Organic Chemistry and Intermolecular Forces Overview
Learning Objectives
Use a variety of molecular representations to illustrate organic compounds.
Identify when atoms with a complete or incomplete octet will have particular formal charge(s)/lone pairs of electrons.
Identify and illustrate functional groups in chemical species, which are groups of atoms/bonds that possess predictable chemical behaviors:
Alkyl halide
Alkene
Alkyne
Alcohol
Ether
Thiol
Sulfide
Ketone
Aldehyde
Carboxylic acid
Acyl chloride
Anhydride
Ester
Amide
Amine
Acetal
Hemiacetal
Ketal
Hemiketal
Identify and apply terms related to functional groups: primary, secondary, tertiary (e.g., primary alcohol, secondary amine) and carbocations (e.g., secondary carbocation).
Name simple alkyl halides, alkenes, alkynes, alcohols, aldehydes, ketones, esters, carboxylic acids, amides, and thiols using IUPAC nomenclature (common names are not required).
Chemical Bonds
Consideration of why DNA is primarily based on carbon instead of silicon:
Atoms interact to achieve electronic configurations analogous to the nearest noble gas configuration (usually 8 valence electrons).
Comparison of Biology and Chemistry
Defining the distinction between Biology and Chemistry:
Biology: Study of the function of the assembly of atoms.
Chemistry: Study of the structure of the assembly of atoms.
Illustrating Organic Compounds
Organic chemists utilize specific chemical illustrations for communication.
Questions raised:
What is the molecular formula of propane?
Draw propane using various chemical representations.
Different illustration techniques include:
Lewis Dot Structure
Line Bond Structure
Condensed Structure
Line Structure
Wedge-Dash Structure
Note that Lewis structures are impractical for representing larger organic molecules (e.g., amoxicillin).
Omitting Hydrogen Atoms
It is customary only to omit C–H bonds while retaining any X–H bonds (where X ≠ C):
Example:
C–C–C–C–O–O-H
H–O–H
N–H
Retaining all H attached to N and O.
Nomenclature
Students are responsible for reviewing nomenclature from Chem 123; no basics will be covered in class.
Functional Group Recognition
Recognizing the classification of nitrogen-containing compounds by the number of carbon atoms directly attached to nitrogen:
Primary (1°)
Secondary (2°)
Tertiary (3°) (Amine, Amide)
For other compounds, the number of carbon atoms attached to the carbon with the functional group is assessed:
Primary (1°)
Secondary (2°)
Tertiary (3°) (Alcohol, Alkyl halide)
Condensed Structures
Usage of condensed structures to indicate the connectivity of compounds without illustrating chiral centers.
Examples include:
Aldehyde
Carboxylic Acids
Esters
Ketones
The notation conventionally indicates R as any carbon framework.
Representing Organic Structures
Questions for drawing line structures for chemicals, such as CH₃COOCH₂CH₃.
New Functional Groups
Ketal:
General structure includes R groups = any carbon group.
Derived from ketones.
When one of the –OR groups is replaced by -OH, it is known as a hemiketal, which is generally unstable and only exists in specific circumstances.
Acetal:
General structure where R = any carbon group.
Derived from aldehydes.
Replacement of one –OR group with –OH yields a hemiacetal, which is unstable.
Practice Questions on Functional Groups
Determination of functional groups based on oxygen atoms incorporated within a compound.
Illustrating Propanone (Acetone)
Instructions to illustrate using various methods including molecular formula, line structure, and condensed structure:
Molecular formula: C₃H₆O
Line structure:
Condensed structure: CH₃C=OCH₂
Formal Charges
Definition: Formal Charge helps to keep track of electron density around an atom in a Lewis structure.
Formula:
Formal Charge = (Number of valence electrons in free atom) - (Number of non-bonding electrons) - 0.5 × (Number of bonding electrons)
Example calculation:
Oxygen (O) has 6 valence electrons.
Additional Methods
Alternative approach: Homolytic bond rupture to assess atomic structures.
Practice Questions on Lone Pairs and Formal Charges
Indications required for determining lone pairs and formal charges on given structures.
Intermolecular Forces Learning Objectives
Define and describe various intermolecular interactions:
Ionic interactions
Hydrogen bonding
Dispersion forces
Dipole-dipole forces
Identify predominant intermolecular forces in chemical species based on functional groups.
Rank melting/boiling points and compare solubility of substances concerning intermolecular forces.
Recognize hydrogen bonds between nucleic acids (DNA) and amino acids in proteins.
Identify intermolecular forces responsible for protein folding.
Chemical Bonding
Two primary types of bonding are recognized:
Covalent Bonds: Formed by electron sharing between atoms.
Ionic Bonds: Formed from the electrostatic attraction between oppositely charged atoms.
Types of Intermolecular Forces
Organic molecules exhibit intermolecular forces, characterized as electrostatic in nature.
Types and their associated energies:
Covalent Bond: 30 – 260 kcal/mol (most around 100 ± 20).
Ionic interactions: = strong due to charge attraction.
Hydrogen bonding: weaker than ionic, yet critical.
Dipole-Dipole interactions: moderate strength.
London Dispersion Forces: weakest, arise from temporary fluctuations in electron density.
Ionic Interactions
Key points about ionic interactions that illustrate the behavior of likewise charged bits.
Negative charged bits repel each other.
Interactions with positive bits include:
Carboxylate (e.g., aspartic and glutamic acid).
Metal ions in biological systems.
Phosphate relevant in DNA & RNA.
Ammonium ions (lysine) and Guanidinium (arginine) as structural components.
Hydrogen Bonds
Characteristics of hydrogen bonds, including their dependence on the polarization of X–H bonds (where X = N, O, S, F, or Cl).
Protons in Water
Description of proton structures in water.
H+ appears as minimal structures encapsulated within water molecules.
Hydrogen Bonding in DNA
Structural components of DNA include:
Sugar-phosphate backbone
Nitrogenous bases are stabilized by weak hydrogen bonds.
Alignments in bonding for nucleotide pairs (e.g., A with T, C with G) and hydrogen-bonding regions illustrated.
Proteins and Their Structure
Explanation of protein primary structure in terms of peptide bonds formation.
Hydrogen Bonding in Protein Structures
Illustrated examples of hydrogen bonding in alpha helix and beta-pleated sheets.
Further Protein Structures
Explaining levels of protein structure:
Primary structure: sequence of amino acids.
Secondary structure: alpha helixes and beta-pleated sheets.
Tertiary structure: overall 3D shape.
Quaternary structure: associations between multiple polypeptide chains.
Denaturing Proteins
Disruption of protein secondary structure due to pH and temperature alterations leads to loss of biological activity (denaturation).
Renaturation refers to regaining biological activity post-denaturation.
Dipole-Dipole Interactions
Discussion on dipole-dipole forces and their impact on the alignment and physical properties of organic compounds.
Ranking Boiling Points of Different Compounds
Exercises presenting various compounds to rank based on boiling points.
π-Stacking Interactions
Explanation of π-stacking as attractions between aromatic rings, explaining both electrostatic and orbital interactions.
The Hydrophobic Effect
Description of the hydrophobic effect and its importance in biological systems, specifically, how nonpolar substances associate while separating from water.
The principle of “like dissolves like,” leading to hydrocarbon behavior in aqueous environments.
Membranes, Vesicles, and Liposomes
Explanation of amphiphatic molecules and their structural properties contributing to membrane formation, highlighting the dual nature of hydrophilic and hydrophobic interactions in biochemistry.
Practice Questions
Questions on identifying hydrogen bonds and understanding definitions surrounding molecular interactions to develop comprehension of chemical bonding principles.