It is with enormous sadness that we must inform visitors that Jack Pridham, Emeritus Professor of Biochemistry, Honorary Fellow of Royal Holloway, and creator of this unique resource, passed away in May 2012.

Having been off-air for some time, the site has now been rebuilt, but with the passing of Jack it is unlikely that there will be further updates. A tribute to Jack by the Principal of Royal Holloway may be found on the College web site, and there are further obituaries at the Times Higher Education and the Telegraph web sites. There is also a very moving and personal eulogy from his friend and colleague Peter Bramley.

Media watch

Welcome to the brighter and more navigable Chemo-Philia site designed by C-P's colleague, the late Dr Gary Warren.

Media Watch, a new addition to the site, will be used for comment on chemical topics reported by the media and where necessary, to put them into perspective and emphasise their value.

There are presently 40 ITEMS (last one 26 July 2010 ) displayed below:


The results of trials with this new drug from the pharmaceutical industry have been widely reported. Its introduction could reduce the reoccurence of breast cancer in older women by 50%.

Many breast cancers are 'nourished' by female hormones, oestrogens (or if you prefer,estrogens), chemicals that first attach themselves to specific tumour cell receptors before encouraging the cells to divide and enlarge the tumour. The successful use of tamoxifen, a so called selective oestrogen receptor modulator, to treat breast cancer is well known. As its description indicates, it works by blocking the tumour cell receptors and stops oestrogen-stimulation. Letrozole, on the other hand, works in a different way - it is described as an aromatase inhibitor. Aromatase is an enzyme which in mammals is involved in producing oestrogens which are aromatic and synthesised from male hormones (androgens) which have structures similar to the oestrogens but are non-aromatic. Letrozole therefore interrupts the supply of oestrogen to the tumour and growth stimulation is reduced.



The word "chemical" continues to be used in a way that suggests danger and promotes fear! The Times(15/10/03) reported that staff in a US electronics company who had developed cancer were turning to litigation as they had been "exposed to chemicals"! They will have little difficulty in persuading the judge that this was so - Chemo-Philia knows of no one that has not been exposed!



Many mothers preparing baby food this morning must have stopped to listen to a report on the BBC 4 "Today" programme. This particular scare story which was tempered by a statement from the Head of the Food Standards Agency, was nothing new - the potential hazard was reported in July of this year by the European Food Safety Authority (EFSA).

The problem is that a compound called semicarbazide:


has been found in several foods which are normally contained in bottles and jars. The maximum amount found was 20 ppb ie 20 millionths of a gram in 1000 grams (1kg) of food which to say the least, is not a lot! Human beings consume thousands of toxic and potentially toxic compounds (mostly from natural sources) at these and higher levels without apparent harm, thanks to the body's cleaner - the liver! However, at much higher doses than parts per billion, semicarbazide is a weak 'rodent carcinogen' which produces tumours in female but not male mice so the situation needs to be monitored. The EFSA believes that the chemical at the levels found, presents little risk for adults or children.

Where does semicarbazide come from? The most likely origin is from the breakdown of azodicarbonamide:


a compound used to produce minute air bubbles in foamed plastics which are used to coat the insides of the metal caps used on jars and bottles. When the filled containers are heat-processed the azodicarbonamide should be completely broken down but apparently traces of it are converted to semicarbazide.

As analytical methods get better and better most if not all chemicals in the environment will be found in our food and in our bodies. At 10-9g and below this does not mean that they are necessarily harmful. Many of them have been there for aeons and the human race still continues to thrive!



A report in the Times Higher Education Supplement (28/11/03) supports the view that there is a use for everything! Apparently, the authorities at the University of Minnesota in the USA were fed-up with citizens stealing their Christmas trees at this time of the year. One would imagine that members of the University Science Faculty were consulted and that they came up with an unique way of detering the thieves - ie by spraying the trees with 'skunk secretion'!

Everyone knows that the North American skunk when threatened, can spray potential predators with an offensive, smelly mixture of chemicals from glands in the base of the tail. In the case of a human target he/she may well have to destroy the clothes being worn at the time of the incident as the odour is quite intolerable and difficult to remove. In the case of the common Striped Skunk, the spray is composed of seven major components which can be divided into two groups: (1), thiols (R--SH; where R represents various chemical structures) and two of these thiols are mainly responsible for the strong odour and (2), acetate derivatives of the thiols (R--S.CO.CH3).

Those responsible for introducing this anti-theft device knew some chemistry and in particular that the chemicals in the spray had low vapour pressures and would not be smelly at cold Minnesotan winter temperatures. However, if someone took a tree indoors it would 'spring to life', so to speak!

Incidentally, the smell may be removed chemically from a contaminated pet. An oxidising agent such as hydrogen peroxide (H2O2) will do the trick but unless you are careful, your black Labrador may look more like a Golden Retriever when you have finished. The melanin in his/her coat is also destroyed by peroxide!

How did evolution produce such an effective, protective, chemical cocktail for skunks - and Christmas trees?!

(Further information on 'skunk chemistry' can be found here) (1/12/03)


Twelve years on from the first Gulf War an editorial summarising what is now known about the so-called Gulf War Syndrome has appeared in The British Medical Journal (327, 1357-1358 (2003)). Considerable research costing some £174 million has been carried out to try and establish whether the symptoms associated with the Syndrome - general pain, fatigue, memory loss, psychological distress, etc - were associated with conditions on the Gulf battlefields.

The Editorial concludes that the complex package of symptoms are real but they are not specifically connected to the Gulf War and can occur in populations, military or otherwise, which have been subjected to various types of stress, eg terrorist attacks and natural and industrial disasters. No excess cancers, birth defects or deaths have occurred in the 'Gulf group' which makes it unlikely that the use of depleted uranium (previously discussed in these pages) and pesticides have played any significant role in the Syndrome. Questions remain over the possible effects of vaccines used in the Gulf. (19/12/03)


Salmon is back in the chemophobic news. C-P last raised the subject in January1991 when dioxins and other organochlorines were reported to be present in this nutritionally valuable fish - as they are in most if not all other foods! The latest report comes from the USA where 'high' levels of dioxins were found in Scottish farmed salmon and it was suggested that in the worst cases of contamination, only one meal of farmed salmon should eaten every four months to avoid increased risk of cancer. These conclusions were reached by employing the ultracautious dosage recommendations of the US Environmental Protection Agency. Our own Food Standards Agency says that the dioxin levels in Scottish salmon are within those that are accepted by the World Health Organization and the European Commission and to lessen the risk of heart attacks, we should eat one portion of oily fish a week which could be salmon. In reality, no one knows the minimum dose that is likely to cause human cancer: for genetic reasons it will probably vary from person to person. Organochlorines are distributed throughout the environment - for example, whenever any organic material, such as wood, is burned they are formed so it is not possible to avoid them completely. In Scottish farmed salmon the contamination mainly comes from the fish food derived from European waters which, in turn, are contaminated by the chlorinated products of European industry.

There is no good evidence to suggest that we suffer from the toxic effects of dioxins and the like, when they are encountered at the existing low environmental levels. Furthermore, the intake of dioxins in food has been reduced by 50% between 1997 and 2001.

As always, the media rushed to emphasise the bad news. The Times for example, on Monday, January 12th published the headlines, "Salmon shunned despite price cuts and reassurances". The next day the same newspaper reported that British consumers were rushing out, "to buy it by the the trolleyful" without the attraction of cut prices. Perhaps the public is tiring of these food scares. (14/01/04)


Alcoholic drinks in moderation for non-pregnant healthy adults are now generally sanctioned by the medical profession but in excessive amounts they can, of course, damage body organs and contribute to crime and fatal accidents on the road and in the workplace.

Various institutions are interested in methods to measure the amount of alcohol (ethanol) that a person has consumed including the police, medical practitioners and, possibly, insurance companies! Several methods have been available for measuring alcohol in the breath for many years. The first method used was essentially blowing down a tube containing yellow potassium dichromate, an oxidising agent which coverts alcohol to acetic acid (see 'Pot' or Pint) and goes green. Later, more sophisticated procedures were developed, such as measuring the amount of alcohol present in the breath by infrared analysis. However, these methods are only useful for monitoring alcohol within a few hours of consumption. Most of the alcohol is destroyed quite quickly by the liver and other tissues. Furthermore, 'breath analysis' data are approximations which need to be confirmed by blood tests

In recent years analysts have been looking for methods that would reveal whether people had drunk alcohol days, weeks or months before testing, by focusing on derivatives of alcohol that are formed in the body and remain there for longer periods than alcohol itself. One of these derivatives is ethyl glucuronide:

CH3CH2 - O - GlcA

The partial chemical structure shown in red is derived from ethanol (by the loss of a hydrogen atom) and glucuronic acid (GlcA), a carbohydrate with a structure very similar to glucose (and synthesised from this sugar) is used to detoxify poisonous substances that enter the body. It makes them more soluble in water so that they may be readily excreted in the urine. (Many drugs and some hormones are also dealt with in this way). Ethyl glucuronide can be detected 3-5 days after all alcohol has been eliminated from the body; it can be found in body tisssues, urine and even hair.

The analysis of a second ehanol derivative, phosphatidyl ethanol, allows alcohol consumption to be detected 2 weeks after the 'binge' has occurred (20/02/04)


C-P has for the first and probably the last time, challenged the BBC children's programme, CBBC Newsround, over its description of the gas, methane, which has been found on Mars and, perhaps originated from living organisms on the planet..

The e-mail sent to the BBC reads as follows:

"Whoops! A schoolboy/girl error! Re methane on Mars (Newsround 29/03/04), both the presenter and the science correspondent seemed to think that methane is smelly. In fact it is odourless and for that reason can be dangerous. It is produced by bacteria in the gut but any smell from this region is likely to be caused by sulphur compounds, not methane".

It should have been mentioned that a smelly compound (a thiol) is added to methane that is used for commercial or domestic purposes (heating or cooking) so that it can be detected if it escapes



In the context of terrorism, we are used to hearing about sarin (a nerve disrupting gas) and ricin and anthrax , natural sources of dangerous toxins. However, in the last few days the media has claimed that an unusual commercial chemical might be used to make a 'dirty bomb'. The compound in question is osmium tetroxide (OsO4) which can be prepared by heating osmium with oxygen. (Osmium is related to the metal platinum and because of its high melting point, was once used instead of tungsten to make electric lamp filaments).

Osmium tetroxide is very expensive and is used by chemists as a catalyst and by biologists to 'fix' /stabilise specimens prior to examining them with powerful (electron) microscopes. It is also a reagent for detecting unsaturated lipids in biological specimens which it achieves by reaction with their double covalent bonds, forming black derivatives.

Osmium tetroxide is a corrosive, volatile compound which is particularly dangerous if it enters the eye or is swallowed or breathed in. It is not explosive but will burn and a 'dirty bomb' based on this material would consist of an explosive mixed with OsO4. When this exploded those near at hand who had not been killed by the blast would suffer stinging eyes, mouths and nasal passages and the psychological effects would probably be greater than the physical. The general consensus is that osmium tetroxide would be rather ineffective as a bomb component (08/04/04).


Barely a week goes by without the media reporting some new relationship between diet and disease and often the comments are conflicting and never surface again. However, as there are so many reports, from time to time one would expect that something of importance would be uncovered!

The research disclosed recently at a meeting of the American Physiological Society which suggests that curry could protect Indians from Alzheimer's disease, may be a case in question.

Curried food, as everyome knows, contains a mixture of herbs and particular attention is being paid to the orange preparation from the tumeric plant which is rich in a compound called curcumin. Curcumin is a powerful antioxidant and anti-inflammatory chemical which protects rat nerve cells from oxidative damage. Oxidative damage is a natural phenomenon affecting DNA and other cell components which is believed to cause cancer and heart disease. The elderly inhabitants of Indian villages have the lowest incidence (less than 1%) of Alzheimer's disease in the world and consequently the question being asked is, " Does a diet high in tumeric provide protection from this serious neurodegenerative disorder?". The situation is unlikely to be simple and other compounds present in curry powders have similar properties to curcumin and therefore may have a role to play.

If nothing else, this report emphasises the fact that our foods contain a wealth of chemicals with highly potent drug-like activities which must be considered alongside commercial chemicals when considering the environment in which we all live.

PS And yet another story - Financial Times (23/04/04) - curcumin may be useful to treat the symptoms of cystic fibrosis! (23 April 2004)


The Bad Science column in The Guardian (26 August 2004) reported a BBC story in which it was said that waste wood chips had been converted to a fuel (to heat parts of a village in Powys in Mid Wales) which would produce no carbon dioxide. A very valuable fuel one would conclude, as it would not contribute to global warming! However, as most readers will know it would be impossible to burn any sort of wood, a mixture of carbon-containing organic compounds, without the production of CO2 :

C + O2 ----> CO2

On consulting the BBC website, there would appear to be confusion all-round. What it actually said was that a sustainable crop of trees to make the chips would absorb CO2 from the atmosphere (for photosynthesis) and the amount of CO2 released on burning the chips would be equal to that absorbed. Hence, the the whole process would not release additional CO2 for global warming.



The title of this report would, to say the least, seem to be obscure but if you suffer from mild breathing problems,chest pain, depression, irritation of the eye, ear, nose and throat, fatigue, headache, lack of concentration, memory loss and skin disorders, perhaps all at once, you might be diagnosed as having IEI! [IEI is also called Multiple Chemical Sensitivity (MCS), Environmental Illness, 20th Century Disease and several other things]. MCS perhaps best describes the condition or conditions, ie the apparent adverse effect of a chemical or a group of related or unrelated commercial chemicals on the human body which produces the often ill-defined symptoms listed above.

Chemo-Philia raises this topic in view of recent reports that air fresheners may be dangerous (The Times 19/10/04) and because of the ongoing campaign against perfumes which is mainly centered on the USA. Both news items, of course, relate to IEI.

"Idiopathic" refers to a disease of unknown origin and this applies to IEI the existence of which most of the medical profession denies - there is presently insuffcient evidence to confirm a relationship between the alleged causes and multiple symptoms. In some quarters, IEI is considered to be a psycogenic illness related to depression and stress. However, thousands of people (10% in the US?) claim to be suffering from exposure to synthetic chemicals and, in particular, fragrances in household products such as cleaning materials and in the products of the perfume industry. Surfing the internet does suggest that the subject is bathed in paranoia with many people who have unexplained symptoms making the most unlikely claims. In general, a single report on the internet that traces of a particular chemical may be associated with IEI symptoms is likely to lead to the establishment of a large focus group that demands the removal of this chemical from the environment - no matter how valuable it is to society! The call to remove all pollutants from the environment is, of course, an impossible task!

To return to a C-P 'chestnut', little or no attention is paid to natural chemicals as possible causes of IEI bearing in mind that plants alone produce more organic compounds in terms of numbers and mass than all global industries combined. Is it not possible, therefore, that some of these may give rise to the IEI-type symptoms? Most people would answer, "No. Natural chemicals are not suspect - only those produced by humankind!" Such beliefs seem to relate back to the early 18th century when the medical profession and many scientists believed that there was a magical side to organic chemicals and that they could only be synthesised with the aid of a 'life force' (Theory of Vitalism) which in turn could only be found in a living cell. This idea was overturned in 1854 when a chemist,Wöhler, synthesised an organic compound, urea, from an inorganic compound, ammonium cyanate, in vitro (ie in glass - a test tube or flask)! Organic chemicals are organic chemicals and there are no fundamental differences between those from anthropogenic and natural sources. Members of most of the chemical 'families' produced by industry are biosphere products ( many of which are volatile and fragrant!) and the natural world produces some of the most toxic compounds known to science - for example, the fungal mycotoxins (which are responsible for thousands of deaths in Asia every year) and the large numbers of plant alkaloids. There are undoubtedly many natural compounds which are readily tolerated by the vast majority of the population but adversely affect a small minority. In examining, further, the possible cause of IEI, if, indeed, such a condition exists, the possible role of biochemicals should surely be pursued. (29/10/04)


Antioxidants have been in the news this last week, ie those chemicals in foods and food supplements which protect the body from the very reactive free radical and other oxidants that are believed to cause cancer and diseases of the cardiovascular system. Oxidant formation is a normal body process although materials in the environment (eg tobacco smoke) can exacerbate the problem.

The Times (11/11/04) had a three-quarter page article mainly concerned with vitamin E, which is consumed in large quantities by the British public: many probably believe that the more antioxidant you consume the better the protection from oxidants and disease. This is not the case, however, and when taking vitamin E doses of 400 IU (International Units) per day - commonly the amount in one capsule - Johns Hopkins University researchers claim that there is a 10% risk of death compared with people not taking the supplement. It is doubtful whether healthy people eating a balanced diet need to take vitamin supplements: vitamin E is present in many green plant foods and in nuts and oils. In the same Times article warnings from the Food Standards Agency were given regarding excessive consumption of ß-carotene, manganese, nicotinic acid (niacin), phosphorus (this would be better described as phosphate - phosphorus even in small quantities, would be lethal!) and zinc.

A second report on antioxidants, entitled, "....the Italian enigma", appeared in the British Medical Journal (6/11/04). Quite unexpectedly it quoted an Italian study which claimed that pizza was good for you! Those eating two or more 200g helpings a week suffered more than 50% fewer heart attacks than those who consumed pizza occasionally. One reader who responded to this report said that the lowered risk was because Italians practised 'relaxed eating' the other said it was because of the lycopene content of the pizza. Lycopene, a constituent of tomato, is a powerful antioxidant. Chemo-Philia gave up eating pizza because of the calorie content but according to the BMJ pizza (Italian at least) is not particularly fattening (presmably it depends on the topping!). So, perhaps, it will again appear on C-P's menu! (12 November 2004)


The New Scientist (26 November 2004) reports on a joint French and Indian publication concerning the "Suicide Tree", so-called because it is associated with many suicides and perhaps murders, in India and South East Asia. The tree's Latin name is Cerbera odollam; it is sometimes referred to as the Odollam tree. The tree contains several poisonous chemicals but the major compound belongs to a chemical family known as the cardenolides or cardiac glycosides These are examples of steroids and the most well known cardiac glycoside is, perhaps, digoxin which in small amounts, is given to patients in heart failure: it stimulates the heart muscle and produces a stronger heartbeat. At higher levels digoxin can be lethal. If anyone wants to sound impressive they can use the 'proper' name for digoxin (which tells the organic chemist exactly what it is) ie:

(3β,5β,12β)- 3 -[(O- 2,6- dideoxy- β- D- ribo- hexopyranosyl- (1,4)- O-2,6- dideoxy- β- D- ribo- hexopyranosyl- (1,4)- 2,6-dideoxy- β- D- ribo- hexopyranosyl)oxy]- 12,14- dihydroxy- card- 20(22)- enolide

The major, related toxin in the Cerbera tree is cerberin; this 'heart poison' accumulates in the seeds of the plant and is not easily detected by forensic investigations. Up until the middle of the 19th century thousands of people a year were dying from Cerbera poisoning in Madagascar in the course of 'trials by ordeal'. (see Journal of Ethnopharmacology 95. 123-126 (2004)). If tribal members were accused of crime they would be forced or would volunteer to eat Cerbera seeds and if they survived (which was unlikely) they were aquitted!" (cf trial by fire or water in Europe). The fear is that the seeds are being used frequently as a poison and that murders by this route are going undetected.

Incidentally, oleander, a decorative shrub which is common in the warmer parts of the world (lining roads to airports, for example) is a member of the same family of plants (Apocynaceae) as Cerbera odollam. Oleander also contans poisonous cardiac glycosides in this case, in all parts of the plant. Anyone preparing a barbeque in California, for example, would not put oleander trimmings on the fire - the smoke is toxic (15 November 2004)


C-P spent 20 early years in a town which was engulfed in tobacco smoke. In the cinema the light beam from the projector had difficulty in reaching the screen, on the tops of double-decker buses the acrid fumes affected eyes, noses and throats and cigarette smoking was the way of life in all public places and most homes; the passive uptake of smoke should, therefore, have been very significant. Despite this, the information recorded on the grave stones in the cemetery do not suggest that the 'locals' suffered an early demise, in fact 70+ years was the expected date of death in this particular area of the country at that time.

Despite these personal observations, C-P has no doubts that active smoking, that produces thousands of biologically active chemicals, should be avoided . Even before World War II it was generally considered to be an unhealthy practice which was associated with hacking coughs and other 'chesty' complaints. However, the general public were not aware of a connection between smoking and lung cancer and cardiovascular disease at that time.

Why discuss smoking, now?

A publication in the British Medical Journal (9 April 2005) again raised the spectre of passive smoking: the title of the article was, "Passive smoking may kill 30 people a day". This was broken down to at least 1 person a week in the entertainment industries (bars, clubs,etc) and 200 in the home. Despite a comment by the Editor of the BMJ that these figures might be overestimated by two-thirds, some of the media accepted them at face value. This distortion may, of course, ensure that more people assign their domestic ashtrays, lighters and tobacco products to their garbage bins, which is good - but, nevertheless, it has to be said that media reports bent the truth - presumably to create concern and attract more readers.

All smokes from burning organic materials (including tobacco and the cigarette papers - not forgetting 'pot' (cannabis)) are potentially toxic and smoke from the burning end of a cigarette (sidestream smoke) and that which has been inhaled and then exhaled (mainstream smoke) contain similar toxic compounds. But, in the former, they are in higher concentrations which makes sidestream smoke potentially more dangerous than mainstream. However, to say that 200 people a week die in the home from passive smoking must at least be qualified by the word "may". Assuming that these alleged deaths arise from breathing in toxic gases then in addition to passive tobacco smoke, the home atmosphere contains gases from all sorts of sources including the furniture, carpets, foods, cooking processes, non-stick pans, etc, etc (confounders) . A very complex system making it difficult to detemine the exact cause of home deaths.

Returning to C-P's early home environment, the scenario described above in the first paragraph obviously requires a deeper investigation and there are several suggestions as to why the majority of the local population appeared to cope with the fug. The first one is that they did not - the information is retospective and, therefore, possibly inaccurate (ie C-P's memory is not what it was !!). Other reasons could include nutritional advantages and the healthy rural environment: it would be going too far to postulate that the population had a 'genetic advantage' but in other scenarios, genetics might have some bearing. One thing that should certainly be remembered is that information obtained from one statistical (epidemiological) study on a small sample should always be questionned. Regarding smoking, one often hears stories concerning people who smoked, say, two packs of cigarettes a day and lived to be nonagenarians. In a large population you would expect to find a few such people but the majority would succumb to far less tobacco smoke. (14 April 2005)

(16) 'POPE SMOKE'(A term borrowed from the USA!)

Chemistry is everywhere and C-P's colleague suggested that it might be interesting to find out what the Vatican used to make black and white smoke. The former, of course, is the signal used to tell the world that the Cardinals in the Sistine Chapel have cast their votes for a new Pope but there has been no consensus: the latter indicates that consensus has been reached. The details of this selection procedure are secretive as (as C-P found) are the modern methods used to make black and white Vatican smoke from the burning ballot papers!

The history of this ritual is interesting and includes in early times, burning the papers in a gun barrel in the Vatican and later, in a furnace which was eventually vented to the exterior because it was felt that the smoke would damage the internal art work. At some period, straw was added to the ballot papers to give the smoke colour but there is confusion on the Internet as to whether wet straw gives black or white smoke! Although C-P has not done the experiment, the former is likely to be correct.

Small, solid particles or liquid droplets suspended in a gas which scatter light are called aerosols, part of a family of materials called colloids. If the suspended particles are solid, the aerosol is commonly called a smoke. The appearance of smokes is a function of the size and colour of the particles.

If you are lost in the jungle with no specialised materials to hand to attract rescuers, survival manuals will tell you to put an oily rag (oil = hydrocarbons - compounds rich in carbon: see "Chocolate & Churches" 2004) on a fire to make black smoke and tree branches with green leaves to make a white smoke - presumably steam produces the white appearance ?)

Smokes intended for military use as markers or for concealment (smoke screens) are more sophisticated and are made by igniting mixtures of chemicals; to aid combustion a chemical rich in oxygen (an oxidising agent) is included ( eg KNO3 ; potassium nitrate). Hence, if an oxidising agent and an organic compound rich in carbon (eg naphthalene or anthracene) are ignited, the carbon particles produced from the burning organic component will turn the smoke black. Many formulations exist to produce white smokes - often they contain zinc dust. Ammonium chloride produces a white smoke; when heated it is converted to hydrochloric acid and ammonia:

NH4Cl <=======> NH3 + HCl

These gases then recombine to give a white smoke of NH4Cl particles.

Coloured smokes - green, red, violet, yellow, etc - are prepared by using organic dyes.

In conclusion, C-P has been unable to discover the secrets of 'Pope smoke' which was said to be undergoing improvement using "chemicals". This improvement was obviously not significant as at the recent conclave, and not for the first time, the public were unsure, initially, whether the smoke coming from the Vatican was white or black. Why not change the sign of success to red smoke by adding rhodamine B to the burning ballot papers? (22 /4/05)


Many people, including some chemists, were probably unaware that in addition to gunpowder (which many small boys once made!) an effective explosive can be made (but should never be attempted!) in a kitchen or garden shed using household materials. C-P refers to media reports which claimed that acetone peroxide (Triacetone triperoxide or TATP) had been found in the house of one of the '7/7' London bombers. Whilst realising that a description of TATP would be better placed in a site labelled "Chemophobia", C-P felt that there would be some interest in knowing something about the material that, because of its instability, has been called "Mother of Satan".

"Acetone peroxide" has been known for many years; it was first made in 1896 by a German chemist, R. Wolffenstein - but what is it?

Its proper name, 3,3,6,6,9,9- hexamethyl- 1,2,4,5,7,8- hexaoxacyclononane, may not be helpful but to know that it is an example of a peroxide, is. All peroxides are potential explosives and are characterised by the presence of one or more peroxide groups:

– O – O –

A simple peroxide is hydrogen peroxide:




This is a commercial product with many uses - in dilute solution as a disinfectant, a bleaching agent, an insecticide, etc - but in concentrated solution it will explode when heated or shaken. Incidentally, hydrogen peroxide is also a natural compound which occurs in all living organisms where it can be both useful, eg by killing invading microorganisms, and harmful, eg by attacking body proteins.

The practical organic chemist, early in training, learns of a second, more dangerous peroxide which he/she may easily encounter. This is diethyl ether peroxide produced slowly from diethyl ether:


Diethyl ether

when the latter is exposed to air (oxygen) and light. The chemical nature of this peroxide seems to be in doubt. It is probably a mixture of compounds with the major component having the following structure:


This compound is a relatively high boiling point, explosive liquid which is likely to be found as a contaminant in diethyl ether that has been stored for long periods. The ether is a common laboratory solvent used, for example, to separate 'fatty materials' (lipids) from ether insoluble/water soluble compounds. Having carried out the extraction, the ether is then evaporated off by heating which leaves the higher boiling point 'ether peroxide' behind. Continued heating of the peroxide causes it to explode - violently! Simple tests are available to see if the peroxide is present and if so, it can readily be removed .

The acetone peroxide (TATP) structure is based on another common laboratory solvent, acetone (aka propanone) which belongs to the ketone family of chemicals which all possess a carbonyl (aka an oxo) group:


Acetone has the structure:


and TATP is composed of three acetone molecules linked together in a circle (a cyclic compound) by three peroxide bonds ie:

(Structures by ACD/ChemSketch Freeware)

The molecule is a good example of an explosive as it possesses parts that are very inflammable containing carbon and hydrogen (the hydrocarbon structures derived from acetone), and plenty of oxygen to support rapid combustion. A simple equation shows how this combustion occurs with the production of lots of vapour/gas (and not shown - heat !) :

2 C9H18O6 + 21 O2 ---> 18 H2O + 18 CO2

[But see the PS below]

Pure samples of TATP are said to explode in response to shock, heat and friction and its instability makes it difficult to employ as an explosive. It degrades on long-term storage. (27 July 2005)

Postscript: Chemo-Philia has just learned from a reader that earlier in the year, a revised mechanism for the decomposition of TATP was published (Journal of the American Chemical Society 127, 1146-1159 (2005)). A multinational group of scientists believe that TATP does not just burn rapidly as surmised above (as is known to be the case with many explosives) but that it has a stressed structure, somewhat akin to a compressed spring, which is the cause of its sensitivity and immense explosive power . This results in the breakdown of one peroxide bond (O—O) to form reactive free radicals and further stresses the remaining peroxide bonds setting off a chain reaction which breaks these bonds and releases acetone . The latter, therefore, does not initially serve as a fuel as originally believed, but in TATP controls the shape of the molecule and raises its potential energy which can be released, for example, in response to heat or shock (9 August 2005)


The news that GM peas that had been fed to mice caused lung inflammation has allowed environmentalists all over the world to say, "I told you so"! This was sad for the Australian scientists who had spent a lot of time trying to develop a hybrid pea which would resist weevils, the scourge of field pea crops. Their approach was to introduce a gene from beans which would direct the synthesis of an amylase inhibitor in the pea. This is a protein that we regularly consume without harm when we eat beans but it can kill weevil larvae. This animal needs to be able to feed on starch when it invades a pea seed and to do this it must first digest it using an enzyme called amylase which the larva produces in its gut. However, if the amylase inhibitor is present, starch breakdown is prevented and the larva will die of starvation.

The fact that GM peas are mildly toxic to mice does not necessarily mean that they would harm human beings. However, as a precautionary measure, the hybrid has been destroyed and the hunt goes on for a safe GM hybrid to control a pest which can result in huge losses (up to 30%) in pea crops.

The good news is that the stringent testing of all GM products is working well. C-P does wonder what the outcome would be if such tests were applied to 'conventional foods'! (28/11/05)


In future, daffodils, the Welsh national flower, growing in the Black Mountains area of Wales may not be intended for the vase or the buttonhole but for the pharmaceutical industry (The Times 29 November 2005). The bulbs of these plants contain the valuable drug galanthamine (aka galantamine). Chemically, this compound belongs to the large family of naturally-occurring, plant alkaloids and like many other compounds in this group, it has powerful pharmaceutical properties. First and foremost, it is an cholinesterase inhibitor and can therefore be used to regulate the activities of nerve cells (neuron(e)s).

Electrical signals to and from the brain are carried by a complex sytem of linked neurons. Chemical signals are also required so that the electrical impulses can be passed across the very small gaps between the neurons in the network. The chemicals which bridge these gaps are called neurotransmitters one of which is acetylcholine (ACh):

CH3CO - O [CH2]2N+ (CH3)3

The electrical signal passing down a neuron reaches the end of the cell and releases ACh into the gap separating it from the next neuron in the chain. The neurotransmitter induces changes in the concentrations of electrically charged sodium and potassium ions in this second neuron and, hence, sets up a new electrical impulse. This again travels down to the end of the cell and releases ACh into the second gap - and the process continues.

It is important that the concentrations of ACh in the gaps rise in response to the oncoming electrical signals and then fall when the signals have passed to the adjoining neurones. Without this wave-lke variation in concentration the passage of the impulses through the network would be disrupted. To lower the concentration of ACh in the gaps following the passing of the impulse, the enzyme acetylcholinesterase (AChE ) is used to destroy the excess ACh by rapidly removing its acetyl (CH3CO -) group. This vital process can be interrupted by chemicals called acetylcholinesterase inhibitors which prevent ACh molecules from binding to AChE. Some nerve gases such as sarin and agent VX , so-called 'weapons of mass destruction', act by completely inhibiting the esterase so that ACh levels build up throughout the neural network and all nerve impulses are blocked with fatal consequences.

However, AChE inhibitors such as galanthamine, in small quantities, can be put to good medical use where there is an ACh deficiency. Such is the case with Alzheimer's disease (6 December 2005)


Two Australians were recently surprised to find a 15kg "stone" on a Queensland beach which was valued at the equivalent of £165,300. The "stone" turned out to be the highly prized chemical (or rather mixture of chemicals) called ambergris, a name derived from the French for 'grey amber'. Amber itself is a natural plant product, a fossilised resin, whereas ambergris is a product of the sperm whale. It is a complex fatty substance produced in the whale's intestine which appears to protect this organ from damage by items in the whale's diet such as the sharp beaks of giant squid. It would seem that ambergris is indigestible and the whale disgorges it and as a fatty substance with a density lower than water, it floats away and is eventually washed up on a beach. During the time it is exposed to sunlight and air the original chemical structure is broken down to a number of smaller molecules and its odour changes from something which is repulsive to a smell which most people find attractive. As such it is used in the perfume industry but its main function seems to be to increase the length of time that other odourants in perfume remain agreeable.

There are reports that a major constituent of ambergris, ambrein, stimulates the sexual behaviour of male rats but there are no reports that it is a human aphrodisiac!

If readers wish to become rich overnight it is best that they comb the beaches in the tropics/subtropics - Barbados seems to be a good place to start. However, global warming may improve the prospects of Northern Europeans operating in their own backyards. Few things are all bad?! (31/1/06)

(21) IT'S ALL RHUBARB! (24 March 2006)

The Times newspaper (9 March 2006) and several food outlets recently described how rhubarb, a vegetable which was very popular in the early 1900s, was again in demand to make puddings which C-P remembers enjoying as a child and also eating raw, young, rhubarb stems - having first and necessarily dipped them in the sugar bowl!

Rhubarb on display in the local supermarket should therefore sell well but not attract particular attention. Compare this with an adjacent display of, say, genetically modified corn (GM corn in a supermarket is at present a theoretical concept, of course!) which is clearly labelled "GM" with details of the exhaustive analysis of the product. In the present anti-GM climate, the latter item would with media aid, be likely to create public paranoia. This difference in attitudes is really ironic and it is clear that the precautionary principle (which in this case is widely interpreted as, "Eat nothing that might harm you") is not being applied equally across the board. Those who fear GM foods should be careful to check on the, so-called, conventional foods. Any number of references to poisonous plants will tell you that rhubarb is toxic! The National Institutes of Health in the US, for example, state that rhubarb can cause a lot disturbing symptoms which include body weakness, difficulty in breathing, nausea, vomiting, coma and (rarely) death. Surely, this should be banned if the precautionary principle is applied? Few, of course, will have known anyone who has ever been poisoned by rhubarb which can also be said with some certainty about GM foods. The risk we all take when eating rhubarb is that we could consume the green leaves which contain most of the poison which is a simple organic compound, oxalic acid:


We do not normally eat these leaves because they are intensely acidic - but we might. Children have been known to eat and drink the most obnoxious things! Something to think about? (24/3/06)

(22) "AO MEI DING!"(6 June 2006)

The Times newspaper (31 May 2006) suggests that the Chinese heading, above, can be translated as "Amaziing Gel" and if the report regarding this material is accurate, then it will provide more valuable ammunition for 'chemophobes'.

Apparently, hundreds of thousands of women in China have received injections of a polymer called polyacrylamide hydrogel ("Amazing Gel") to produce breast enlargements. Unfortunately thousands are now having to have the material removed as it is migrating around the body causing a number of medical problems including infections and discoloured lumps which sometimes necessitates breast removal.

Chemo-Philia is not sure of the exact composition of this particular gel but as a polyacrylamide derivative, one might well expect that it would be risky to use it for internal medicine..

Polyacrylamides in general are synthesised from acrylamide which has the following structure:


This is then polymerised by a strong oxidising agent to give polyacrylamide, a long chain of repeating acrylamide units:


Furthermore, individual polyacrylamide chains can be chemically cross-linked to give a porous structure with the degree of cross-linking determining the size of the pores. In the latter form, the gels are extremely important in biochemistry for separating mixtures of large protein molecules in an electric field (electrophoresis). The method has valuable applications in biology and medicine and before the advent of polyacrylamides, such separations were extremely difficult if not impossible. Polyacrylamides are also widely used in the construction industry and in agriculture. For example, they are employed as pesticide additives and to stop water erosion of soils, to clarify water and to seal leaky irrigation ditches.

Acrylamide, the precursor of the gel, is a well known toxic compound which may cause cancer and is certainly a neurotoxin (a nerve poison). Polyacrylamide itself in the laboratory, is treated with respect but is normally believed to be non-toxic. Crude polyacrylamides, however, may contain traces of acrylamide (was this the problem in China?) and heat and light are said to release acrylamide from the polymer although this degradation process is controversial.

Some scientists have noted this latter possibility and believe that the widespread industrial use of polyacrylamide may be the cause of the acrylamide contamination of foods. (NB This contamination is generally believed to be caused by high temperature cooking procedures and the reaction of sugars with amino acids. (See ARCHIVES: "Poisonous Bread....." (25 April 2002) and "Now We May Know...."(8 October 2002)). (6/6/06).

(23) IN THE NEWS - STINGRAYS! (6 September 2006)

This week's tragic accident again reminds Chemo-Philia that if you are looking for dangerous chemicals the best results can be obtained by 'going natural' and in this case it was into a warm marine environment.

The person in question was of course Steve Irwin the Australian "Crocodile Hunter" who entertained many and upset others with his expeditions into the wilds where he handled huge numbers of dangerous animals. Steve was killed rather unexpectedly by a physical blow to the chest from a stingray's spine or 'stinger' which penetrated his heart. These flat fish carry a fin spine or several fin spines (depending on the species) on their backs near the tails, which can be used to ward off predators such as sharks. Some spines can be up to 30 cm in length and provide the animal with a formidable weapon which can be deployed by an upward swing of the tail.

To make the connection to dangerous chemicals, the stingray can wound and kill by physical means and/or by employing neurotoxins (also called venoms - which target the nervous system) and are produced from cells which cover the spine. This venom appears to be poorly defined. but probably contains several proteins some of which are hydrolytic enzymes which destroy important cell constituents. This produces constriction of the blood vessels and lowering of the blood pressure and a number of other potentially lethal symptoms. The intense pain caused by the venom can be alleviated by applying hot water (45oC) to the wound. Most references say that the water is effective because it destroys heat-labile proteins in the venom but this may be incorrect as, in vitro, much higher temperatures than 45oC are needed to destroy them. Interestingly, applying a 'meat tenderiser' such as papain from the kitchen, to the wound may be helpful as a way of destroying the offending proteins. There is no specific antivenoms for this toxin as there are for many snake and spider venoms.

The powers of the stingray spines were known as early as 29 AD when they were ground to make a powder which was used to treat toothache!

About a thousand different marine organisms produce toxins when aroused so it may be best when next you paddle to wear thick boots! (6/9/06)

(24) Toxic Chemicals Influenced the Greeks (1 November 2006)

The Times (24 October 2006) reported research from Greece which suggested that the prophecies that came from the Oracle of Delphi via a priestess or Pythia, may have been influenced by chemical pollution.

It is alleged that the Oracle often provided obscure information and that the Pythia was in a trance both of which are not surprising as she was suspended over a large hole which penetrated to a great depth into the earth and apparently emitted volcanic gases. According to the Greek scientists the gases included:

Carbon dioxide (CO2) - an asphyxiant (causing suffocation: NB 1600 people were killed in 1986 when CO2 escaped in large amounts from the bottom of Lake Nyos in Africa). The gas also has toxic properties at high concentrations

Ethanol (aka ethyl alcohol, alcohol; CH3-CH2-OH) - no further comment is really needed!

Methane (CH4) - another asphyxiant which will prevent oxygen from reaching the blood cells;

It was also alleged that there was a sweet odour associated with the Oracle; this may have been ethylene (aka ethene; CH2==CH2) a gas which is a mild narcotic which also would have affected the output of the Pythia. No ethylene appears to be present in the volcanic gases today, however.

An additional factor which would not have improved the performance of the Pythia was that she is thought to have sniffed hallucinogenic herbs and chewed laurel leaves. The latter when damaged produce cyanide so one assumes that the priestess did not eat too many! (1/11/06)

(25) Chemtrails (12 December 2006)

Chemo-Philia has belatedly unearthed a large nest of chemophobes which can be contacted by entering the word 'Chemtrail' in the Google search box. This could be an entertaining activity which would occupy the whole of the Christmas break!

To be fair, C-P has only skimmed through the literature on this subject but if it is to be believed, then, perhaps, living near to an airport might constitute a hazard, not from crashing aeroplanes but from the chemicals that are deliberately pumped out of planes into the air, for unknown, devious purposes. It has been suggested for example, that governments are attempting to control the weather and are assessing biological weapons including those for mind control.

Chemtrails are not to be confused with contrails - the water that condenses from aeroengines at high altitudes. Chemtrails are said to have a different appearance from contrails. Furthermore, some believe that they are associated with strange human disorders such as Morgellons disease which presents as a skin condition where the tissue contains fibres which might come from the atmosphere.

Read Wikipedia for a concise, rounded discussion of this phenomenon (12/12/06)

(26) Alcohol - Not all bad? (29 March 2007)

A re-classification of drugs was reported by the media (cf The Times 23 March 2007) in which alcohol was rated as only slightly less dangerous than heroin and cocaine and more dangerous than ecstasy and cannabis.  The re-classification was based on the physical and social harm that drugs cause and how addictive they are. In this context the word “alcohol” must refer to alcoholic drinks which are, of course, not pure alcohol/ethanol but a complex mixture of chemicals. (Strictly speaking the word "alcohol" refers to a family of organic chemicals possessing one or more hydroxyl (-OH) groups but it is commonly used to mean one specific alcohol, ethanol (CH3CH2OH) or drinks containing ethanol. For "alcohol" below read "ethanol")

The main difference between alcohol, as normally consumed in the form of  beers, wines and spirits, and the other drugs is that the latter, apart from a short-term feeling of well-being, offer no benefits to the consumer whatsoever, either in small or large doses. They are in fact, all harmful.

Alcoholic drinks often contain vitamins and micronutrients including antioxidants that are believed to protect from some cancers and cardiothoracic disease.  Red wine is one of the richest sources of antioxidants and there is now general agreement that the consumption of wine and probably other alcoholic drinks, in moderation, provides significant health benefits.  Furthermore, alcohol itself, unlike the other drugs that have been considered, could be classed as a food.  It provides the body with kilocalories/kilojoules, energy at a level which is somewhere between carbohydrates and fats.  In this connection, excessive amounts of alcohol are often associated with obesity.

Alcohol has inadvertently been part of the natural diet for as long as human beings have consumed plant foods. This may relate to the high levels of alcohol-destroying enzymes (alcohol dehydrogenases) that we have in our body tissues, particularly the liver.  They protect us!

Most plant tissues contain fermentable carbohydrate (glucose, sucrose, etc) and when the tissue ages or is physically damaged, microorganisms can produce ethanol from these carbohydrates. Relatively large amounts of ethanol are produced when some fruits such as apples, begin to deteriorate.  Overripe fruits can intoxicate birds and insects. Any human foods that have been produced by a fermentation process may contain alcohol, eg bread– but in this case most of it will have been removed by the baking process. However, there are early reports from Canada (1920s) of bread that contained approximately 2% ethanol - at a time when  North Americans were concerned with alcohol prohibition laws! Obviously, the alcohol content will vary according to the dough-making and baking conditions

Having criticized the re-classification of drugs, it is best to leave the subject on a note of caution. Alcohol in large doses is undoubtedly one of the most harmful of the addictive drugs!

(29/3/ 07)

(27) Another Probable Human Carcinogen ! (3 May 2007)

It will soon be possible for food miserabilists to argue that bread and wine, two of the earliest items on the human menu, are unfit for consumption.  The same applies to other foods which have been subjected to a fermentation process!

The culprit that has been resurrected and reclassified as a Group 2A human carcinogen – a probable carcinogen – by the World Health Organization, is ethyl carbamate (aka urethane):


a compound originally listed as a Group 2B carcinogen – a possible human carcinogen – which  is formed when urea and ethanol (two naturally occurring compounds) are mixed, particularly at elevated temperatures.

H2N-CO-NH2  + HO-CH2-CH3 ------>  H2N-CO-O-CH2-CH3  +  NH3

 Urea is derived from the breakdown of the natural amino acids, arginine and citrulline by yeast, a fermentation agent :


H2N-CO-NH- (CH2)3-CH-(NH2)-CO2H

Ethyl carbamate, is not acutely toxic - it is used as an anaesthetic – but in high doses, it is carcinogenic in rodents.  There are no studies which clearly suggest that it is responsible for human cancer.

The fear of bread has presumably been exacerbated (in California at least) by the State’s Attorney General’s Office insisting that baked potatoes, chips and crisps from fast food restaurants be labelled with a cancer-warning.  The problem here is the carcinogen, acrylamide:


which is produced in high temperature cooking procedures and is also found in bread   However, once again, there is no direct evidence that acrylamide is a human carcinogen.

Will the ‘food activists’ continue along this pathway, employing the precautionary principle as they go? Arguably, all foods should be labelled as dangerous; most contain carcinogens as well as other poisonous compounds.  However, Chemo-Philia will continue as before remembering that ‘the proof of the pudding is in the eating’! (3 May 2007)

(28) The Smallest Chunk of Ice (13 August 2007)

Water, H2O (or dihydrogen monoxide – an accurate name but rarely used except in humour cf is one of the simplest but most important chemical structures on this planet. Without it, life as we know it, would not exist.  Despite its molecular simplicity much remains to be discovered about its structure.

Perhaps the most important thing to know about liquid water is that, normally, the molecules do not exist in the monomolecular form, ie as isolated H2O molecules. If it did, much of the 326 million cubic miles (or 1360 million cubic kilometres) in the oceans, rivers and lakes would leave the surface of the earth, as monomolecular H2O is a gas.

A water molecule with its angular structure is polarized with small (partial) electrical charges (Fig.1.).
The water molecule has this basic geometric structure

Fig.1 Polarized water molecule
Adapted from Wikipedia (

(To explain this, imagine that the two chemical bonds between the hydrogens and the oxygen are negatively charged clouds equivalent to two electrons each, then electron attraction by the O will make the density of the cloud near to this atom greater than it is in the vicinity of the hydrogens.  In other words, the O now carries a partial negative electrical charge leaving the hydrogens with a partial and balancing, positive charge.  It is important to emphasize that these are partial charges, as indicated by the Greek letter ‘δ’ (delta) placed before the + and – signs.  The signs without the deltas would indicate full electrical charges which would result if a whole electron was gained or lost, as is the case when water ionizes:

H-O-H  --------> H+   +  OH-

Here, one O–H bond breaks leaving the hydroxyl radical (H-O) with an extra electron and a full negative charge and the H without an electron and, hence, a full positive charge).

The polarity of water molecules causes them to aggregate with the positive side of one molecule being attracted to the negative side of another.  This attraction between molecules is shown below (Fig.2), and the attachment links are called  hydrogen bonds.

Snapshot from a simulation of liquid water. The dashed blue lines from the molecule in the center of the picture represent hydrogen bonds.

Fig.2. Water molecules (Red O; Grey H) linked by hydrogen bonds (- - - -)
Adapted from Wikipedia (

The H-bond which is an important structure in many biological molecules, is a very weak bond which readily breaks and reforms and in liquid water, hundreds of water molecules can aggregate together in this way in a dynamic structure which is continually changing. In solid water, ice, there is extensive hydrogen bonding with large aggregates of molecules and in water vapour (steam) where the molecules are relatively far apart there is less tendency for H-bond formation and monomolecular water will be present.
There have been claims that liquid water can occur in several different, stable forms suggesting different degrees of hydrogen bonding.  In the 1960s it was reported that water could exist as Polywater which was syrupy and had a higher boiling point and lower freezing  point than conventional water  Eventually it was shown that these unusual properties were caused by impurities.  There is also Pentawater  which is manufactured by treating water with high energy sound which is said to convert the large hydrogen-bonded molecular aggregates into smaller ones.  It is claimed that Pentawater has useful medical properties although more investigations are required to substantiate these claims

Recent work by German and UK scientists has shown that at very low temperatures (approx -268o C) the smallest possible ice crystal with six water molecules H-bonded together can form (see Fig.1):

Fig. 3. “The “smallest particle of ice” - a water ‘hexamer’ Published with permission from University College, London

Using a special microscope, the individual water molecules can be seen (as blue spheres in Fig. 2) with different spacings between them suggesting that the H-bond strengths are different.  The ‘hexamer’ was the smallest particle seen but clusters of 7, 8 and 9 molecules of water were also observed. (13/08/07).

(29) Practical Grossology?

Although this has little to do with chemistry, Chemo-Philia felt that an article in the newspaper, Metro (1st November 2007), was worthy of mention particularly as Christmas approaches and C-P, just a few days ago, had covered a topic related to that in the newspaper..

In the C-P discussion of  C. difficile treatment (Grossology, 29th October 2007) it was said that the use of faeces as a medication was really a practical demonstration of ‘grossology’, the term used to describe the method of teaching science to children by reference to ‘gross (some would say ‘revolting’) ‘biological  items’!

It now appears that it will be possible to buy ‘gross items’ in the form of cuddly toys as Christmas presents (see  They include soft toys named Ebola, Syphilis and Malaria and toys relating to the ‘bugs’ which cause ‘bad breath’ and ‘athlete’s foot’. In addition to the common names, politically doubtful nicknames are given to these organisms as well as proper Latin names and some details of their impact on human beings.  Conclusion?  Education with humour for the budding scientist! (6/11/07)

(30) Human Foods may not be a Dog’s Best Friend (14 March 2008)

We still have a lot to learn about food chemistry in terms of what’s good for you and for your pets and why.

Chemo-Philia  was interested to read of the many foods that were recommended for humans that could prove fatal for dogs.  In contrast, most if not all foods recommended for dogs (provided they are not contaminated with microbial pathogens) would be tolerated by humans.

Large amounts of  fruit cake can be lethal for dogs and it is the currants and sultanas in the cake that are responsible for the problem .  Indeed, grapes and any product derived from them can cause canine kidney failure.  Why this is so appears to be unknown:  these foods are a recommended source of antioxidants for humans.  An unrelated plant material that might also be included in a fruit cake recipe is macadamia nut.  This would make the cake even more toxic for dogs. Why?  Again, we don’t know!

Similarly, the toxic effects of members of the Allium (onion) family on dogs are not well understood. Garlic, leeks, onions and shallots (and even chives) should not be fed to these animals in large amounts.  The edible parts of these plants are packed with sulphur-containing compounds which are probably there to defend against agricultural pests.  However, in humans they appear to protect against cancer, heart disease, infections and a myriad of other complaints in ways that are still largely a mystery.  One or more of these compounds appears to make the red blood cells (erythrocytes) of dogs fragile and haemolysis (the loss of oxygen-carrying haemoglobin) occurs.  Haemoglobin also becomes bound to sulphur.

The response of dogs to chocolate is better understood.  The toxic component in this case is the alkaloid, theobromine, which comes (along with caffeine) from the cocoa

(formula from Wikipedia:

Theobromine affects the central nervous system of dogs and raises blood pressure and rate of heart beat. In man it is effectively destroyed by the liver which seems not  to be so in the case of the dog. The LD 50 (the dose which is lethal for 50% of a population of animals) varies significantly with theobromine.  For man it is calculated to be 1000mg/kg (ie a massive amount of chocolate – in the region of 6kg for the average man) and for dogs only 300mg/kg.

Animal tests remain as a major method for assessing the toxicity of chemicals -  it is difficult to see, for example, how a drug with multiple effects on living cells can be examined in any other way.  However, the differences between species which are illustrated above shows that there is a need to be cautious when extrapolating from one to another.  In the majority of ways the chemistry of one mammal is likely to be similar or the same as that of another.  However, in some cases there may be significant differences in the ways two species metabolise particular compounds. (14/3/08)

(31) Flowers don’t smell as good as they used to! (21 April 2008)                                      

In general, ‘commercial flowers’ such as carnations and roses have lost their smell.  Few would argue otherwise and many would say that in breeding for flower size and colour other characteristics such as fragrances have been inadvertently lost.

However, another reason for the loss of flower fragrances has recently been reported (see The Express 28 March 2008) which could have serious environmental consequences.  The study in question was carried out at the University of Virginia in the USA and in essence suggests that bees and other pollinating insects in some environments may not be able to detect flowers by their scents.  In these cases the flowers are producing volatile, fragrant chemicals but they are being destroyed when they enter the atmosphere by pollutants such as ozone (O3) and free radicals (aka radicals)The latter are highly reactive chemical structures;  eg the hydroxyl radical, which can be formed from water thus:

H : O : H   ----->     H*    +    * O : H

Note that in water, the two hydrogen atoms are linked to the oxygen by two single covalent bonds which consist of  pairs of electrons (:).  When one of these bonds (on the left) is broken (by ‘homolysis’) one of the electrons stays with the hydrogen (H*) and one with the hydroxyl group (*OH) forming hydrogen and hydroxyl free radicals, respectively. Chemical structures such as these with unpaired electrons are unstable and  extremely reactive and regain their paired electron structures by reacting rapidly with other molecules, eg a hydrocarbon (RH), close by, eg:

R : H  +  *O : H  ----> R* + H : O : H


The new radical (R*) that has been formed can now react with another molecule starting a ‘chain reaction’ which is characteristic of radical reactions.

If atmospheric pollution is present free radicals and ozone (a strong oxidising molecule) react and destroy the structures of  flower fragrance molecules – molecules such as linalool, β-myrcene and β-ocimene.  (These compounds belong to a large family of chemicals called terpenes which, in turn, are composed of one or more molecules of isoprene:

CH2==C(CH3) --CH==CH2

The study showed that as a result, fragrance molecules in the field were not spreading so far from the parent plants as they would have in the absence of pollution. The difference between the two situations could be of the order of 100s of metres (dependant on the weather conditions) with bees and other insects, therefore, having less success in targeting the flowers.  Hence, plants requiring insect pollination in order to produce fruits and seeds would be harmed.  Many years earlier than this present study, it was clearly demonstrated that atmospheric pollutants could also damage the internal chemistry of plants, a double whammy for agricultural practices.(21/4/08).

(32) Dietary Advice (2 June 2008)

As a nation we are inundated with dietary advice – 5 helpings of fruit and veg a day, 21 units of alcohol (male maximum) a week, 7g (max) of salt a day and just recently, 3 mugs of cocoa (special – high in antioxidants) a day - to improve impaired arteries!  C-P could go on! As well as the official advice, we now have ‘small screen’ celebrities jumping on the dietary bandwagon and, all in all, many of our fellow citizens must feel confused and, perhaps, persecuted.

The question of salt (sodium chloride; NaCl) intake was addressed by the media last month when workers in the Albert Einstein College of Medicine in the US added to the confusion by reporting that too little salt is equated with cardiovascular disease! This was announced in the face of the many organizations which try to reduce salt in the diet as well as many food manufacturers who have or are intending to ‘de-salt’ their products.

The studies in the USA which suggest  that less than 2g of salt a day may be harmful will need to be confirmed by independent studies.  However, one can begin to understand these results by appreciating that sodium is involved a wide range of biochemical reactions and is absolutely essential for all living cells. At some level of NaCl (the main external source of sodium), therefore, life processes must fail, .  Defining this level is difficult because it will be determined by, amongst other things, the physical activity of in this case, the human being, and his/her genetic make up.

Although sodium levels in the body can be reduced to a dangerous level, eg by excessive exercise, the main attention in medicine is the consumption of too much salt rather that too little.  Excessive salt in the diet is linked with high blood pressure (hypertension) and heart disease (see: and this is exacerbated if it is accompanied by kidney disease which reduces the body’s ability to rid itself of salt. There is also a condition called salt-sensitive hypertension where an individual’s blood pressure shows an exaggerated rise in response to salt.  The consensus of opinion does favour a general, positive relationship between salt and hypertension although not all support this idea (see: and reach your own conclusions).

As generally believed, we have all evolved from an aqueous environment which was presumably ‘salty’, and one would expect the body to be well adapted to gaining and removing sodium in order to regulate  metabolism. This appears to be true for healthy people who may well be able to cope with dietary salt levels in excess of what is normally recommended.  Again, however, there must be levels which ‘swamp’ the body’s mechanisms for salt removal but there will be individual variations. 

In summary, there are upper and lower levels of dietary salt intake but in reality these will vary from individual to individual.  The RDA (recommended daily allowance) figure for the upper limit (7g a day) is for general guidance. However, some members of the public may well believe that the lower they go below the RAD the healthier they will be! This is clearly not the case and in view of the Albert Einstein studies, it might be advisable for an adult to take note that perhaps 2g of salt a day may be excessively low.

Official attempts to govern the intake of components of a population’s diet may run into difficulty and the dietician’s highly unpopular hamburger could be a life-saver in some situations! (2/6/08).

(33) We have Ways and Means of Discovering where you’ve been! (13 June 2008)

Forensic science (the application of science to legal problems) relies heavily (you could argue totally) on chemistry for  progress.  In particular, very accurate and irrefutable chemical analysis is at the core of forensic science.  Much of this analysis is concerned with the identification and quantitative assay of elements and compounds found at the scene of the crime including more recently the identification of DNA. Now, some forensic scientists have turned to the analysis of chemical isotopes  to help with criminal investigations.

Chemo-Philia has discussed isotopes on a previous occasion (“Eat isotopes to live longer”;  4th April 2007) but to recap,  isotopes are closely related forms of an element with different neutron contents and, hence, different relative atomic masses .  More than 3,500 isotopes are known.  For example, in the simplest case, an atom of the most abundant form of the naturally-occurring element, hydrogen (H), contains 1 proton (heavy and positively charged) and 1 electron (light and negatively charged) giving a relative atomic mass of 1 and an electrically neutral atom, designated, 1 H.    Hydrogen can also exist naturally in another isotopic form, 2H  (aka deuterium;  D) where in addition to the proton and electron found in 1H,  a neutron ( heavy but not charged) is also present.  This isotope therefore has a relative atomic mass of 2.  The chemical properties of 1H and 2H are identical but because the latter is double the mass of 1H the rates of reactions of the two forms are different.

In the case of the element, oxygen (O)composed of more complex atoms, several isotopes exist. The most abundant form of O has a relative atomic mass of 16 and is composed of  8 protons, 8 neutrons and 8 electrons.  The other naturally occurring isotopes of oxygen are 17O and 18O of which the latter is the most common and is equivalent to 16O plus 2 additional neutrons giving a relative mass of 18.

All of the isotopes listed above are stable and naturally-occurring, others such as 14C and 32P are unstable (aka radioisotopes) and usually not naturally-occurring;  they decay by the loss of radiation.  (A few radioisotopes are naturally-occurring as their rates of decay are extremely small  eg 238Uranium, 4.5 x 109 years, and 232 Thorium, 1.4 x 1010 years).

Isotopes have many scientific, medical and industrial uses.  In chemotherapy for example, tumours are destroyed by high energy radiation (γ-radiation) emitted by 60Cobalt and isotope radiation is also used widely to examine systems as diverse as water flowing through pipes to the metabolism of food molecules in the body.  In archaeology the decay of isotopes provides information about the age of materials.

Hair has been a target for forensic scientists for many years.  Criminals have been identified from microscopic analysis and more recently from the analysis of the DNA found in hair roots.  Hair which can grow at an approximate rate of 1cm per month can hold the ‘chemical history’ of its owner – for example, the drugs and the metals that he or she has encountered.

The analysis of the stable isotope content of hair is now being used to establish in what location in the USA a person has been living.  This information is derived from the fact that:  (i), the hydrogen and oxygen in drinking water (H2O) are incorporated into the chemical structure of  growing hair and (ii), drinking water from different geographical areas contains different proportions of hydrogen and oxygen isotopes. For example, the two ratios, 2H / 1H and 18O /16O  in water are both high  in the south-east corner of the USA and low in the western half of the country.  The ratio differences are large enough to distinguish between general geographic areas such as Texas and Utah but do not show exact locations where the suspect or the victim had drunk water.

Water from different locations clearly does have different isotope ratios.  For example, the ratios in seawater, polar ice and atmospheric water vapour are all different.  Furthermore, when seawater evaporates to form clouds and then rain the
18O / 16 O ratio decreases – ie  the rainwater is enriched  with 16O.  This can be explained by the lighter isotope of water evaporating more rapidly than the heavier.  This situation, often referred to as isotope fractionation, over a large land mass is obviously complex involving the physical properties of the water, temperatures and probably other factors. (13/6/08)

(34 ) The Smallest of Parasites (13 August 2008)

“So, naturalists observe, a flea
Has smaller fleas that on him prey;
And these have smaller still to bite ’em;
And so proceed ad infinitum”

This verse from a poem (Rhapsody) by Jonathan Swift provides a very suitable introduction to breaking news from the virus world.  It is not clear how much Swift knew about conventional science but he did venture into exotic science fiction. For example, in Gulliver’s Travels he described “a project for extracting sunbeams out of cucumbers, which were to be put in phials hermetically sealed, and let out to warm the air in raw inclement summers”. The verse suggests that Swift was at least aware of parastism and he tells us that ‘parasites have parasites that have parasites’ which is a truism but within limits which are still being explored.

What is a parasite?  Thoughts immediately go to organisms such as the malarial parasite, Plasmodium, and the tapeworm in animals and mistletoe in plants but there are huge numbers of other parasites to be found right across the spectrum of living organisms.  A parasite can be defined as an organism which in order to exist and reproduce must have a close and complex association with the living cells of another species (the host).  The host is normally harmed by the association.

Viruses, the exception, are not usually classified as living organisms, but are accepted as the ultimate parasites. They exist as inert chemical particles composed of nucleic acid and protein when outside of living cells. They are obligate parasites, which means that they are only able to manufacture new virus particles by entering host cells and ‘hijacking’ their machinery for making the component viral chemicals.

Viruses can normally only be seen by the use of electron microscope.  However, one virus, called the mimivirus, is about 400 nm (400 billionths of a metre) in diameter and can be seen with a light microscope. It is found in water cooling towers where it infects amoeba;  it may also be responsible for some cases of human pneumonia. A second strain of mimivirus which is larger, was found in a similar environment.  This was named mamavirus and when examined with an electron microscope was seen to possess its own parasitic virus a parasite of a parasite -  which was named Sputnick. This very small virus (about 50nm in diameter) is said to possess only 20 genes and when parasitizing mamavirus it targets its DNA-synthesizing machinery. 

Sputnick can be classed as a virophage – a virus infecting a virus – just as a virus infecting a bacterium is called a bacteriophage. It is conceivable that virophages could be used to treat human viral diseases.  Prior to the development of antibiotics there was considerable interest in curing bacterial diseases with bacteriophages but the success of antibiotic therapy brought much of this ‘bacteriophage therapy’ to an end.

This leads us back to the last line of Swift’s verse, “And so proceed ad infinitum”, where the Latin phrase needs to be replaced. It is very unlikely that Sputnick has its own parasite and in general the search for smaller and smaller parasites would encounter a molecular size-barrier where replication would not be possible – the necessary chemical tools would not be there.  So, a Latin scholar is perhaps needed to replace ad infinitum” with a more appropriate and, of course, rhyming, phrase, implying “onwards” but not “onwards” for ever.  Swift would probably not object! (13/8/08)

(35) 'Plastic Mines' (17 November 2008)

In an earlier article - Ban the Plastic Bag? (9 April 2008) - the fact that landfill sites were being filled with waste plastic was aired and listed as one of the reasons why the environmental lobby was seeking a ban on plastic shopping bags (a news item which, incidentally, now seems to be of little interest to the media in the present financial crisis!).

However, for those who wish to argue that, unsightly as they may be, landfills at the present time are an essential facility, may like to read that some also consider them to be a valuable resource! The Environment Agency in its magazine, "Your Environment" (Issue 21 Nov 2008 - Jan 2009) discusses 'landfill mining' an activity occurring in many countries where plastic and metals are being recovered from landfills and reused. The plastics are mainly being recovered to use as fuel; polyethylene bags and oil, of course, are both hydrocarbons. Landfill mining is apparently only happening on a very small scale in the UK. The downside of the activity is that it can release pollutants - leachate for example - although there is every reason to suppose that this can be controlled (17/11/08)

(36) The Marvels of Chemistry - with help from Wikipedia (11 March 2009 )

Having read this note, when your GP says he is going to put you on a course of  vancomycin, to cure your Staphylococcal infection you will be able to say, “Oh, you 
 mean (1S,2R,18R,19R,22S,25R,28R,40S)- 48- {[(2S,3R,4S,5S,6R)- 3- {[(2S,4S,5S,6S)- 4- amino- 5- hydroxy- 4,6- dimethyloxan- 2- yl]oxy}- 4,5- dihydroxy- 6- (hydroxymethyl)oxan- 2- yl]oxy}- 22- (carbamoylmethyl)- 5,15- dichloro- 2,18,32,35,37- pentahydroxy- 19- [(2R)- 4- methyl- 2- (methylamino)pentanamido]- 20,23,26,42,44- pentaoxo- 7,13- dioxa- 21,24,27,41,43- pentaazaoctacyclo[,6.214,17.18,12.129,33.010,25.034,39]pentaconta- 3,5,8(48),9,11,14,16,29(45),30,32,34,36,38,46,49- pentadecaene- 40- carboxylic acid”.

This will surely impress your doctor although it is highly unlikely that he/she will be able to produce a chemical structure for you from this jargon:  the same can be said for Chemo-Philia in the case of this particular compound!

In order produce a systematic name for vancomycin or, indeed, any chemical, you need to know the rules of nomenclature which have been established by the International Union of Pure and Applied Chemistry (IUPAC). These allow you to name a compound so that others will be able to understand and accurately draw its chemical formula. For example, the popular (often called 'trivial') name, "glucose", is given to one of the best known carbohydrates. However, this name tells you nothing about the structure of the compound except that it is probably a sugar/carbohydrate because the name ends in 'ose'. The IUPAC name is:

(2S,3R, 4S,5R,6R)-6-methyloltetrahydropyran-2,3,4,5-tetrol

which is the name given to glucose in its 6-membered ring form:

glucose molecule - now with missing H on C5 added

Information can be added to the trivial name, glucose, providing more details about its structure (A more completetrivial name for the above structure is α-D-glucopyranosewhich tells the reader more about the ring size and the arrangement of the hydroxyl groups (-OH))). However, the IUPAC nomenclature is more informative for chemists. (11/3/09).

(37) Dangers in the Kitchen (20 July 2009)

Kitchens are potentially hazardous places with sharp implements, electrical equipment and hot liquids, not forgetting the hundreds of toxic, naturally-occurring chemicals that foods contain – luckily in low concentrations! Most pesticides, for example, are naturally-occurring.   Furthermore, we should be somewhat concerned by what happens to these complex chemical mixtures when they are baked, boiled or fried.  High temperature cooking certainly gives rise to carcinogenic compounds.

It would now appear that some of the methods normally used by trained personnel in science laboratories are being employed in kitchens by  ‘molecular  gastronomes’: this  raises concern to an even higher level.  The German chef who recently lost both hands in an explosion involving liquid nitrogen (LN2) ( is an early warning to culinary enthusiasts that they should perhaps be very wary of methods that are not described in popular cookery books.

It is common knowledge that the intensely cold LN2 (boiling point –195.8  Deg.C) can cause serious burns and that there have been deaths by asphyxiation caused by  nitrogen gas coming from LN2 :  one volume of liquid can produce about 700 volumes of gas.  However, it is not well known that LN2 causes oxygen gas to condense out of the atmosphere as a liquid (LOX) which is an extremely hazardous substance.  It is used in rocket motors and at one time, in combination with organic materials, as a commercial explosive.  However, it has now been abandoned in the latter role because of its unstable properties.

The explosion in the German kitchen (or was it “bathroom”) was described as “enormous” and C-P wonders if it was caused by LOX condensing from the atmosphere or whether it was produced by trying to keep LN2 in a sealed container. In the former case, a mixture of LOX, organic material such as clothing, and a spark would have ‘done the trick’! (20/7/09)

(38) Champagne Bubbles (4 December 2009)

Champagne like all drinks derived from plant extracts contains hundreds of organic chemicals giving it a characteristic aroma and taste which is difficult to mimic in a laboratory.

Champagne can be distinguished from still wines by its high level of carbon dioxide (CO2) which supersaturates the liquid under pressure in the bottle.  CO2 is derived from the fermentation reaction produced by yeast acting upon the sugar from the grapes in a series of reactions that can be summarized thus:

C6H12O6  →→  2CH3CH2OH  +  2 CO2
                              Glucose                    Ethanol

In this primary fermentation the CO2 is allowed to escape and then more CO2 is made by adding more sugar and yeast to the wine (a secondary fermentation) which is now in stoppered bottles which are placed so that the necks face downwards.  This allows sediment to collect in the necks of the bottles which is removed by freezing and allowing the frozen ‘plug’ of unwanted material to be pushed out by the pressure of the CO2.  Some sugar together with sulphur dioxide (SO2) as a preservative is added and the bottles are then quickly corked and wired.

When the cork is removed, CO2 comes out of solution as bubbles, aided by condensation nuclei (small specks of impurities coming from the wine or the bottle glass), which rise to the surface and break at the air/liquid interface. Wine glasses that have been etched on the inside are said to produce more bubbles than smooth glasses.

The unique aroma and flavour experience in drinking champagne is a function of the bubbles which contain hundreds of chemicals (including esters, fatty acids and alcohols) which are continually being brought to the surface to be smelled and tasted.  The bubbles (the gas phase) contain much higher concentrations of many of these chemicals than the champagne (the liquid phase).

Interestingly, the bubbles display some basic chemistry as the chemicals they contain are in part made up of ‘surface active’ compounds which distribute themselves between the gas in the bubble and the liquid of the wine. To do this the molecules must be amphiphilic, ie have two ends, one (hydrophilic) which is attracted to water and the other (hydrophobic) which is not.

A typical amphiphile is stearic acid:

Stearic acid.svg

(Structure taken from Wikipedia:

This molecule is composed of 18 carbon atoms, 17 of which are fully saturated with hydrogen atoms and 1 which is part of the acidic carboxyl group (-CO2H)(-CO2H). The latter is the hydrophilic part of the molecule which is attracted to water and the long 17 carbon chain favours a non-aqueous environment such as an organic solvent or a gas such as air. As a result of these structures a stearic acid molecule in champagne would be found stretched across the aqueous/ CO2 bubble interface thus:

                               CO2 PHASE    | AQUEOUS PHASE
   Stearic acid.svg

A knowledge of chemistry is therefore needed to understand champagne and all the other foods and drinks that are consumed during the holiday season – and for that matter, pretty well everything else on this planet! (4 December 2009)

(39) Antimony in Fruit Juices (10 March 2010)

The Royal Society of Chemistry recently reported that high levels of the element antimony (Sb), above the EU limit for drinking water, have been found in fruit juices produced in the UK.  Antimony is in the same family of elements as arsenic (As) and so it is understandable that there are some who are worried about this discovery.

Sb and its derivatives are not as toxic as As  although they are thought to be  carcinogens and cardiovascular poisons which can perhaps interfere with reproductive processes.  Readers may also remember that in early 1990s there was considerable public concern that Sb was causing cot deaths (SIDS: Sudden Infant Death Syndrome)The hypothesis was that antimony trioxide (Sb2O3), a fire retardant added to cot mattresses, was being converted to trimethlystibine (Sb(CH3)3), a poisonous gas, by microorganisms living in the damp environment of the cot.  However, a thorough investigation of this hypothesis gave it no support.

The source of the Sb in the fruit juices has so far not been determined although a possibility that should be investigated is that it comes from the packaging.  Fruit juices are commonly found in plastic bottles made from a polymer named polyethylene terephthalate or PET. To synthesize this material a catalyst is required which is commonly antimony trioxide!

Polyethylene terephthalate
(Structure from Wikipedia:

It is therefore possible that contaminating Sb was leached out from the plastic by the fruit juices.  The acidity of the juice may have aided this process. It is not clear whether all of the juices examined were contained in PET bottles, however.(10 March 2010)

(40) REACH has reached the USA (26 July 2010)

A new bill, The Toxic Chemicals Safety Act 2010, has started on its way through the US Congress to amend the Toxic Substances Control Act 1976 (
In this case the USA  is, unusually, following in the ‘environmental wake’ of the EU in that the  TCSA appears to be very like Europe’s REACH (Registration, Evaluation, Authorisation & Restriction of Chemicals) and embarking on an expensive safety review of thousands of chemicals many of which have served as domestic friends of US citizens for decades and longer. Chemophobia marches on! (26 July 2010)