Colorimetry

I was sitting with some friends drinking tea in glasses.
I noticed some people like "weak" tea and others like their tea "strong".
Technically "weak" tea isn't "weak" at all ... it's really a more dilute solution of tea, while "strong" tea is a more concentrated solution of tea.
But what I noticed most is that "weak" tea is less of a brown colour than "strong" tea, so it ought to be possible to guess the concentration of "tea" in a glass of tea by looking at its colour.
However, I wouldn't have to guess the concentration if I had a colorimeter because a colorimeter would measure the absorbance of each tea solution.
It may seem like a lot of hard work for very little reward ... "I'll like a 0.341 absorbance glass of tea please..." .... but colorimetry is useful tool for measuring the concentration of coloured solutions as you will find out in AUS-e-TUTE's new set of colorimetry resources.
AUS-e-TUTE Members should log-in to use the colorimetry resources listed under "Spectroscopy" and the subheading "Absorption Spectroscopy".
Non-members can access a "free-to-view" tutorial at https://www.ausetute.com.au/colorimetry.html

Mass Spectroscopy and Organic Molecules

What happens when an organic chemist makes a new molecule?
How do they know what the structure of the new molecule is?
They use lots of different techniques to determine the molecular mass and structure of the new molecule, one of which is mass spectroscopy.
Mass spectroscopy tells you the molecular mass of the molecule, and, it gives a good indication of how the atoms making up the molecule are put together. And it does this by breaking the molecule up!
Find out more about how mass spectroscopy can be used to determine the structure of organic molecules in our tutorial
AUS-e-TUTE Members can log-in to play the corresponding game, and to answer test and exam questions (which give you immediate feedback about your answer)

The man who proved the moon isn’t cheese

Meet Emeritus Professor Ross Taylor AC, the Australian who analyzed the first moon rock samples in 1969, in Volume 46 Number 4 of the ANUreporter,

"With emission spectroscopy you can put a tiny amount of material into the flame and quickly identify any of 70 different elements from the spectral lines they produce. But those 70 elements could produce 100,000 possible lines," he says.
At 11.45am on 28 July, Taylor received the first samples. By 4pm, he delivered preliminary results to a press conference - significantly faster than the usual scientific process and with much more at stake.
The high-speed analysis had not been without hiccups. Taylor almost missed one of the most significant traits of the moon's chemistry, its significantly lower sodium levels than Earth.
The moon is also rich in chromium, which has a spectral line that almost perfectly disguised the low sodium result. Only moments before the press conference Taylor realised the mistake and corrected it.
"It would have ruined my reputation," he says.

Reference:
The man who proved the moon isn't cheese

Further Reading:
http://www.ausetute.com.au/emissions.html 
http://www.ausetute.com.au/flametest.html

Suggested Study Questions
1/ What is an emission spectrum?
2/ How can you produce the emission spectrum of metallic elements at school?
3/ How is the emission spectrum of an element used to confirm the existence of energy levels in atomic structure?
4/ What is a flame test?
5/ How does a flame test differ from emission spectroscopy?
6/ How is a flame test similar to emission spectroscopy?
7/ "With emission spectroscopy you can put a tiny amount of material into the flame and quickly identify any of 70 different elements from the spectral lines they produce." 
Explain how emission spectroscopy can be used to identify different elements.
8/ "But those 70 elements could produce 100,000 possible lines,"
Explain how such a huge number of lines can be produced from what seems like a much smaller number of elements.
9/ "The moon is also rich in chromium, which has a spectral line that almost perfectly disguised the low sodium result"
Explain how a chromium spectral line could disguise the low sodium result.
10/ Imagine you have helped Emeritus Professor Ross Taylor AC analyse these moon rock samples. Produce a scientific poster to communicate the results of this experiment to your class.

Molecule with Anti-Cancer Kick

In 2013, medical researchers found a molecule that fights cancer in animals by boosting the cell's production of a powerful natural antitumor protein known as TRAIL. The Researchers referred to this anti-cancer molecule as TIC10, short for TRAIL Inducing Compound number 10.
The structure of this molecule, as confirmed by mass spectroscopy, was published at this time as is shown below:

Chemists at The Scripps Research Institute (TSRI) found a way to synthesize this molecule in the laboratory. However, when the Chemists gave their molecule to Biologists to test on cancer cells, this molecule failed to show any anti-cancer activity!
So, the Chemists asked the Biologists to supply some of the TIC10 that had shown anti-cancer activity. The Chemists spent months analyzing both TIC10 molecules to determine their exact molecular structure. And they discovered that the molecule the biologists had shown to fight cancer did not have the structure that was originally published, so the molecule that the Chemists had synthesized in their laboratory would not fight cancer cells,.
However, the Chemists found that the molecule that DOES fight cancer cells has a very similar structure. The structure of the active molecule is shown below:

Note that the structure originally published for TIC10 had the three nitrogen containing rings in a straight line. This new, correct, structure for TIC10 has two of the nitrogen containing rings in a straight line, but the third ring sticks out at an angle from the other two. Only this "angular" isomer (the molecule with a kick) shows any anti-cancer activity.

Kim D. Janda, the Ely R. Callaway Jr. Professor of Chemistry and member of the Skaggs Institute for Chemical Biology at TSRI has been quoted as saying, "One lesson from this has got to be: don't leave your chemists behind".
(http://www.sciencedaily.com/releases/2014/05/140519184505.htm)

Reference:
Nicholas T. Jacob, Jonathan W. Lockner, Vladimir V. Kravchenko, Kim D. Janda. Pharmacophore Reassignment for Induction of the Immunosurveillance Cytokine TRAIL. Angewandte Chemie, 2014; DOI: 10.1002/ange.201402133

Further Reading
Molecular Formula  
Condensed Structural Formula 
2-Dimensional Structural Formula
Skeletal Formula
Percent Composition
Functional Groups
Benzene
Mass Spectroscopy for Structural Determination

Suggested Study Questions:

1. Refer to the structure of TIC10 as shown above. In one molecule, how many
   • carbon atoms are present?
   • hydrogen atoms are present?
   • oxygen atoms are present?
   • nitrogen atoms are present?
2.  Write the molecular formula for a molecule of TIC10.
3. For the TIC10 molecule, calculate the percent by mass of
   • carbon
   • hydrogen
   • oxygen
   • nitrogen
4. Convert the skeletal structure for the active anti-cancer molecule into a 2-dimensional structural formula.
5. Circle one benzene ring in the structure of the active anti-cancer molecule.
6. Circle and name the functional group containing an oxygen atom on the active anti-cancer molecule.
7. What value do you expect for the mass-to-charge (M/Z) peak on a mass spectrum of the anti-cancer TIC10 compound ?
8. Do you think mass spectroscopy alone could be used to distinguish between the two structures proposed for TIC10 above? Explain your answer.

Chemistry in Eclipses

The 14th November 2012 excites students of physics and those interested in astronomy. This is the date of a total eclipse of the sun. The area of totality will pass over northern Australia, from east of Darwin in the Northern Territory to the Cape York Peninsula of Far North Queensland, turning morning into darkness. The rest of Australia will see a partial eclipse.

But why would chemists get excited about a solar eclipse?

The story begins more than 200 years ago ...

Gaps in the Solar Spectrum?

In 1802 an English Chemist, William Hyde Wollaston, was the first person to record the appearance of a number of dark lines in the emission spectrum of light from the sun.

In 1814, German physicist Joseph von Fraunhofer began measuring the wavelengths of over 570 of these lines.

Fingerprinting the Sun

Robert Gustave Kirchhoff and Robert Bunsen, developed a better prism-based spectroscope and observed that the spectral lines emitted by a gas occurred at the same wavelength as the absorption lines observed when incandescent light from Bunsen's burner shone through the same gas heated at the same temperature.

Then Kirchhoff,  proposed the laws of spectroscopy which bear his name:

1. A hot solid object produces light with a continuous spectrum
2. A hot tenuous gas produces light with spectral lines at discrete wavelengths (an emission spectrum)
3. A hot solid object surrounded by a cooler tenuous gas produces light with an almost continuous spectrum with gaps at discrete wavelengths (an absorption spectrum)

A star, like the sun, will create an absorption line spectrum because the continuous spectrum emitted by the dense, opaque gas that makes up most of the star passes through the cooler, transparent atmosphere of the star.

In 1859, Kirchhoff  demonstrated that all pure substances display their own characteristic spectrum, so it is possible to use the spectrum of elements to identify elements in a mixture, just like each person's fingerprints are unique and can be used to identify them. He proposed  that the lines in the solar spectrum are caused by the absorption of light by elements in the solar atmosphere and set out to identify the elements present in our sun.

New Element Discovered

On the 18th August 1868 there was a total solar eclipse. In India, French astronomer Pierre Janssen observed this eclipse using a spectroscope. He recorded a bright yellow line with a wavelength of 587.49 nm in the spectrum of the solar prominences. The same result was also recorded by British astronomer Norman Lockyer. This line could not be due to sodium, because although sodium produces a bright yellow line (actually more than 1), the wavelength of sodium's 'line' is about 589.3 nm. Lockyer proposed that this line was due to a new element which he called helium after the greek word 'helios' meaning 'sun'.

About 10 years later, Scottish chemist William Ramsay isolated helium on earth ...... but that's another story.

References:

http://eclipse.aaq.org.au/

http://www.csiro.au/en/Outcomes/Understanding-the-Universe/Tracking-spacecraft/History-of-total-solar-eclipses.aspx

Further Reading:

Emission Spectra 

Suggested Study Questions:

1. speed of light (m/s) = frequency (s^-1) x wavelength (m)
   If the speed of light is 3 x 10⁸ ms^-1 calculate:
• find the frequency of the 'yellow line' in sodium's spectrum
• find the frequency of the yellow line for the new element found in the solar spectrum
2.  speed of light (m/s) = frequency (s^-1) x wavelength (m)
   If the speed of light is 3 x 10⁸ ms^-1 calculate:
• wavelength of blue light with a frequency of 6.9 x 10¹⁴ s^-1
• wavelength of red light with a frequency of 4.6 x 10¹⁴ s^-1
  
3. The energy of light emitted, E, is Planck's constant,h, multiplied by the speed of light divided by the wavelength of light emitted. Write a mathematical equation to represent this.
4. Use your equation above to calculate
   • energy of the blue light in question 2 above
   • energy of the red light in question 2 above
5. Complete the following generalizations:
   • The longer the wavelength of light, the ___________ energy it has
   • The shorter the frequency of light, the _________ energy it has.
6. Compare the wavelength of the 'yellow line' in sodium's spectrum and the yellow line for the 'new element'. Which element has
   • the longest wavelength
   • the shortest frequency
   • the most energy
7. Describe the difference in the spectrum of light from the sun as seen in a spectroscope compared to the spectrum of light from a fluorescent light as seen in a spectroscope.
8. Explain the differences between the two spectrum in question 7 above.

Green Hair

Imagine you are living in a small town in Sweden.
You go to bed one night, naturally blonde.
When you wake up in the morning and look in the mirror your blonde hair has turned green!
Not only that, but your naturally blonde neighbour also has green hair!

This actually did happen in 2011, and, no doubt, caused a certain amount of distress.

Where would you begin in order solve the "green hair" mystery?
What could turn hair green?

Blonde hair often turns green after swimming in chlorinated pool water.
Copper, used in compounds to reduce algae growth in water, can be present in concentrations of about 0.5 ppm in pool water. When bleach (often sold as "liquid chlorine") is added to the pool water it oxidizes the copper resulting in a pretty green colour, and the oxidized copper binds to the proteins in the hair.
If you happen to have copper pipes in your bathroom, you've probably seen "green stains" on the pipes where the copper has been oxidized.

So, back to the story in Sweden.
Samples of drinking water were taken from a number of homes in order to measure the amount of copper present but the concentration of copper in the water did not exceed the recommended guidelines (that is, the copper ion concentration was less than 1 ppm).

However, in new houses, when hot water was left overnight and tested the next morning, the concentration of copper in the water increased dramatically. On further investigation it was discovered that the hot water pipes in new houses lacked the coating that the pipes in older houses had. So, overnight, when the water in the pipes was still and not being continuously "flushed" through the pipes, copper particles were being added to the water.

For solving the "Swedish Green Hair Mystery" Johan Pettersson was rewarded with a 2012 Ig Nobel Prize for Chemistry.


References:
http://www.thelocal.se/37994/20111217/
http://www.improbable.com/ig/winners/#ig2012

Further Reading 
http://www.ausetute.com.au/waterana.html 
http://www.ausetute.com.au/aas.html 
http://www.ausetute.com.au/partspm.html 
http://www.ausetute.com.au/concsols.html 
http://www.ausetute.com.au/weightpc.html 
http://www.ausetute.com.au/corrosion.html 

Suggested Study Questions:

1. Describe 2 methods you could use to detect the presence of copper ions in water.
2. Describe the process by which Atomic Absorption Sepctroscopy (AAS) could be used to measure the concentration of copper ions in a water sample.
3. Describe a way that you could prevent copper from entering the water in the copper water pipes in this Swedish town.
4. Copper is often present in soils at a concentration of around 50 ppm. What mass of copper would be present in 0.5 tonne of soil?
5. A particular pool contains 40,000 L of water. If the pool water contains 0.5 ppm copper ions, what is the concentration of copper ions in mol L^-1 ?
6. Chocolate can contain 10 mg/kg  copper. What mass of copper is present in a 250 g bar of chocolate?
7. Doses of copper that exceed 50 mg/kg of body mass can be lethal. Calculate the mass of copper that would be the lethal limit for an 80 kg adult.
8. What advice could you give the inhabitants of this Swedish town in order for them to avoid having green hair?

Elemental Fluorine

Fluorine, the most electronegative element, is extremely chemically reactive. Fluorine chemically combines with every other element in the Periodic Table, except helium and neon, to form fluorides, and these reactions are often sudden or explosive. For this reason, Chemists didn't believe that it could be found in nature in its elemental form, they thought it would only ever be found in nature in ionic compounds such as in the mineral fluorite or fluorspar (CaF₂).
Chemists have now used ¹⁹F NMR spectroscopy to identify the presence of elemental fluorine in "stinking fluorspar" (antozonite, stinkspat, stinkfluss, stinkstein, fetid fluorite). As the name suggests, stinking fluorspar has an unpleasant, pungent odour when crushed.

For 200 years, scientists have tried to establish the cause of this unpleasant odour. Suggestions have included iodine and ozone, even sulfur, but Chemists doubted that elemental fluorine could be the cause of the odour. The elemental fluorine in stinking fluorspar is produced when the tiny amounts of uranium existing in the mineral emit ionizing radiation which splits the fluorite into calcium and element fluorine.

Reference
1.Jörn Schmedt auf der Günne, Martin Mangstl, Florian Kraus. Occurrence of Difluorine F2 in Nature-In Situ Proof and Quantification by NMR Spectroscopy. Angewandte Chemie International Edition, 2012; DOI: 10.1002/anie.201203515


Further Reading
Interactive Periodic Table
Trends in Group 17 (Halogens)
Electronegativity
Electron Configuration
Writing Ionic Formula
Name and Formula of Covalent Compounds
Balancing Chemical Equations

Suggested Study Questions

1. Give the symbol for each of the following elements:
   • fluorine
   • helium
   • neon
   • calcium
   • iodine
   • oxygen
   • sulfur
   • uranium
2. Explain what is meant by the term electronegative.
3. Give the electron configuration for fluorine in
• simple (shell) notation
• sub-shell notation
4. Give the chemical formula for elemental fluorine.
5. Explain why elemental fluorine is expected to exist as a covalently bonded molecule.
6. Give the formula for each of the following fluorides:
• calcium fluoride
• sodium fluoride
• lithium fluoride
• magnesium fluoride
• silver fluoride
• iron(II) fluoride
• tin(IV) fluoride
• gold(III) fluoride
• xenon difluoride
7. Write a balanced chemical equation to describe the reaction in which calcium fluoride in stinking fluorspar is split into elemental calcium and elemental fluorine.
8. Write balanced chemical equations for the production of the fluoride in each of the following reactions
• sodium metal and fluorine
• calcium metal and fluorine
• silver metal and fluorine
• iron metal and fluorine
• xeonon gas and fluorine
• hydrogen gas and fluorine

NMR Without Magnets

Nuclear Magnetic Resonance (NMR) is an important tool in analyzing the structure of organic compounds, and, its relative, Magnetic Resonance Imaging (MRI) is used in medical diagnosis.

Nuclear Magnetic Resonance (NMR) depends on the fact that many atomic nucleii possess spin and their own dipolar magnetic fields. During conventional NMR spectroscopy these nuclei are lined by a strong external magnetic field, then knocked off axis by a burst of radio waves. The rate at which each kind of nucleus then wobbles, or precesses, is unique and identifies the element. For example, a hydrogen-1 nucleus (a lone proton) precesses four times faster than a carbon-13 nucleus (6 protons and 7 neutrons).

Being able to detect these signals depends first of all on being able to detect net spin. If the sample were to have as many spin-up nuclei as spin-down nuclei it would have zero polarization, and the signals would cancel out. But since the spin-up orientation requires slightly less energy, a population of atomic nuclei usually has a slight excess of spin ups, if only by a few in a million.

The lines in a typical NMR spectrum reveal more than just different elements. Electrons near precessing nuclei alter their precession frequencies and cause a "chemical shift", moving the signal or splitting it into separate lines in the NMR spectrum. This is the principal goal of conventional NMR, because chemical shifts point to particular chemical species; for example, even when two hydrocarbons contain the same number of hydrogen, carbon, or other atoms, their signatures differ markedly according to how the atoms are arranged. But without a strong magnetic field, chemical shifts are insignificant.

The down-side is that NMR relies on huge, very low-temperature, superconducting magnets so it is an expensive and non-portable tool. Scientists at Berkeley Lab and UC Berkeley have shown that chemical analysis with NMR is practical without using any magnets at all.

Firstly the scientists have increased the net spin orientation via hyperpolarization which increases the proportion of parahydrogen (in which the proton in each hydrogen nucleus spins in the opposite direction resulting in spin 0) in relation to orthohydrogen (in which the proton in each hydrogen nucleus spins in the same direction resulting in spin 1).

Second, the scientists use optical-atomic magnetometers instead of the huge superconducting magnets used in conventional NMR. Optical-atomic magnetometers measure whole atoms, not just nuclei. An external magnetic field is measured by measuring the spin of the atoms inside the magnetometer's own vapor cell, typically a thin gas of an alkali metal such as potassium or rubidium. Their spin is influenced by polarizing the atoms with laser light; if there's even a weak external field, they begin to precess. A second laser beam probes how much they're precessing and thus just how strong the external field is.

Third, the scientists use J-coupling, instead of chemical shift, for the chemical analysis because you cannot detect chemical shift in a zero field. Discovered in 1950 by the NMR pioneer Erwin Hahn and his graduate student, Donald Maxwell, J-coupling provides an interaction pathway between two protons (or other nuclei with spin), which is mediated by their associated electrons. The signature frequencies of these interactions, appearing in the NMR spectrum, can be used to determine the angle between chemical bonds and distances between the nuclei. You can even tell how many bonds separate the two spins.

Experiments to date have been performed on molecules that are easily hydrogenated and therefore easily hyperpolarized. Beginning with styrene, a simple hydrocarbon, J-coupling has been measured for a series of hydrocarbon derivatives including hexane and hexene, phenylpropene, and dimethyl maleate, important constituents of plastics, petroleum products, even perfumes.

Reference
T. Theis, P. Ganssle, G. Kervern, S. Knappe, J. Kitching, M. P. Ledbetter, D. Budker, A. Pines. Parahydrogen-enhanced zero-field nuclear magnetic resonance. Nature Physics, 2011; DOI: 10.1038/nphys1986

Further Reading
¹H NMR Spectroscopy
Quantum Numbers
Isotopes

Study Questions

1. For conventional ¹H NMR, define the following terms:
   • chemical shift
   • magnetic coupling or spin-spin coupling
   • J-coupling
   • internal standard
2. In conventional ¹H NMR, what is the purpose of an internal standard such as TMS?
   
   
3. In conventional ¹H NMR, what does the number of signals tell you about a sample molecule?
4. In conventional ¹H NMR, what does the relative area of each signal tell you about the sample molecule?
5. In conventional ¹H NMR, what does the relative position of the signals tell you about the sample molecule?
6. For an atom of hydrogen-1, given the possible value(s) for the spin quantum number, m_s.
7. Consider a diatomic molecule of hydrogen, H₂. For each possible spin quantum number for each hydrogen atom, draw a representative diagram using ↑ to represent up-spin and ↓ to represent down-spin.
   
8. For each diagram above, add the values of the spin quantum number for each nucleus in the molecule to find the net spin on the molecule.
9. How many parahydrogen and orthohydrogen molecules did you draw?
   

Your Phone: Your Spectrometer

Professor Alexander Scheeline of the University of Illinois has developed a method to turn a mobile (cell) phone into a portable spectrometer.

In a spectrometer, white light shines through a sample solution. The solution absorbs certain wavelengths of light. A diffraction grating then spreads the light into its colour spectrum like a prism. Chemists analyze the spectrum to tell them about the properties of the sample.

In Scheeline's device, a single light-emitting diode (LED) powered by a 3-volt battery (as used in key fobs to remotely lock a car) is used as the light source. Diffraction gratings are available from scientific supply companies, as are cuvettes, the small, clear containers to hold the sample solutions. The mobile (cell) phone is used to take a photo of the spectrum obtained. Then the JPEG photo is analyzed using a software program freely accessible online:
http://www.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/index.html

Further Reading
http://www.ausetute.com.au/spectros.html

Further Activities

1. Build a spectrometer as per the instructions given in here : http://www.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/HSFiles/3.html
   
2. Follow the instructions in the preparation of a solutions of different concentrations, including a blank.
3. Record each spectrum produced by taking a photo of it.
4. Upload the photos into the programme which you should download using the link above.
5. Data will be available as an exported csv file for excel.
6. Plot absorbance versus concentration.
7. Obtain a solution of unknown concentration.
8. Use the plot above to determine the concentration of this solution.
   

Diacetylene in Space

Diacetylene, C₄H₂, has previously been discovered in the atmosphere of Titan and on the Moon. Polish scientists have recently observed it in translucent interstellar clouds.

The density of translucent interstellar clouds is extremely small, much less than the best vacuum we can produce in a laboratory, but because they are huge in size their gas molecules have a chance to interact with penetrating radiation, so scientists can use spectroscopy to study the composition of these translucent interstellar clouds.

Molecules absorb and emit photons of specific energies, and therefore wavelengths, corresponding to the differences between energy levels in their atomic structure. The light from stars that reaches the Earth is slightly changed as a result of interactions with gas particles in translucent clouds, it lacks the wavelengths absorbed by intervening interstellar atoms and molecules. Until now, compounds composed of no more than a few atoms have been found in these clouds, molecules such as C₃ andH₃⁺. It is possible that diacetylene is quite a common component of the interstellar medium, having now been located in two carbon-rich galaxy regions and in the averaged data coming from a dozen other lines of sight.

Reference
Institute of Physical Chemistry of the Polish Academy of Sciences (2010, September 17). Surprisingly complicated molecule found in outer space. ScienceDaily. Retrieved September 18, 2010, from http://www.sciencedaily.com­ /releases/2010/09/100915084456.htm

Further Reading
Spectroscopy : http://www.ausetute.com.au/spectros.html
Nomenclature : http://www.ausetute.com.au/namctut1.html
Alkynes : http://www.ausetute.com.au/namsynes.html

Study Questions:

1. Draw the structural formula for diacetylene, C₄H₂.
2. Give the systematic IUPAC name for diacetylene.
3. To which homologous series does the diacetylene molecule belong?
4. Give the empirical formula for the diacetylene molecule.
   
5. Is diacetylene an example of a saturated or unsaturated hydrocarbon? Explain your answer.
6. In Titan's atmosphere, diacetylene could be produced from the reaction between acetylene, C₂H₂, and the ethynyl radical C₂H. Write a possible chemical equation to represent this reaction.
7. Would you expect diacetylene to react with bromine water? Explain your answer.
8. Would you expect diacetylene to be easily oxidized? Explain your answer.
   

Protonated Water Clusters

Water molecules are polar. This causes neighbouring water molecules to be attracted to each other, forming hydrogen-bonds that link them into chains or clusters. The evaporation of water requires relatively large amounts of energy in order to break the hydrogen-bond networks apart.

Protonated water clusters, which have protons bound to them, are important model systems for the study of proton hydration in aqueous solutions, the process that determines the acidity (pH) and electrical conductivity of water.

The smallest protonated water cluster is the hydronium cation consisting of a single water molecule with an associated proton.
The Zundel ion is another protonated water cluster and is formed when a single proton is shared by two water molecules.

Scientists have been using infrared spectroscopy to determine the bond strengths, geometrical structures and chemical properties of protonated water clusters. When molecules are irradiated with infrared light, they vibrate in ways that depend on the wavelength, the colour, of the light. The frequency of the resulting vibrations allows scientists to deduce the three-dimensional structure of the molecule and the strength of the bonds between its atoms.

Reference:

1. Marcel sBaer, Dominik Marx, Gerald Mathias. Theoretical Messenger Spectroscopy of Microsolvated Hydronium and Zundel Cations. Angewandte Chemie, 23 August 2010 DOI: 10.1002/anie.201001672
2. G. Mathias, D. Marx. Structures and spectral signatures of protonated water networks in bacteriorhodopsin. Proceedings of the National Academy of Sciences, 2007; 104 (17): 6980 DOI: 10.1073/pnas.0609229104

Study Questions

1. Draw the molecular structure of a water molecule.
2. Use the structure above to explain what is meant by water being a polar molecule.
3. Draw a diagram to show how a hydrogen-bond can be formed between two water molecules.
4. Write the molecular formula for the hydronium cation.
5. Give the structural formala for the hydronium ion.
6. Based on the description of the Zundel ion given above, write the molecular formula for the Zundel ion.
7. Give the structural formula for the Zundel ion.
8. Another protonated water cluster is the Eigen ion, H₉O₄⁺ . Give a possible structural formula for the Eigen ion.
   

Buckyballs in Space

In 1970, Japanese professor Eiji Osawa predicted the existence of buckyballs.
In 1985, Buckminster Fullerenes were first observed in the laboratory.
In 1996, Sir Harry Kroto, Bob Curl and Rick Smalley shared the Nobel Prize in chemistry for the discovery of buckyballs.
They were named after the architect Buckminster Fuller because they resemble his geodesic domes which have interlocking circles on the surface of a partial sphere. Buckyballs, 60 carbon atoms arranged into a three-dimensional spherical structure resembling a soccer ball, are allotropes of carbon.
Buckyballs have been found on Earth in candle soot, layers of rock and meteorites.

Astronomers using NASA's Spitzer Space Telescope have now discovered buckyballs in space, in a planetary nebula named Tc 1. Planetary nebula are the remains of stars that shed their outer layers of gas and dust as they age. A compact, hot star, or white dwarf, at the centre of the nebula illuminates and heats these clouds of discarded material. The buckyballs were found in these clouds when the astronomers used Spitzer's spectroscopy instrument to analyze infrared light from the planetary nebula and see the spectral signatures of the buckyballs. The data from Spitzer were compared with data from laboratory measurements of the same molecules and showed a perfect match.

Reference:
Jan Cami, Jeronimo Bernard-Salas, Els Peeters, and Sarah Elizabeth Malek. Detection of C₆₀ and C₇₀ in a Young Planetary Nebula. Science, 2010; DOI: 10.1126/science.1192035

Study Questions:

1. What is an allotrope?
2. Name two naturally occurring allotropes of carbon other than buckminster fullerenes.
3. In what ways are these allotropes above the same?
4. In what ways are these allotropes above different?
5. It has been suggested that buckyballs could be used in armour, drug delivery, and, superconductors. What do you think the physical and chemical properties of buckyballs are likely to be?
   
6. Name the other allotrope of oxygen besides (bi)molecular oxygen.
   
7. In what ways are the two allotropes of oxygen the same?
8. In what ways are the two allotropes of oxygen different?
9. There are several allotropes of phosphorus. Discuss the similarities and differences of these allotropes.
   

Lunar Graphite

Scientists have been analyzing 3.8 billion year old Mare Serenitatis lunar samples brought back to Earth by astronauts in 1972. Raman spectroscopy of the sample allowed scientists to create an image of the minerals it contained. The scientists were surprised to find graphite and graphite whiskers, formed under very hot conditions between 1273K and 3900K. The graphite whiskers appeared to be a few microns in diameter and up to 10 microns long.
The scientists believe that the carbon they detected came either from the object that made the impact crater, or, that it condensed from the carbon-rich gas that was released during the impact.

Reference:
A. Steele, F. M. McCubbin, M. Fries, M. Glamoclija, L. Kater, and H. Nekvasil. Graphite in an Apollo 17 Impact Melt Breccia. Science, 2010; 329 (5987): 51 DOI: 10.1126/science.1190541

Study Questions:

1. Carbon is present on Earth in different forms. What is the term given to these different forms?
2. Name two different natural forms of carbon found on Earth.
3. In what ways are the two different forms of carbon named above similar?
4. In what ways are the two different forms of carbon named above different?
   
5. Name two different synthetic forms of carbon.
6. Give a use for each synthetic form of carbon named above.
7. Why do you think the scientists were surprised to find graphite in these lunar samples?
   

Art Meets Science

Scientists have been using state-of-the-art gas-chromatography-mass-spectroscopy (GC-MS) to study the organic chemistry of old master paintings in the UK National Gallery's collection. GC-MS has been used to study the characterisation and composition of paint binding media, additions to paint media such as resins, and the composition of old varnishes.

Paint binding media include drying oils such as linseed oil, walnut oil and poppy seed oil. Analysis can show whether the oil was pre-treated by heat-bodying, or thickening, before use by the painter. Added resins can be identified and the state of degradation of the binder assessed. Paintings in other media such as egg tempera can be identified, as well as complex combinations of media.

One such painting studied was The Virgin and Child with an Angel, originally attributed to the Renaissance painter-goldsmith Francesco Francia and dated ~1490. The authenticity of the painting was queried in 1954 when another version of the same painting appeared on the market. In 2009, GC-MS was used to test the paint media and varnish, with the conclusion that the painting in the UK collection was a fake painted in the 19th century.

If you happen to be in the UK during July, you can get to see the results of this research for yourself:
http://www.nationalgallery.org.uk/about-us/press-and-media/close-examination

Now, if you happen to be in Australia, you have only a few days left to get yourself to Federation Square in Melbourne to see Rafael Lozano-Hemmer's amazing "Solar Equation" installation. This incredible piece of physics-meets-art is a simulation of the Sun, 100 million times smaller than the real thing, and compresses the entire 11 year solar cycle including solar flares and sunspots into a few short minutes of visual excitement.
http://www.fedsquare.com/index.cfm?pageID=373

Heavy Fermions

Scientists are interested in studying heavy fermion behaviour because it could lead to the design of new materials for high temperature super-conductors.

Cornell University Scientists imaging the electronic properties of a material composed of uranium, ruthenium and silicon, have found that the effects of heavy fermions begin to appear as the material is cooled below 55K, and, an even more unusual electronic phase transition occurs below 17.5K.

This phase transition was studied using spectroscopic imaging scanning tunneling microscopy (SI-STM) which measures the wavelength of electrons on the surface of the material in relation to their energy. From the wavelength and energy measurements scientists calculated the effective electron mass and found that these electrons were either very heavy, or, that they were acting like very heavy electrons because they were being slowed down. This suggests that these electrons are interacting with the uranium atoms, that is, acting as particles rather than acting as a wave.

Reference:
A. R. Schmidt, M. H. Hamidian, P. Wahl, F. Meier, A. V. Balatsky, J. D. Garrett, T. J. Williams, G. M. Luke & J. C. Davis. Imaging the Fano lattice to 'hidden order' transition in URu₂Si₂. Nature, 2010; DOI: 10.1038/nature09073

Study Questions

1/ What is a fermion?

2/ What is a super-conductor?

3/ What could high temperature superconductors be used for?

4/ What is the atomic symbol for:

• uranium
• ruthenium
• silicon

5/ To which group of the Periodic Table do each of the following elements belong?

• uranium
• ruthenium
• silicon

6/ Convert the following temperatures in Kelvin to ^oC.

• 55K
• 17.5K

7/ What is the relationship between mass, energy and wavelength that would allow Scientists to calculate the effective mass of an electron?

8/ Why would electrons appear to be heavier if they are slowed down?

MALDI-MSI and Fingerprints

A fingerprint is made up of material from the surface of the skin and from gland secretions, which can be detected and analysed. Fingerprints found at a crime scene are often lifted using a powder, and compared with prints on a database to identify a suspect.

Matrix-Assisted Laser Desorption/Ionisation Mass Spectrometry Imaging (MALDI-MSI) is usually used to map different molecules within tissue sections, but, scientists at Sheffield Hallam University have just used the technique to analyse and produce images of fingerprints. Fingerprints analysed this way provided a wider range of information, eg, the technique can detect the presence of drugs and medication, and can provide information about a person's diet.

Reference:
Rosalind Wolstenholme, Robert Bradshaw, Malcolm R. Clench, Simona Francese. Study of latent fingermarks by matrix-assisted laser desorption/ionisation mass spectrometry imaging of endogenous lipids. Rapid Communications in Mass Spectrometry, 2009; 23 (19): 3031 DOI: 10.1002/rcm.4218