OBJECTIVES

This "dry lab" is intended to provide an introduction to several aspects of molecular structure in inorganic chemistry. As well as introducing a number of molecular shapes and their geometrical features, the questions scattered throughout often require you to draw molecules so that their shapes are clear to others. Take the time to practice this skill, and hand in a good quality report: hastily prepared answers will lose you marks. Also, when writing down formulae, be careful to get the charges, if any, correct. All questions, including the three "review questions" are to be answered.

INTRODUCTION

While the "molecular" formulae tell us the number of the atoms in a molecule, they provide no information as to the arrangement of atoms relative to one another. The molecular formula is a very compact way of representing the molecule, or the substance, but for many purposes this representation is entirely inadequate. There are times when a formula that shows how the atoms are arranged vis a vis one another proves very useful. Such a formula is called a "structural formula".

Review Question 1.

Give a real example of a pair of different substances which have the same molecular formula but different molecular structures.

For polyatomic molecules, on the other hand, the structural formula can be much more revealing. Consider the following molecules:

Molecule/Molecule-Ion	Molecular Formula	Possible Structural Formulas
Carbon dioxide	CO2
Water	H2O
Ammonia	NH3
Boron trichloride	BCl3
Silicon tetrachloride	SiCl4
Dibromodichloroplatinate(II)	[PtBr2Cl2]2-
Hexabromostannate(IV)	[SnBr6]2-

We notice that we can show more than one way in which we can arrange the atoms in a molecule. Consider the two triatomic molecules, CO₂ and H₂O. Which of the two possible structural formulas shown above is the correct one? In order to choose between the two possibilities (by experiment) we resort to some physical property of the molecule in question. Experimentally it has been found, for example, that the molecule of carbon dioxide, CO₂, has a dipole moment of zero and water, H₂O, has a dipole moment of 1.87 Debyes. We are now in a position to make a choice.

The fact that carbon dioxide has an experimental dipole moment of zero suggests that the linear structural formula (where the bond moments cancel each other) is the correct one. (The bent formula (where the resultant is not zero) would very likely have a dipole moment greater than zero.) In the case of water we have to eliminate the linear structural formula since this formula says that the dipole moment of water should be zero, contrary to the experimental observation.

Review Question 2.

The diagram at the right shows schematically apparatus in which the effect molecular dipole moments might be detected. The cell contains a pair of electrically charged plates. Copy the diagram, and sketch in between the plates a molecule of CO₂ showing how it would tend to orient if it were, in fact, bent.

Do the same for H₂O and OF₂ which really are bent.

Although structural formulae are generally a much more informative way of representing a molecule than the ordinary molecular formulae, they still suffer from a great disadvantage. They all appear to be flat or planar (ie. two-dimensional). In fact, molecules do not exist in a two-dimensional world: molecules are not flat, they are three-dimensional. In order to convey the three-dimensional structure of a molecule, it is necessary to use a three-dimensional model - or a picture of such a model. The drawing of such a three-dimensional model is referred to as a "perspective structural formula".

There are three common forms of commercially available molecular models in which the atoms are represented by spheres (or sometimes polyhedra). These spheres are usually made of different colours and sizes so as to distinguish between the various kinds of atoms.

The crudest models are those in which the spheres are connected by rigid sticks, the so-called "ball and stick" models. In a variant, springs or flexible rods are used to replace the sticks. "Ball and spring" models, are more realistic because they show the flexibility of molecules more realistically. The third kind of model, in which the balls are fitted directly together, are called "space-filling" or "filled-space" models. They are in many ways the most realistic for several reasons. Firstly, they show just how atoms that are not directly bound to one another may nevertheless be rather crowded together: a phenomenon called steric hindrance. Also, they can show how closely separate molecules might approach one another. In addition, they can show the bond lengths more correctly. (In ball and stick or ball and spring model kits there is usually only a very limited number of stick or spring lengths.) A disadvantage is the loss of flexibility since the bond/sticks are eliminated and the inter-bond angles are fixed at idealized values.

Some illustrative pictures of models of common molecules are tabulated below:

Molecule	Ball and Stick Model	Space-filling Model
HCl
H2O
NH3

Comparatively recently, a number of computer programs (e.g. PCModel and RasMol) have been written which show molecular diagrams corresponding to each of the above model types (and more). Many allow the user to manipulate the view using the mouse. A very simple version of such a program has been built into this lab. The diagrams with the buff-coloured background are of this type - "drag" the mouse pointer across the diagram to alter the view of the molecules. As a result, the use of real (and sometimes expensive) models has decreased. You may have purchased such models, or they may be made available for this lab if you do it in the Department, but you might not need them.

Review Question 3.

Make a sketch similar to the space-filling diagram of HCl (above) and label it to distinguish between the covalent radii and van der Waals radii of the hydrogen and the chlorine.

Coordination compounds are compounds containing one or more coordinate covalent bonds. These coordination compounds or complexes consist of a central metal atom or ion bonded by coordinate covalent bonds to a definite number of atoms, molecules, or ions arranged about it in a definite stereochemistry. For example, in the [Pt(NH₃)₄]²⁺ complex ion shown below, the Pt(II) central ion is surrounded by the N atoms of the four NH₃ molecules, the Pt(II) and the four N atoms lying in the same plane. Each N atom of an NH₃ molecule donates its lone electron pair to the Pt(II) forming a coordinate covalent bond, resulting in the formation of a complex ion. In general the central atom or ion acts as an electron-pair acceptor (Lewis acid) and the NH₃ molecule as an electron-pair donor (Lewis base). The ammonia molecules are known as ligands or coordinating groups.

	Missing Applet
[Pt(NH3)4]2+

Question 1.

Manipulate the diagram on the right to show a view looking directly down along a N-Pt-N axis (along a diagonal of the square molecule). Are the hydrogen atoms on the two ammonia groups eclipsed or staggered?

Look at the square edge-on as well. Are the hydrogen atoms on adjacent NH₃ ligands as far apart as they could be?

Coordination number is the total number of ions or molecules which may be directly associated with another ion or molecule (or may also be defined as the number of sigma bonds associated with the central atom or ion). For example the coordination number (C.N.) of Pt(II) in [PtBr₂Cl₂]^2- is 4. In the ion, SnBr₆^2- the Sn(IV) central ion has a C.N. of 6. in the molecule PCl₅, the P might be said to have a C.N. of 5. Aluminum in AlCl₄^- has a C.N. of 4 but in AlF₆^3- it has a C.N. of 6.

The central atom or ion and the ligands immediately surrounding it define what is known as a coordination sphere.

The coordination geometry is the geometry which a coordination compound or complex ion possesses. For example, the AlCl₄^- complex ion possesses a tetrahedral coordination geometry; AlF₆^3- possesses an octahedral coordination geometry; [PtBr₂Cl₂]^2- possesses a square-planar geometry. We will restrict ourselves here to those geometries of coordination compounds which have a coordination number of 3, 4, 5, and 6.

The word arrangement is used here to describe the disposition of the ligands around the central atom without regard to the lone-pairs whose presence is usually inferred rather than "seen".

(a) Coordination Number Three

This coordination number occurs quite rarely. Two of the arrangements expected for C.N. 3 are trigonal planar (eg. BF₃, NO₃^-) and the trigonal pyramid (eg. NH₃, ClO₃^-) where lone pairs occupy a fourth "site" on the central atom, which could therefore be considered to have a tetrahedral coordination geometry. The presence of more lone-pairs can lead to other arrangements e.g. "T" shaped (with two lone-pairs in equatorial sites of a trigonal-bipyramidal coordination geometry).

Missing Applet

Missing Applet

Question 2.

Look at the three molecules below: are they all the same, are there two which are the same (which two), or are they all different?

(b) Coordination Number Four

There are two geometries that compounds having C.N. = 4 can adopt: the tetrahedral geometry and the square planar geometry.

The tetrahedral geometry occurs fairly commonly for complexes of non-transition metal ions. The preference for this geometry is attributed to two factors:

1. covalence in the bonds achieved by use of sp³ hybrid orbitals and,
2. from an electrostatic point of view the ligand are farthest from each other.

Some complex ions having tetrahedral geometry are BF₄^-, BCl₄^-, ZnCl₄^2-, ZnBr₄^2-, [Cd(CN)_4]^2-, BF₃NH₃, and others. Among the transition metals, CoCl₄^2-, CoBr₄^2-, [Co(NCS)₄]_2-, FeCl₄^-, and a few other CoX₄^2- species have this geometry. It occurs particularly when the ligands are sterically demanding and/or when there is no strong reason to adopt one of the alternatives, notably octahedral or square planar (see below).

The square-planar geometry is especially characteristic of certain transition metals (mostly d⁸ ions) and otherwise not very common. The ions Rh(I), Ir(I), Pt(II), Pd(II), Au(III) are frequently found in this form of coordination geometry. For the elements Ni(II) and Cu(II) this geometry is also very common and very important.

Missing Applet

Missing Applet

Question 3.

Which coordination geometry, tetrahedral or square-planar, would you anticipate for the following species? Explain.

1. GeF₄
2. GeBr₄
3. [AuCl₄]^3–
4. [AuCl₄]^–

This geometry is also relatively rare. A note of caution here is appropriate. The coordination number is not always the number of atoms bonded to a central atom as implied by the empirical (simplest) formula; eg. in the crystalline compounds NbCl₅, NbBr₅, TaCl₅, and MoCl₅, the C.N. is not 5. These compounds all contain dimeric M₂X₁₀ molecules consisting of two octahedral MX₆ groups sharing an edge using bridging X groups:

	Missing Applet
Nb2Cl10

There are two regular forms of 5-coordination geometry. One in which the atoms lie at the vertices of a trigonal-bipyramid and one in which they lie at the vertices of a square-pyramid.

The compounds Fe(CO)₅ (shown above), [Mn(CO)₅]^-, and gaseous PCl₅ all have the trigonal-bipyramidal geometry. The square-pyramidal geometry is espoused by complex compounds such as [Ni(CN)₅]^3- (with certain cations) (also shown above) NiBr₃[P(C₂H₅)₃]₂, and a few others.

Question 4.

The trigonal-bipyramidal geometry has two different sites called equatorial and axial, and the square-pyramidal geometry also has two different sites called basal and apical. Draw sketches of the two geometries with the sites labelled.

The geometric form for 6-coordination is very common and is found in almost exculsively in one geometrical arrangement - the octahedron, which is a figure of very high symmetry. There are two common ways to draw this geometry shown to the left and right of the ball and stick diagram. Note that most of the actual bonds are not shown, and sometimes even the central atom label is omitted if it is clear from the context what it must be.

	Missing Applet
[PtCl6]2–

There are huge numbers of complexes with this geometry, a very few examples of which are: [Cr(H₂O)₆]³⁺, [Rh(H₂O)₆]³⁺, AlI₆^3-, CoCl₆^3-, [Ti(H₂O)₆]³⁺, SnBr₆^2-, TeCl₆^2-, [Cr(NH₃)₆]³⁺.

Question 5.

Copy the two sketches (to the left and right of the ball and stick model above) and then mark the position of the actual bonds.