CHEM 2060 Lecture 1: Structure and Shape PART ONE ... · CHEM 2060 Lecture 1: Structure and Shape L1-3 Question: What is an “X-ray crystal structure”? [Def] Crystallography is

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 e.g., C-H bond 1 Å = 1 x 10-10 m ca. 1.1 Å 1 pm = 1 x 10-12 m

CHEM 2060 Lecture 1: Structure and Shape L1-2 Example of a “small” molecule:

C16H10N2O2 P. Susse, et al., Z. Kristallogr. 1988, 184, 269. CSD Refcode: INDIGO03 Bond distances:

* NOTE: The H atom positions are usually estimated, not actually measured, in an X-ray crystal structure.

C=O 1.24 Å C=C 1.34 Å C--Caromatic 1.39 Å C-C 1.43 and 1.46 Å N-H 0.98 Å

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 Water, H2O Psoralen, C11H6O3

- a Lewis acid - 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 Hexachlorophosphate W(CO)6 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 AUD polymer banknotes

Cellulose, (C6H10O5)n

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)