Chemistry and Biochemistry Experiment Notes
Experiment 05: Molecular Models
Foundations of Chemistry
Theory of Electronic Character:
Discusses the nature of atoms and ions.
Theory of Spatial Arrangement:
Concerns three-dimensional arrangements of atoms in molecules.
Importance of three-dimensional visualization in understanding molecular properties.
Two-Dimensional Representations:
Chemists use two-dimensional symbolic representations for molecular structures.
Limitations arise when translating three-dimensional molecular shapes into two dimensions, often requiring artists for accurate representations.
Molecular Models:
Constructed to visualize the properties of molecular structures accurately.
Models serve as three-dimensional representations of Lewis electron dot structures, where each bond signifies an electron pair.
Bonds between atoms represented differently based on orientation:
Curved Bonds:
Facilitate representation of multiple electron pairs between atoms.
Each type of atom has specific electron pair capacities:
Carbon and Nitrogen: can accommodate four electron pairs.
Hydrogen and Chlorine: can accommodate one electron pair.
Oxygen: can accommodate two electron pairs.
Laboratory Experiment Overview
Entire lab session focused on constructing and manipulating molecular models.
Models will be translated into written molecular structural formulas.
Each student works individually on construction but collaboration is encouraged within and between groups.
Reporting:
Reports may be filled out during the experiment without prior notebook entry.
Reports must be neat, legible, and written in pencil.
Three-Dimensional Bonds Visualization
To represent three-dimensional bonds in two dimensions:
Wedges: represent bonds protruding out of the paper plane.
Hatches: represent bonds extending behind the paper plane.
Lines: represent bonds lying flat in the plane of the paper.
Report Sheet Details
1. Molecular Models Construction
Students construct models for the following molecules, drawing both Lewis and structural formulas indicating three-dimensional geometry:
Ammonia (NH₃):
a. Molecular geometry around nitrogen atom.
b. Identify what occupies the fourth bonding position of the nitrogen atom.
c. Assessment of NH₃ polarity.
Formaldehyde (CH₂O):
a. Geometry of bonds around carbon atom.
b. Assessment of CH₂O polarity.
Chloromethane (CH₃Cl):
a. Geometry of bonds around carbon atom.
b. Assessment of CH₃Cl polarity.
Water (H₂O):
a. Geometry of bonds around the oxygen atom.
b. Identify what occupies the other two bonding positions of the oxygen atom.
c. Assessment of H₂O polarity.
2. Proton Transfer Reaction
Using water and ammonia:
a. Remove one proton from water and insert into unshared electron pair of ammonia.
b. Identify the two species produced.
c. Write the chemical equation for this reaction.
3. Chloromethane Reaction with Hydroxide Ion
Utilize a hydroxide ion (OH⁻) from water to remove the chloride ion from chloromethane and insert hydroxyl ion into the carbon atom's open position.
a. Write the reaction equation represented.
4. Hydrocarbons Structural Models
Construct models for the following hydrocarbons and draw structural formulas indicating bond rotation:
Ethane (C₂H₆)
Acetic Acid (CH₃COOH)
Methyl Amine (CH₃NH₂)
Assessment of polarity for each molecule presented.
5. Acid and Amine Reaction
Using the models of acetic acid and methyl amine, remove the proton of the hydroxyl group from the acid and insert it into the unshared electrons of the amine nitrogen. Write the resulting equation for this reaction.
6. Hydrocarbon Models Construction
Build models and write structural formulas for the following hydrocarbons, representing electron pairs with lines:
Methane (CH₄)
Ethane (C₂H₆)
Propane (C₃H₈)
Butane (C₄H₁₀): Write both structural isomers.
Pentane (C₅H₁₂): Write all structural isomers.
Structural Isomers Definition
Definition: Molecules with the same empirical formulas but different bonding arrangements.
7. Phosphorus Bonding
Phosphorus can bond with up to five atoms/groups (e.g., PF₅).
Construct the two structural isomers of PF₄Cl and complete their structural formulas.
8. PF₃Cl₂ Isomers
PF₃Cl₂ can form three structural isomers. Construct and complete the structural formulas for each isomer.
9. Platinum Complexes isomers
The platinum complex [Pt(NH₃)₂Cl₂] has four groups coordinated in a square planar arrangement, leading to two cis-trans isomeric forms. Construct each isomer and represent with structural formulas showing three-dimensional geometry.
10. Cobalt Complex Ligands
The complex [Co(NH₃)₄Cl₂]⁺ has six ligands in an octahedral arrangement leading to two cis-trans isomers. Construct and complete each structural formula.
Note: Ligands should be represented as whole molecules without individual bond representation.
11. Co(NH₃)₃Cl₃ Isomers
Construct and complete structural formulas for the two isomers of Co(NH₃)₃Cl₃.
12. Structural Isomers for [Co(NH₃)₃(H₂O)Cl₂]⁺
This complex has three structural isomers. Construct and complete each isomer's structural formulas.
13. Enantiomers and Chiral Molecules
Enantiomers: Defined as molecules that are mirror images but non-superimposable, also referred to as chiral. The complex [Co(NH₃)₂(H₂O)₂Cl₂]⁺ has five structural isomers, one of which form an enantiomeric pair. Construct all six structures and indicate the enantiomeric pair. Use viewing method to analyze mirror images.
14. Octahedral Arrangement of Ethylenediamine Complex
The complex [Pt(en)₃]⁴⁺, where en represents ethylenediamine (NH₂CH₂CH₂NH₂), has three ligands coordinated to platinum in an octahedral arrangement.
Each en ligand binds twice to different platinum sites forming five-membered rings. Construct each structure and denote the enantiomer pair. Representation of en as loops or rings in structural drawings is acceptable.
Collaboration with peers is necessary for the construction of these molecular arrangements.