Archive for March, 2011

Top Ten most-read PCCP articles in February

The latest top ten most accessed PCCP articles

See the most-read papers of February 2011 here;

Ekaterina I. Izgorodina, Phys. Chem. Chem. Phys., 2011, 13, 4189-4207
DOI: 10.1039/C0CP02315A
 
Ferdi Schüth, Phys. Chem. Chem. Phys., 2011, 13, 2447-2448
DOI: 10.1039/C1CP90005F
 
Sandra Engelskirchen and Chandrashekhar V. Kulkarni, Phys. Chem. Chem. Phys., 2011, 13, 3003-3003
DOI: 10.1039/C1CP90008K
 
Christopher J. Cramer and Donald G. Truhlar, Phys. Chem. Chem. Phys., 2009, 11, 10757-10816
DOI: 10.1039/B907148B
 
Chandrashekhar V. Kulkarni, Wolfgang Wachter, Guillermo Iglesias-Salto, Sandra Engelskirchen and Silvia Ahualli, Phys. Chem. Chem. Phys., 2011, 13, 3004-3021
DOI: 10.1039/C0CP01539C
 
Katsuhiko Ariga, Phys. Chem. Chem. Phys., 2011, 13, 4780-4781
DOI: 10.1039/C1CP90016A
 
Matthew B. Boucher, Simone Goergen, Nan Yi and Maria Flytzani-Stephanopoulos, Phys. Chem. Chem. Phys., 2011, 13, 2517-2527
DOI: 10.1039/C0CP02009E
 
Stephen Berkebile, Thomas Ules, Peter Puschnig, Lorenz Romaner, Georg Koller, Alexander J. Fleming, Konstantin Emtsev, Thomas Seyller, Claudia Ambrosch-Draxl, Falko P. Netzer and Michael G. Ramsey, Phys. Chem. Chem. Phys., 2011, 13, 3604-3611
DOI: 10.1039/C0CP01458C
 
Chun-Jiang Jia and Ferdi Schüth, Phys. Chem. Chem. Phys., 2011, 13, 2457-2487
DOI: 10.1039/C0CP02680H
 
Ilkeun Lee, Manuel A. Albiter, Qiao Zhang, Jianping Ge, Yadong Yin and Francisco Zaera, Phys. Chem. Chem. Phys., 2011, 13, 2449-2456
DOI: 10.1039/C0CP01688H

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PCCP on PhysOrg.com: organic aerosol chemistry

The Perspective article which was a joint collaboration by PNNS and the University of California, Irvine reviews the use of high resolution mass spectrometry (HR-MS) for studying the fundamental chemistry of organic aerosols.

PCCP cover 9Read the full PhysOrg.com article: Molecular-level analysis of organic particles put in perspective

This Perspective article also featured on the cover of PCCP issue 9!

Full PCCP article:
Molecular chemistry of organic aerosols through the application of high resolution mass spectrometry

Sergey A. Nizkorodov, Julia Laskin and Alexander Laskin
Phys. Chem. Chem. Phys., 2011, 13, 3612-3629
DOI: 10.1039/C0CP02032J

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Studying liquid atom interactions

Paul Popelier and his team have used quantum chemical topology (QCT) to reveal the dynamics of atom–atom interactions in a liquid.

Liquid mixtures, such as ethanol–water and methanol–water, are useful for research into molecular studies of the hydrophobic effect, which governs biological structures and plays a role in protein folding. Also, in the case of ethanol, its specific use as a bio-fuel creates an interest in understanding its interaction with water.

The team studied the behaviour of water and ethanol molecules in terms of O-H…O, C-H…O and H…H interactions. They found that the water molecule formed one to six C-H…O and one to four O-H…O interactions as a proton acceptor.

Also, the more localised a dynamical bond critical point distribution, the higher the average electron density at its bond critical points. The formation of multiple C-H…O interactions affected the shape of the oxygen basin of the water molecule. They also found that the hydrogen atoms of water strongly preferred to form H…H interactions with ethanol’s alkyl hydrogen atoms over its hydroxyl hydrogen.

Reference:
The dynamic behavior of a liquid ethanol-water mixture: a perspective from Quantum Chemical Topology
Paul L. A. Popelier et al, Phys. Chem. Chem. Phys., 2011, DOI: 10.1039/c0cp02869j

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PCCP article featured in Science Daily

A recent PCCP article about a new way to use light to predict molecular crystal structure has featured in Science Daily this week.

coverIn the paper, Timothy Korter and colleagues use low-frequency light to predict London-type dispersion forces using solid-state density functional theory.

This work also featured on the cover of issue 10 of PCCP earlier this month.

Read the Science Daily article

See the PCCP paper in full:
Application of London-type dispersion corrections to the solid-state density functional theory simulation of the terahertz spectra of crystalline pharmaceuticals
Matthew D. King, William D. Buchanan and Timothy M. Korter
Phys. Chem. Chem. Phys., 2011, 13, 4250-4259

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Study of ionic liquid/gold surface interface

Further understanding of the processes that occur at the interface between ionic liquids and metal surfaces has been gained following Frank Endres and colleagues study into the 1-butyl-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate/Au(111) interface.

STM images of the herringbone structure of the Au(111) surface.

STM images of the herringbone structure of the Au(111) surface.

At −1.2 V versus the Pt quasi-reference, in situ scanning tunnelling microscopy revealed that the Au(111) surface undergoes a reconstruction to to a herringbone superstructure. Atomic force microscopy showed that that multiple ion pair layers are present at the interface, which are dependent on the electrode potential. Finally, electrochemical impedance spectroscopy revealed three distinct processes at the interface, including a capacitive process occurring between −0.84 V and −1.04 V, which is slower than the electrochemical double layer formation, and is thought to be related to the herringbone reconstruction.

Read more about this hot new research here.

Rob Atkin, Natalia Borisenko, Marcel Drüschler, Sherif Zein El Abedin, Frank Endres, Robert Hayes, Benedikt Huber and Bernhard Roling
Phys. Chem. Chem. Phys., 2011, DOI: 10.1039/C0CP02846K

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A database of new zeolite-like materials – with over 2.6 million structures

US scientists have described a database of computationally predicted zeolite-like materials

Positions of Si atoms as well as unit cell, space group, density, and number of crystallographically unique atoms were explored in the construction of this database. The database contains over 2.6 M unique structures. Roughly 15% of these are within +30 kJ mol-1 Si of α-quartz, the band in which most of the known zeolites lie.

These structures have topological, geometrical, and diffraction characteristics that are similar to those of known zeolites. The database is the result of refinement by two interatomic potentials that both satisfy the Pauli exclusion principle. The database has been deposited in the publicly available PCOD database.

Read the PCCP article in full:

A Database of New Zeolite-Like Materials
R Pophale, P A Cheeseman and M W Deem
Phys. Chem. Chem. Phys., 2011, DOI: 10.1039/ c0cp02255a

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Interfacial processes and mechanisms – special collection

cover2cover1PCCP is delighted to present issue 12 as a special collection on Interfacial processes and mechanisms in celebration of John Albery’s 75th birthday, Guest Edited by PCCP Advisory Board member,  Professor Rob Hillman.

The issue includes a great collection of Perspectives, Communications and papers on this exciting area of chemistry:

The mechanism of hydrazine electro-oxidation revealed by platinum microelectrodes: role of residual oxides
Leigh Aldous and Richard G. Compton
Phys. Chem. Chem. Phys., 2011, 13, 5279-5287

Stochastic electrochemistry with electrocatalytic nanoparticles at inert ultramicroelectrodes—theory and experiments
Seong Jung Kwon, Hongjun Zhou, Fu-Ren F. Fan, Vasily Vorobyev, Bo Zhang and Allen J. Bard
Phys. Chem. Chem. Phys., 2011, 13, 5394-5402

Microscopic structure and dynamics of air/water interface by computer simulations—comparison with sum-frequency generation experiments

Yanting Wang, Nathan O. Hodas, Yousung Jung and R. A. Marcus
Phys. Chem. Chem. Phys., 2011, 13, 5388-5393

Take a look at the whole issue today!

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Seong Keun Kim Interview – Inspirational science

Recently I interviewed new PCCP Editorial Board member Professor Seong Keun Kim, we talked about his latest research, how he was inspired by a comic book character and the importance of science in Korea.

Read on to find out more…

Seong Keun Kim is head of the Molecular Reaction Dynamics Laboratory at Seoul National University, Korea. He uses spectroscopic, microscopic and computational methods to investigate a wide range of subjects from molecular physics and nanoscience to cell biology.

S K Kim

Korea is becoming a major player in chemical research. How important is chemistry to the future development of the country?

Korea is very strong in the electronics, automobile, ship building and steel industries, but it is also the world’s fifth largest producer of chemicals by volume. So chemistry plays a critical role in the day-to-day operations of virtually every Korean industry, and strong chemical research is compulsory for innovation and product development.

Why did you choose to specialise in the nano-bio area?

I am a physical chemist by training but have always been interested in what goes on in other areas, within and beyond chemistry. The nano-bio area serves as a good window through which we can probe nature in a broader sense at a manageable level. And it turns out that my chemical knowledge, and the array of powerful techniques from the physical chemistry toolbox, can be very handy for nano-bio research.

What projects are you working on?

We have been working on a wide range of topics, from atomic and molecular physics to surface science to genetic assays. Lately, however, we have been focusing on elucidating the molecular interactions and reaction mechanisms for biologically relevant problems.

What’s going to be the next big thing in your field?

‘Seeing’ the chemical transformation of molecules, such as DNA and proteins, in a cell in real time.

What’s the trickiest problem you’ve had to overcome in your research? How did you solve it?

I’ve had my share of puzzles, but the trickiest one happens to be the one I am wrestling with now. A well-known, simple, non-fluorescing compound becomes highly fluorescent upon photoirradiation. We are trying to understand the photochemical reaction pathway, which has so far been quite evasive.

Who or what inspired you to become a scientist?

A Korean comic book character from the early 1960s that depicted a Mr Know-It-All scientist. Later, the Apollo mission and the vivid, flaming images of a rocket launch left an indelible impression.

In high school, a short film shown in the classroom about molecules moving, jittering and bouncing off each other was taken as a providential sign pointing in the direction of my calling. Six years later, I found myself running a crossed molecular beam experiment between ‘flaming’ Rb and CO2 clusters in Dudley Herschbach’s lab at Harvard in the US. It felt like déjà vu.

What is the most rewarding aspect of your career?

Teaching students of all ages and backgrounds. At the end of the summer vacation or during sabbaticals, I invariably find myself bored and defunct because I don’t get to teach. I never turn down invitations for extramural lectures, which are mostly for non-scientific audiences, because the general public are just as susceptible as scientists to the wonder and awe that nature inspires.

Can you tell us a little known fact about yourself?

In every aptitude test I took as a student, I was never predicted to become a scientist. Instead, I was supposed to be a journalist, painter, psychiatrist, pilot or soldier. I now realise that the life of a scientist involves being all of these!

What do you do in your spare time?

Listening to Mahler and Ludwig van Beethoven in my car while it’s going at 150 km per hr (and ending up with a speeding ticket half the time!).

And finally, if you weren’t a scientist, what would you do?

Be a John Horgan.


Check out the themed issue series that Seong Keun Kim Guest Edited on Biophysics and Biophysical Chemistry

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Tracking the early stages of Alzheimer’s disease

UK researchers can track the early steps of formation of peptide clumps linked to Alzheimer’s disease using the peptide’s fluorescent ability. This could help design effective therapies for the disease at an early stage.

A peptide known as beta-amyloid forms amyloid plaques that are found in Alzheimer’s disease. Scientists believe that the toxicity of the smallest peptide aggregates formed during the earliest stages of the aggregation process contribute to the neurological damage in the disease. But it’s difficult to study the earliest aggregation steps to find out why the peptide starts to clump together.

Amyloid fibrils
To help shed light on the process, Olaf Rolinski and colleagues at the University of Strathclyde monitored the decay of tyrosine fluorescence (tyrosine is an amino acid present in beta-amyloid) as the peptides started to self-associate. The decay happens in stages as tyrosine’s surroundings change, producing three different forms, or conformers, of tyrosine. The three forms give different fluorescent signals that can be picked up with a fluorescence spectrometer. Using the peptide’s intrinsic fluorescence avoids introducing a bulky, unnatural fluorophore, which could affect the aggregation process.

Fluorescence is sensitive to interactions on the Ångström to nanometre scale so it can be used to monitor processes between individual molecules at the early stages of amyloid aggregation,’ explains Rolinski.

The team measured the decay in tyrosine fluorescence at eight different peptide concentrations enabling them to detect early single peptide-peptide interactions, which are invisible in conventional fluorescence experiments. They found that the initial peptide concentration influences what conformation is adopted by individual peptides and determines the rate of their aggregation.

Read the rest of the Chemistry World story by Russell Johnson

Or read the PCCP paper in full:

Beta-amyloid oligomerisation monitored by intrinsic tyrosine fluorescence
Mariana Amaro, David J. S. Birch and Olaf J. Rolinski
Phys. Chem. Chem. Phys., 2011, DOI: 10.1039/c0cp02652b

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US Energy Secretary talks biophysics

Stephen Chu, Secretary of Energy for the US government, gave a plenary lecture at the Annual Biophysical Society meeting earlier today.

Dr Chu began his scientific career as a physicist and went on to win the Nobel Prize for his biophysics research. Today he talked about his group’s current research interests into sub-wavelength imaging and detecting protein binding events in real-time. 

He then went on to discuss the influence fundamental biophysics is having on the search for future energy sources, including new metabolic pathways for biofuels synthesis and Li-ion batteries.  

Chu then went on to say that if new alternative energy sources are really going to take off – then the government need to set directives that will force the current energy industries to make these changes happen – just like they did in the 50’s with frost-free refrigerators!!     

Take a look at the great energy research published in both PCCP and Energy & Environmental Science today

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