Organic & Biomolecular Chemistry Blog

Organic & Biomolecular Chemistry Editor Richard Kelly will be visiting several North East universities next week as part of the RSC US Roadshows 2012.

Week 4 sees the Royal Society of Chemistry visiting four universities in Pennsylvania and New York:

May 7th – University of Pittsburgh
May 8th – Pennsylvania State University
May 10th – University of Pennsylvania
May 11th – Columbia University

Read more about the US roadshows 2012:

Starting in mid April 2012, RSC Publishing has been touring the United States of America to share more than 170 years experience of publishing in the chemical sciences. Sixteen universities across the country are hosting these one-day events, which are open to all members of the hosting institute.

Attendees have the opportunity to explore RSC’s apps on mobile devices and meet informally with RSC editors. Lunchtime discussion groups explore reading habits and opportunities in the 21st century and an afternoon seminar give an insight into the world of scholarly publishing, with tips on how to get published in high impact journals. A demonstration of ChemSpider, and a guest lecture from an RSC associate editor or board member are available at many of the roadshows.

Follow the RSC Roadshows on Twitter – just look for #RSC2012.

A collagen-binding peptide with applications in wound healing has been developed by scientists in the US. The peptide is able to invade the strands of collagen, forming a strong and stable non-covalent bond at room temperature. Pendant drug molecules could be attached to the peptide and anchored at the wound site to aid wound healing…

Read the full article at Chemistry World, or read the OBC paper:

Peptides that anneal to natural collagen in vitro and ex vivo
Sayani Chattopadhyay, Christopher J. Murphy, Jonathan F. McAnulty and Ronald T Raines
DOI: 10.1039/C2OB25190F

A highly selective indicator for the amino acid cysteine has been designed by scientists from the US and China to monitor levels in human plasma. Elevated cysteine levels have been linked with motor neurone disease, Parkinson’s disease and Alzheimer’s disease.

Cysteine is an essential amino acid and plays an important role in cell functions. Its structure contains both a sulfhydryl (-SH) and an amino group (-NH₂), both of which are reactive. Previous detectors have focused on reactions with the sulfhydryl group, but it has been tricky to detect cysteine over other SH-containing biomolecules in the blood, such as glutathione and the closely related homocysteine.

The indicator molecule reacts with the sulfhydryl and amino parts of the cysteine molecule to form a pink compound that's fluorescent under UV light. No such reaction is seen with other biothiols

Robert Strongin from Portland State University, Portland, and co-workers, have found a way to overcome this problem, by designing a fluorescent sensor called a chemodosimeter (so called because the visible change is due to an irreversible reaction). They used an indicator molecule that reacts with both the sulfhydryl and amino parts of the cysteine molecule.

‘We can detect cysteine selectively due to its unique chemistry, which we have complemented with our indicator design,’ explains Strongin. ‘There is a very selective reaction that turns the indicator on.’ The cysteine’s sulfhydryl group reacts with the indicator molecule to form a colourless compound. The amino part attacks an ester group on the indicator molecule to form a pink compound that is fluorescent under UV light. When tested with other amino acids or SH-containing molecules, no colour change or fluorescence could be seen.

‘Compared to designing probes for the detection of metal ions or inorganic anions, analytes such as cysteine tend to be far more problematic. The work provides convincing evidence that a clever design can overcome such obstacles,’ says Michael Heagy, an expert in fluorescent chemosensors for biological molecules at the New Mexico Institute of Mining and Technology, US.

In the future, Strongin plans to develop the approach to make other specialised indicators for non-polar metabolites, such as amino acids, sugars and phospholipids.

A seminaphthofluorescein-based fluorescent chemodosimeter for the highly selective detection of cysteine
Xiaofeng Yang , Yixing Guo and Robert M. Strongin
DOI: 10.1039/C2OB25178G

Read the original article at Chemistry World

Theoretical chemistry could answer some questions about how life on earth originated, say Australian researchers.

Although we know amino acids were vital in the genesis of life, how they first appeared on earth is still under much debate. One theory is that they were introduced from space, having been synthesised in molecular clouds from simpler radicals. However, at almost absolute zero temperatures, it would be very difficult for any molecular collision to overcome the activation energy barrier. Unfortunately, owing to these extreme conditions, it is impossible to conduct laboratory experiments to investigate this.

Noticing that a number of possible interstellar reactions involve hydrogen transfer, John Bowie and Tianfang Wang at the University of Adelaide considered the possibility that they may be assisted by hydrogen tunnelling effects. Hydrogen tunnelling occurs when hydrogen atoms or nuclei take part in a reaction without having to overcome an energy barrier; instead they ‘tunnel’ through it. The team used high level computational methods to study how tunnelling affects isomerisation reactions that may either help or hinder the synthesis of biologically important molecules.

Molecules of life are thought to have been introduced to earth by collisions from comets or meteorites

‘Let us propose, for example, that ?CH₂NH₂ and ?CN react to form the glycine precursor NH₂CH₂CN,’ explains Bowie, ‘if [?CH₂NH₂] isomerises rapidly to CH₃NH?, then the proposed synthesis is not practical.’

They found that although these reactions show significant tunnelling effects, the rate constants for most of them would still be too slow for reaction to occur.

Holger Somnitz, a theoretical chemistry expert at the University of Duisburg-Essen, Germany, appreciates the information obtained. ‘The [researchers] have quantified the effect of tunnelling. and provided valuable information on the potential energy along the minimum energy path,’ he says. However, he points out that the true impact of the work will only be revealed after experimental confirmation of the interstellar existence of the studied radicals.

Recognising the usefulness of the information obtained from their calculations, the researchers are now turning their attention to tunnelling effects in other fields of interest, such as in proteomics.

Hydrogen tunnelling influences the isomerisation of some small radicals of interstellar importance. A theoretical investigation.
Tianfang Wang and John H. Bowie
DOI: 10.1039/C2OB07102A

Read the original article at Chemistry World

Goverdhan Mehta talks to Sheena Elliott and Elinor Richards about the progress of science in India and the challenges scientists face

Goverdhan Mehta is a researcher, specialising in organic synthesis. He has helped to build institutions in India – the Indian Institute of Technology, Kanpur, the University of Hyderabad, and the Indian Institute of Science, Bangalore. He was director of the Indian Institute of Science (1998-2005) and vice chancellor of the University of Hyderabad (1994-1998).

Your research is focused on organic chemistry. What attracted you to that field?

There is something intrinsically fascinating about organic chemistry. In my early high school years, when I was exposed to interesting chemical structures, I was attracted to them. I had a sense of appreciation for art and organic molecules to me provided a wonderful expression of art at a molecular level.

What are your main achievements in the field?

I have worked in many areas of organic chemistry, but it’s synthesis that’s given me the greatest pleasure. As organic chemistry advanced, different contemporary challenges came to my attention. The main driver for me to pursue those challenges was the intricacy of the target structure synthesis. There was also an element of expectation that perhaps our research might become useful to society. We continue to need new drugs for a variety of disorders, so we synthesised a large number of natural products; many of them are biologically active and it is quite possible that some of them can provide leads for new drug discovery.

Over the last few years, I have become interested in how to address a problem that the ageing population is facing – neurodegeneration. It has been shown that some natural products can slow down neurodegeneration. In some cases, there is also an indication that they can help restore lost cognitive function. So I have been working on the synthesis of such lead molecules. As I’m getting older, I recognise the need for doing something in that area!

You’ve won numerous awards. Which achievements are you most proud of?

I don’t think that awards and recognition have necessarily brought me a great sense of joy. They do bring a sense of satisfaction because your peers have recognised your work. But I don’t think any serious researcher works for awards. It is the sheer joy of research that keeps people going. Recognition has come my way, but don’t think that I can equate that with the joy of doing research.

What are the challenges facing scientists in India and how could these be overcome?

Scientists all over the world are facing challenges on two fronts. The first problem is that scientists are not being supported by society as much as they should and some governments are not always forthcoming in terms of providing budgetary support. The second problem is that scientists, and science in general, have become isolated both in terms of discipline and, to some extent, in terms of geographical location. This is being redressed now with increasing international collaborations, so in the geographical sense, the isolation is being reduced. But I think disciplinary isolation vis a vis other knowledge streams and fragmentation of science is still a serious challenge.

It is a good time for scientists in India because the government is very supportive of science. Funding is no longer as serious a problem as it is in other parts of the world. Recently, our prime minister said that the budget for science will be almost doubled over the next few years. But I’m not too sure that we as a scientific community are steering science in India in the direction that it ought to be heading. I believe that the government and the scientific community must set a goal that in the next 10 years, India will be among the world’s leading scientific countries.

What is your opinion on the perception that Indian science and research is falling behind the rest of the world, following recent comments by Prime Minister Manmohan Singh?

Prime Minister Singh’s statement referred mainly to China. China has made more progress in science and technology than India. Scientific productivity in India has increased, but not as much as in China. Since we are behind, to simply say that we are walking and walking well is not enough. We should be galloping to catch up. My judgement is that our progress is not commensurate with the support that the government is providing, and not commensurate with the capacity, capability, enthusiasm and the vibrancy that our youth have. We can achieve much more.

How do the different industries compare (the pharmaceutical industry in particular or the more general chemical industry)?

It is only over the last 10 or 12 years, since the economic reforms, that industry in India has grown at such a rate so as to be in a position to invest in research and development. I expect that investment by industry is going to rise; however, the current level of investment is not in an acceptable range. There are certain sectors – pharma, for example – and some other chemical industries, where I think India’s potential is immense, but there are some challenges with the policies that are being pursued. We have to devise a well thought out strategy.

The prime minister’s Science Advisory Council reported that there in an absence of any Indian universities among the world’s best. What is your opinion on the quality of universities in India?

I’m not a great believer in the ranking systems being followed, but the fact is that no Indian university features among the top few hundred  universities. However, if we were to look at undergraduate teaching, India has institutions that produce graduates through excellent teaching and training. The graduates are probably as good as they are anywhere else in the world. If you were to grade an institution on the quality of undergraduates, I would say that the Indian Institutes of Technology rank among the top 10 institutions in the world. But, if you bring in research and other elements, they will not feature anywhere near the top. So the quality of research is a serious problem. I think it is high time that the scientific community and scientific leadership in our country sort out an effective, implementable strategy to make a major shift.

You experienced difficulty obtaining a visa to travel to the US in 2006, when you were invited to give a lecture at the University of Florida. At the time, a report from the National Academy of Sciences in the US said that at least 3000 scientists had faced a similar problem. Have things improved since then or do you believe that the visa problem is hampering scientific progress and career development for scientists?

It was ironic that I and a leading scientist from the US, Jane Lubchenco (who at that time was president of the International Council for Science before I succeeded her), wrote an editorial about the principle of universatility of science and the visa regime in Science a few months before this happened. We wrote that it was important for the international growth of science that scientists were able to travel. Little did I realise that soon I would be a victim of this! I think the situation has improved, but a lot more needs to be done. While the US National Academy of Sciences is playing a very positive role towards this end, the academies can only do the advocacy. Eventually, it is the government and the state department of security staff that makes the final judgement.

If you have any spare time, how do you fill it?

For most scientists, and I’m no exception, your research is a hobby. What other profession can give you that pleasure and privilege? In a previous interview, I was asked what I would wish for. I said we Indians believe in rebirth and so the only wish I have is that if I were to be born again, I would be a scientist. I would like to be a chemist, hopefully a better one.

Read some of Goverdhan Mehta’s recent research:

Towards a temperature-guided molecular switch: an unusual reversible low-temperature polymorphic phase transition in a conformationally locked environment
Goverdhan Mehta and Saikat Sen, Chem. Commun., 2009, 5981
DOI: 10.1039/b905651c

Understanding the self-assembling process in crystalline cyclooctitols: an insight into the conformational flexibility of medium-sized rings
Goverdhan Mehta, Saikat Sen and Kotapalli Pallavi, CrystEngComm, 2008, 10, 534
DOI: 10.1039/b712877k

Additive induced polymorphous behavior of a conformationally locked hexol
Goverdhan Mehta, Saikat Sen and Kailasam Venkatesan, CrystEngComm, 2007, 9, 144
DOI: 10.1039/b613949c