Author Archive

Bringing DNA to life – an interview with Clyde Hutchison

In July I met up with Clyde Hutchison (J. Craig Venter Institute) at ISACS5 in Manchester, UK. He gave a great talk at the meeting and afterwards I caught up with him to find out more about his career. A short excerpt from the interview is copied below but you can read the full version in Chemistry World.

Clyde Hutchison Clyde Hutchison is a distinguished professor at the J. Craig Venter Institute, San Diego, US, and is also Kenan Professor Emeritus at the University of North Carolina, Chapel Hill. His research focuses on the search for improved methods to learn about gene function from DNA sequence information.

Why did you decide to become a scientist?

My father was a chemist. He called himself a chemical physicist. He worked on paramagnetic resonance absorption problems and did some really major work in that area. He always encouraged me to learn about science. As a physical scientist, he had a tendency to think of biology as a bit on the messy side. I think in the end, though, he came to like what I did.

You did an undergraduate degree in physics. How did you make the transition to synthetic biology?

I knew I wanted to be a scientist but I didn’t know I wanted to be a biologist. I was also considering a maths major but it came down to office hours. At Yale there was a particular day that you had to declare your major field of study and before you did so, you had to go and speak to the advisor in that field. The physics advisor’s office hours ended later than the maths advisor’s so that’s why I chose physics.

To find out how Professor Hutchison ended up being a biologist, read the full interview.

For more information about ISACS5, check out my conference blog.

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Changing polymer’s backbone to improve organic electronic devices

Incorporating selenium into a polymer backbone can improve the polymer’s electron transport and could lead to improved organic electronics, reports scientists from the UK and Australia.

Ambipolar conjugated polymers, which can transport both holes and electrons, are of great interest as a method to mimic silicon-based logic circuits. Thiophene copolymers have been shown to be good hole transporters but are let down by their ability to transport electrons. 

Replacing thiophene with selenophene results in a significant reduction in polymer band gap, enabling the polymers to effectively transport electrons as well as holes. The resulting polymers display one of the highest hole mobilities reported for any device structure.

Graphical abstract: Low band gap selenophene–diketopyrrolopyrrole polymers exhibiting high and balanced ambipolar performance in bottom-gate transistors

Download the Chemical Science Edge article to find out more.

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The next generation of foldamers

Scientists in Germany have reported a novel foldamer structure based on perylene bisimide (PBI) dyes and rigid oligophenylene ethynylene (OPE) backbones. The work was born out of the desire to create a well-defined macromolecular framework with predictable geometries. The group, from the University of Würzburg and lead by Frank Würthner, designed an OPE-fused PBI oligomer in which the π-π interactions between the molecules of PBI direct the folding geometry. 

Graphical abstract: Foldamer with a spiral perylene bisimide staircase aggregate structureWhile the influence of π-π interactions on systems which fold into highly ordered structures, or foldamers, has been previously studied, the system designed by Würthner and his team is unique in that the rigid OPE backbone played no part in directing the folding geometry; π-π interactions in the PBI units were the sole influence on the backbone conformation and lead to the final geometry. 

A typical OPE-fused PBI oligomer was found to contain between 8 and 9 PBI units, as determined by gel permeation chromatography and diffusion NMR. Further studies using MALDI-TOF ruled out impurities or side production in the oligomer. With this structural data in hand, they used UV-vis spectroscopy to prove that only the PBI, not the OPE, units participated in π-π stacking; a feature that is unique to their oligomer system. The authors then proved, through a series of elegant UV-vis analyses in chloroform and methylcyclohexane, that the oligomer was able to fold and unfold with changes in solvent polarity. These conclusions were also supported by molecular modeling studies. 

The PBI oligomer reported in this work, in which the OPE backbone does not play a role in π-π stacking, resembles interactions in nucleic acids. Therefore, this system could be an ideal mimic for functional biological systems such as DNA or may also prove to have very interesting photophysical properties.

Find out more by downloading Würthner’s Edge article.

Posted on behalf of Patricia Pantos, Chemical Science web writer.

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Domino diastereoselectivity

Huw Davies’ group have developed a domino sequence for the asymmetric synthesis of highly functionalised cyclopentanes.

The researchers from Emory University have combined scandium catalysis with a previously reported asymmetric rhodium-catalysed dienol formation to afford cyclopentanes in good to excellent levels of enantioselectivity. Four new stereogenic centres are formed in the reaction sequence and the cyclopentane products are obtained as single diastereoisomers.

domino sequence for the asymmetric synthesis of highly functionalised cyclopentanes

The one-pot procedure commences with a tandem oxygen ylide formation and [2,3] sigmatropic rearrangement between racemic allyl alcohol 1 and vinyl diazoacetate 2, resulting in formation of chiral dienol 4. Upon heating, an oxy-Cope rearrangement provides enol 5 in quantitative yield albeit with slight erosion of enantiomeric excess. Subsequent tautomerisation yields ketone 6, which is primed for a scandium triflate-catalysed carbonyl ene reaction on elevation of temperature, affording the cyclopentane product.

The impressive diastereoselectivity of this reaction combined with the complexity of the enantioenriched cyclopentane products highlights the synthetic power of reactive metal carbenoids in such thoughtfully designed reaction sequences. Download Davies’ Edge article to find out more.

Researcher’s perspective:
“The discovery of new carbenoid reactions is always an exciting time: often the products generated are high energy and capable of further transformations. Needless to say, it was thrilling the first time the crude NMR indicated the domino sequence was viable.” Brendan Parr, from the Davies group

 Posted on behalf of Alice E. Williamson, Chemical Science web writer.

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ACS Denver – making chemical connections

On Tuesday I met up with Chem Soc Rev editorial board member Huw Davies and the speakers from the young academic investigator session he organised. It was a really great session, with 16 of the best emerging investigators in organic chemistry showcasing their recent, and very impressive, research. They included Zachary Ball and Neil Garg, both of whom have recently published in Chem Sci (see Proximity-driven metallopeptide catalysis: Remarkable side-chain scope enables modification of the Fos bZip domain and Nickel-catalyzed amination of aryl carbamates and sequential site-selective cross-couplings). We all went out for dinner after the session then on to a bar which claimed to have the world’s largest selection of draft beer – no wonder we found lots of other conference delegates in there!

I also attended some of the inorganic nanoscience award symposium in honour of Catherine Murphy, one of ChemComm‘s advisory editorial board members. I was treated to a double dose of Northwestern excellence, first from Chad Mirkin then Chemical Science associate editor Teri Odom. You can find out about Teri’s work in her recent Chem Sci Perspective.

Wednesday was another great day. I met up with Haw Yang, another Chemical Science associate editor and had lunch with Michel Orrit and Johan Hofkens, whom I had met previously at ISACS2 and ISACS5 respectively. They’ve both published exceptional articles in Chem Sci (see Detection limits in photothermal microscopy; DNA fluorocode: A single molecule, optical map of DNA with nanometre resolution; Fluorescent probes for superresolution imaging of lipid domains on the plasma membrane).

One of my highlights in the afternoon was Byron Purse‘s talk on unusually stable encapsulation complexes. By assembling pyrogallolarene hexamers under thermal conditions in the absence of solvent, he found he could efficiently load guest molecules, producing kinetically trapped assemblies.

My time in Denver ended on a high as Duncan Graham, Chem Sci advisory board member, signed me in to the exclusive airport lounge where I sipped sparkling wine in the company of high-flying chemists. Proof that who you know as well as what you know counts in chemistry!

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ACS Denver – will it blow me away?

The hurricane might be thousands of miles away but we’re feeling its effects here at the ACS meeting in Denver. Flight cancellations from the East coast have thwarted the travel plans of a number of speakers and delegates, leaving some noteable holes in the program. Nonetheless, day one, which included the lively RSC reception, was great and there are so many excellent-looking sessions today I am having trouble deciding which to go to. I have time to decide though as I’ve been up since 4 am….stupid jet lag!

Follow my tweets throughout the coming days @chemicalscience to find out who is saying what at ACS Denver.

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Indole annulation or indole ring-opening

Researchers have shown that acid-catalysed condensations of aminobenzaldehydes with indole result in the formation of different products depending on whether the aminobenzaldehyde is primary or secondary.

Daniel Seidel’s group at Rutgers, The State University of New Jersey, found that N-methylbenzaldehyde reacts with indole to form neocryptolepine-related structures in a single step. Neocryptolepine (5) and its analogues are attractive targets for synthesis as they display promising antimalarial activity.

acid catalysed reactions of aminobenzaldehydes with indoles

Conversely, primary benzaldehydes such as aminobenzaldehyde react under similar conditions to form quinolines (7). The mechanistic pathways leading to the formation of both indoles (5) and quinolines (7) are initially identical, with aminobenzaldehyde 1 condensing with indole 2 to form the corresponding azafulvenium ions (3), which undergo ring closure to yield tetracyclic products (4). At this point the mechanisms diverge; secondary systems (4a) undergo proton loss and oxidation to give neocryptolepine analogues (5), whilst primary systems (4b) undergo proton transfer to give products of type 6, which aromatise to form quinoline products (7) on ring opening.

The group made a range of both neocryptolepine analogues and quinoline systems in good to excellent yields, representing important scaffolds for medicinal chemistry.

Researcher’s perspective:
“From the confirmation of the formation of neocryptolepine to the surprising results of the reactions of primary aminobenzaldehydes, this project was a fun experience with its intricacies and challenges” Aaron X. Sun, from the Seidel group

Seidel’s Edge article is free to download. Let me know what you think of this work by leaving your comments below.

Posted on behalf of Alice E. Williamson, Chemical Science web writer.

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Straight to the point

Researchers from the University of Delaware have reported a total synthesis of hyacinthacine A2, an attractive target owing to its selective glycosidase inhibition and activity against HIV. 

Joseph Fox’s research group achieved the synthesis in less than ten steps from sucrose by designing and synthesising a functionalised 5-aza-cyclooctene system (1) that would undergo a novel transannular hydroamination, following stereocontrolled photoisomerisation.

hyacinthacine synthesis

The efficiency of the photoisomerisation process was improved by using a flow system that removes trans-isomers by selective complexation with silver salts, thereby enabling the cis-isomer of 1 to be recycled. Incorporation of a fused acetonide ring system in 1 imposed significant conformational constraints to favour formation of the desired trans-diastereosiomer 2 in good yield and in 8:1 diastereomeric ration following decomplexation from the silver salts.

Following separation of the major diasteroisomer of 2, and cleavage of both trifluoroacetyl and acetonide protecting groups, the corresponding ammonium salt was obtained. The planar chirality present in 2 was perfectly transferred in a transannular hydroamination to give the point chirality present in the natural product.

Find out more by downloading Professor Fox’s Chemical Science Edge article, which is free to access.

Posted on behalf of Alice E. Williamson, Chemical Science web writer.

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1st Chemical Science Symposium

We’re heading to Nanjing in China – because our first symposium is taking place in that city on 6th September 2011.

Professor Wenbing Hu from the School of Chemistry and Chemical Engineering at Nanjing University will be our host for the one-day meeting, which has the topic of Supramolecular Chemistry and Organic Materials. 

Among the speakers is our Associate Editor for Organic Materials Colin Nuckolls. His lecture is titled ‘From Molecules to Materials’. 

The winner of the very first ChemComm Emerging Investigator Lectureship, Scott Dalgarno, will deliver his lecture on Metal-Organic Calixarene Assemblies. 

Attendance at the symposium is free of charge – find out more about the speakers and the schedule on our website.

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‘Dial a molecule’ approach controls antibiotic production

UK scientists have used genetic methods to control the chemical structures of pacidamycin antibiotics produced in bacteria. Their approach allows them to ‘dial into’ particular molecules, and to generate new pacidamycins.

The pacidamycins are uridyl peptide antibiotics with specific activity against Pseudomonas aeruginosa, a common cause of hospital infections. They target a protein in the bug’s cell wall. Around 20 pacidamycins are produced naturally by Streptomyces coeruleorubidus, although they have never been used clinically.

TelephoneAs with many natural products, purifying one from a suite of similar compounds can be tricky. But Rebecca Goss and colleagues at the University of East Anglia say their approach allows them to steer production in the direction they choose. ‘We’ve been able to introduce the genes into an organism that doesn’t naturally produce pacidamycin and rather than it making a whole forest of different peaks – of different antibiotics – which would be a separation nightmare, we’ve been able to bolt in the genes to make the different members of the family,’ explains Goss. ‘So we’ve been able to “dial a molecule” within the bug.’

Find out more in Chemistry World and download Goss’ Chemical Science Edge article for free.

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