Elemental

New Year

2008-01-05T17:57:00.000-08:00

Happy new year to all, especially to the students of the 2008 batch in 6.08, 6.09 and 6.12 Chemistry HL classes.

Life is not easy. In fact, we are quite certain that life is tough. But Chem HL is easy, and you will get a high grade if you read through every single entry in this blog and do your homework. Heh.

Reasons For Colour

2007-10-02T20:13:00.000-07:00

There's a beautiful little web-exhibit on the reasons why things are coloured. You can find it here. The page which is probably most relevant for students doing spectroscopy is here.

Take A Break

2007-07-08T02:03:00.001-07:00

For all the sad and depressed would-be analytical chemists, here is an entertaining look at the electromagnetic spectrum. There are a lot of weird things making waves out there...

Professional Development

2007-07-07T23:17:00.000-07:00

This is for those of you who are thinking of becoming professional chemists or taking up a career in which chemistry will play a role in your professional development.

The first place to begin with is, of course, your university life. Many good universities exist at which a chemical education is possible. This is not the place to discuss them.

Next, consider your membership of the local chemical sciences organisation, by state or country. For example, having settled for the time being in the Republic of Singapore, I am a member of the Singapore National Institute of Chemistry (SNIC). I am also a member of the American Chemical Society (ACS).

Also consider your membership of blanket organisations which extend your professional role. As an educator, I am a member of the American Association for the Advancement of Science (AAAS). It is often interesting to see how your professional area dovetails with others. My membership of the New York Academy of Sciences (NYAS) helps with this.

In general, you don't have to be a member of every organisation which comes your way. But take time to look at organisations whose annual events, publications and activities help to maintain, extend and update your professional knowledge and role.
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pH Indicators

2007-07-03T09:35:00.000-07:00

For no particular reason, I have surmised that it is good for all alchemical scholars to understand one of the key concepts in analytical alchemy – the use of coloured indicators to determine the endpoint of a neutralisation reaction.

A wonderful link can be found HERE.

Remember, not all indicators change colour at the equivalence point. And that link will show you the truth in false but reasonable true colours. Haha.

Advice To Chemistry Extended Essay Students

2007-05-26T21:58:00.000-07:00

1. If you have hazy ideas about doing a Chemistry EE, stop. Ask yourself the following questions.

1.1 What is the chemical subject – the compound, experimental set-up or reaction – you intend to examine?
1.2 What is the scope – the reactions of a compound, the applications of a set-up, the variables of a reaction – of your examination?
1.3 What hypothetical outcomes do you expect? Even if you have no specific expectations, what areas of theory inform your research?

2. Make sure you have discussed every one of these points with your EE supervisor. This is your FIRST MAJOR SESSION with your supervisor. Following the discussion, draft a one-page summary (about 300-500 words) of that discussion and submit it for checking and further comments.

3. Based on the returns, plan a research and experimentation schedule; aim for about 40 hours of planning and research, about 20-30 hours of lab work (spread into 4-6 hour shifts, not longer, and not too much shorter). You need to have a channel of discussion (MSN, email etc) open for SHORT communications with your supervisor.

4. Execute the plan, drafting a short account (100 words or a bit more) after each session to keep your supervisor informed of progress. Make sure that you reflect on that progress, figuring out how to improve things, get better results, clarify concepts etc. Make notes of your own cognitive processes as you execute the plan.

5. Write up by assembling your notes and findings.

5.1 Start by doing the easiest thing – assemble them in chronological order.
5.2 Next, assemble them in the order the rubric demands: research question, methodology/approach, analysis/interpretation, argument/evaluation, conclusion.
5.3 Write your abstract.
5.4 Ensure that all the formal presentation guidelines are observed (biblio, formatting, word count etc).
5.5 Your holistic judgement grade depends to a large extent on how much intelligent work you have done, the quality of the intelligent behaviour you have shown, and your communication of this and other things to your supervisor.

6. Submit the first draft to your supervisor by the end of the last term in Year 5. This is the absolute latest realistic time for a first draft. The earlier the better, as long as you don't compromise on quality.

7. Let your supervisor say as much as possible for discussion of this first draft; it is the SECOND MAJOR SESSION with your supervisor. If you don't intend to listen to your supervisor, you shouldn't be doing this EE anyway. So pay attention with a view to major holiday homework.

8. Try to give a first draft update within a week or two, for minor corrections (if you have been good) or a barracking (if you haven't been good).

9. When Year 6 starts, you should be able to submit your second draft at near-final or final quality. You will then have a fair amount of time to prettify your work before the real final submission.

10. Have fun!
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Quick Organics

2007-05-06T22:15:00.000-07:00

This is a quick revision source for those of you still coping with organic chemistry. It's a very neat summary, and it's been around a long time. I still wish that students would show the driving intelligence to learn which is oft shown by the creation of personal data structures.

Notes given by an instructor are fine. But they are first of all a communication coded by one brain in the hope that another, completely different, brain will decode it similarly and be guided by it equivalently. This is not as efficient as a brain working on established information and reconfiguring such material for its own use.
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Phenol

2007-04-26T17:55:00.000-07:00

For those of you who have been wondering how phenol can possibly be made by electrophilic aromatic substitution... well, it isn't. As would more reasonably be expected, it's commonly made by nucleophilic aromatic substitution in which sodium hydroxide supplies a strong nucleophile that replaces another group (the 'leaving group') such as -Cl or -SO3H.

Phenols are also made by direct catalytic oxidation of benzene, nowadays. This kind of direct synthesis at the elemental level is the 'Holy Grail' of modern organometallic chemists.

Here is a convenient summary of methods for preparation of phenol, with links to related topics. It's a good reason why you should buy Carey's text.
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Colours

2007-04-09T19:00:00.000-07:00

Just a couple of very useful pages for people who like that sort of thing:

The relationship between UV-Vis absorptions and TM complex colours

and

ways of seeing redox reactions.

Enjoy!

[6.01/6.09] Preparation: Practical Planning

2007-03-29T09:23:00.000-07:00

All students please note that this takes place immediately after school tomorrow. We will be looking at physical chemistry, mostly reaction kinetics. You are advised to read up in advance.

This is one of the many useful sites for a preliminary discussion. Here is another good starting point for the sufficiently enterprising. I shall leave you to dig around for more sites. Googling 'chemical kinetics' is good enough.

Infrared Spectroscopy

2007-03-28T21:20:00.000-07:00

This is an excellent site for examining IR spectra. It is especially good because it shows molecular models and animates the vibrations that give rise to specific absorptions. You will need to download the CHIME plug-in.

Thanks to CKW for providing the URL.
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Alkenes

2007-03-04T00:17:00.000-08:00

I am quite impressed by the thoroughness shown in this summary of the addition and oxidation reactions of alkenes.

In fact, if my students were to look at this and figure out the common threads, I would be even more impressed.
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Musical Mnemonics

2007-03-01T07:51:00.000-08:00

I surrender to popular sentiment and post this very funny link suggested by Sam.

It will help you somewhat if your chemistry is really bad. Then again, it might provide steric hindrance to understanding.

Mock Examination Material

2007-01-30T19:28:00.000-08:00

For those who would like to have some experience in past years' papers from the A-Level system, this page has been kindly provided by the people who administer that.

Look here. Answer schemes are provided as well!

In Summary

2007-01-30T05:12:00.000-08:00

I'd just like to point out that at this present moment, all classes should be aware of the following points:

1. There are four important areas to examine in organic chemistry, compounds, reactions and mechanisms. These are: electronic factors, steric factors, thermodynamic factors and kinetic factors.

2. There are a few major mechanisms with variations. One way to look at the range of mechanisms is: a) look at the attacking species - nucleophile, electrophile, free radical etc; b) look at the outcome - substitution, addition, elimination etc; c) consider the molecularity - likely to be unimolecular or bimolecular. Another way is to put these together and get mechanisms such as free radical substitution, electrophilic addition, electrophilic substitution, Sn1, Sn2, E1, E2 and so on. You should be able to explain all the reactions to some extent at this point, using structural diagrams and arrows.

3. This doesn't take away your responsibility to be able to classify compounds, name the easier ones (8 or fewer carbon, I'd say, but 6 or fewer is OK), and draw them. You should know these kinds at least: alkanes, alkenes, haloalkanes, alcohols, aldehydes, ketones, carboxylic acids, amides, acyl halides, acid anhydrides, esters, and simple (one ring) aromatic compounds. It's nice if you know alkynes and other stuff, but we'll cover some of that later on.
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Reaction Mechanisms

2007-01-11T18:15:00.000-08:00

'Reaction mechanisms in organic chemistry' is pretty straightforward topic if you remember a few key ideas.

1. Factors to consider: electronic, steric, thermodynamic, kinetic

2. Active species involved: free radical, nucleophile, electrophile

3. Overall consequence: substitution, addition, elimination

Here are two very helpful links:

1. List of Wikipedia entries for organic chemistry reaction mechanisms

2. ChemGuide index for organic chemistry reaction mechanisms

Personally, I prefer Wikipedia when I am looking for many related concepts and how they work together. I prefer Chemguide when I'm looking for clear specific ideas related to academic course requirements. Between the two, students should be able to figure out the basic principles of organic reactions.
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Organic Chemistry 102

2007-01-03T06:17:00.000-08:00

For those who still don't know what's being covered in the IBDP syllabus, please look at:

Organic Chemistry - Topic 20 (HL)
Further Organic Chemistry - Option H

Also check out related links on the rest of the page.
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Organic Chemistry 101

2007-01-02T07:20:00.000-08:00

Hello, ladies and gentlemen.

Welcome to a new year of chemical exploits (not explosions!)

Please go to this site to do some basic reading in organic chemistry before you will be ready. Explore as much as you can in the given sequence by the second week of term.

More advanced students might want to take note of this resource as well.

Thank you!
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Special Report on the Next 50 Years - New Scientist

2006-12-02T03:24:00.000-08:00

Special Report on Brilliant Minds Forecast the Next 50 Years - New Scientist is an interesting page. It isn't (strictly speaking) a chemistry page, but it is significant to the future of science education in many ways.

Please read it.
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Consciousness

2006-11-07T07:28:00.000-08:00

For a long time I debated with myself about whether the following resource had a place on this blog. "Online papers on consciousness" is a superb compilation of materials on this matter, related to the section on 'mind-affecting drugs' only tangentially.

Students of TOK will find this thought-provoking; if the chemistry students hate it enough, I'll remove the link.

Anaesthetic Readings

2006-11-07T05:12:00.000-08:00

No, I do not mean to make you fall asleep. However, the following readings can help you understand some of the finer points of anaesthesia which I am not covering in the last lecture of the series.

1. Mayo Clinic's guides are always useful. Anaesthesia: A look at local, regional and general anaesthesia is a good outline to the facts and issues related to anaesthesia.

2. Would you believe... Wikithesia? Yes, a Wikipaedia just for anaesthesia.

3. Sadly, GASNet is no more. However, you can still explore the extensive archive and learn more about being an anaesthetist or whatever it is you want to do with anaesthesia.

Combinatorial Chemistry

2006-11-06T08:28:00.000-08:00

Combinatorial Chemistry: A Guide for Librarians is a useful article for students seeking to understand basic combinatorial libraries using 'mix-and-split' teabag approaches.

Just think of it as a simple probability-tree thing, and you will understand what it's all about...

Computational Chemistry

2006-11-05T01:49:00.000-08:00

I have realised that some of you would like to see 3D molecule models of the substances we've been examining. A nice new (but still quite small) resource is the Computational Chemistry Wiki.

Essentially, you type in "http://www.compchemwiki.org/index.php?title=" followed by the name of the compound.

For example, Lecture 4 contains a discussion on how the xanthines inhibit adenosine reception.

You could follow this link to adenosine. Or even this one to caffeine.

There are quite a few more. Enjoy!

Medicines By Design

2006-11-04T06:04:00.000-08:00

Medicines By Design is a nice publication with links and associations to the rest of the very useful National Institutes of Health site(s). Please have a look!

Life Cycle of HIV Infection

2006-11-02T08:55:00.000-08:00

There's a nice little Flash animation about the Life Cycle of HIV Infection here. This is helpful when trying to visualise exactly what a virus does when it invades a cell and 'borrows' the 'copying engine'.

Medicines and Drugs

2006-10-26T08:35:00.000-07:00

And so it comes to pass that I will be giving five two-hour lectures on this topic. People who intend to attend, please look at the following links:

Lecture One: Introduction to Medicines and Drugs

Modern Drug Discovery website
GlaxoSmithKline website
Merck website
The Vioxx Case
The Thalidomide Case
Further Reading: The Promise of Thalidomide

[5.09] All Kinds of Bondage

2006-09-25T09:36:00.000-07:00

Chemical bonding in all its many varieties can be a confusing field of exploration. However, I have found a webpage which actually tries to explore all the main kinds of bonding. Of special note is the teasing little mention of two of my favourite chemical entities - the bifluoride and the triiodide ions.

I suppose that since the hint provided eliminates obvious ways of drawing these entities, students should look up things like 'resonance' and '3c-2e bonding'. The more advanced might want to look up 'Walsh orbitals'. And if even more advanced, might want to take a nap and prepare to study something else. Like this, for example. Heh heh.

[5.01/5.09] Organic Chemistry as a Second Language

2006-09-20T21:13:00.001-07:00

Sometimes, I wonder why we teach organic nomenclature as if it were some sort of esoteric sub-discipline. It is a second language, one which is eminently rational, and mostly consistent - unlike English, for example.

Here is an HTML version of IUPAC's Recommendations on Nomenclature of Organic Chemistry(1979 & 1993). You have to admire the orderly manner in which this is handled. You don't really need a textbook or a teacher if you examine this ruthlessly to the end of each hierarchical sequence.

The only quibble I have is the use of the word 'recommendations'. IUPAC is the authority on pure and applied chemistry - whatever it says goes, and so it should not be 'recommendations', but 'directives' (or at weakest, 'guidelines'). It's a small quibble.

[5.01/5.09] Physical Chemistry

2006-09-17T07:01:00.000-07:00

Here is a link to ChemGuide's page on physical chemistry - mainly reaction kinetics and equilibria. You will be surprised as to how easy the ChemGuide people make it look. As of course, it should be.

Please read the Phase Equilibria section for the week ahead.

Neutrality

2006-08-26T20:39:00.000-07:00

Neutrality is an interesting situation to be in. How interesting? Well, here is some simple evidence that a pH of 7 does not define neutrality; rather, neutrality is defined independent of pH. It all goes back down to how people who digest pre-digested information don't get to enjoy the taste of the precursor materials.

Project 2061

2006-08-21T22:36:00.000-07:00

Project 2061, named after the next year of arrival of Halley's Comet, provided the basis for the integrated programme I helped to design many years ago. Since then, the programme has evolved. Those of you who have experienced the programme but are unsure of the theoretical basis for it might find many interesting points of difference and areas of incongruence (no, no, not 'incongruity'). Check out the Publications tab and you will find free downloadable source material which we used for the initial plans.

Those of you who are radically interested in educational curriculum design might want to email me for details. Note: this part only works for those of you who already know where my email address can be obtained. Obviously, I will never reveal any information for which I have signed an NDA or which I am otherwise contractually obliged not to disclose. There's still a lot in my head though.

Entropy and the Second Law of Thermodynamics

2006-08-17T20:37:00.000-07:00

This is one of the reference sites for the material in our course. It's in the reference list, but I gather that there are a few people who look at this site and not at their notes! Mastery of the content on this site provides the physics background that some of you lack when needing to handle chemical energetics.

Referencing Accuracy

2006-08-05T20:20:00.000-07:00

Those who think that Wikipedia is an inadequate reference should read this. Note, however, that the article refers to science articles. Highly contentious issues remain over other kinds of wikimatter.

Natural Science

2006-07-30T01:18:00.000-07:00

Suddenly, all the links converged. And thus is a revelation achieved. Or maybe, archived. Take a look at Natural Science...

Readings on the Nature of Science

2006-07-29T07:32:00.000-07:00

I am indebted to the University of Illinois for assembling what I think is the best collection of Nature of Science readings on the Net. It is best to me because it covers everything a sensible student needs to know without being overly technical.

I highly, seriously and specifically recommend this page. All my students should read all the links on it.

Sulphur

2006-07-18T21:24:00.000-07:00

Sulphur is how most of us spell it. Of course, by IUPAC reckoning, this is not how it should be spelt. The problem is that the 'ph' is a Greek sound, and not a Germanic one, and 'sulphur' was originally spelt 'sulfur', from OE seolfor.

This is not a new problem. Color, center, theater, and more... all these spellings were used by Shakespeare. The problem arose when the common trans-Atlantic language diverged during the Enlightenment and thereafter. For some reason, the English decided that 'classical' spellings and words (i.e. Frenchified or Romanticised) looked better. So 'color' became 'colour' (to look more like French 'coleur', I suppose); the same is true of the rest.

The great thing about chemistry, of course, is that we can (and indeed, should) just use symbols for chemical expressions, and then it will not matter how we spell 'sulphur' - which is Dr Beavon's point exactly.

[5.01/5.09] The Atypical Chemistry of Beryllium Chloride

2006-06-11T01:00:00.000-07:00

This provides some answers for any lingering questions surrounding the behaviour of beryllium chloride. Rather good answers, too.

Tetrahedral Bond Angles

2006-06-11T00:24:00.000-07:00

This article gives mathematical proofs of why the bond angle in a tetrahedral molecule such as methane should be about 109.5 degrees. I suppose some people are more mathematically inclined than graphically, so this should help such hard-core types.

Invisibility

2006-06-01T06:28:00.000-07:00

This article is the proof, in its own way, of what chemists have been saying all the time - repeat after me: bonding leads to structure, and structure leads to properties. Only theoretical so far, this invisibility...

Pharmacopoeia

2006-05-26T08:26:00.000-07:00

Quite a lot of my students - whether of chemistry, alchemy, natural philosophy, or unnatural philosophy - have expressed an interest in medical and pharmaceutical knowledge. Well, one of the modern bearers of the great caduceus is Merck & Co., Inc., a "global research-driven pharmaceutical products company" best known for its excellent manuals, an interesting history, and some rather unusual drug-related events.

The link above leads to one of its great public-service endeavours - free manuals for the masses, available online. Enjoy.

Printable Periodic Tables

2006-05-23T23:43:00.000-07:00

Printable Periodic Tables are available at the eponymous webpage. A large and entertaining range, for those of you who collect such things and who want to see the world in new and interesting ways. Might give you ideas for your own design too!

Holiday Stuff

2006-05-21T02:23:00.000-07:00

If you can really still bring yourself to think about science in the coming summer break, you can be vastly entertained for free (and for days if you're the sort) at LiveScience.com. Enjoy.

Molecular List

2006-04-16T08:04:00.000-07:00

This is for any students of chemistry who are hungrily searching for online molecular models. Flick's list contains many common molecules, ions, and fragments - and some rare ones as well.

[5.01/5.09] Rethinking Hybridization

2006-04-16T08:01:00.000-07:00

Rethinking Hybridization is an interesting article. Warning: only for advanced students who have some idea about what symmetry (and group theory) are about. Essentially, the article argues that hybridization isn't always the best description of how bonds are formed. If you can understand this article, you're probably at Year II university level.

[5.01/5.09] Hybrid Orbitals

2006-04-10T10:27:00.000-07:00

Hybridization, for the visually challenged. Link provided by the industrious BC. I'm sure there are more beautiful ones, and I shall post them if anyone finds them.

[5.01/5.09] An Age of Uncertainty (updated from 04 Mar 2006)

2006-03-18T02:30:00.000-08:00

After many dark nights spent poring over semi-legible manuscripts purporting to be lab reports, I sought wisdom on the Internet which could be shared with the children of the wyvern. And this is what I found: Mathematical Wisdom. Enjoy, my children.

Other URLs on this topic are listed below:

1. Combining experimental error is an excellent page from Rod Beavon's website (which has been cited elsewhere, though not sited elsewhere... haha!) The rest of the site is worth looking through too.

2. Chemsheets is a great source of interesting test-yourself assignments from Richard Grimes. Answers are there, but not obviously so.

[5.01/5.09] Preparing To Bond

2006-03-12T07:50:00.000-08:00

Bonding is the topic for next term, and this link takes you to the place found in the bibliography of your notes. You may explore the entire ChemGuide if you wish. It will help you somewhat. But you MUST do your readings faithfully...

[5.01/5.09] The Plambeck Course

2006-02-28T06:00:00.000-08:00

The Introductory Chemistry Course is a PSIGate offering from Dr James Plambeck, a chemist retired from the University of Alberta. Material is reliable and made freely available to all students of chemistry. Warning: University-level course, heavily text-based. May therefore not be suitable for some young people.

[5.01/5.09] ChemWorld

2006-02-20T07:00:00.000-08:00

ChemWorld at Thinkquest.org is a pretty well-designed site for those aiming at post-secondary courses like AP Chemistry and IBDP HL Chem. I would like to draw attention to the friendly formatting and reasonably well-designed pages. The layout is OK, although sometimes the text is too close for comfort. Enjoy. And revise for the test, which I shall endeavour to hold on the day latest in the week.

[5.01/5.09] Definitions

2006-02-11T19:00:00.000-08:00

Why do you think this is important at all?

In fact, for those who can spare the time, it is extremely instructive to read about the criteria for recognising new elements. Read, especially, section II.2 on the linked page. It is almost like a class in the Theory of Knowledge. Definitions are indeed somewhat arbitrary, while saving us from arbitrariness. This is the glorious paradox of definition.

[5.01/5.09] Electronic Structure Slides

2006-02-07T06:00:00.000-08:00

Here is a Media Portfolio containing many interesting diagrams of explanatory nature. (Prentice-Hall materials are pretty good, should you be looking for alternative textbooks.) If you navigate backwards through the page (i.e. through the links at the top), you will find that you can download the whole thing as a PowerPoint file, and even find other useful materials.

[5.01/5.09] Atomic Theory/Electronic Structure

2006-02-04T04:00:00.000-08:00

Readings for this topic:
Electronic Configuration of Atoms — material from basic to in-depth.

Note that subunits 4.1 to 4.5 will take you up to the current topic, while the remainder will take you up to the end of the term or so. Have fun.

[5.01/5.09] Avogadro's Number

2006-02-02T02:00:00.000-08:00

As supplementary reading, please look at: Avogadro's Number.

Wisdom

2006-02-01T08:00:00.000-08:00

Wittgenstein once remarked, "That Newtonian mechanics can be used to describe the world tells nothing about the world. Nevertheless it tells us something: that it can be used to describe the world in the way in which we do in fact use it."

I don't personally know any Newtonian mechanics, although I have friends who are perfectly capable mechanics. It strikes me, in particular, however that many scientists fail to pay sufficient homage to the common-sense realities of life - that people can be stupid, or venal, or careless, or insensitive; that science is an excellent way of making a particularly rigorous but not necessarily useful construct for dealing with life; that we are all in charge of reality by virtue of interpreting it however we want.

But in this House of the Wyvern, my dear apprentices, you must first learn to measure, to count, to recount, and to account.

I leave you with a quote from the ancient canon of Moses, the great thaumaturge of the Hebrews. The Second Book of Law says, in chapter 25, verse 15, "You must have accurate and honest weights and measures, so that you may live long in the land the Lord your God is giving you." And that is the beginning of practical alchemy.