Progress in Chemistry 2018

Last year, the Nobel Prize in Chemistry 2017 was awarded to Jacques Dubochet, Joachim Frank & Richard Henderson for their work in cryo-electron microscopy. Their work in the past has definitely revolutionized how we see molecules and was a great step forward in Biochemistry.

The concept of ‘ dynamic equilibrium’ alone has taught us that even when a reaction has ‘stopped’, reactions are still occurring. It’s the net change that is zero, which leads to our perception that the reaction has ‘stopped’. Knowing this, one can see why we would need to slow down molecules drastically in order to properly visualize them.

By slowing the molecules down drastically, for instance, with the Zika virus, proper rendering and visualization can be done more accurately. With that information, researchers could analyze the molecules (receptor sites, active sites, etc) and provide a more accurate target for pharmaceuticals.

People always misuse the quote “A picture is worth a thousand words” but in reality, it’s much more important to know WHICH WORDS they actually are. With the progress in the area of cryo-EM, a new era of Biochemistry began.

Now, look to yourselves, and ask, “What was my progress during the holidays in December 2017?” It is easily possible for one to learn and develop one’s self much more during a month of holidays, than in an entire year at school. It’s the time that we spend by ourselves (minus procrastination) that leads to eventual development and success. Let’s take a great and effective first step into 2018!



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Chemistry of “D” Presentations 2017

24th July 2017

It was that time of the year again, where students presented their findings from their voluntary research endeavors. Last year, it was the Chemistry of “C”, which included some very interesting presentations like The Chemistry of Cough Syrup, The Chemistry of Coffee ❤ & The Chemistry of Chocolate! ❤ ❤ ❤

These were the topics for this year:

Chemistry Presentation 2017

Learning content for examinations is crucial, but I believe that learning how to learn effectively is much more vital! Cramming for exams is temporary… but self-motivated research & commitment to learning can last a lifetime. Furthermore, if the content can be related to real life, it becomes even more embedded into ones’ memories!

Here are some photos from the event. Click on the photo below to view the photos from Dropbox!

Photo Jul 24, 10 23 18 AM


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Happy Holidays!

Last day of Term 1, and here’s what we’ve done so far:Chem Topic 1 syllabus

Now, the above should only exist a a checklist. The questions from Jim Clark listed in your holiday homework & reading lists should help consolidate your proficiency in Topic 1 – Atoms, Molecules & Stoichiometry.

Holidays are meant to be enjoyed, so please do! However, spend some time and rack up some hours in your 100 Hour Revision Cards, and look up the Duke of Edinburgh Awards. Hopefully, we can find more information as to how it can be done in Brunei. Speak to people at Careers Section, and find out if there are any available internships, or job placements to more productively spend your holidays. Pick up a new skill, learn a new language, hone your sports skills, become more valuable as a person than you were before the holidays!

Need any help? You know who to contact =)

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Flame ON!

With the arrival of our new batch of L6, here’s hoping they all come in with a fiery desire to excel in Chemistry! Remember the MOTTO of our Chemistry Department!

1% Exams, 99% Exploration!

There is no point doing well in exams… if you haven’t really learnt anything beyond plain memorization. Remember Bloom’s Taxonomy!


How far up the pyramid are you in terms of learning? One should always aim all the way up to Analysis at A-Level… and then constantly be attempting Synthesis & Evaluation for all steps along the way.

Now let’s get right into it. Here are some Flame Test Colours!


One of the oldest methods of identifying traces of metal ions, all that has to be done, is to burn the sample with a flame and observe the color given off. Now, this method of analysis is simple and quick. However, if the sample isn’t pure, what you will observe would be a mixture of colors.

Look forward to learning about electronic configuration, energy levels & theory of color for transition metal complexes in aqueous solution to find out more about why a given ion would give off a certain color!

Until the next post, work hard! 100 Hours Revision Cards can be downloaded here.

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The Chemistry of Roses

A day after the anticipated, or in some cases, dreaded Valentine’s Day, I’ve decided to look up an infographic for the Chemistry of Roses. Going at $1.50 usually, they were, as expected, marked up to $3 for a single rose, and with a few floral arrangements that are individually cheap per piece, you could end up with corsages that costed $40 and above!

Now what is it actually about roses that entices people so much? Is it the color? The aroma? Tradition? Some conspiracy made up by florists in ages past to boost their economy for a few days around the 14th of February?

Nonetheless, let’s take a deeper look at the Chemistry. (from Compound Interest)


Red may be the traditional color for roses during Valentine’s Day, but there are various other shades that may be desirable. Carothenoids and anthocyanins are responsible for the color of the petals. Now, there are over 75 different carothenoids across 40 different yellow rose petals alone! However, for red roses, the anthocyanins are surprisingly not as diverse, and hence… more unique in a fashion.

Strange to say, there are colorless compounds that exist in rose petals, that can interact with common colored compounds such as cyanin and pelargonin to influence the shade that we actually see via a phenomenon called ‘copigmentation’.

Color may attract attention, but what about the aroma? Compounds such as (-)-cis-rose oxide (quite a generic name to be honest), rose ketones e.g. beta damascenone and terpene compounds e.g. geraniol, nerol, citronellol, and farnesol may also contribute to the scent. What’s really interesting is that these compounds crop up in other flowers as well, but it takes an expert nose to be able to tell the difference without the gift of sight.

Hope everyone had an enjoyable (and not-so-expensive) Valentine’s Day!

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Another new year in Chemistry!

2016 was a really exciting year for Chemistry indeed! With the latest Nobel Prize in Chemistry having such interesting content, and so many new discoveries, here’s to 2017 being an even more successful year!

PTES is currently undergoing some new Professional Development for staff and Study Skills for students. At the moment, Dr. Makarimi Kassim has already shown the staff how Mindmaps are generated, and have helped the students begin to use them in their studies. The Chemistry students have made some Mindmaps from the topic: Organic Chemistry – Carbonyl Compounds. Here are some of the lovely products from our students:

So which of the Mindmaps above suits your preference? Which ones would truly aid you in more efficient revision?

Personally, I prefer infographics! As usual, our go-to source of Weekly Infographics is Compound Interest. Here’s one that tries to summarize the reasons for why some bodily fluids are coloured as they are.

Do you want to know more about why a certain fluid from any source has a certain colour? Glowsticks maybe? Drop us an email at and we may make that the subject of our next post! Until then, have a great week!

The Machine – Admin 0014

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Everyday Chemicals: Piperine


This infographic was taken directly from Compound Interest and I have no ownership nor do I claim to have made this myself =) As I’ve told my Lower Sixth students, it is very important not just to Know and to Understand what we learn in class, but even more important to Apply it to real life situations. Chemistry has Chemicals in abundance! We should be able to know what each chemical does… whether it has one function, multiple functions and ESPECIALLY if they cause side effects. That is among the crucial roles of a Research Chemist.

Piperine is a nitrogenous organic compound of plant origin that has pronounced physiological action on humans. Other alkaloid compounds, as they are called, include morphine, quinine (drugs) and atropine (poison). Now one may view the name of the compound itself with the suffix -ine to denote an amine, which would be technically correct. However, the full name of this compound is 1-[5-(1,3-Benzodioxol-5-yl)-1-oxo-2,4-pentadienyl]piperidine. What a mouthful! You have to understand that every compound with a shockingly short name hides a possibly incredibly long IUPAC name.

Piperine is basically an essential component of black pepper. The ‘hot’ taste is due to piperine (similar to capsaicin – found in chilli peppers). According to the infographic above, piperine causes a spicy taste that is only 1% of that from capsaicin. It is also contained in various homeopathic remedies and even in Chinese medicine. Now there is a chemical that we often use, but never really cared about why or how it works. I wouldn’t say this is Molecule of the Month material, but if anyone has a molecule to suggest, please email me at

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Compound Interest-ing!

This blog has not been updated for a while, and that’s because I’ve been sharing posts via Facebook using infographics from Compound Interest! But as of this term, I shall begin linking the posts from Facebook over here.

To begin with, let’s take a look at the article regarding Pyrimidanes. At A-Level, you will most definitely be taught about the pyramidal shape of P4 (white or yellow phosphorus). There may be some chelating compounds that you may encounter that have a similar shape, but the mysterious thing about these Pyrimidanes lay in the geometry.

Using VSEPR, an atom of carbon would prefer to form bonds that would be tetrahedral in shape. Limiting carbon to 3 bonds would violate the rules of valency.


The above diagram was taken directly from the site for the article regarding Pyrimidanes, and the curious geometry of both the covalent and ionic forms is seen. Yes, the carbons have 4 bonds in the covalent form, but the bond angle would not be 109.5 degrees as expected. There would be some strain on the compound structure due to the near 90 degree bond angles in the base (although even cyclopropane compounds exist).

Interesting stuff!

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Elixir of the Month – The Aroma of Coffee

Just in case anyone did not realize it… the molecule of the month for April was Adrenaline ^_^;;

And due to the complexities that surround this upcoming BRILLIANT beverage… an Elixir of Life of sorts… COFFEE!!!! Over the years I’ve been a barista at Starbucks (best months of my life as an employee), a barista at college cocktail bars serving alcoholic and non-alcoholic drinks (including, of course, COFFEE!!!), as well as an overall lover of anything that can taste bittersweet and make you feel alive!

I remember walking in to my shift at Starbucks… probably feeling slightly down due to workload… but as soon as I entered the door, I would take in a huge breath, slip on my apron (smile automatically comes onto my usually unsmiling face), and it would always be 6 hours of energetic bliss! As a result of my vigor, I was given the honor as Employee of the Month (Twice!), and also made Head Barista on my final month working there (sadly). The pay was awesome, but nothing could compare with the smell I was blessed with during my shift, and for hours after… lingering on my clothes and hair. I have to admit I was tempted at most times to just skip showering! ^_^;;;;

Now to start off, I just simply HAVE to mention caffeine, the world’s most widely consumed psychoactive drug. More specifically, it is a central nervous stimulant (CNS) of the methylxanthine class of psychoactive drugs. As a substance, it is a bitter, white crystalline purine, a methylxanthine alkaloid and closely related to adenine, which is found in DNA and RNA. What’s important is that it can stave off drowsiness, definitely useful in many situations. But it also has negative side effects like insomnia, gastric, etc. Nothing is free in this world… what we have to do is weigh the pluses and minuses… and decide!


This infographic above, taken from Compound Interest in 2014, details some of the most important aspects of coffee. Not only does it summarize the action of caffeine, but also explains why coffee is bitter. Now, not many would be interested in bitter things. Most fairy tale wannabe believers just want the sweetness in life. Although it takes a special kind of maturity to love bitter things, it doesn’t take much to love coffee. The key to brewing the ultimate coffee, is love! Depending on the levels of chemicals like 5-caffeoylquinic acid in coffee beans, different grades of roasting can reduce that enough to give a great taste.

However, the most important aspect of coffee to me, lay in the smell… the sweet aroma of the bitterness (see what I did there?). The next infographic summarizes it very well, and once again, THANK YOU Compound Interest.


I don’t know what else I need to say… I’m printing out this infographic in a large size and pasting it on my bar counter wall. Once the cupboards are done, and the coffee machine is here… there will be a very nice aroma in my living room ^__^

P.S. Although caffeine is listed as the molecule of the month, it’s up to you to decide which chemical that is found in Coffee, the Elixir of Life, that interests you the most, and research them individually.

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Fight or Flight Response – Adrenaline

It’s less than a week away from Floyd Mayweather, Jr. vs Manny Pacquiao, and the world is trembling in anticipation of the Fight to Watch for this generation! Personally, the adrenaline rush I get when I view all those promo videos (official and fan made ones) is mind blowing. Talk about butterflies in the stomach early in the morning in the absence of any threat! However, it is this very feeling that will be the subject of this post at the end of April 2015. How often are we subject to ‘threatening’ situations where our basic instinct of survival kicks in? Not so much? Well, even during sports, especially when we are put on the spot, where winning or losing a major game would fall entirely on our shoulders… that’s when Adrenaline can make or break us. Would we succumb to panic? Or would the hormone steer our heightened senses to victory?

An interesting infographic that depicts the stages of the Fight or Flight Response. The symptoms seem rather debilitating and detrimental to our survival. However, if they are honed and focused, they can bring us back to what we may have been created originally to be, not the domesticated creatures we are now.

Now, firstly we need to address the actual system itself. Our Autonomic Nervous System is a control system that acts largely unconsciously and regulates heart rate, digestion, respiratory rate, pupillary response, urination, and sexual arousal. The role of this system is mediated by the Sympathetic Nervous System, which has the main function of activating the physiological changes that occur during the fight or flight response, and the Parasympathetic Nervous System, which has the main function of activating the “rest and digest” response and return the body to homeostasis after the fight or flight response. Basically like an “ON” (norepinephrine) and “OFF” (acetylcholine) switch respectively.



Now imagine the build up to the fight on May 2nd. Neither of them will run. They’ve been wanting this for years! Once they are both in the ring, let’s take a look at what will happen.

The amygdala will trigger a neural response in the hypothalamus. The initial reaction is followed by activation of the pituitary gland and secretion of the hormone adrenocorticotropic hormone (ACTH). The adrenal gland is activated almost simultaneously and releases the neurotransmitter epinephrine. The release of chemical messengers results in the production of the hormone cortisol, which increases blood pressure, blood sugar, and suppresses the immune system (AKA ENERGY BOOST!). Epinephrine basically binds with liver cells and glucose production spikes. Additionally, the circulation of cortisol functions to turn fatty acids into available energy, which prepares muscles throughout the body for response. Catecholamine hormones, such as adrenaline (epinephrine) or noradrenaline (norepinephrine), facilitate immediate physical reactions associated with a preparation for violent muscular action.

There is a huge list of these, which includes acceleration of heart and lung action, dilation of blood vessels for muscles, pupil dilation, tunnel vision (this can be a problem, which requires focus and training to hone), loss of hearing (better known as auditory exclusion as you focus only on the sounds you need!), shaking (well DUH!), inhibition of erection (not THIS is interesting!). Also, you will have increased strength and speed! Awesome, isn’t it?

However, as with all things, nothing is free. During the reaction, the intensity of emotion brought about by the stimulus may be too high for most. Individuals with high levels of emotional reactivity may be prone to anxiety and aggression. A burst of energy such as these ones would require some form of trade off. It leaves us feeling drained after. Tired. Weak. Wet pants (for some).

Do you have problems with butterflies in the stomach? Anxiety? Stress? Unable to stand up in public or unable to solve your big problems due to fear? Then you have lost to adrenaline… rather than befriended and used it. Fear is our greatest enemy, but we were all born with the tools to combat it. Use your fear, channel it into something positive. Transcend your past self, and FIGHT!

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