Unveiling the behavior of hydrogen molecules

Dr. William Yim had the opportunity to collaborate with Toshiaki Iitaka from Riken Advanced Science Institute and Prof John Tse from Canada’s University of Saskatchewan last year. The team of researchers discovered the physical basis to explain the newly discovered vibration behavior of molecular hydrogen, including ‘silane’ - hydrogen bound to silicon, under high pressure.

The two-month project resulted in a paper, ‘Pressure-induced intermolecular interactions in crystalline silane-hydrogen’, that was published in Physical Review Letters 105.

The cross-disciplinary team was like a dream team, made possible by the mutual introductions given by Prof John Tse and Dr. Wu Ping, IHPC’s Director of Material Science and Engineering Department.

“Prof. John Tse’s expertise is on experimental and computational research on materials science and he is famous in high pressure research field” said William. “Dr. Toshiaski Iitaka is a permanent staff member at Riken working on solid state research and program development for linear scaling computational method.”

As William himself has a track record on ab initio vibrational frequency calculations applying to surface science, it was a good match of expertise.

His motto is “Be Prepared”, so the challenge of taking on the project was a welcome one.

“I like to learn new skills, and I made sure I learnt all the necessary computational techniques before this project. Good preparation and speed are the key factors in benefitting from such a good opportunity.”

It was a classic collaboration case study, in which everyone played an important role in making the breakthrough.

“When Prof. Tse mentioned an interesting problem of H2 vibron softening, we were well prepared to puzzle out the scientific question” William said.

William contributed the ‘Donor-acceptor interaction in compression regime’, which is a brand new idea.

The team performed molecular dynamic simulations to study the interactions between hydrogen and silane molecules, which gave a better fundamental understanding for the materials under extreme conditions.

The results provided a good basis to potentially develop a hydrogen economy.

William said “the knowledge of physical interaction in compressed regimes, as indicated by vibrational spectroscopy and chemical bonding, will be very helpful for further engineering the mixing process and hence the H2 transport capability.”

The project is another feather in the cap for IHPC.

Dr. Toshiaki Itaka, from Riken’s Computational Astrophysics Laboratory commented: “It was an exciting experience that I could work with William and IHPC for the study of SiH4 under pressure. As a physicist, I learned a lot from the chemist's viewpoint of William.”

“I also noted that IHPC has strength not only in academic research but also in its application to important problems in real world. This is what Riken is aiming at, and would like to learn from IHPC.”

William too had an enriching experience working closely with the other researchers, commenting “the most important skill I’ve learnt is to understand how to translate research work into an impactful and engaging story. It is an art to turn lots of boring numbers into an interesting story so that people can understand the significance of the discovery.”

Provided by Institute of High Performance Computing, Singapore

Sugar synthesis hits the sweet spot

A new strategy for synthesizing the kind of complex molecules that certain bacteria use to build their protective cell walls has been developed by Akihiro Ishiwata and Yukishige Ito from the RIKEN Advanced Science Institute in Wako, Japan. The strategy applies to Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), so it could lead to much-needed new medicines to combat the spread of multi-drug-resistant strains of the pathogen. 

Disrupting the formation of the cell wall of M. tuberculosis is already a proven strategy for treating TB, with several of the current front-line drugs working in this way. However, the cell wall skeleton is a complex, highly branched structure, and its biosynthesis is not yet fully understood.

According to Ito, the compound he and Ishiwata made—a sugar-based structure known as the arabinan motif (Araf22) (Fig.1)—should be a useful biological probe, helping to unravel cell wall biosynthesis. Perhaps more importantly, however, the success of their strategy suggests that larger, more complex cell wall components could be made in the same way. 

Sugar-based compounds are notoriously difficult to make. Sugars are bristling with reactive alcohol groups, so molecules made from more than 20 sugar units pose a significant synthetic challenge. Nevertheless, Ishiwata and Ito succeeded in clipping together the branching chain of 22 sugar units needed to make Araf22. 

Their strategy involved synthesizing small sub-structures of the mycobacterial cell wall skeleton and building from there. To make the compound, they conceptually broke down Araf22’s structure into several simpler fragments, chemically synthesized those fragments, and then clipped them together to make Araf22. This aspect of the strategy has been applied before, but Ishiwata and Ito built the fragments such that they clipped together at linear rather than branching points in their structure. 

The researchers’ strategy makes the individual fragments more difficult to build, but it makes the coupling process much more efficient. Crucially, that means the strategy should work just as well as a way to make even larger and more complex components of the cell wall.

“One of the main points of this work is for us to show the way to construct the more complex compounds,” says Ishiwata. “We are now planning to synthesize more complex but structurally reliable glycans of cell wall skeletons for biological studies.” However, such compounds could even prove to be useful drugs in themselves, if they are able to disrupt the cellular machinery responsible for mycobacterial cell wall biosynthesis.

More information: Ishiwata A. & Ito Y. Synthesis of docosasaccharide arabinan motif of mycobacterial cell wall. Journal of the American Chemical Society 133, 2275–2291 (2011)

Provided by RIKEN (news : web)

Pentagonal tiles pave the way towards organic electronics

 New research paves way for the nanoscale self-assembly of organic building blocks, a promising new route towards the next generation of ultra-small electronic devices.

Ring-like molecules with unusual five-fold symmetry bind strongly to a copper surface, due to a substantial transfer of charge, but experience remarkably little difficulty in sideways diffusion, and exhibit surprisingly little interaction between neighbouring molecules. This unprecedented combination of features is ideal for the spontaneous creation of high-density stable thin films, comprising a pavement of these organic pentagonal tiles, with potential applications in computing, solar power and novel display technologies.

Currently, commercial electronics use a top-down approach, with the milling or etching away of inorganic material, such as silicon, to make a device smaller. For many years the computing power of a given size of computer chip has been doubling every eighteen months (a phenomenon known as Moore's law) but a limit in this growth is soon expected. At the same time, the efficiency of coupling electronic components to incoming or outgoing light (either in the generation of electricity from sunlight, or in the generation of light from electricity in flat-screen displays and lighting) is also fundamentally limited by the development of fabrication techniques at the nanometre scale (a nanometre being one billionth of a metre).

Researchers are therefore looking for ingenious solutions in the creation of ever smaller electronics. The field of nanotechnology is taking a bottom-up approach of creating electronics using naturally self-assembling organic components, such as polymers, which will be capable of spontaneously forming devices with the desired electronic or optical characteristics.

The latest findings are from scientists at the University of Cambridge and Rutgers University who are working on the development of new classes of organic thin films on surfaces. By studying the fundamental forces at play in self-assembling thin films, they are developing the knowledge that will allow them to tailor these films into molecular-scale organic-electronic devices, creating smaller components than would ever be possible with conventional fabrication techniques.

Dr Holly Hedgeland, of the Department of Physics at the University of Cambridge, one of the co-authors of the paper reporting the research, said: "With the semiconductor industry currently worth an estimated $249 billion per year there is a clear motivation towards a molecular scale understanding of innovative technologies that could come to replace those we use today."

It is not simply the electronic properties of a molecule on a surface that will control its potential to form part of a device, but also whether it will move by itself into the required structural configuration and remain stable in that position even if the device becomes heated in use.

Molecules that are strongly bound to the substrate with a high degree of transfer of charge offer a range of new possibilities, though little is currently known of their behaviour. A number of organic molecules, usually featuring carbon rings across which electronic charge can conduct, potentially demonstrate the right electronic properties, but the long-range forces which will govern their self-assembly during the first phases of growth often remain a mystery.

Now the interdisciplinary team based in the Departments of Physics and Chemistry at the University of Cambridge, and the Department of Chemistry and Chemical Biology at Rutgers University, have reported the first dynamical measurements for a new class of organic thin film where cyclopentadienyl molecules (C5H5) receive significant electronic charge from the surface, yet diffuse easily across the surface and show interactions with each other that are much weaker than would typically be expected for the amount of charge transferred.

Hedgeland explained: "By coupling the experimental helium spin echo technique with advanced first-principles calculations, we were able to study the dynamic behaviour of a cyclopentendienyl layer on a copper surface, and to deduce that the charge transfer between the metal and the organic molecule was occurring in a counter-intuitive sense."

Dr Marco Sacchi, of the Department of Chemistry at the University of Cambridge, who carried out the calculations that helped explain the startling new experimental results, said that "the key to the unique behavior of cyclopentadienyl lies in its pentagonal (five-fold) symmetry, which prevents it latching onto any one site within the triangular (three-fold) symmetry of the copper surface through directional covalent bonds, leaving it free to move easily from site to site; at the same time, its internal electronic structure is just one electron short of an extremely stable `aromatic' configuration, encouraging a high degree of charge transfer from the surface and creating a strong non-directional ionic bond."

The researchers' findings, reported in Physical Review Letters on May 6, highlight the potential of a new category of molecular adsorbate, which could fulfill all the criteria required for useful application.

Hedgeland concluded: "The unusual character of the charge transfer in this case prevents the large repulsive interactions between adjacent molecules that would otherwise have been expected, and hence should enable the formation of unusually high-density films. At the same time, the molecules remain highly mobile and yet strongly bound to the surface, with a large degree of thermal stability. In all, this is a combination of physical properties that offers huge potential benefit to the development of new classes of self-assembled organic films relevant for technological applications."

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by University of Cambridge.

Journal Reference:

H. Hedgeland, B. Lechner, F. Tuddenham, A. Jardine, W. Allison, J. Ellis, M. Sacchi, S. Jenkins, B. Hinch. Weak Intermolecular Interactions in an Ionically Bound Molecular Adsorbate: Cyclopentadienyl/Cu(111). Physical Review Letters, 2011; 106 (18) DOI: 10.1103/PhysRevLett.106.186101

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

A renewable twist on fossil fuels

 Pulling valuable fuels out of thin air? It sounds like magic, but Joel Rosenthal, a chemist at the University of Delaware, is working to transform carbon dioxide (CO2), a greenhouse gas in the atmosphere, into gas for your car and clean-energy future fuels.

Such a feat could help reduce the rising CO2 levels implicated in global warming and also offer a new method of renewable energy production.

Oak Ridge Associated Universities (ORAU), a consortium of 98 Ph.D.-granting universities, of which UD is a member, has selected Rosenthal to receive the Ralph E. Powe Junior Faculty Enhancement Award to pursue the novel research. Rosenthal is one of 30 award winners nationwide.

The competitive award, which provides $5,000 in seed funding from ORAU and $5,000 in matching funding from the faculty member's university, is intended to enrich the research and educational growth of young faculty and serve as a springboard to new funding opportunities.

Rosenthal and his team are designing electrocatalysts from metals such as nickel and palladium that will freely give away electrons when they react with carbon dioxide, thus chemically reducing this greenhouse gas into energy-rich carbon monoxide or methanol.

Besides its use in making plastics, solvents, carpet and other products, methanol fuels race cars in the United States and currently is being researched as a hydrogen carrier for fuel cell vehicles.

Carbon monoxide is an important precursor to liquid hydrocarbons in the energy arena, in addition to its applications as an industrial chemical for producing plastics to detergents to the acetic acid used in food preservation, drug manufacturing and other fields.

"The catalytic reduction of carbon dioxide to carbon monoxide is an important transformation that would allow for the mitigation of atmospheric CO2 levels, while producing an energy-rich substrate that forms a basis for fuels production," Rosenthal says.

"The chemistry we're doing is energetically uphill -- it's an energy-storing process rather than a downhill, energy-liberating process," he notes. "And our goal is to make liquid fuel renewably from wind and solar sources, not from typical fossil fuel bases."

As early as junior high, Rosenthal said, he realized that basic life processes are linked to molecular energy conversion. Then his undergraduate and graduate research took off on renewables.

He earned his undergraduate degree in organic chemistry from New York University and his doctorate in inorganic chemistry at MIT while studying how metals catalyze various energy conversion processes. His doctoral adviser at MIT was Dan Nocera, a leading scientist in renewable energy research.

The strong reputation of the chemistry and biochemistry department lured Rosenthal, a New York City native, to UD. He joined the UD faculty this past fall and already has a research group of eight focusing on the project -- one postdoctoral researcher, four graduate students and three undergraduates.

"The CO2 problem is very important, and people have to tackle it," Rosenthal says. "It's my hope to be able to map out the molecular design principles for efficient CO2 conversion into fuels. Then you can think about doing this on a commercially relevant scale."

Conservative estimates predict that by 2050, the rate of global energy consumption will roughly double the rate recorded at the end of the 20th century. Most scientists believe that rising carbon dioxide levels are leading to global climate change.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by University of Delaware.

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.