ATENEO DE MANILA UNIVERSITY

CH 114.1 INORGANIC CHEMISTRY LABORATORY

Experiment 3A: Synthesis of the Linkage Isomers Nitrito- and

Nitropentaamminecobalt(III) Chloride
1. Introduction

[(NH3)5Co(Cl)]Cl2 reacts with sodium nitrite NaNO2 such that the nitrite ion NO2- replaces the
chloride ion Cl- to form [(NH3)5Co(nitrite)]Cl2. The ionic equation for the reaction is given below. The
reaction involves substitution of the coordinated chloride ligand for nitrite. Such a reaction is an example of
a ligand substitution reaction.

[(NH3)5Co(Cl)]2+ + NO2-  [(NH3)5Co(nitrite)]2+ + Cl- (1)

There are two possible structures of [(NH3)5Co(NO2)]2+ depending on how the NO2- ligand coordinates
with Co. These are the nitrito complex [(NH3)5Co(ONO)]2+, in which the oxygen is directly bonded to Co,
and the other one is the nitro complex [Co(NH3)5(NO2)]2+, in which the nitrogen is directly bonded to Co.
Since both have the same formula but differ only in the way the nitrate ligand is linked to Co, then these
two compounds are called linkage isomers.

Q1. Describe the geometry about the central metal atom for all three cobalt complexes.
A. __________________________________________________________________

Q2 What do you think is the role of the uncoordinated Cl (underlined) in [(NH3)5Co(Cl)]Cl2 and
[(NH3)5Co(nitrite)]Cl2? (Hint: What do you think is the role of sodium in sodium nitrite?).
A. ____________________________________________________________________

Q3. Are these Cl bonded directly to the metal? What is the term used to indicate that an atom or a group of
atoms is bonded to the metal?
A. ____________________________________________________________________

In this experiment, you will synthesize both the nitrito and nitro isomers. However, both isomers
cannot be obtained at the same time. You will first get isomer A. After about an hour, isomer K slowly
becomes isomer T. (You will determine through experiment and modeling which nitrite isomer is A or B.)
Why? This is because isomer A is the kinetic product (K) of the reaction. Isomer B is the thermodynamic
product (T). A diagram showing the energy versus reaction coordinate will be helpful (Figure 1).

Figure 1. Energy along a reaction coordinate for a reaction

with two products K and T and a common intermediate I.

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 The reactants, R, in his case [(NH3)5Co(Cl)]2+ and NO2- , will need to overcome the activation
energy EA (the first hill) to become the common intermediates, I. The common intermediates can then
become the kinetic product K and the thermodynamic product T. From the diagram, which do you think
will be more readily formed: K or T? Hint: Compare E AK as the hill for K and EAT as the hill for T. The
diagram shows EAK < EAT, so that the kinetic product K will be formed faster relative to the product, T.

Now consider further: if we run the reaction at a temperature such that there is roughly EK energy
available but not ET, then the back-reaction from K to the common intermediate will have enough energy
to occur but not the back-reaction from T to the common intermediate. Note that EK > EAT. This means
that when we have EK worth of energy available, so that the common intermediate re-forms from the
back-reaction of K, we also have enough energy available to overcome the activation energy for formation
of T. Therefore, under these conditions, any K that forms has a chance of back-reacting to form the
common intermediate, and then forward-reacting to form the product T. But, any T that forms does not
have sufficient energy to back-react to form the common intermediate. The product T will therefore
accumulate at the expense of the K product. Note that this is not an equilibrium situation, since T cannot
back-react.

After the synthesis component of this experiment, you will do molecular modeling (Spartan®) to
obtain the total energy values for the nitrito- and nitro- complexes. From computational results, you will
make predictions as to which one is the kinetic and which one is the thermodynamic product. Will these
theoretical data be in agreement with experimental fact? That is what you are going to verify in this
experiment.

2. Objectives

1. To prepare the linkage isomers nitritopentaamminecobalt(III) chloride and nitropentaamminecobalt(III)

chloride.
2. To determine experimentally which of the synthesized cobalt complexes is the kinetic product and which
is the thermodynamic product.
3. To confirm whether the results of the computational chemistry experiment on the cobalt complexes are
in agreement with those found experimentally.

3. Procedure

A. Preparation of Isomer K.

1. Turn on the hot plate and heat beaker containing a mixture of 0.8 mL of conc. aqueous ammonia in 8 mL
of distilled water. Cover the beaker to avoid loss of NH3. Make sure the magnetic stir bar is functioning
properly. The temperature is not critical.
2. Add 0.50 g of chloropentaamminecobalt(III) chloride or [(NH 3)5Co(Cl)]Cl2 to the mixture. Continue
heating and stirring until the solid dissolves completely. If the solid does not dissolve completely, you may
filter off the remaining solid and proceed to step 3. If a dark brown or black precipitate of cobalt oxide
forms, filter it off and use this filtrate for step 3.
3. Using a pair of tongs, remove the mixture from the hot plate. The solution should be clear. Let cool to
room temperature for a few minutes then cool further by running tap water. Place this in an ice-water bath
(use a large beaker) and let cool for 5 minutes. Save 1-2 drops of the solution for UV-Vis analysis.
4. Neutralize the solution by adding several drops of 2 M HCl slowly and testing with red and blue litmus
paper. Keep the solution immersed in the ice-water bath during this step.
5. Add 0.50 g sodium nitrite to the cold mixture in step 4. Stir until all the sodium nitrite dissolves. Why is
the mixture kept cold as nitrite is added? Save 1-2 drops of the solution for UV-Vis analysis.
6. Transfer the set up (beaker and ice-water bath) into the hood. Add 0.5 mL of 6 M HCl. (Be careful when
handling the acid!) Keep the solution in the ice bath until salmon pink crystals precipitate off.

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7. Filter the product (decant if filtrate is too fine to filter) and wash with 2 mL of cold distilled water.
Proceed to Part B immediately.
8. Leave some product to air-dry for FTIR analysis.

B. Conversion of Isomer K to Isomer T

1. Boil 2 mL of distilled water in a small beaker to remove any dissolved CO 2. Keep the beaker covered.
Then remove this from the hot plate using a pair of tongs. Add a few drops of conc. aqueous ammonia into
the beaker.
2. Obtain a spatula of the wet product you obtained in step A.7. Add this to the contents of the beaker
above and heat until dissolved. Stir well while heating and wait for the color to change to yellow or orange.
If color does not change, heat the solution further until the color is observed. Save 1-2 drops of the solution
for UV-Vis analysis.
3. As the mixture cools to room temperature, add 2 mL of conc HCl. Cool in an ice-water bath and observe
the appearance of crystals. Is there any difference in color between the two isomers?
4. Filter off the crystals or simply decant and wash with 3 mL (about 60 drops) of cold ethanol. Air-dry on
your bench top.
5. Run FTIR analysis using pellet technique.
6. Transfer remaining product to a vial. Label properly and submit to your instructor.

C. Room Temperature Conversion of Isomer K to Isomer T

Return to the remaining wet isomer K you obtained in step A.7. Transfer this wet product to a vial and label
properly. Allow this to sit on the bench top and see what happens when you come back after one week.
What can you conclude?

Q4. Can you relate the colors of the isomers and the starting compound [(NH 3)5Co(Cl)]2+, to the
spectroscopic series? (CO, CN– > phen > NO2– > en > NH3 > NCS– > H2O > F– > RCO2– > OH– > Cl– > Br–
> I– )
A.__________________________________________________________________________

4. References

1. Tanaka, J.; Suib, S. ―Experimental Methods in Inorganic Chemistry;‖ Prentice Hall: New Jersey, 1999.
2. Pass, G.; Sutcliffe, H. ―Practical Inorganic Chemistry,‖ 2nd ed.; Chapman and Hall: New York, 1982.

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Experiment 3B: Kinetic vs. Thermodynamic Reaction Product: A
Molecular Modeling Experiment on Nitrito- and
Nitropentaamminecobalt(III) Chloride Complexes

1. Introduction

Computational chemistry uses mathematical models to describe molecular and atomic interactions.
The goal of producing an accurate mathematical description of a molecule is to be able to predict all of its
properties, both physical and chemical. The rapid growth of computational chemistry as a discipline
paralleled the phenomenal development of fast computers so that today, ―good theories could now be
applied to real systems.‖

Molecular modeling involves the rendering of a 2D- or 3D-model of a molecule’s structure and
properties. These structure and property data are the results of computations based on molecular mechanics
and/or quantum mechanical methods, which are rendered graphically by the aid of computers. Generally,
there are two types of molecular modeling studies: Molecular Dynamics and Simulations, which are used to
study dynamic processes, and Structural Molecular Modeling, mainly for the study of structure/reactivity
relationships. The type of data and quality of the computed parameters obtained are largely dependent on
the computational method used. Cost and computer time are also important factors to consider when
carrying out computational studies.

In this session, you will be carrying out a computational chemistry experiment using Spartan®.
You will be introduced to a computational method based on molecular mechanics to study the linkage
isomers nitrito- and nitropentaamminecobalt(III). Molecular Mechanics methods are applied routinely to
find molecular equilibrium geometries and conformations and these are applicable to large systems of even
more than 1000 atoms.

ETOTAL = ESTRETCH + EBEND + EVDW + ETORSION + EELECTROSTATIC + EH-BOND + …

The force fields depend on which energy terms are included in the computation of the total energy (ETOTAL)
and how these energy terms are treated. In this molecular modeling experiment, you will experience the use
of molecular mechanics to describe the atomic interactions of the linkage isomers [(NH3)5Co(ONO)]2+ and
[(NH3)5Co(NO2)]2+. The computational method to be used in this experiment is the Merck Molecular Force
Field (MMFF ’94).

You will use the calculated minimum energy to predict which of the two isomers is the kinetic and
which is the thermodynamic product. In Experiment 2A, you synthesized the linkage isomers nitrito- and
nitro-pentaamminecobalt(III). Verify the predictions made based on computational chemistry. This
experiment will show you how computational chemistry is used as a tool in inorganic chemistry and how it
complements actual experimental data.

2. Objectives

1. To use molecular mechanics method (MMFF94) to describe the atomic interactions of two linkage
isomers of a cobalt(III) complex: [(NH3)5Co(ONO)]2+ and [(NH3)5Co(NO2)]2+.
2. To use the total energy values obtained from molecular mechanics to predict which would be the kinetic
and which would be the thermodynamic product when the two linkage isomers are synthesized from
[(NH3)5Co(Cl)]Cl2.

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3. Procedure

1. Draw the nitritopentaaminecobalt(III) complex ion, [(NH3)5Co(ONO)]2+. Try to draw a chemically

reasonable input structure.

2. Minimize the input structure. (Click on Minimize).

3. Record the total energy obtained for [(NH3)5Co(ONO)]2+. Save the image.
4. Repeat steps 1-3 above with the nitropentaamminecobalt(III) isomer.

Q1. Based on the computed total energies of [(NH3)5Co(ONO)]2+ and [(NH3)5Co(NO2)]2+ in Table 1, which
may be assigned as the kinetic product and which one is the thermodynamic product?
A.__________________________________________________________________

5. Examine the minimized structures of both isomers. Record the internal coordinates (bond lengths and
bond angles) indicated in Tables 1a and 1b. To measure the internal coordinates, choose Geometry then
Bond Length (or Bond Angle), then click the bond (two bonds or three atoms for bond angle).

Table 1a. Bond lengths for minimized structures of nitrito and nitro complex ions.
[(NH3)5Co(ONO)]2+ bond lengths/ Å [(NH3)5Co(NO2)]2+ bond lengths/ Å
Co–O (ONO) Co–N (NO2)
Co–N (NH3) Co–N (NH3)
O*–N
N–O
N–O
N–H N–H
*coordinated to Co

Table 1b. Bond angles for minimized structures of nitrito and nitro complex ions.
[(NH3)5Co(ONO)]2+ bond angles/ ° [(NH3)5Co(NO2)]2+ bond angles/ °
Co–O–N Co–N–O
O–N–O O–N–O
O*–Co–N (NO2) N–Co–N (NH3)
(NH3) N–Co–N (NH3) (NH3) N–Co–N (NH3)
H–N–H H–N–H

Q2. Based on the computed internal coordinates of [(NH 3)5Co(ONO)]2+ and [(NH3)5Co(NO2)]2+ in Tables
1a and 1b, comment on the following:
a. Geometry/coordination sphere around cobalt(III)
b. Geometry around the nitrogen in the ammine ligands
c. O—N—O bond angles in nitrito and nitro ligands
d. Bond lengths in Co—N(NH3) and Co—N(NO2) in [(NH3)5Co(NO2)]2+.
e. Bond lengths in Co—N(NH3) and Co—N(ONO) in [(NH3)5Co(ONO)]2+.

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Q3. Comment on the limitations of the molecular mechanics computational method.
A. _________________________________________________________
Let us now examine the effect of input structure on the computed energy of the system.

6. Draw input structures for [(NH3)5Co(ONO)]2+ and [(NH3)5Co(NO2)]2+ which include the following
―distortions‖. For each distortion (a—d) minimize the structure. Record the changes made and the total
energy computed for each distortion in Table 2. Your demonstrators will guide you how to set/constrain
bond angles and bond lengths to carry out ―distortions‖ on the complexes.

Table 2. Effect of input structure on the computed total energy.

[(NH3)5Co(ONO)]2+ [(NH3)5Co(NO2)]2+
Co–N (NH3) elongation
Change O–N–O bond angle*
Change N–H bond length in one
NH3 ligand*
Change H–N–H bond angle in one
NH3 ligand*
*increase and decrease the bond angle/ length

Q4. Compare the computed total energies of [(NH3)5Co(ONO)]2+ and [(NH3)5Co(NO2)]2+ in Table 1 and in
Table 2. What is the general effect of the ―distortions‖ on the computed total energy of the isomers? Offer
an explanation, bearing in mind that the computational method used is based on molecular mechanics.
Account for those results that do not follow the general trend.
A.___________________________________________________________________

4. Reference

Tanaka, J.; Suib, S. ―Experimental Methods in Inorganic Chemistry;‖ Prentice Hall: New Jersey, 1999.

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