Life Of A Chemist

Group 6 dinuclear compounds have been of interest have been of interest for over 40 years due to their formation of metal to metal quadruple bonds, σ2π4δ2 [1], with bond order ranging from 0 to 4. The δ bonds are formed from overlap of the dxy orbitals from each metal forming a bonding and antibonding orbital, where z is the internuclear axis. These orbitals are considerably more diffuse and therefore achieve poorer overlap resulting in an order of bond strength of σ > π > δ.[2]

A pair of d4 transition metals can achieve a bond order of 4[1] by filling the σ, π and δ bonding orbitals with no extra electrons in the anti-bonding orbitals, such as in [Re2Cl4].[2]

This is in contrast to the bond orders found in organic chemistry which ranges from 0 to 3, which is a direct consequence of the number s and p orbitals used in bonding.

 Figure 1.[3] (a) Paddle-wheel structure of a dinuclear compound with 4 bridging ligands, Mo2X4 such as [Mo­2­(O­­2CCH3)4]. (b) Structure of Mo2X8 such as K4[Mo2Cl8].2H2O. (c) Structure of Mo2X4L4 with D2h symmetry.[4,5]

Quadruple bonded metals then form 4 further bonds to ligands, depending on the nature of the ligands, this creates different structures. [Mo­2­(O­­2CCH3)4] has a quadruple bond, high in electron density, is of particular interest due to its particular, due to its unique paddle-wheel structure, spectroscopic properties and potential to be used as a reducing agent.[6]

Over a thousand Mo-Mo compounds have been reported and structures determined using various analytical techniques such as Raman spectroscopy[7], NMR[8] and X-ray crystallography.[1] The Mo-Mo bond length has been extensively researched. The bond length, and thereby bond strength has been determined by X-ray crystallography for 467 compounds containing a Mo-Mo quadruple bond, of which, 442 were within the range 2.06 Å- 2.07 Å.[1] Aforementioned compound [Mo­2­(O­­2CCH3)4] has a Mo-Mo bond length of 2.09 Å [1] and K4[Mo2Cl8].2H2O has a Mo-Mo bond length. [1] This experiment aims to investigate a series of dinuclear Mo compounds containing quadruple bonds and to characterise using NMR and IR.[4]

One of the uses of NMR is to investigate the arrangement of ligands in structure C, Mo2X4L4such as {Mo2Cl4[(C4H9)3]4}. The cis- and trans- forms are of two different symmetry groups and therefore are expected to have different NMR spectrum.[5]

Bibliography

“Diamond Light Source is the UK’s synchrotron. It works like a giant microscope, harnessing the power of electrons to produce bright light that scientists can use to study anything from fossils to jet engines to viruses and vaccines.”

“The linac and the booster synchrotron both work to accelerate the electrons so that they are travelling at nearly the speed of light. 

The storage ring is what gives Diamond its iconic doughnut shape. It has a huge circumference. The storage ring is not a true circle, but a type of polygon called a tetracontakaioctagon, made of 48 straight sections angled together with 48 bending magnets, and this magnetism is used to steer the electrons around the ring. Third generation synchrotrons like Diamond also use special arrays of magnets called insertion devices. These cause the electrons to wiggle around, which produces even more intense light. When the path of the electron beam is bent by Diamond’s powerful magnets, the electrons lose energy in the form of light. This light can then be channelled out of the storage ring and into the experimental stations, called beamlines.

It is inside these beamlines that scientists carry out their experiments. The beamline contains three different sections; the optics hutch, where the light is filtered and focused; the experimental hutch, where the sample sits and the experiment is carried out; and the control cabin, where the scientists control the experiment. The beams of light are so strong that, in the case of Diamond’s X-ray beamlines, it is not safe to be in the same room whilst they are being fired at the sample.”

Crown ethers consists of R chains, typically CH2CH2 groups between oxygen molecules. The first number denotes the number of atoms in the ring and the last number denotes the number of oxygen.  

Crown ethers are supramolecular molecules which are excellent chelating agents due to the pre-organisation of the ring (favorable entropic effects) and as they have so many donor atoms (chelate effect).

There are two main types of adsorption, physisorption and chemisorption.

Physisorption is defined as adsorption in which the forces involved are intermolecular forces (van der Waals forces) and which do not involve a significant change from the gas phase electronic orbital patterns of the species involved. Energies associated with physisorption is typically less than 40 kJ mol-1.

Journals are assigned an factor. This number expresses the average number of weighted citations received in the selected year by the documents published in the journal in the three previous years.

Journal of the American Chemical Society (J. Am. Chem. Soc.) is given a rating of 7.123 which is very high. Therefore only papers with an expected high impact will be able to publish in this journal. 

This is my write up of a simple experimental procedure to produce furoin in the style which the Journal of the Chemical Society (JCS) would publish its works. 

3-benzyl-5-(2-hydroxyethyl)-4-methyl-1,3-thiazolium chloride (0.67 g, 2.5 mmol) dissolved in absolute ethanol (15 cm3) was kept under a  N2 atmosphere. Triethylamine (2.1 cm3, 0.015 mol) was added to the mixture, then 2-furanaldehyde (4.2 cm3, 0.05 mol) was added dropwise over 6 min. The reaction mixture was stirred at room temperature and monitored using TLC (eluent 1:1 Et2O: light petroleum), visualised by UV light then 2,4-DNP. After 24 h, 2-furanaldehyde (Rf = 0.48) was not detected in the reaction mixture. The mixture was cooled at 0°C to form crystals which were dried and washed with ice cold absolute ethanol (3 x 2 mL). A solution of CH3OH (40 mL) with 3 drops of acetone at 80°C was used for recrystallization to produce furoin crystals as a sandy yellow crystalline solid (3.767 g, 78 %); (Rf = 0.29); mp = 134-137 °C (from CH3OH/acetone); (solid state IR using ATR attachment)/ cm-1 3409(OH), 3127(CH), 3963 (CH), 1674(CO).

Key things to note:

Making standard solutions to make a calibration curve. 

This is a common analytical technique used to determine the concentration of an unknown solution. In this case I was using UV-vis however you can make these for flame atomic spectroscopy and other techniques too. You plot a graph of your absorption readings against your known concentrations, get a linear line of best fit. Measure the absorbance of your unknown and read off the graph to determine your concentration. 

One of the major challenges in drug development is to create target specific drugs, this would reduce the number of side effects. Photoliable protecting groups (PLPG) could be the answer.

PLPG are a group of light sensitive chemical compounds. They bind to a drug; temporarily deactivating it, this forms a caged molecule. A caged molecule can be safely delivered to target area, such as a tumour, without the drug acting on the healthy tissue it passes on its way. Once at the tumour, the caged molecules are exposed to light, the PLPG group is removed and the active form of the drug is released around the tumour. This method of drug delivery has huge implications, by reducing the side effects as active drug and reducing the amount of active drug required to have the same effect as the drug would be concentrated where needed. PLPG can already be attached to a range of biological molecules; drugs, DNA, nucleotides, neurotransmitters and fluorescent dyes for research.

Although through the diagram; this mechanism seems easy to employ, PLPG requires ongoing research before it can be applied in medicine. Firstly, identify a PLPG complementary to your drug/ biological molecule and then run various tests to determine: 

- The speed at which the PLPG releases the active drug (the faster the better) - Any side products much be non-toxic - The amount of active drug which is released per gram of the caged form - The wavelength of light used should be of low energy i.e. visible light

One of the major hurdles in the advancement of PLPG is the lack of PLPG which can operate with low energy light. High energy light such as UV light can cause damage to living tissue, and long term exposure can lead to skin cancer. Therefore it is important that PLPG uses visible light. However, it is very difficult to predict based on a chemical structure whether a molecule will react to light, let alone which type. Therefore a more practical method is commonly used; to start with a known PLPG such as o-nitrobenzyl, and then alter its chemical structure slightly and to test it. This has been an effective method and produced PLPG which releases the drug more quickly and uses a slightly lower energy of UV light, although not ideal it is a significant improvement.

Another hurdle lies within delivering light to a target area which is embedded deep within your body. Flusburg B.A. and his team has used fibre optic implants to deliver neurotransmitters to the brain; one of the most difficult to reach places. This development has enabled neurotransmitter research. PLPG are currently being used in multiple fields of research such as enzymes, the movement of Calcium in cells, and also in controlling gene expression in rats.

CIP rules are used to assign stereo chemistry of a molecule, at a chiral centre (R or S). There are many methods you can use to get the correct assignment- this is the one I use, and the one my university has taught me.

 1) Orientate the molecule so that the atom with the lowest atomic number is facing away from you, in this case hydrogen.

2) Order the 3 atoms immediately bonded to the chiral carbon, with the atom of highest atomic number being 1st. Sulphur (atomic number of 16) is 1st and then Oxygen (atomic number of 8) is 2nd and Carbon (atomic number 6) is 3. 

3) Write the numbers 1,2,3 next to their atoms. If reading clockwise gives you 1, 2, 3 then you have an R- isomer. If you read anticlockwise gives you 1, 2 ,3 then you have an S- isomer. In this case we would read from Sulphur (1) to Oxygen (2) to Carbon (3) in an anticlockwise fashion and therefore this is the S isomer. 

This is different to the l and d (or + and -) assignment as this is based on its structure. l and d assignment is determined experimentally and have no correlation to R and S.