This course is concerned with the properties of Molecules and (ordered) Solids. Ø i.e., species with regular atomic positions

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Eleanore Tyler
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1 PART ONE: Structure and Shape CHEM 2060 Lecture 1: Structure and Shape L1-1 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 m ca. 1.1 Å 1 pm = 1 x m

2 Example of a small molecule: CHEM 2060 Lecture 1: Structure and Shape L1-2 C 16 H 10 N 2 O 2 P. Susse, et al., Z. Kristallogr. 1988, 184, 269. CSD Refcode: INDIGO03 Bond distances: C=O C=C C--C aromatic C-C N-H 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.

$[Def] Diffraction is the apparent bending of waves (e.g., light) around very small objects and spreading out of waves that travel through small openings.$

3 Question: What is an X-ray crystal structure? CHEM 2060 Lecture 1: Structure and Shape L1-3 [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)

$CHEM 2060 Lecture 1: Structure and Shape L1-4 When X-rays are shone through a crystal, they are diffracted by the atoms (specifically by the electron cloud, not by the nucleus) and emerge according$

4 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.

5 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.

6 Example of a large molecule: CHEM 2060 Lecture 1: Structure and Shape L1-6 G. Christou, et al., Angew. Chem. 2004, 43, We will now get our first look at the shapes of: molecules polymers solids surfaces

7 1) Examples of Planar Molecules ( Flat ) CHEM 2060 Lecture 1: Structure and Shape L1-7 Benzene, C 6 H 6 Crystal T = 150 K Refcode: BENZEN18 Nayak, et al., Cryst. Eng. Comm. 2010, 12, Boron trifluoride, BF 3 Water, H 2 O Psoralen, C 11 H 6 O 3 - a Lewis acid - a type of furanocoumarin - a phototoxin - a mutagen

8 2) Examples of Octahedral Molecules (C.N. = 6) CHEM 2060 Lecture 1: Structure and Shape L1-8 Question: What is an octahedron? 8 faces 12 edges 6 apices Octahedral Spinel (see Solids) Tungsten hexacarbonyl W(CO) 6 Hexachlorophosphate PCl 6

9 3) Examples of Tetrahedral Molecules (C.N. = 4) CHEM 2060 Lecture 1: Structure and Shape L1-9 Question: What is a tetrahedron? 4 faces 6 edges 4 apices

10 4) Examples of Other Shapes CHEM 2060 Lecture 1: Structure and Shape L1-10

11 5) Examples of Polymers CHEM 2060 Lecture 1: Structure and Shape L1-11 Polypropylene, [-CH(CH 3 )CH 2 -] n AUD polymer banknotes Cellulose, (C 6 H 10 O 5 ) n

12 6) Examples of Molecular and Ionic Solids CHEM 2060 Lecture 1: Structure and Shape L1-12 Ice, H 2 O Table Salt, Sodium Chloride, NaCl

13 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)

At the end of this lesson, students should be able to :

At the end of this lesson, students should be able to : (a) Explain Valence Shell Electron Pair Repulsion theory (VSEPR) (b) Draw the basic molecular shapes: linear, planar, tetrahedral, and octahedral.