Molecule of the Month – March 2015

Explosions explosions EXPLOSIONS!! I knew a Chemistry Tutor in the UK… who simply loved explosions. He studied thousands of explosive compounds, and even demonstrated a few in a Lecture on Explosive Reactions in Chemistry (with the proper safety precautions, of course!). One would think that it takes years and years of experience to perform such feats of wonder and danger. But what about those who discovered the explosives in the first place? They must have spent years, risking their lives all the way, to discover, and implement. But not all discoveries were from well-known, experienced, brilliant scientists who put everything on the line for the advancement of science.

During a fifth-grade class in 2012 conducted by a Science teacher Kenneth Boehr, ten-year-old Clara Lazen assembled a complex model using ball-and-stick model set and asked whether it was a real molecule.

Clara Lazen with her molecule in 2012

Unsure of the answer, Boehr sent a picture of the model to a chemist friend, Robert Zoellner, a Professor in Chemistry at Humboldt State University. Zoellner checked the molecule against the ‘Chemical Abstracts‘ database and confirmed that Lazen’s had a unique and previously unrecognized structure.

Professor Robert Zoellner admires a model of the new molecule in 2012

Zoellner wrote a paper on the molecule, published in Computational and Theoretical Chemistry, crediting Lazen and Boehr as co-authors.

Tetranitratoxycarbon consists of oxygen, nitrogen, and carbon, with molecular structure C(CO3N)4. As an oxygen-rich compound of carbon and nitrogen, similar to nitroglycerin, it is predicted to have explosive properties, but to be too thermally unstable for practical use.

(Notice the Schrödinger equation on the blackboard in the background!)

This is not the first time a young aspiring scientist has been a direct or indirect cause of the discovery of a new molecule, and it will not be the last. Especially to our Lower Sixth intake of 2015/2016, it falls to YOU to be innovative, to be proactive, to be brilliant and be the next Clara.

Rush headlong into Chemistry A-Level with a strong desire to EXCEL! Welcome, Lower Sixth Students, to our wonderful world ^___^

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Molecule of the Month (April 2013) – Luminol

Ever watch CSI or any series or movies that involve forensic science? Ever wonder how they find bloodstains on the carpet or in various areas where the stain is actually so faint that you can’t see it with the naked eye? Well, Luminol is one such answer…

This molecule of the month was suggested by LJY 2013 =)
From Wikipedia, the free encyclopedia:
Molecular formula C8H7N3O2
Molar mass 177.16 g/mol
Melting point 319 °C, 592 K, 606 °F

Luminol (C8H7N3O2) is a versatile chemical that exhibits chemiluminescence, with a striking blue glow, when mixed with an appropriate oxidizing agent. It is a white to slightly yellow crystalline solid that is soluble in most polar organic solvents, but insoluble in water. Luminol is used by forensic investigators to detect trace amounts of blood left at crime scenes as it reacts with iron found in hemoglobin. It is used by biologists in cellular assays for the detection of copperiron, and cyanides, in addition to the detection of specific proteins by western blot. For analysis of an area, luminol can be sprayed evenly across the area, and trace amounts of an activating oxidant will cause the luminol to emit a blue glow that can be seen in a darkened room. The glow lasts for about 30 seconds, but the effect can be documented by a long-exposure photograph. It is important that the spraying be evenly applied to avoid creating a slanted, or biased impression, such as blood traces appearing to be more concentrated in areas which received more spray. The intensity of the glow does not indicate the original amount present, but only the distribution of trace amounts of substances left in the area.

Luminol may be synthesized by a reverse phosphorescence 2-step process. It begins from 3-nitrophthalic acid. First, hydrazine (N2H4) is heated with the 3-nitrophthalic acid in a high-boiling solvent such as triethylene glycol. An acyl substitution condensation reaction occurs, with loss of water, forming 3-nitrophthalhydrazide. Reduction of the nitro group to an amino groupwith sodium dithionite (Na2S2O4), via a transient hydroxylamine intermediate, produces luminol.


Luminol synthesis.png Luminol was first synthesized in Germany in 1902, but the compound was not named “luminol” until 1934.


Chemiluminescence of luminol

To exhibit its luminescence, the luminol must first be activated with an oxidant. Usually, a solution of hydrogen peroxide (H2O2) and a hydroxidesalt in water is used as the activator. In the presence of a catalyst such as an iron compound, the hydrogen peroxide is decomposed to form oxygen and water:

2 H2O2 → O2 + 2 H2O

In a laboratory setting, the catalyst used is often potassium ferricyanide. In the forensic detection of blood, the catalyst is the iron present inhemoglobinEnzymes in a variety of biological systems may also catalyze the decomposition of hydrogen peroxide. When luminol reacts with the hydroxide salt, a dianion is formed. The oxygen produced from the hydrogen peroxide then reacts with the luminoldianion. The product of this reaction, an organic peroxide, is very unstable and is made by losing a nitrogen, electrons going from excited state to ground state, and energy emitting as a photon. This emitting of the photon is what ultimately gives off the blue light.

Reactions leading to the chemiluminescence of luminol.

Use by crime scene investigators


In 1928, the German chemist H. O. Albrecht found that blood, among other substances, enhanced the luminescence of luminol in an alkaline solution of hydrogen peroxide. In 1936, Karl Gleu and Karl Pfannstiel confirmed this enhancement in the presence of hematin, a component of blood. In 1937, the German forensic scientist Walter Specht made extensive studies of luminol’s application to the detection of blood at crime scenes.


Luminol is used by crime scene investigators to locate traces of blood, even if it has been cleaned or removed. The investigator prepares a solution of luminol and the activator and sprays it throughout the area under investigation. The iron present in any blood in the area catalyzes the chemical reaction that leads to the luminescence revealing the location of the blood. The amount of catalyst necessary for the reaction to occur is very small relative to the amount of luminol, allowing the detection of even trace amounts of blood. The glow lasts for about 30 seconds and is blue. Detecting the glow requires a fairly dark room. Any glow detected may be documented by a long exposure photograph.


Luminol has some drawbacks that may limit its use in a crime scene investigation:

  • Luminol chemiluminescence can also be triggered by a number of substances such as copper or copper-containing chemical compounds, and certain bleaches; and, as a result, if a crime scene is thoroughly cleaned with a bleach solution, residual cleaner will cause the entire crime scene to produce the typical blue glow, effectively camouflaging any organic evidence, such as blood.
  • Horseradish sauce, via the enzyme horseradish peroxidase, catalyses the oxidation of luminol, emitting light at 428 nm (blue in the visible spectrum), which may result in a false positive.
  • Luminol will also detect the small amounts of blood present in urine, and it can be distorted if animal blood is present in the room that is being tested.
  • Luminol reacts with fecal matter, causing the same glow as if it were blood.
  • Luminol’s presence may prevent other tests from being performed on a piece of evidence. However, it has been shown that DNA can be successfully extracted from samples treated with luminol reagent.

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Molecule of the Month (March 2013) – Ibuprofen

Reposted from Feb 2012, since not many students seemed to even realize what drugs they’ve been prescribed =)

Please send any suggestions for Molecule of the Month (April 2013) to (you WILL be credited on the post)
Please state what reasons you have for choosing the stated molecule as well.

From Wikipedia:

Ibuprofen (INN); from the nomenclature iso-butyl-propanoic-phenolic acid) is a nonsteroidal anti-inflammatory drug (NSAID) used for relief of symptoms of arthritisfever, as an analgesic (pain reliever), especially where there is an inflammatory component, and dysmenorrhea.

Ibuprofen is known to have an antiplatelet effect, though it is relatively mild and somewhat short-lived when compared with aspirin or other better-known antiplatelet drugs. In general, ibuprofen also acts as a vasodilator, having been shown to dilate coronary arteries and some other blood vessels. Ibuprofen is a core medicine in the World Health Organization‘s “WHO Model List of Essential Medicines“, which is a list of minimum medical needs for a basic healthcare system.

Ibuprofen was derived from propionic acid by the research arm of Boots Group during the 1960s. It was discovered by Andrew RM Dunlop, with colleagues Stewart Adams, John Nicholson, Vonleigh Simmons, Jeff Wilson and Colin Burrows, and was patented in 1961. Originally marketed as Brufen, ibuprofen is available under a variety of popular trademarks, including Motrin, NurofenAdvil, and Nuprin.

Chemical Structure of Ibuprofen

Athletes, the young, the old, the sick alike all use Ibuprofen. Can you recall the last time you were prescribed this chemical? Take care though… from personal experience, this drug, as well as most drugs… cause gastric discomfort 😦

Ibuprofen Tablets



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Molecule of the Month (January 2013) – Green Fluorescent Protein (GFP)

When we were little, we’ve always wondered about things that make weird sounds, or look out of the ordinary. Now this GFP is pretty interesting. Various uses, and definitely eye catching. I found it appropriate to begin this year’s MotM with one from Biochemistry, since we will be dealing quite heavily with proteins in P4 in your A2 year. As a Chemist, you have to focus more on the actual chemical processes that accompany such molecules, and how their structure leads to their uses.

Maxim Yap C.S.
HoD Chemistry 2013

From RSC, Protein Data Bank


The green fluorescent protein, shown here from PDB entry 1gfl, is found in a jellyfish that lives in the cold waters of the north Pacific. The jellyfish contains a bioluminescent protein– aequorin–that emits blue light. The green fluorescent protein converts this light to green light, which is what we actually see when the jellyfish lights up. Solutions of purified GFP look yellow under typical room lights, but when taken outdoors in sunlight, they glow with a bright green color. The protein absorbs ultraviolet light from the sunlight, and then emits it as lower-energy green light.

So What?

You might be saying: who cares about this obscure little green protein from a jellyfish? It turns out that GFP is amazingly useful in scientific research, because it allows us to look directly into the inner workings of cells. It is easy to find out where GFP is at any given time: you just have to shine ultraviolet light, and any GFP will glow bright green. So here is the trick: you attach the GFP to any object that you are interested in watching. For instance, you can attach it to a virus. Then, as the virus spreads through the host, you can watch the spread by following the green glow. Or, you can attach it to a protein, and watch through the microscope as it moves around inside cells.


GFP is a ready-made fluorescent protein, so it is particularly easy to use. Most proteins that deal with light use exotic molecules to capture and release photons. For instance, the opsins in our eyes use retinol to sense light (see the Molecule of the Month on bacteriorhodopsin). These “chromophores” must be built specifically for the task, and carefully incorporated into the proteins. GFP, on the other hand, has all of its own light handling machinery built in, constructed using only amino acids. It has a special sequence of three amino acids: serine-tyrosine-glycine (sometimes, the serine is replaced by the similar threonine). When the protein chain folds, this short segment is buried deep inside the protein. Then, several chemical transformations occur: the glycine forms a chemical bond with the serine, forming a new closed ring, which then spontaneously dehydrates. Finally, over the course of an hour or so, oxygen from the surrounding environment attacks a bond in the tyrosine, forming a new double bond and creating the fluorescent chromophore. Since GFP makes its own chromophore, it is perfect for genetic engineering. You don’t have to worry about manipulating any strange chromophores; you simply engineer the cell with the genetic instructions for building the GFP protein, and GFP folds up by itself and starts to glow.

Engineering GFP

The uses of GFP are also expanding into the world of art and commerce. Artist Eduardo Kac has created a fluorescent green rabbit by engineering GFP into its cells. Breeders are exploring GFP as a way to create unique fluorescent plants and fishes. GFP has been added to rats, mice, frogs, flies, worms, and countless other living things. Of course, these engineered plants and animals are still controversial, and are spurring important dialogue on the safety and morality of genetic engineering.

Improving GFP

GFP is amazingly useful for studying living cells, and scientists are making it even more useful. They are engineering GFP molecules that fluoresce different colors. Scientists can now make blue fluorescent proteins, and yellow fluorescent proteins, and a host of others. The trick is to make small mutations that change the stability of the chromophore. Thousands of different variants have been tried, and you can find several successes in the PDB. Scientists are also using GFP to create biosensors: molecular machines that sense the levels of ions or pH, and then report the results by fluorescing in characteristic ways. The molecule shown here, from PDB entry 1kys, is a blue fluorescent protein that has been modified to sense the level of zinc ions. When zinc, shown here in red, binds to the modified chromophore, shown here it bright blue, the protein fluoresces twice as brightly, creating a visible signal that is easily detected.

 Exploring the Structure

You can take a close look at the chromophore of GFP in the PDB entry 1ema. The backbone of the entire protein is shown here on the left. The protein chain forms a cylindrical can (shown in blue), with one portion of the strand threading straight through the middle (shown in green). The chromophore is found right in the middle of the can, totally shielded from the surrounding environment. This shielding is essential for the fluorescence. The jostling water molecules would normally rob the chromophore of its energy once it absorbs a photon. But inside the protein, it is protected, releasing the energy instead as a slightly less energetic photon of light. The chromophore (shown in the close-up on the right) forms spontaneously from three amino acids in the protein chain: a glycine, a tyrosine and a threonine (or serine). Notice how the glycine and the threonine have formed a new bond, creating an unusual five-membered ring.

This picture was created with RasMol. You can create similar pictures by clicking on the accession code above and then picking one of the options under View Structure. The chromophore is called “CRO” in this file, and it is residue number 66 in the protein chain.

Additional information on green fluorescent protein

Roger Y. Tsien (1998): The Green Fluorescent Protein. Annual Review of Biochemistry 67, pp. 509-544.

The Green Fluorescent Protein – annotation of GFP and its family relationships, available from InterPro.

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Partition Coefficient

A new page has been added with some details on Kpc. Please go and read! Thanks =)

The page can also be accessible via the drop down menus above (under Applications – Analytical)

Please send any notes you wish to donate for publishing on this website to

Maxim Yap
HoD Chemistry 2012

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Molecule of the Month (November 2012) – Varenicline

Now students, it is not a secret. Many students abuse nicotine. If you wish to clear your life of it, now is the time! There are numerous ways, but here is one pharmacological way. There are risks however, so please read carefully. Nonetheless, ENJOY this post =)

Maxim Yap
HoD Chemistry 2012

From Wikipedia, the Free Encyclopedia

Varenicline (trade name Chantix in the USA and Champix in Canada, Europe and other countries, marketed by Pfizer, usually in the form of varenicline tartrate), is a prescription medication used to treat smoking addiction. Varenicline stimulates nicotine receptors more weakly than nicotine does, that is, it is a nicotinic receptor partial agonist. In this respect it is similar to cytisine and different from the nicotinic antagonist, bupropion, and nicotine replacement therapies (NRTs) like nicotine patches and nicotine gum. As a partial agonist it both reduces cravings for and decreases the pleasurable effects of cigarettes and other tobacco products. Through these mechanisms it can assist some patients to quit smoking.

Medical uses

Varenicline is indicated for smoking cessation. It is more effective than NRTs and nicotine agonists. In a 2006 randomized controlled trial sponsored by Pfizer, after one year the rate of continuous abstinence was 10% for placebo, 15% for bupropion and 23% for varenicline.In a 2009 meta-analysis of 101 studies funded by Pfizer, varenicline was found to be more effective than bupropion (odds ratio 1.40) and NRTs (odds ratio 1.56).

A Cochrane systematic review concluded that both varenicline and bupropion improved smoking cessation. More people quit with varenicline than with bupropion, but the difference was not statistically significant.

The FDA has approved its use for twelve weeks. If smoking cessation has been achieved it may be continued for another twelve weeks.

Varenicline has not been tested in those under 18 years old or pregnant women and therefore is not recommended for use by these groups.

Adverse effects

Nausea occurs commonly in people taking varenicline. Other less common side effects include headache, difficulty sleeping, and abnormal dreams. Rare side effects reported by people taking varenicline compared to placebo include change in taste, vomiting, abdominal pain, flatulence, and constipation. In a recent meta-analysis paper by Leung et al, it has been estimated that for every 5 subjects taking varenicline at maintenance doses (1mg twice daily), there will be an event of nausea, and for every 24 and 35 treated subjects, there will be an event of constipation and flatulence respectively. Gastrointestinal side-effects are important factors compromising the compliance of varenicline.

Depression and suicide

In November 2007, the FDA announced it had received post-marketing reports that patients using varenicline for smoking cessation had experienced several serious side-effects, including suicidal ideation and occasional suicidal behavior, erratic behavior, and drowsiness. On February 1, 2008 the FDA issued an alert to further clarify its findings, noting that “it appears increasingly likely that there is an association between Chantix and serious neuropsychiatric symptoms.” It is unknown whether the psychiatric symptoms are related to the drug or to nicotine withdrawal symptoms, although not all patients had stopped smoking. The FDA also recommended that health care professionals and patients watch for behavioral and mood changes.In May 2008, Pfizer updated the safety information associated with varenicline, noting that “some patients have reported changes in behavior, agitation, depressed mood, suicidal thoughts or actions.” While it is unclear whether or not a small subgroup of people develop depression and suicidal ideation as a result of varenicline or smoking cessation itself, there is evidence that varenicline, similar to nicotine, has antidepressant properties and the use of varenicline for smoking cessation leads to a reduced rate of initiation of antidepressant pharmacotherapy.

As of July 1, 2009, the US Food and Drug Administration requires Chantix (varenicline) to carry a black box warning, the agency’s strongest safety warning, due to public reports of side effects including depression, suicidal thoughts, and suicidal actions.

Cardiovascular disease

On June 16, 2011, the FDA issued a safety announcement that Chantix may be associated with “a small, increased risk of certain cardiovascular adverse events in patients who have cardiovascular disease.”

On July 4, 2011, four scientists published a review of double-blind studies in the Canadian Medical Association Journal. They found that varenicline has increased risk of serious adverse cardiovascular events compared with placebo.

Mechanism of action

Varenicline is a partial agonist of the α4β2 subtype of the nicotinic acetylcholine receptor. In addition it acts on α3β4 and weakly on α3β2 and α6-containing receptors. A full agonism was displayed on α7-receptors.

Acting as a partial agonist varenicline binds to, and partially stimulates, the α4β2 receptor without producing a full effect like nicotine. Thus varenicline does not greatly increase the downstream release of dopamine. Due to its competitive binding on these receptors, varenicline blocks the ability of nicotine to bind and stimulate the mesolimbic dopamine system, akin to the action of buprenorphine in the treatment of opioid addiction.

Varenicline also acts as an agonist at 5-HT3 receptors, which may contribute to mood altering effects of varenicline.


Most of the active compound is excreted renally (92–93%). A small proportion is glucuronidated, oxidated, N-formylated or conjugated to a hexose. The elimination half-life is about 24 hours.


Varenicline was discovered at Pfizer through the research aimed at modifying the structure of cytisine.

Varenicline received a “priority review” by the U.S. Food and Drug Administration (FDA) in February 2006, shortening the usual 10-month review period to 6 months because of its demonstrated effectiveness in clinical trials and perceived lack of safety issues. The agency’s approval of the drug came on May 11, 2006. August 1, 2006, varenicline was made available for sale in the United States and on September 29, 2006, was approved for sale in the European Union.

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Welcome to our Cohort 2 Students!

Happy Leap Year 29th February 2012 everyone! With the start of March comes a new beginning for our Cohort 2 Chemistry students. Start off fresh and on the ball, and you will end up with better results than you expected! On behalf of the PTEK Chemistry Department, I bid you all welcome, and wish you all the very best in your endeavors in A-Level Chemistry.

Do NOT underestimate this subject (as well as any other subject for that matter), and you will be well on your way towards a successful future.

Before we begin anything, please take the time to read about Safety in the Laboratory. It is imperative that we behave as scientists in the science laboratory. For more information, here is the full document regarding Safety!

Please download a copy of the CIE 9701 A-Level Chemistry Syllabus for your reference. I advise that you use this as a checklist for your revision purposes. Put a tick after each time you have been delivered material by your tutors, and then a second tick when you have understood the concept. That way you will be able to plan your revision well in the future. Of course, by the time you see 3 ticks on every objective in the syllabus, you should be ready for almost ANY question that CIE can throw your way. Also, you should print out a copy of the Practical Assessment (Qualitative Analysis) Notes as they will be used in EVERY Practical Session. They can be found on pages 69-70 of the Syllabus.

We INSIST that you all visit this website often to keep yourself up to date with anything involving PTEK Chemistry. Resources will be put up as we go along, maybe some worksheets, mark schemes and please take note at the very bottom of this page… the COUNTDOWN to your First APR. =) They should begin roughly around the 9th of April, 2012.

Being prepared is half the battle won!

Maxim Yap
HoD Chemistry 2012

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Molecule of the Month (March) – Ibuprofen

From Wikipedia:

Ibuprofen (INN); from the nomenclature iso-butyl-propanoic-phenolic acid) is a nonsteroidal anti-inflammatory drug (NSAID) used for relief of symptoms of arthritis, fever, as an analgesic (pain reliever), especially where there is an inflammatory component, and dysmenorrhea.

Ibuprofen is known to have an antiplatelet effect, though it is relatively mild and somewhat short-lived when compared with aspirin or other better-known antiplatelet drugs. In general, ibuprofen also acts as a vasodilator, having been shown to dilate coronary arteries and some other blood vessels. Ibuprofen is a core medicine in the World Health Organization‘s “WHO Model List of Essential Medicines“, which is a list of minimum medical needs for a basic healthcare system.

Ibuprofen was derived from propionic acid by the research arm of Boots Group during the 1960s. It was discovered by Andrew RM Dunlop, with colleagues Stewart Adams, John Nicholson, Vonleigh Simmons, Jeff Wilson and Colin Burrows, and was patented in 1961. Originally marketed as Brufen, ibuprofen is available under a variety of popular trademarks, including Motrin, Nurofen, Advil, and Nuprin.

Chemical Structure of Ibuprofen

Athletes, the young, the old, the sick alike all use Ibuprofen. Can you recall the last time you were prescribed this chemical? Take care though… from personal experience, this drug, as well as most drugs… cause gastric discomfort 😦

Ibuprofen Tablets




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Electrochemistry Revision & Reading

Below is an excerpt taken from RavenslarkChem Blogspot site. Echoes from the past will always return… but use them wisely, and you will succeed in the future!
From April 11th, 2010

There isn’t much on chemguide about A2 Electrochemistry. You folks are going to have to depend quite heavily on my notes this time. There’s some on AS Electrochemistry on Chemguide, which includes Electrolysis of Brine

Basic pointers regarding the drawing of the experimental setup:
1) Standard Hydrogen Electrode (SHE) is always on the left in diagram
2) Sign of electrode potential as measured from voltmeter = charge of RHS electrode
3) Labeling of direction of flow of electrons is done ONLY on the voltmeter wire

Basic pointers regarding the construction of a cell diagram:
1) (-) on the left; (+) on the right
2) | to denote a boundary between electrode & electrolyte
3) // to denote the salt bridge
4) Either side of a cell diagram will be the solid electrodes
5) Electrons are lost on the left, and gained on the right

N.B. DO NOT CONFUSE THE Cell Diagram with the experimental setup diagram.

If anyone has good links for Electrochemistry A2 please feel free to post!

Update: So far, in class, we’ve gone through the cell diagrams / experimental setup for measuring the electrode potentials for Zn2+/Zn, Cu2+/Cu & Cl2/Cl half-cells.
The class will go home and research on the case for measuring the standard electrode potentials for Cr3+/Cr2+ & Fe3+/Fe2+ systems.

Update (14/4/2010): Pt(s)|Cr2+(aq),Cr3+(aq)//Fe3+(aq),Fe2+(aq)|Pt(s)


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24/7 Access to Chemistry @ PTEK

A very warm welcome to all students, AE and BE (cohort 1 and 2) alike! Welcome to 2012 PTEK Chemistry. Be proud… for you are among those who will pioneer our latest approach to Chemistry that prioritizes communication online.

We are currently in the process of moving archives from as well as various excerpts and notes from revision guides found online. Please be patient with us as we will get this blog running as soon as possible.

Here you will find various resources, lesson notes, test papers, mark schemes, etc.

Moreover, you will be able to post questions to specific tutors or all tutors and peers in general. However, we would prefer that smaller questions be sent to our FaceBook Group PTEK Chemistry, and larger questions be sent to individual emails that your respective tutors will supply you if they wish.

Once again, welcome to a new Academic Year in PTEK Chemistry. All the best in your endeavors and on behalf of the Chemistry Department, I wish you all the best of luck in your studies!

Maxim Yap
HoD Chemistry 2012


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