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> en > NH
3
> NCS
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2
O > F
> RCO
2
> 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.
School of Science and Engineering page 4 of 6
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 molecules 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.
E
TOTAL
= E
STRETCH
+ E
BEND
+ E
VDW
+ E
TORSION
+ E
ELECTROSTATIC
+ E
H-BOND
+
The force fields depend on which energy terms are included in the computation of the total energy (E
TOTAL
)
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 [(NH
3
)
5
Co(ONO)]
2+
and
[(NH
3
)
5
Co(NO
2
)]
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: [(NH
3
)
5
Co(ONO)]
2+
and [(NH
3
)
5
Co(NO
2
)]
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
[(NH
3
)
5
Co(Cl)]Cl
2
.
School of Science and Engineering page 5 of 6
3. Procedure
1. Draw the nitritopentaaminecobalt(III) complex ion, [(NH
3
)
5
Co(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 [(NH
3
)
5
Co(ONO)]
2+
. Save the image.
4. Repeat steps 1-3 above with the nitropentaamminecobalt(III) isomer.
Q1. Based on the computed total energies of [(NH
3
)
5
Co(ONO)]
2+
and [(NH
3
)
5
Co(NO
2
)]
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.
[(NH
3
)
5
Co(ONO)]
2+
bond lengths/ [(NH
3
)
5
Co(NO
2
)]
2+
bond lengths/
CoO (ONO) CoN (NO
2
)
CoN (NH
3
) CoN (NH
3
)
O*N
NO
NO
NH NH
*coordinated to Co
Table 1b. Bond angles for minimized structures of nitrito and nitro complex ions.
[(NH
3
)
5
Co(ONO)]
2+
bond angles/ [(NH
3
)
5
Co(NO
2
)]
2+
bond angles/
CoON CoNO
ONO ONO
O*CoN (NO
2
) NCoN (NH
3
)
(NH
3
) NCoN (NH
3
) (NH
3
) NCoN (NH
3
)
HNH HNH
Q2. Based on the computed internal coordinates of [(NH
3
)
5
Co(ONO)]
2+
and [(NH
3
)
5
Co(NO
2
)]
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. ONO bond angles in nitrito and nitro ligands
d. Bond lengths in CoN(NH
3
) and CoN(NO
2
) in [(NH
3
)
5
Co(NO
2
)]
2+
.
e. Bond lengths in CoN(NH
3
) and CoN(ONO) in [(NH
3
)
5
Co(ONO)]
2+
.
School of Science and Engineering page 6 of 6
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 [(NH
3
)
5
Co(ONO)]
2+
and [(NH
3
)
5
Co(NO
2
)]
2+
which include the following
distortions. For each distortion (ad) 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.
[(NH
3
)
5
Co(ONO)]
2+
[(NH
3
)
5
Co(NO
2
)]
2+
CoN (NH
3
) elongation
Change ONO bond angle*
Change NH bond length in one
NH
3
ligand*
Change HNH bond angle in one
NH
3
ligand*
*increase and decrease the bond angle/ length
Q4. Compare the computed total energies of [(NH
3
)
5
Co(ONO)]
2+
and [(NH
3
)
5
Co(NO
2
)]
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.