical reactivity.

Bonding Geometry and Hybridisation

• Various examples of bonding geometry and hybridisation are shown.

Organic Building Blocks

• Hydrocarbons

• Carbohydrates & Lipids

Common Functional Groups

• Alcohol, R—OH

• Aldehyde, R—C(H)=O

• Ketone, R1—C(=O)—R2

• Carboxylic acid, R-C(=O)—OH

• Oxygen is divalent; in alcohols, sp3 hybridised; in aldehydes and ketones, sp2 (flat geometry) with s & p bonds.

• Generally more polar than hydrocarbons.

• Chemical reactivity: condensation (alcohols, acids), oxidation (aldehydes), acidity (carboxylic acids).

Nomenclature (Functional Groups)

• Alcohols: suffix “-ol” (methanol, ethanol, propanol).

• Aldehydes and ketones: differ in carbonyl positioning (terminal or internal, respectively); aldehydes are more reactive, suffix “-al” (methanal, ethanal).

• Ketones: suffix “-one” (propan-2-one or acetone).

• Carboxylic acids: suffix “-oic acid” (n-hexanoic acid); release $H^+$ to produce a carboxylate anion (n-hexanoate).

Structural Isomers of Oxygen-Containing Compounds

• Example: Molecular formula of $C<em>2H</em>6O$ may be ethanol or methoxymethane (an ether).

Examples of Condensation Reactions

• Alcohol + carboxylic acid = ester + water.

• 2 alcohols à ether + water.

Oxidation of Organic Compounds

• Oxidation: Removal of electrons from C by removing H or adding O (energy released).

• Reduction: Addition of electrons to C by removing O or adding H.

Example: Pyruvic Acid

• Identify functional groups, name the compound, and predict properties.

• Contains a keto group and a carboxylic acid group (2-oxo-propanoic acid).

• May deprotonate at C-1 (weak acid) and be reduced at C-2 (to lactic acid).

• Very polar and water-soluble.

Summary

• Tetravalent carbon produces diverse structures.

• Hydrocarbons may be straight-chain, branched, or cyclic; saturated or unsaturated.

• Oxygen adds functionality (alcohols, carbonyl compounds, carboxylic acids).

• Oxidation, reduction, and condensation reactions.

• Carboxylic acids are weak acids.

• Observe polarity, hydrogen bonding, and higher m.p./b.p. than alkanes.

• Isomerism: structural and geometric isomers.

• Nomenclature rules: https://iupac.qmul.ac.uk/BlueBook/; https://en.wikipedia.org/wiki/IUPACnomenclatureoforganicchemistry