Lab Report Guidelines & Marking Scheme for Practical

Section 1 Lab Performance (Total 20%)

1. Pre-entering lab (5%)
Score Criteria
0 No preparation of experimental procedure, no proper attire-shoes; goggle; lab
coat.
1-2 Summary of procedures too brief, lack of details and confusing; incomplete
safety attire.
3-5 Presents easy to follow steps in lab experimental, logical and adequately
detailed; safety attire checked.

2. Skill & Techniques (15%)

Score Criteria
0 No skill is demonstrated.
1-5 Wrong glassware used, wrong technique, spillage and wasting of chemicals.
6-10 Right glassware used, incorrect or lack of lab technique.
10-15 Presents correct lab skill, clean and tidy.

Section 2: Lab report (Total 80%)

Section Total Rubric

Mark
Title 5 0-1 • No title, or
• Too brief (e.g. “Lab report”; “Mercury in fish”;
Ascorbic acid in fruits”, etc).
2-3 • Too long, or
• Does not identify the complete subject of study
(E.g “Determination of mercury”; “Determination
of lead”, etc).
4-5 Identify the complete subject of study and
encapsulates the purpose of the report/study.
Objective 15 0 Section missing completely.
1-7 • Be too vague, ambitious or broad in scope.
• Just repeat each other in different terms.
• Just be a list of things related to the topic.
• Contradict with methods.
• Does not identify subject of study.
8 - 15 • Concise and brief.
• Be interrelated and describes how to achieve that
objective.
• Clearly identify the subject of study.
• Related to the experiment that has been done.
Introduction 10 0 Section missing completely.
1-5 Background info only from lab manual
6 - 10 • Clearly written, well structured, with
 evidence of extra reading.
• Clear outline of study’s hypotheses.
• Does show something novel in it as
compared to the supplied handout/laboratory
manual.
• Does include the rationale for performing the
experiment.
Experimental 10 0 Section missing completely.
1-5 • One or more subsections (e.g. chemicals or
instrumentation) are missing.
• Confusing statement.
• Parts have been included under the wrong sub-
section.
6-10 Contains all of the relevant information about the
method used; clearly and systematically described
in such a way that a reader could replicate the
study from the description.
Results 20 0 No Discussion section.
1-6 Very lack attempt to relate experiment findings and
collected data.
6-12 Showing attempt to discuss the findings and
collected data, but using inaccurate theories and
justifications.
13-20 Able to demonstrate analysis skill in discussing the
and appropriate statements to justify the
experiment outcome.
.

Discussion 20 0 No Discussion section.

1-6 Very lack attempt to relate experiment findings and
collected data.
6-12 Showing attempt to discuss the findings and
collected data, but using inaccurate theories and
justifications.
13-20 Able to demonstrate analysis skill in discussing the
and appropriate statements to justify the experiment
outcome.

Safety caution 5 0 Section is not present.

1-3 Sentences are not in complete, focusing on minor or
lack important steps.
4-5 Tabulate at least 3 major and most important safety
caution.
Conclusions 10 0 Section missing completely
1–5 • Conclusion is drawn but not supported by
experimental evidence.
• No sensible conclusion is drawn.
• No clear evidence of a thorough understanding of
the experiment and/or theory behind the
experiment.
 6 – 10 • Conclusion is drawn and supported by
experimental evidence.
• Sensible conclusion is drawn.
• Shows clear evidence of a thorough
understanding of the experiment and/or theory
behind the experiment.
References 5 0 Reference not included in the report

1-3 Incomplete references to the books or any other

sources used in report.

4-5 • References in the text and in the reference list

conform in all respects to the formatting
convention (e.g. APA format)
• Complete references to the books or any other
sources used in report.
• References in text are matched with references in
reference list (e.g. no missing references)
Total Mark 100

Late Submission of Report -1 marks / day

Department of Chemistry
Faculty of Science
Universiti Putra Malaysia

Module 1 Title
Introduction and briefing on Good Laboratory Practice (GLP)
COURSE CODE CHM4301

Module Code/No UPM/FS/CHM4301-01

DURATION 3 hours

Learning Resources 1. “Good Laboratory Practice” retrieved from

https://www.stir.ac.uk/media/schools/naturalscience/bes/do
cuments/hs/goodLabPractice.pdf on 7 September 2017
PRIOR Knowledge Good laboratory practice

TERMS TO KNOW -
Learning Outcomes At the end of this module, students are able to:

1. Familiarize themselves with the laboratory, the lecturer,

demonstrators and lab staffs
2. Understand and follow the rules and regulations
throughout the practical course
3. Implement the GLP
Course Contents AND Introduction:
LEARNING Activities
Good laboratory practice (GLP) is essentially the safe laboratory
practice which needs to be implemented in order to ensure the
health and safety of staff and students working in the lab.
Nevertheless it also includes correct techniques of conducting
experiments and also data recording. As a matter of fact, there are
many chemicals that may be encountered by laboratory workers,
some will have known and well documented health hazards,
others will be a byproduct of work, and sometimes new substances
will be generated with unknown health hazards. It is therefore
extremely important that laboratory workers undertake their work
and conduct themselves in a manner that ensures that exposure to
hazardous chemicals is minimised and that where this occurs both
exposure, by all available routes, and physical hazard, is
adequately controlled so as to prevent risk to health or safety.
1.1. Principles of Good Practice

There are four basic principles that summarize good practice in all
laboratory work.

i. Forward planning

Any potential hazards associated with laboratory work,

including, the hazards posed by chemicals used, or
produced, should be determined well before the
commencement of the project. To do this you will have to
consult literature, this could be: Material Safety Data
Sheets (MSDS) supplied by the manufacturer, data bases
of generic MSDS, textbooks, toxicity reviews and any
approved chemical database.

ii. Risk assess, minimize risk and control exposure to

chemicals.

You must undertake a risk assessment of the entire

laboratory work project including; equipment and any
chemicals you use, or produce, during the work. The aim
of the risk assessment is to minimise the risk to persons
health or safety from physical hazards (glass, fire,
explosion, etc.), and from health hazards (chemical
vapours, fume, dusts, toxic powders, corrosives, etc.) by
implementing risk control measures such as safe
equipment, use of fume cupboards, suitable protective
clothing and equipment, etc.

iii. Do not underestimate the risk

It is sensible to assume that where more than one chemical

is used in an activity that the resultant mixture will be more
toxic than its most toxic component. Do not assume that a
fume cupboard will prevent the buildup of explosive
atmospheres, especially when working with very volatile
chemicals that have a low flashpoint e.g. ethers. If a
substance or preparation is classified as explosive,
oxidising, extremely flammable, highly flammable or
flammable then it is a dangerous substance and you are
 required by law to undertake a risk assessment. In addition,
laboratory workers should be prepared for emergency
situations such as a chemical spill, or unintentional release
of gas or vapour.

1.2. Behaviour in the laboratory

The highest standards of professional personal behaviour are

expected of all workers in the laboratory:

● Always wear laboratory coats of a type suited to the

hazard (long sleeved coat, etc.) and always wear them
properly fastened.

● Laboratory coats, or coveralls, must not be worn outwith

laboratories e.g. 3 common rooms, dining rooms, libraries,
computer labs, etc

● In order to prevent cross contamination chemical resistant

gloves must not be worn outside the laboratory, or in
designated write up areas, where telephones, door handles,
pens, etc. may subsequently be touched by persons not
wearing protective gloves.

● Long hair must be secured behind the head when working

in a laboratory to reduce the risk of it dipping in chemicals
or catching fire.

● Open-toed shoes or sandals should never be worn in a

laboratory where chemicals are used and trousers are to be
preferred.

● Do not indulge in horseplay or practical jokes in the

laboratory.

● Never run in a laboratory, or hurry through doorways.

● Make sure equipment is used only for its designated

purpose.

● Never alter the design, or construction, of any purchased

 equipment.

● Make sure all equipment is serviceable and suitable for the

intended use.

1.3. Exposure routes and minimizing risks

Ingestion

● Eating, drinking, applying cosmetics in the laboratory is

strictly prohibited.

● Smoking is prohibited in all University buildings.

● Food, and drinking or eating utensils must not be stored

within laboratories.

● Laboratory refrigerators, freezers, ovens, etc. must never

be used for food storage or preparation.

● Water supply points within a laboratory should never be

used for drinking purposes.

● Laboratory glassware must never be used for food

purposes.

● Mouth pipetting is prohibited. Automatic pipettes, bulbs,

or aspirators should be used to pipette chemicals or start a
siphon.

● Gloves should be washed before being removed and hands

washed following work with any laboratory chemicals.

Inhalation

● Chemicals, or chemical by-products, that are very toxic, or

toxic by inhalation, must be worked with only in a glove
box, or fume cupboard, the appropriate mechanical control
having been chosen as a result of thorough and documented
risk assessment.

● Chemicals that are classed as harmful, or irritant, by

inhalation should be used whenever possible within a fume
cupboard.

● You should keep hazardous chemicals and any reactions at

least 15 cm behind the plane of the sash.

● You should never insert your head inside a fume cupboard

to check a procedure.

● Always work with the sash in the lowest practicable

position and always close the sash when leaving the fume
cupboard unattended.

● Do not clutter fume cupboards with unnecessary

equipment, or store bottles of chemicals within them as this
may restrict the airflow and affect containment.

● Always ensure that the space below the fume cupboard sill
is kept clear of obstruction so as to ensure optimum airflow
and thus containment.

● Never use a fume cupboard that is suspected to be

malfunctioning, or override a warning indicator and always
report any malfunction

● If PPE in the form of Respiratory Protective Equipment

(RPE), commonly referred to as masks, is to be worn as a
control measure then care must be taken that the correct
respirator and appropriate filters is chosen.

Dermal Contact

Dermal hazards are varied; excesses of heat or cold,

corrosives, toxic chemicals that can be absorbed through the
skin, skin irritants, etc. and the exposure route is not
confined to the hands, but may also include the forearms,
face, and any other area of exposed skin. Gloves of a type
 suitable to protect against a particular hazard should be
worn; the following is general good practice that applies to
the selection and use of gloves. More specific and detailed
guidance can be found at: Personal Protective Equipment

● Only wear gloves that you know to be suitably resistant to

the chemical in use and for the type and duration of use e.g.
splash contact or immersion contact. Do not assume that,
general nitrile disposable laboratory glove, will protect
against the particular chemicals in use, it may not, different
chemicals permeate through differing glove materials at
different rates. Wearing gloves of the wrong material can be
more hazardous than not wearing gloves at all, as a chemical
could become trapped in contact with the skin for a
prolonged period.

● You should always inspect gloves as you put them on for

any holes or tears.

● Reusable gloves should be washed as appropriate before

removal to prevent prolonged chemical residue contact and
premature degradation. Disposable gloves should be rinsed
before removal as this helps to prevent contamination
transfer to the hands on removal.

● Always wear your laboratory coat sleeves rolled down in

case of accidental splashing and always wear close fitting
chemical resistant safety spectacles. In the case of work with
corrosive liquids a chemical resistant face shield should be
worn.

● Close fitting chemical resistant safety spectacles, or

goggles, should always be worn when working with
chemicals. When working with corrosive chemicals, or
chemicals which toxicity can be absorbed through skin, a
chemical resistant full face shield should be worn. Safety
glasses or goggles must be worn at all times.

1.4. General Housekeeping

The following general points must be adhered to in all

 laboratories:

● The laboratory floor and in particular traffic areas should

be kept free of obstructions, items such as chemical
containers, boxes, apparatus, etc, should not be stored on the
floor.

● Access to emergency exits, emergency showering

facilities, or emergency equipment such as fire extinguishers
and first aid boxes must never be obstructed.

● Benches should be clean and tidy and free from clutter by

chemicals or apparatus that is not in use.

● Floors should be cleaned regularly and spills dealt with

immediately, in the appropriate manner.

● Correctly label all containers containing chemicals with

detail of the content; this is particularly important in the case
of materials that have been decanted from a larger container,
or where solutions have been made from two or more
substances.

1.5. Closing laboratory

Listen to the instructions given by the demonstrator.

Everyone is responsible to ensure all glass wares used are
cleaned thoroughly. The last person to leave a laboratory
should check that any gas, water and electricity supplies not
in use have been turned off, and that all stocks of flammable
reagents and solvents have been returned to their fire-
resistant cupboards, cabinets or bins. Apparatus left running
overnight must be clearly marked with a notice giving the
name and telephone number of the person to contact in any
emergency. Water connections to experiments left running
overnight must be made secure by a screw clip, or similar
device and a water failure cut-out switch should be fitted,
where appropriate.

Summary The students will be required to adhere to the GLP.

Assignment Students will be introduced to the demonstrators and lab staffs for
 the particular course. They will also be briefed on the rules and
regulations while being in the laboratory. Towards the end,
students will be asked to write a one page summary (in a mind
map) of Good Laboratory Practice and submit the following week.

Assessment* Summary of GLP in a mind map.

Department of Chemistry
Faculty of Science
Universiti Putra Malaysia

Module 2 Title
Computer simulation to understand supramolecular chemistry

COURSE CODE CHM4301

Module Code/No UPM/FS/CHM4301-02

DURATION 6 hours

Learning Resources 1. Steed, J. W. & Atwood, J. L. (2009) Supramolecular

Chemistry, 2nd ed. Chichester: John Wiley & Sons, Ltd.
2. Schneider, H. J. (2012) Applications of Supramolecular
Chemistry, Boca Raton: CRC Press

PRIOR Knowledge Concept of supramolecular chemistry, molecular recognition,

receptor, substrate and interaction site complementarity.

TERMS TO KNOW Receptor, host-guest, substrate, macrocyclic, macrocycles,

ligands, complementarity

Learning Outcomes At the end of this module, students are able to:

a) Understand the following important concept of

supramolecular chemistry: molecular recognition, receptor,
substrate and interaction site complementarity.
b) Familiarize with various aspect of cation recognition by
macrocyclic ligands: spherical recognition, linear
recognition and binding selectivity as a function of the size
of the macrocyclic cavity and the conformational
flexibility of the macrocycles.
c) Self-manipulate the Accelrys Discovery Studio Visualizer
2.5 software in understanding Supramolecular Chemistry.
Course Contents AND Introduction:
LEARNING Activities Supramolecular chemistry is a highly interdisciplinary field of
science involving chemical species assembled from smaller
molecular fragments, which are held together and organized by
means of intermolecular (non-covalent) binding interactions. The
field has its root in synthetic organic chemistry, the metal ion-
ligand complexes of coordination chemistry, the physical
chemistry of molecular interactions, the binding and recognition
of biological substrates, materials science, and the mechanical
properties of solids.

The thermodynamic selectivity of a given host for a particular

cation represents the ratio between the host’s affinity for a given
metal and other guest cations. Strong but selective binding is the
basis of molecular recognition. Designing a synthetic host that
will be selective for a given cation is a very complicated task
because the selectivity is governed by an enormous number of
factors.

Molecular recognition is the specific binding of a guest molecule

to a complementary host molecule to form a host–guest complex.
Often, the definition of which species is the "host" and which is
the "guest" is arbitrary. The molecules are able to identify each
other using non-covalent interactions. Key applications of this
field are the construction of molecular sensors and catalysis.
PART A

Experimental Details

At the computer:

1. Open a software named “Accelrys Discovery Studio 2016

2.5.5”.

18-Crown-6 in the Solid State: Understanding the Steric Fit

Approach

To preview the structure

a) [18]crown-6 (L)

1. Go to “File” on toolbar → “Open” → “Desktop” → “Expt

3” → “hoocd-5.msv” → “Open”

The selected structure will be shown in this window.

2. Go to “View” at toolbar → “Display Style”.

A new dialogue box of Display Style will appear.

3. Choose “Ball and Stick” and click “OK”.

4. Go to “View” at toolbar and select “Spin”.

The structure will rotate 360 ° to give you a better visual of the
molecule. Or else you can view the structure at different angle by
simply hold left click and moving the mouse.

6. Go to “Chemistry” at toolbar and select “Element

Properties”.

From the periodic table, you can see the colors that represent each
element.
Examples:
Atom Color
Oxygen Red
Carbon Grey
Hydrogen White

To learn how to determine the distance between atoms

7. Left click on one oxygen atom of the 18-crown-6 and hold

“Shift” button while clicking the opposite oxygen atom.

8. Go to “Structure” at toolbar → “Monitor” → “Distance”.

This will give you the distance between the selected oxygen
atoms. The distance unit is in Ångstrom.

To convert structure to image format for publication purpose.

9. Select the line connecting the two atoms, go to “View” at

toolbar → “Display Style” → “Label” → “Coloring” →
Select black color → “OK” → “Apply” → “Graphics” →
“Background color” → Select white background color →
“OK” → “Apply” → “Close”

10. Go to “Files” at toolbar → “Save as”→ Desktop → “Files

of type: Image files” → “Save.”

b) L.Na+.H2O

11. Repeat step 1, but in this case open a file named

“nathod_5.msv”.

A new structure will appear. This is the structure of 18-crown-6

with one sodium ion inside the cavity and one mole of water
molecule.

12. Repeat steps 2, 3 and 4.

To determine the distance between oxygen and sodium (Na+) atom

13. Left click on Na+ atom and hold “Shift” button while
clicking one of the oxygen atom.

14. Repeat step 8.

Note down the distance between the Na+ and that particular
oxygen atom.

15. Repeat step 13 for the distance between Na+ with the rest
of the oxygen atoms.

16. Repeat step 9 and 10.

c) L.K+

17. Repeat step 1, but in this case open a file named

“kthod_5.msv”.

18. Repeat 2, 3 and 4.

19. Left click on K+ atom and hold “Shift” button while

clicking one of the oxygen atom.

20. Repeat step 8.

In this case, you need to measure the distance between

oxygens and potassium (K+) atom.

21. Repeat step 19 for the distance between K+ with the rest of
the oxygen atoms.

22. Repeat step 9 and 10.

d) 2(L.Rb+.NCS-)

23. Repeat step 1, but in this case open a file named “rbthxd-
5.msv”.

24. Repeat step 2, 3 and 4.

25. Left click on Rb+ atom and hold “Shift” button while
clicking one of the oxygen atom.

26. Repeat step 8.

In this case, you need to measure the distance between oxygens
and Rubidium (Rb+) atom.

27. Repeat step 25 for the distance between Rb+ with the rest
of the oxygen atoms.

28. Repeat step 9 and 10.

e) L.Cs+

29. Repeat step 1, but in this case open a file named “csthxd-
5.msv”.

30. Repeat 2, 3 and 4.

31. Left click on Cs+ atom and hold “Shift” button while
clicking one of the oxygen atom.

32. Repeat step 8.

In this case, you need to measure the distance between oxygens

and Cesium (Cs+) atom.

33. Repeat step 31 for the distance between Cs+ with the rest
of the oxygen atoms.

34. Repeat step 9 and 10.

PART B

Interaction Sites Complementarity and Linear Recognition

1. Open a software named “Accelrys Discovery Studio

Visualizer 2.5”.

To preview the structure

a) L.NH3+-C2H4-NH3+

2. Go to “File” on toolbar → “Open” → “Local Disk (C:)”

 → “Expt 6” → “bafzen-27b.msv”.

The selected structure will be shown in a new window.

3. Go to “View” at toolbar → “Display Style” → “Ball and

stick” → “OK”.

4. Go to “Structure” at toolbar → “Monitor” → “HBonds”.

You will see the H-bonding between the cation and the receptor.
Note down how many hydrogen bonds involve in the interaction
between the host and guest.

To convert structure to image format for publication purpose

5. Go to “View” at toolbar → “Display Style” → “Graphics”

→ “Background color” → Select white background color
→ “OK” → Apply

6. Go to “Files” at toolbar → “Save as” → “Files of type:

Image files” → “OK.”

b) L.NH3+-(CH2)5-NH3+

7. Go to “File” on toolbar → “Open” → “Local Disk (C:)”

→ “Expt 6” → “bexnat-52.msv”.

8. Repeat step 3.

To determine the length of guest

8. Left click on nitrogen atom of one end and the nitrogen

atom of the other end of the guest.

9. Go to “Structure” at toolbar → “Monitor” → “Distance”.

10. DO IT YOURSELF: Determine the molecular length of

the receptor.

Note down the length of both substrate and receptor.

11. Repeat steps 5 and 6.

Summary The study of non-covalent interactions is crucial to understanding
many biological processes from cell structure to vision that rely on
these forces for structure and function. Design based on
supramolecular chemistry has led to numerous applications in the
creation of functional biomaterials and therapeutics. It is thus
important to study the formation of these host-guest complexes in
order to build specific supramolecules that meet certain
application.

Assignment Questions

1. Fill in the table for each of the 18-crown-6 complexes (File

name: nathod_5.msv, kthod_5.msv, rbthxd-5.msv and
csthxd-5.msv).

Atom Distance to guest atom, Å

O1
O2
O3
O4
O5
O6

2. Determine the best fit cation in the 18-crown-6 cavity.

Explain why (based on the atomic distance).
3. Define non-covalent binding interaction.

Table 1: Some ionic and van der Waals Radii.

Ionic Radius/Å
Li+ Na+ K+ Rb+ Cs+
0.68 0.97 1.33 1.47 1.67

van der Waals Radius/Å

O N C H
1.40 1.50 1.85 1.20

1. The pioneering work of Charles J. Pedersen (1988), Jean

M. Lehn (1988) and Donald Cram (1988) ignited interest
in supramolecular chemistry and was recognized with the
award of the 1987 Nobel prize for chemistry. One of its
key player, Donald Cram has summed up the principle of
 preorganization and complementarity. Define this
principle.
2. What factor that contributes to the binding of NH3+-C2H4-
NH3+ with tetra-tartaro-18-crown-6 (file name: bafzen-
27b.msv).
3. What are the other factors that contribute to the affinity of
a host for a guest?

Assessment* Laboratory Report

Your report must include the introduction to supramolecular

chemistry and host guest systems, images of supramolecular
molecules obtained from Part A and Part B of the experiment and
answers for all the questions in both parts of the experiment.
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia

Module 3 Title
Docking of small molecules into DNA/protein molecule via
simple docking software

COURSE CODE CHM4301

Module Code/No UPM/FS/CHM4301-03

DURATION 6 hours
Learning Resources J. Chem. Inf. Model. 2008, 48, 1602–1615
PRIOR Knowledge Concept of supramolecular chemistry, receptor, ligand, binding
energy, docking

TERMS TO KNOW Receptor, ligand, drug-DNA interaction, intercalator, binding

affinity, docking
Learning Outcomes At the end of this module, students are able to:

1. Understand the concept of drug-DNA interaction

2. Visualize and manipulate the drug-DNA interaction in
docking software
3. Understand the concept of molecular docking and
familiarize the steps and aspect in molecular docking

Course Contents AND Introduction:

LEARNING Activities The accurate in silico prediction of small molecule-receptor
complex geometries, for example molecular docking, offers great
promise in driving the rational development of novel small-
molecule therapeutics. Molecular docking usually uses as a
screening tools during the synthesis and development of small
molecule drugs that selectively target protein or nucleic acids. The
technique gives valuable information comprising the interaction
and mechanism of action of the small molecules with the target
and this may have medicinal value.

Often, the interaction of small molecules with nucleic acids at

multiple sites may lead to alteration of the nucleic acid function.
Small molecules may bind to duplex DNA in three different
modes: electrostatic, minor and major groove and also
intercalation. The structures of the ligands are responsible for the
different mechanism of binding (i.e. minor groove is particularly
attractive target for small molecules with crescent shape due to the
complementary shape between the ligand and the target.
Intercalators, on the other hand, would prefer to stack between the
duplex bases due to the presence of extended planar aromatic
ligand of the intercalator. Two well-known and well-characterized
minor groove binders are the antimalarial drug pentamidine and
the antiviral drug distamycin, which we selected for our studies. In
addition, we selected two prototypical intercalators, daunorubicin,
a drug commonly used to treat certain forms of leukemia, and
ellipticine, another antineoplastic drug, for docking experiments.

Among the commonly use docking GUI are autodock Vina and
AutoDock 4.2. These 2 docking software are among the simplest
to use thus making them suitable for beginners. Vina is known to
implement Broyden-Fletcher-Goldfarb-Shanno algorithm in its
calculation while Autodock 4.2 offered a few options that can be
chosen. Hence making it a good candidate for comparison with
Vina.

Software required

1. MGL tools (http://mgltools.scripps.edu/downloads)

2. Discovery Studio Visualizer
(http://accelrys.com/products/discovery-
studio/visualization-download.php)
3. Autodock Tools
(http://autodock.scripps.edu/resources/adt)
4. Autodock Vina (http://vina.scripps.edu/download.html)
5. Open Babel (http://openbabel.org/wiki/Main_Page)

Part A: Getting the required target and ligand

1. The required target and ligands can be downloaded from

major databases such as RCSB-PDB, PubChem and drug
bank.
2. Download the PDB file of the listed molecules from:
(https://www.rcsb.org/)
I. 152d
II. 2dnd
III. 1z3f
IV. 1d64
 3. Download the ligand listed from PubChem
(https://pubchem.ncbi.nlm.nih.gov/)
I. daunorubicin
II. distamycin
III. ellipticine
IV. pentamidine

Part B: Preparation of the macromolecules (protein) and

ligand using DS Visualizer and Autodock Tools

1. Initiate the DS Visualizer software to prepare the protein

file (receptor).
2. Click file, open the 1d64 pdb file that has been
downloaded. Check the structure of the protein and delete
water molecules and heteroatom. Also delete the co-
crystallizes molecule present.
3. Then save the protein as “receptor.pdb”.
4. Next, convert the ligand file from SDF format to pdb
format using Open Babel software. Then save as
ligand.pdb.

At this point, each of you would have two files in PDB format.
(receptor.pdb and ligand.pdb). Next step is to prepare both ligand
and receptor for docking. This is done following the listed steps:

5. Open the AutoDock Tools, click Read Molecule and open

the file receptor.pdb. This will put up the protein molecule
on the screen to be edited.
6. Click Edit, delete water molecule, then again click Edit to
add H (use the default setting). The next step is to add
charge to the protein. This is done by clicking Edit,
Charges, choose Add Kollman Charges. After that, save
the receptor to pdbqt format. Click Grid, then
Macromolecule, Chose the receptor file and save as
receptor.pdbqt.
7. Next, open the ligand file using the AutoDock Tools. To
do this, Click Ligand tab, then click Input and Open the
ligand.pdb file (saved during Part A)
8. The software would prompt a “summary” to add charges to
the ligand file. Click OK and save as ligand.pdbqt file.

At this stage, each one of you should have two files

(receptor.pdbqt and ligand.pdbqt). The next step is to prepare the
Grid for docking. This is done by:

9. Click Grid then Chose Macromelcule, click the receptor

 file and you will be prompted a few dialog boxes, use the
default option. Then save as receptor.pdbqt file (Overwrite
the previous file).
10. Then click Grid, go to Grid Box. A Grid Options dialog
box will appear, and a box can be observed in the protein
structure. A grid box defines the set point and site for the
docking to be calculated.
11. Then, click File, choose Output and dimension file. This
is to save the grid file. Save as Grid.txt.

Part C: Setting the run configuration file and run docking

1. Create a config.txt file. The text is as below:

receptor = receptor.pdbqt

ligand = ligand.pdbqt

center_x =

center_y =

center_z =

size_x =

size_y =

size_z =

energy_range = 4

exhaustiveness = 8

2. The center for x,y,z and size x,y,z is key in as save from
the grid.txt file.
3. Then save as config.txt file. To run Autodock Vina, click
search “cmd” to open the command prompt box.
4. Set the pathway to run the docking in the command
prompt. To do this, type in the command prompt box as
below:
 cd_Pathway of the docking file folder. Then hit Enter

C:Users\win pathway to docking file “C:\Program Files

(x86)\The Scripps Research Institute\Vina\vina.exe” –receptor
receptor.pdbqt –ligand ligand.pdbqt –config config.txt –log
log.txt –out output.pdbqt

5. Then hit Enter to run docking.

Part D: visualization of the docking result and analysis of the

scoring

1. The docking results can be open in the AutoDock Tools.

All the poses and the ligand binding affinity/energy can be
referred in the log.txt file.

In order to run AutoDock 4.2, the protein and ligand need to be

prepared as pdbqt file. This step can be done by repeating every
step in Part A and Part B. To set the grid box for docking,
grid.gpf file is created.

1. Click Grid, chose macromolecule then click receptor,

then save as receptor.pdbqt.
2. Again, click Grid then Set Map Types, chose Ligand and
Select ligand.
3. Set the grid box by clicking Grid, select Grid Box. Set the
grid box parameter then click File, chose Close saving
current. To save the GPF file, click Grid then chose output
save as grid.gpf.

At this point, each of you should have 3 files (receptor.pdbqt,

ligand.pdbqt and grid.gpf)

4. To run autogrid, click Run tab, chose Run AutoGrid then

select the pathway and file. Click Launch to execute the
process.

The next step is to set up the dock parameters. To do this:

5. Click Docking, go to Macromolecule, set Rigid Filename

then chose receptor.pdbqt file.
6. After that again click the Docking tab, chose ligand, and
select ligand then click Accept.
7. Set the search parameter by clicking Docking and chose
Genetic Algorithm. Use the default value for now by
clicking Accept.
 8. The output is set by clicking Docking and select Output
then chose Lamarckian GA (4.2). Save as output.dpf.

Now, all the required file for docking is complete. You should
have 4 files (receptor.pdbqt, ligand.pdbqt, grid.gpf and
output.dpf). All the docking parameters also has been set and it is
now to run the docking algorithm using AutoDock 4.2. The steps
are as follow:

1. Click Run then chose Run AutoDock, select the

Autodock 4.2 and click the output.dpf file and then
Launch to execute the docking process.

Summary Computational tools have come to the rescue and have

undoubtedly played a pivotal role in rationalizing the path to drug
discovery by reducing the tedious process of hunting a lead
molecule. Molecular docking is an alternative approach to fulfil
the screening of millions of compounds within a few days when
the 3D structure of target protein is available. This method could
predict both the binding affinity between ligand and protein and
the structure of protein–ligand complex, which is useful
information for lead optimization.

Assignment Question:
1. Explain the concept of molecular docking with example.
What are the files required in the process?
2. List all the non-bonding interactions of the ligand docked
in the receptor. (Vina and AutoDock 4.2)
3. Visualize the best pose of each ligand dock in the receptor
and compare the pose between Vina and Autodock 4.2.
4. Compare the ligand dock in the receptor with the co-
crystallized ligand. Comment on the different of the ligand
dock and co-crystallized.
5. Explained the important of setting a suitable Grid box in
the docking process.
6. Define Kollman and Gasteiger charges and what are the
differences between these 2 charges?

Assessment* Laboratory Report

Department of Chemistry
Faculty of Science
Universiti Putra Malaysia

Module 4 Title
Study on the structural properties of mixed sandwich Ru(II)
complexes involving η6-p-cymene with fluorinated phosphines
or phosphites ligands

COURSE CODE CHM4301

Module Code/No UPM/FS/CHM4301-04

DURATION 6 hours
Learning Resources J. Coord. Chem. 2016, 69, 20-38
PRIOR Knowledge Ligand substitution reaction, geometry

TERMS TO KNOW Phosphines, phosphites, ligand susbtitution reaction, p-cymene

Learning Outcomes At the end of this module, students are able to:

1. Understand the setup of organometallic compounds

that need inert atmosphere
2. Visualize and analyze crystal structures of complexes
using Mercury
3. Describe the bonding between the arene and the Ru
using qualitative MO theory

Course Contents AND Introduction:

LEARNING Activities The coordination chemistry of monometallic half-sandwich
complexes has been of significant interest in inorganic and
organometallic chemistry and have found wide application in
bioinorganic and medicinal chemistry. The 6-p-cymene ligand
can be utilized to prepare new organometallic Ru(II) complexes
that in general are piano-stool pseudo-octahedral complexes. The
p-cymene ligand is relatively inert to ligand substitution reactions,
and can be functionalized to tune the properties of the arene-Ru
complex. [Ru(p-cymene)(L)Cl2] is an example of piano-stool
complex which can be prepared by cleaving the bridging chlorides
in {[Ru(p-cymene)Cl2]}2 in the presence of a two-electron donor
(L). The reaction is rather straightforward and has been used to
prepare variety of complexes ranging from L = C- (e.g., N-
heterocyclic carbene), N-, O-, or P-donor ligands.
In this experiment, the p-cymene-Ru(II) moiety serves as a stable
electron-rich platform to explore the structural properties of
fluorine-containing phosphine and phosphite ligands. The
reactivity of organometallic compounds in both stoichiometric and
catalytic reactions have been known to relate to the steric and
electronic properties of phosphines and phosphites. It is well
known that the addition of fluorine or trifluoromethyl groups to
trivalent phosphorus donor ligand resulted in unique electronic
properties of the complexes. This is due to the electron-
withdrawing property of fluorine or trifluoromethyl. This study
would be useful for the rational design of a homogeneous catalyst.

Procedure:

Virtual lab: Synthesis of the Ru(II) precursor and its

complexes

Part A: Synthesis of [(ƞ6-p-cymene) RuCl2]2.

form 1 dimer
1. RuCl3.3H2O is reflux with α-terpinene in a 1:2 mole ratio.
Reflux the mixture in Ethanol for approximately 5 hours.
2. Then concentrate the resultant red solution under reduced
pressure before addition of diethyl ether.
Leave the mixture in a fridge for overnight to yield a red-
brown precipitate. Filter and dry the precipitate.

Part B: Synthesis of [Ru(ƞ6-p-cymene)(L)Cl2] complexes.

1. [(ƞ6-p-cymene) RuCl2]2 is dissolves in dichloromethane

and L (ligand) is added in a mole ratio of 1:2 with respect
of the metal precursor.
2. The mixture is stir for 3 hours at room temperature.
3. After that, the solvent was removed under reduced
pressure to obtain a dark red oil. Hexanes is added to
obtain solid precipitate.
4. The solid is then filter by vacuum filtration.
5. Repeat the steps from 1 to 4 to get all the complexes listed
in the table below.
 Complex L(ligand)
No.
1 P(C6H4F)3
2 P(C6H4CF)3
3 P(C6H3(CF3)2)3
4 P(C6H5)3
5 (P(OCH2CF3)3
6 P(OCH(CF3)2)3
7 P(O(CH3))3
Solvent
Dichloromethane
Tetrahydrofuran
Tetrahydrofuran
Tetrahydrofuran
Tetrahydrofuran
Tetrahydrofuran
Tetrahydrofuran

Analysis of the crystal of [Ru(ƞ6-p-cymene)(L)Cl2] complexes

using Mercury

Part C: Study on the structural properties of the mixed sandwich

Ru(II) complexes involving η6-p-cymene with fluorinated
phosphines or phosphites ligands

In this part, Mercury will be used to view the structure of

complexes synthesised in the previous part. Mercury can be
downloaded from:

https://www.ccdc.cam.ac.uk/support-and-resources/Downloads/

Go to CSD -Community Tab and select Mercury

(incorporating enCIFer) then click Download. Then you have to
install the software.

1. The crystal data of complexes needed in this section can be

downloaded from
(https://www.ccdc.cam.ac.uk/structures/).

• Crystals 1, 3, 5, 6 and 7

2. Open the Mercury Software. Click Open your crystal

structure and the molecule will be displayed Mercury
viewer window. The packing of the crystal can be viewed
by clicking Packing on the Display tab. Record the type of
packing and its space group.
3. Click Asymmetric Unit in the Display tab to show the
crystallographically unique part of the crystal structure.
4. The bond length of the metal complexes is measured by
clicking Picking Mode and select Measure Distances.
Measure and record all the bond length around the metal
center and the arene ring.
 5. Then the angle of bonds of the complexes are measure by
clicking Picking Mode and select Measure Angles. Record
angle around the metal center and ligand.
6. Repeat step 2 to 5 for all the crystal structure and discuss
on how ancillary ligand would affect the structure of the
metal complex and conformation of the ligand.

Summary Organometallic chemistry has had a dramatic impact in the field

of catalysis, particularly in the field of synthetic organic chemistry
where homogeneous organometallic complexes have been used to
bring about transformations that in many cases cannot occur under
typical laboratory conditions, and/or bring about selectivity in an
organic reaction. In many homogeneous systems, determining the
mechanism of a transformation is possible and critical to catalyst
design. In order to make rational choices in complex design, an
understanding of the coordination chemistry of a series of ligand
can be useful.

Assignment Question:
1. Write balanced chemical reaction for the preparation
of the complexes in general.
2. Propose a likely mechanism for this ligand substitution
reaction.
3. Discuss why didn’t anyone make [Ru(p-
cymene){P(C6F5)3}(Cl)2]?
4. Describe the bonding between the arene and the Ru
using qualitative MO theory.
5. Use crystallographic data for this series to comment on
the general structure and draw comparisons between
the Ru-P bond lengths. Search the literature for related
compounds such as [Ru(p-cymene){P(R)3}(Cl)2] (R =
Ph, -OC6H5, -C6H5, and -CH3).
6. Determine the point group of [Ru(p-
cymene){P(C6H4F-p)3}(Cl)2].

Assessment* Laboratory Report

Department of Chemistry
Faculty of Science
Universiti Putra Malaysia

Module 5 Title
Synthesis and Characterisation of Tetraphenylporphyrin H2(TPP),
Metalloporphyrins ZnII(TPP) And NiII (TPP) Using Electronic
Absorption Spectroscopy
COURSE CODE CHM4301

Module Code/No UPM/FS/CHM4301-05

DURATION 9 hours

Learning Resources 1. Marsh, Diane. (1996). Microscale Synthesis and Electronic

Absorption Spectroscopy of Tetraphenylporphyrin
H2(TPP) and Metalloporphyrins ZnII(TPP) and NiII(TPP),
Journal of Chemical Education - J Chem Educ. 73.
10.1021/ed073p1188.

PRIOR Knowledge Electronic absorption spectroscopy, fluorescence spectroscopy,

reflux

TERMS TO KNOW Porphyrins, fluorescence, orbitals, electronic absorption

Learning Outcomes At the end of this module, students are able to:

a) Carry out the synthesis of porphyrins and

metalloporphyrins.
b) Investigate the spectroscopic properties (UV-Vis and
fluorescence) of the resulting porphyrin and
metalloporphyrins.
c) Discuss the differences between free-base porphyrin and
metalloporphyrins.
Course Contents AND Introduction:
LEARNING Activities
Metalloporphyrin complexes play significant roles in many
biological and catalytic systems. The diversity of their function is
due in part to the variety of metals that bind in the “pocket” of the
porphyrin ring system (Figure 1).

Figure 1: Metallated tetraphenylporphyrin

Metalloporphyrins can be divided into two groups based on their

UV-Vis and fluorescence properties. Regular metalloporphryins
contain closed-shell metal ions (d0 or d10) – for example ZnII, in
wich the dπ (dxz, dyz) metal-based orbitals are relatively low in
energy. These have very little effect on the porphyrin π to π*
energy gap in porphyrin electronic spectra (Figure 2).
Hypsoporphyrins are metalloporphyrins in which metals are of dm,
m = 6-9, having filled dπ orbitals. In hypsoporphyrins there is
significant metal dπ to porphyrin π* orbital interaction (metal to
ligand π-backbonding). This results in an increased porphyrin π to
π* energy separation causing the electronic absorptions to undergo
hypsochromic (blue) shifts.
 dx2-y2
π*
dz 2
ΔE

π
dxz, dyz
dπ
dxy
Porphyrin Metal

Figure 2: Simplified molecular orbital diagram for

metalloporphyrins. Interaction between metal dπ and π* porphyrin
orbitals occurs in hypsoporphyrins

Experimental Details

Materials
Propionic acid, benzaldehyde, pyrrole, methanol, ice bath, boiling
hot distilled water, zinc chloride, dimethylformamide and Ni(II)
chloride hexahydrate.

Apparatus
Round bottom flask (50 mL), water condenser, stirrer bar, 0.1 mL
graduated pipette, glass rod, heating mantle, beaker (100 mL),
filter funnel, Hirsh/Buchner funnel, round bottom flask (5 mL),
filter paper, UV-Vis spectrometer and UV lamp.

PART A

Synthesis of Tetraphenylporphyrin, H2(TPP) (1)

1. Heat a propionic acid (12 mL) (~120 ºC) and reflux for 5
minutes.
2. Add 0.06 mL of benzaldehyde using a 0.1 mL graduated
pipette to the refluxing propionic acid.
3. To the mixture, add pyrrole (0.04 mL) from a freshly
opened bottle using a pipette.
4. The color darkens to orange-yellow and becomes dark
brown-black as the reaction proceeds.
5. After 30 min, cool the mixture to room temperature.
6. Pour the cooled mixture into a flask containing 10 mL of
methanol. (Place the flask in an ice bath with stirring).
7. Scratch the sides of the flask with a glass rod to induce
crystallization. Filter the deep-purple crystals using
 Buchner or Hirsch funnel and subsequently wash with
three 0.5 mL portions of boiling hot distilled water.
8. Air-dry the crystals and store in a vacuum dessicator over
a drying agent until the next laboratory period.

PART B

Synthesis of ZnII(TPP) (2)

1. Dry a zinc chloride in a 110 ºC oven overnight before

use. (Zinc chloride is very hygroscopic). Avoid the
exposure to moisture.
2. Dissolve 1 (1-2mg) in 3 mL of dimethylformamide
(DMF) in a 5mL round bottom flask containing a stir
bar.
3. To the solution, add zinc chloride (10 mg).
4. Reflux the reactants for 30 min. The resulting solution
(1 mL) can be diluted with DMF (2 mL) to measure the
visible spectrum.

Synthesis of NiII(TPP) (3)

1. Anhydrous nickel(II) chloride must be used.

2. Dry a green Ni(II) chloride hexahydrate by heating the
crushed solid in an evaporating dish until the color is
yellow-orange.
3. Dehydrated Ni(II) chloride should be kept in an oven at
110 ºC until used.
4. The synthesis of NiII(TPP) uses 10 mg of dry nickel(II)
chloride but is otherwise identical to the synthesis of
ZnII(TPP).

Characterizations

The visible spectra (300-660 nm) of DMF solutions (0.1 mg/mL)

of H2(TPP), Zn(TPP), and Ni(TPP) can be obtained by UV-Vis
spectrophotometer. The three solutions in DMF can be tested for
fluorescence with UV lamp (short wave) in a dark room.
Summary
Porphyrins possess extended π-electron systems and exhibit
stability, and due to that, they are finding use, to an increasing
extent, in advanced materials, as components in organic metals,
molecular wires, and other devices. This module exposes the
students to the synthesis of metalloporphyrins.

Assignment Questions
 1. What are the observations when the three solutions in
DMF are tested for fluorescence with UV lamp?
2. Explain the observations on Question 1 based on the
energy level diagram.
3. Plot the absorption spectra of the three solutions in DMF.
Note down the absorption peaks for each compounds.
4. What are the changes for visible spectrum upon metalation
with nickel and zinc? Explain the changes based on
symmetry element.

Assessment* Laboratory Report

Your report must include the introduction to porphyrin and

metalloporphyrins and answers for all the questions and discuss on
the UV-Visible spectra obtained.
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia

Module 6 Title
Study on the formation of ß-cyclodextrin inclusion complex with
iodine
COURSE CODE CHM4301

Module Code/No UPM/FS/CHM4301-06

DURATION 3 hours

Learning Resources 1. Steed, J. W. & Atwood, J. L. (2009) Supramolecular

Chemistry, 2nd ed. Chichester: John Wiley & Sons, Ltd.
2. Schneider, H. J. (2012) Applications of Supramolecular
Chemistry, Boca Raton: CRC Press

PRIOR Knowledge intermolecular forces, host-guest

TERMS TO KNOW dissolution, receptor, inclusion complexes, cavity

Learning Outcomes At the end of this module, students are able to:

a. Understand the role of intermolecular forces on the

behaviour and macroscopic properties of substances.
b. Detect the formation of inclusion compounds
comprising a host, ß-cyclodextrin and a guest
molecule, I2 or I3-.
c. Observe the influence of the formation of inclusion
complexes on the process of iodine extraction from
aqueous medium by organic solvent.
d. Discuss their results in terms of the effect of
intermolecular forces on the dissolution processes.

Course Contents AND Introduction:

LEARNING Activities
Cyclodextrin, which is the host or molecular receptor, forms
inclusion complexes with various compounds, called guests or
substrates, by including the latter in its cavity. In an inclusion
compound two substances are intimidately linked but not through
covalent bonds. The elucidation of the intermolecular forces
between host and guest in an inclusion complex belongs to realm
of supramolecular chemistry.

Inclusion complexes may be formed either in solution or in the

solid state. Although water is the usual solvent, formation also
takes place in other solvents. The formation is detected by various
methods (e.g. NMR, electronic absorption, fluorescence).
Inclusion complexes in solution are not static species. Substrates
included in the cavity not only exchange rapidly with free
substrate molecules but also reaccomodate themselves by
presenting several molecular orientations.

Experimental Details

Materials
Anhydrous ß-Cyclodextrin, elemental iodine, potassium iodide,
chloroform, distilled water and ethyl ether.

Apparatus
Test tubes (20 mL) and graduated pipettes.

Labels for the tubes

The starting solutions are contained in four 20 mL test tubes
labelled reagent a, b, c and d (Figure 1). Mixtures are then
prepared in tubes as described below.
a. Lightface lower-case letters, a, b,…, indicate solutions in
which the reagent is merely diluted and no observations
are necessary.
b. Boldface upper-case letters, E, F,… indicate tubes in
which a chemical reactions occurs. Students should record
their observations, such as color changes, precipitate
formation, phase separation, and volume changes for each
phase.

Observations should be carried out at the moment of the

experiment. The student is advised to perform a second
observation one or two days later.
 Figure 1: Sequence of solution mixing.
Mixing
When mixing is necessary this has been indicated by “mixture”.
Whenever a heterogeneous mixture is obtained, the test tubes
should be vigorously shaken and then left to stand to allow phase
separation before recording the observation. The mixing process
starts from tubes labelled a, b, c and d with reagents and follows
the arrows, with the volumes indicated in each case.
Reagent a – Dissolve 3.3 mg of iodine in a small amount of ethyl
ether. Then add 3 mL of water, followed by shaking. Once the
ether has evaporated, the solution is decanted, and the volume is
taken to 10 mL. The colour of solution is aqueous orange-brown.
Reagent b – contains a colourless and transparent 10 mmol
solution of ß-Cyclodextrin (white powder, 0.1135 g/10mL of
water).
Reagent c – contains a colourless 10 mmol solution of KI (0.0166
g in 10 mL of water).
Reagent d – contains 10 mmol of I2 (0.033 g) in 10 mL of CHCl3.
(Chloroform has a limited evidence of a carcinogenic effect).
Avoid prolonged exposure through inhalation.
 Using the flowchart

Example:

Solution “a” is prepared by adding 1 mL of water to 1 mL of the

reagent solution of tube “a”. Because this is only a dilution, you
do not need to write out any observation. If at this point the left
arrow is followed, then prepared the solution in tube “E” by
simply mixing, in a clean tube, 1 mL from the tube with 1 mL of
CHCl3. Here you have to observe a chemical interaction and
records observations.
Summary The students will appreciate the knowledge on host-guest
chemistry.
Assignment
Questions

1. Note down all the observations when required (tube E, F,

G, H, I, J, K, L, M, N) and discuss the results in term of
intermolecular forces on the dissolution processes.
2. Explain on how the ß-Cyclodextrin dissolve in water and
what cause the inclusion compounds of ß-Cyclodextrin
with guest in water?

Your report must include the introduction on the ß-Cyclodextrin

(e.g. characteristic of ß-Cyclodextrin, factors that govern the
formation of inclusion complex of ß-Cyclodextrin, etc.),
discussion on the experimental methods and answers for all the
questions in this experiment.

Assessment* Laboratory Report

Department of Chemistry
Faculty of Science
Universiti Putra Malaysia

Module 7 Title
Synthesis, Characterisation and Electrophilic Substitution of
Tris(2,4-Pentanedionato) Complexes of Chromium(III) and
Cobalt(III)

COURSE CODE CHM4301

Module Code/No UPM/FS/CHM4301-07

DURATION 9 hours

Learning Resources 1. N.N. Greenwood and A. Earnshaw "Chemistry of the

Elements"
2. F. Cotton & G. Wilkinson "Advanced Inorganic Chemistry"
3. K. Nakamoto "Infrared Spectra of Inorganic and
Coordination Compounds"

PRIOR Knowledge Infrared spectroscopy, thin layer chromatography, NMR

spectroscopy, recrystallization

TERMS TO KNOW chelate, keto-enol tautomer, hydrolysis

Learning Outcomes At the end of this module, students are able to:

a) To synthesis and purify [M(acac)3] complexes (M = either

CrIII, CoIII)
b) To brominate/nitrate [M(acac)3]
c) To determine the purity of the complexes by using
chromatography
d) To characterize the complexes by using spectroscopy
Course Contents AND Introduction:
LEARNING Activities
Pure acetylacetone (2,4-pentanedione, acacH) exists as a keto-enol
tautomer:

H
O O O O

This is evidenced by IR and NMR spectroscopy. The enol is

stabilised by intramolecular hydrogen-bonding.

Acetylacetone is a typical diketone in that it ionises in aqueous

solution as a weak acid:

H3CCOCH2COCH3 H3CCOCHCOCH3- + H+

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metal ions, forming stable metal complexes with six-membered
chelate rings:

H3C H3C
O O
Mn+
HC - HC M(n-1)+
O O
H3C H3C .

If the coordination number of the metal ion is twice its charge,

neutral complexes of the stoichiometry [M(acac)n] (n = 2, 3, 4)
result. In such complexes the six-membered M-acac rings are
planar with delocalised p electrons.

The metal complex shows some of the characteristics of an

aromatic system. For example, the C(2)-C(3) and C(3)-C(4) bond
lengths are equal. Because of this aromatic character, the
hydrogen atom on C(3) can be substituted, for example:

• by bromine to give the Cr(III) chelate of the 3-bromo-2,4-

pentanedionato ligand
• by nitro to give the Co(III) chelate of the 3-nitro-2,4-
pentanedionato ligand.

EXPERIMENTAL
Safety
Handle organic solvents in the fume hood.
Alkanes are very flammable.

PART A

Synthesis of Tris(2,4-pentanedionato)chromium (III)

[Cr(acac)3]

CO(NH2)2 + H2O ® 2NH3 + CO2

Cr3+ + 3CH3COCH2COCH3 + 3NH3 ® 3NH4+ +
Cr(CH3COCHCOCH3)3

Urea undergoes a slow hydrolysis; the liberated ammonia controls

the pH of the reaction mixture.

Weigh directly into a 100 ml conical flask CrCl3.6H2O (1.4 g) and

dissolve it in distilled water (50 ml) (FUME HOOD). Weigh out
urea (10.0 g) and add it in four portions with stirring to the deep
green chromium chloride solution. After all of the urea has
dissolved, add acetylacetone (3.0 ml), cover with a watch glass
and heat the solution rapidly with stirring on a hot plate to 80 -
90°C (almost boiling). The solution is initially very dark, almost
black in appearance. As the reaction continues, deep maroon
plate-like crystals forms.

After 1 hour of heating, cool the reaction mixture to room

temperature and into an ice bath. Filter off the product using the
Buchner funnel. Do not wash. Air dry and record the yield.

Synthesis of Tris(2,4-pentanedionato)cobalt (III) [Co(acac)3]

CoCO3 + 2CH3COCH2COCH3 ®
Co(CH3COCHCOCH3)2 + CO2 + H2O
2Co2+ + H2O2 ® 2Co3+ + 2OH-
2CoCO3 + 6CH3COCH2COCH3 + H2O2 ®
2Co(CH3COCHCOCH3)3 + 2CO2 + 4H2O

In this reaction, the Co2+ complex is formed first; this is then

oxidised by H2O2, giving the resulting overall equation.

Weigh directly into a 50 ml conical flask CoCO3 (1.25 g) and add

acetylacetone (8 ml) (FUME HOOD). Cover with a watch glass
and heat with stirring on a hot plate to ~90°C. While maintaining
this temperature and with stirring, add dropwise a 10% H2O2
solution (15 ml), slowly using a dropping pipette (CARE); this
addition should take about 15 min. Cover the flask with a watch
glass between additions. Continue stirring for a further 15 min.
Note the colour of the solution. Cool to room temperature then in
an ice bath and filter off the product. Do not wash. Air dry and
then dry in the oven at 110°C. Record the yield.

PART B

Recrystallisation of Tris(2,4-pentanedionato)chromium (III)

[Cr(acac)3]

Recrystallise about 1.2 g of the crude product from toluene-

petroleum spirit (5 mL:5 mL). Add slowly until completely
dissolved. Collect the deep-red crystals (water pump) and air dry.

Determine the melting point and record the IR (nujol mull,

solution) and electronic (in toluene) spectrum.

Recrystallisation of Tris(2,4-pentanedionato)cobalt (III)

[Co(acac)3]

Recrystallise about 1 g of the crude product from toluene-

petroleum spirit. Collect the crystals (water pump) and air dry.

Determine the melting point and record the IR (nujol mull,

solution) and electronic (solution) spectrum.

PART C

Bromination of [Cr(acac)3]

Dissolve recrystallised [Cr(acac)3] (0.6g) in chloroform (12 ml)

and add N-bromosuccinimide (1 g). Boil the solution with stirring
(hot plate, FUME HOOD) for 5 min. The solution turns green and
a brown precipitate forms. Transfer the mixture to a 500 ml
beaker and let the solvent evaporate.

Place the solid in a fluted filter paper inside a filter funnel. Make
sure the solid is at the bottom of the fluted filter paper and wash
successively with 95% ethanol (5 ml), two portions of 5% aqueous
NaHSO3 (5 ml), water (5 ml) and two portions of hot 95% ethanol
(5 ml) and air dry.

Recrystallise as follows: dissolve the product in boiling

dichloromethane (4 ml) (FUME HOOD) and add boiling hexane
(~5 ml). Let cool to room temperature and cool in an ice-bath.
Collect the brown crystals and wash with two portions of 95%
ethanol (5 ml) and air dry.

Determine the melting point and record the IR (nujol mull,

solution) and electronic (solution) spectrum.

Nitration of [Co(acac)3]

Recrystallised [Co(acac)3] (0.5g) and crushed Cu(NO3)2.3H2O

(1.08 g) were placed in a dry flask and acetic anhydride (20 ml)
was added (FUME HOOD). The flask was firmly stoppered and
the mixture was stirred vigorously for 30 min. The reaction
mixture was poured into an ice-cold solution of sodium acetate
(7.6 g of sodium acetate and 60 g of ice). An oil separates; this can
be solidified by adding ethanol and stirring until the solution
becomes cloudy. Filter off the product and wash with small
amounts (8 ml) of water and ethanol and air dry.

Recrystallise from chloroform-ethanol, wash with cold ethanol (4

ml) and air dry.

Determine the melting point and record the IR (nujol mull,

solution) and electronic (solution) spectrum.

Project

Investigate one of the following:

• Does N-bromosuccinimide brominate [Co(acac)3]?

• Does the Cu(NO3)2 nitration proceed with Cr(acac)3]?

How would you determine that a reaction has taken place and
what product was formed?

Characterisation

Physical Measurements

1. Determine the melting points of the complexes.

2. Compare the solubility of the compounds.
3. Record the IR spectra in the range 4000 - 400 cm-1 (nujol)
and 2000 – 1000 cm-1 (solution).
4. Record the electronic spectra in solution (ca. 10-3 M; 10 ml)
in the range 700 - 250 nm.

Thin Layer Chromatography

 Dissolve a few mg of each compound in a few drops of
dichloromethane. Spot onto silica TLC plates and develop with
1% methanol in dichloromethane. Use [M(acac)3], crude and
recrystallised, and [M(Xacac)3] (M = Cr, Co; X = H, Br, NO2).

NMR Spectra

The NMR spectra of acacH are attached.

Summary The students will appreciate the knowledge on coordination

compounds, electronic absorption, crystal field splitting for the
complexes and the effect of halogenation/nitration on the crystal
field splitting.

Assignment Place your products in labelled sample bottles and hand them in at
the end of the session.

Questions

1. Calculate the percentage yields for your syntheses.

2. Tabulate the properties of all the compounds, e.g. colour,
melting point, solubility.
3. Tabulate the infrared spectra of the compounds.
4. Can you identify the C-Br stretching band and the NO2
bands?
5. Compare the spectrum of [M(acac)3] with that of acacH.
6. Are there any distinct changes in the spectrum of acac of
coordination?
7. Tabulate the electronic spectra of the compounds.
8. How many d-d transitions are expected for an octahedral
Cr(III)/Co(III) ion?
9. How many are observed?
10. From the d-d transitions calculate the crystal field splitting
for the complexes.
11. What is the effect of halogenation/nitration on the crystal
field splitting?
12. Compare the crystal field splitting with that of other O-
donor ligands.
13. Interpret the attached 1H and 13C NMR spectra of acacH.
14. What would be the magnetic moment for these complexes?
15. Is TLC useful for this type of complex? Why?
Assessment* Laboratory Report
NMR Spectra of acetylacetone in CDCl3.
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia

Module 8 Title
Identification of vibrational spectra and bonding in metal carbonyl

COURSE CODE CHM4301

Module Code/No UPM/FS/CHM4301-08

DURATION 6 hours

Learning Resources 1. Miessler, G. L., Fisher, P.J & Tarr, D. A. (2014) Inorganic
Chemistry, 5th ed. Harlow: Pearson-Prentice Hall
2. Crabtree, R. H. (2014) The Organometallic Chemistry of
Transition Metals, 5th ed. Hoboken: John Wiley & Sons
3. Duward Shriver, D., Weller, M., Overton, T., Rourke, J.,
Armstrong, F. (2014). Inorganic Chemistry, 6th ed. Oxford:
Oxford University Press

PRIOR Knowledge Donor ligands, acceptor ligands, metal carbonyl complexes

TERMS TO KNOW Structure and bonding of metal carbonyl complexes

Learning Outcomes At the end of this module, students are able to:

a) To synthesis a series of Group 16 carbonyl complexes

b) To characterize the complexes and relate the bonding
model of the M-CO bond to the structure
Course Contents AND Introduction:
LEARNING Activities The transition metal binary carbonyls are non polar volatile
compounds. The carbonyl ligands are easily substituted by a vast
range of ligands with a wide variety of donor atoms (C, N, O, P, S
etc.). The degree of substitution depends on the ligand (both
electronic and steric factors).

The carbonyl ligands give rise to intense CO stretching bands

(nCO) in the infrared spectrum (2200 - 1600 cm-1). The spectrum is
usually recorded as a dilute solution. The number of carbonyl
bands depends on both the number of carbonyls and the structure
of the complex. Hence, the IR spectrum can be used as a structural
tool.

The exact frequency of the CO bands depends on the

donor/acceptor properties of the other ligands in the complex.
Thus, the IR spectrum is sensitive to other factors such as the
electronic properties of the ligands and the oxidation state.

The changes in nCO can be easily rationalised from the bonding

model of the M-CO bond, i.e. a OC®M σ-bond and a M®CO p-
bond.

Safety

All metal carbonyl complexes are toxic. These chemicals are fairly
rapidly absorbed through the skin. Do not touch the materials with
your fingers and you must be careful not to spill solutions onto
your skin. If you do so, wash your hands thoroughly.

Handle organic solvents and bromine in the fume hoods.

Petroleum ether is very flammable.

Solid metal carbonyls are usually air stable; however, they tend to
be more air sensitive in solution. Consequently, reactions,
especially those involving heating, are carried out in an inert
atmosphere such as nitrogen. The suitable experimental setup is
shown in Figure 1. Before commencing the heating, flush the
system with nitrogen, during the reflux maintain a slow flow of
gas and afterwards while allowing the apparatus to cool increase
the flow rate again to prevent suck-back.
 Nitrogen out
to a gas bubbler

In

Nitrogen
from cylinder

Simple gas
bubbler

water

Heating mantle
plus stirrer

Figure 1. Experimental setup for a reflux in an inert atmosphere

Gentle flow of gas (~ 1 bubble per second)

Syntheses

NOTE: All reactions are to be carried out in an atmosphere of

nitrogen.

For all the syntheses determine the yield and the percentage yield.
Record the melting point, infrared spectrum in dichloromethane
and the electronic spectrum.

1. Bis(pyridine)tetracarbonylmolybdenum [Mo(CO)4(py)2]
Mo(CO)6 (0.125g) in pyridine (2 ml) is heated under reflux for
about 50 min. Allow the solution to cool and add petroleum
ether (~15 ml). After crystallisation has finished, filter the
orange-red solid and wash with petroleum ether and dry in
vacuo. Record the IR spectrum. If necessary, recrystallise from
acetone/water.

2. 2,2'-Bipyridinetetracarbonylmolybdenum
[Mo(CO)4(bpy)]
Mo(CO)6 (0.125g) and 2,2'-bipyridine (0.08g) are heated under
reflux in toluene (6 ml) for ~2 hr. After cooling collect the
brick-red crystals, wash with toluene and petroleum ether and
dry in vacuo.

3. Bis(triphenylphosphine)tetracarbonylmolybdenum
[Mo(CO)4(PPh3)2]
Mo(CO)6 (0.10 g) and PPh3 (0.225g) are heated under reflux in
toluene (5 ml) for ~2 hr. After cooling collect the yellow
crystals, wash with toluene and petroleum ether and dry in
vacuo.

Characterization

Infrared Spectroscopy

Solution spectra are recorded using a solution cell (CaF2 windows

separated by a thin teflon spacer). The cell is filled using a syringe
or a Pasteur pipette. After use rinse the cell twice with solvent and
return it to the desiccator.

Before recording the spectrum of a compound in either the X, Y or

Z channel, you need to record the spectrum of the solvent in the
background channel of the Perkin Elmer spectrophotometer.

Prepare a dilute solution of the complex (a few crystals in about

10-15 drops) in dichloromethane. Fill the solution cell and record
the spectrum in the range 2200 - 1600 cm-1.

NOTE: the baseline should be a smooth straight line with no

solvent bands.
 Electronic Spectroscopy

Prepare a dilute solution of the complex (~ 5 x 10-4 M). Using

quartz cuvettes, record the spectrum in the range 700 - 300 nm.

Use a solvent such as dimethyl formamide or acetone.

Summary Apart from X-ray crystallography, important analytical technique

for the characterization of metal carbonyls are infrared
spectroscopy. Infrared active vibrational modes, such as CO-
stretching vibrations are often fast compared to intramolecular
processes. The energies of the νCO band for the metal carbonyls
correlates with the strength of the carbon-oxygen bond, and
inversely correlated with the strength of the π-backbonding
between the metal and the carbon.

Assignment Questions

1. Calculate the percentage yields for your syntheses.

2. Do the compounds have a melting point?
3. Tabulate the infrared spectra of all the compounds.
4. Outline any trends in the CO stretching frequencies.
5. Are your compounds pure?
6. Is the IR spectrum of each compound consistent with its
structure?
7. Which compounds can exist as geometric isomers? Which
isomer was produced in your synthesis?
8. Tabulate the electronic spectra of all the compounds. Are
there any trends?
9. Interpret the mass spectra of the compounds.

Assessment* Laboratory Report