CHEM 2060 Lecture 1: Structure and Shape L1-1
PART ONE: Structure and Shape
• This course is concerned with the properties of Molecules and (ordered) Solids.
Ø i.e., species with regular atomic positions
• Later, we’ll see how these are dictated by their electronic structure (how
electrons occupy orbitals).
• First, we will consider the shape of these species…
Atomic and Molecular Dimensions – units of measure
• Typically, Angstroms (Å) are the unit of distance used when discussing atoms and
molecules.
1 mm = 1 x 10-3 m
1 nm = 1 x 10-9 m
1 Å = 1 x 10-10 m
1 pm = 1 x 10-12 m
e.g., C-H bond
ca. 1.1 Å
CHEM 2060 Lecture 1: Structure and Shape L1-2
Example of a “small” molecule:
C16H10N2O2
Bond distances:
C=O
C=C
C--Caromatic
C-C
N-H
P. Susse, et al., Z. Kristallogr. 1988, 184, 269. CSD Refcode: INDIGO03
1.24 Å
1.34 Å
1.39 Å
1.43 and 1.46 Å
0.98 Å
* NOTE: The H atom positions are
usually estimated, not actually
measured, in an X-ray crystal
structure.
CHEM 2060 Lecture 1: Structure and Shape L1-3
Question: What is an “X-ray crystal structure”?
[Def] Crystallography is the theory of spatially periodic, perfectly long-range
ordered patterns.
[Def] Diffraction is the apparent bending of waves (e.g., light) around very small
objects and spreading out of waves that travel through small openings.
[Def] X-rays are electromagnetic radiation with wavelengths of ~100 pm.
(i.e., 10 Å)
CHEM 2060 Lecture 1: Structure and Shape L1-4
• When X-rays are shone through a crystal, they are
diffracted by the atoms (specifically by the electron cloud, not by the nucleus) and
emerge according to a diffraction pattern.
• By rotating the crystal in the X-ray beam, it is possible to collect a complete set of
diffraction patterns at each angle that they occur.
Left: Two diffraction patterns for crystals of
benzene.
Right: Using mathematical algorithms,
a 3D picture of the electron density
distribution (i.e., atom positions and
atom identities) in the crystal can then
be solved.
CHEM 2060 Lecture 1: Structure and Shape L1-5
• It should now be apparent why protons (H atoms) normally do not “show up” in an
X-ray crystal structure…
…too little electron density to diffract the X-ray!
• Atom positions relative to one another in space help determine which atoms are
bonded to one another and by what type of bond.
Ø e.g., double bonds are shorter than single bonds, so the atoms will be
closer together.
• The geometry of non-rigid molecules might be different in the solid state than in
the liquid (or solution) state.
Ø e.g., rotation around a single bond can occur in solution, but the atom
positions are “locked” in the solid state.
CHEM 2060 Lecture 1: Structure and Shape L1-6
Example of a “large” molecule:
G. Christou, et al., Angew. Chem. 2004, 43, 2117.
We will now get our first look at the shapes of:
molecules
polymers
solids
surfaces
CHEM 2060 Lecture 1: Structure and Shape L1-7
1) Examples of Planar Molecules (“Flat”)
Benzene, C6H6
Crystal Structure @ T = 150 K
Refcode: BENZEN18
Nayak, et al., Cryst. Eng. Comm. 2010, 12,
3112-3118.
Boron trifluoride, BF3
- a Lewis acid
Water, H2O
Psoralen, C11H6O3
- a type of furanocoumarin
- a phototoxin
- a mutagen
CHEM 2060 Lecture 1: Structure and Shape L1-8
2) Examples of Octahedral Molecules (C.N. = 6)
Question: What is an octahedron?
8 faces
12 edges
6 apices
Octahedral Spinel (see Solids)
Tungsten hexacarbonyl
W(CO)6
Hexachlorophosphate
PCl6¯
CHEM 2060 Lecture 1: Structure and Shape L1-9
3) Examples of Tetrahedral Molecules (C.N. = 4)
Question: What is a tetrahedron?
4 faces
6 edges
4 apices
CHEM 2060 Lecture 1: Structure and Shape L1-10
4) Examples of Other Shapes
CHEM 2060 Lecture 1: Structure and Shape L1-11
5) Examples of Polymers
Polypropylene, [-CH(CH3)CH2-]n
Cellulose, (C6H10O5)n
AUD polymer banknotes
CHEM 2060 Lecture 1: Structure and Shape L1-12
6) Examples of Molecular and Ionic Solids
Ice, H2O
Table Salt, Sodium Chloride, NaCl
CHEM 2060 Lecture 1: Structure and Shape L1-13
Molecular Shapes
Source: “Chemical Structure and Bonding”, R.
L. DeKock and H. B. Gray
• VSEPR theory to predict shapes!
• Recall: Valence Shell Electron Pair
Repulsion Theory
• Note that in more advanced classes,
you will learn about VALENCE
BOND theory as an improved method
of predicting structures (“tweaks”
VSEPR theory results).
Sapling Users: VSEPR theory
refresher (not a graded assignment)
(see Sapling Online Assignment)