Saturday, June 25, 2011

Powerful computers, experiments provide insights into ion's behavior near interfaces

 From renewable energy sources to pharmaceuticals, iodide ions are a common actor, and now, thanks to scientists at Pacific Northwest National Laboratory, the ion's behavior can be better predicted. By considering electrons' subtler choices about where to reside, Dr. Chris Mundy and Dr. Marcel Baer showed the negatively charged iodine ion congregates at the air-water interface. However, the ions gather at a lower concentration than previously predicted.

The team obtained answers about the iodide ion's choices to be at the surface or under bulk solvation, surrounded by liquid, using the laws of quantum mechanics in conjunction with Newton's to describe the evolution of aqueous electrolytes, or .  The aforementioned calculations were extensive and required the use of leadership-class computers through the Department of Energy's INCITE award. Previous studies relied on empirical potentials, which are simpler mathematical models of molecular motion that do not explicitly consider .

Understanding the nature of ions where air and water meet and at similar interfaces could change how we conduct basic energy research, climate studies, and biological investigations. However, the fundamentals of an ion's propensity to be present at an interface and the important interactions that wrap ions in liquid are still not understood. This research sheds new light on the effects of ions in the vicinity of hydrophobic environments.

"Our work shows where some models may fail and where you may have to take into account the more subtle effects of when performing calculations," said Mundy, the physical chemist who co-authored the study.

It begins with large polarizable anions, negatively charged particles where the electrons slosh back and forth around the atom's central core in response to nearby electric fields produced by the motion of surrounding water molecules. The new conventional wisdom since 2002 is that these ions can exist in significant population at the air-water interface.  The now nearly universally accepted results were pioneered by Dr. Liem Dang at PNNL and independently by Profs. Jungwirth and Tobias at the University of California at Irvine. These studies were done using empirical potentials in conjunction with a parameterized model for how electrons respond to different charged environments, namely polarization.

"Simply put, electric fields felt by an ion at the interface are different than those felt in the bulk of the liquid," said Mundy.

The earlier results have influenced a generation of both experimental and theoretical studies dedicated to understanding this phenomenon.  Although there is now a consensus regarding ions at interfaces Mundy and Baer wanted to understand the precise interactions that drive ions to the air-water interface. 

To understand how ions adsorb onto surfaces and provide the more accurate data to scientific models, the researchers integrated experimental research, theory, and leadership-class computing. The researchers performed extensive density functional theory calculations to mathematically represent the electrons and ions and determine their interactions.

To justify the computationally expensive calculations, the team compared the detailed structure of iodide in water to extended x-ray fine structure experiments conducted by John Fulton at PNNL. Results of this joint theoretical and experimental study suggested that quantum mechanical models reproduced the local solvation structure of iodide more accurately than the models based on empirical polarizable interaction potentials, known as multipole expansions.  Here, a multipole expansion breaks down a complicated arrangement of charges into concepts, such as a monopole, dipole, etc., and is a good description when you are looking at charges from far away.

"Multipole expansions are good from far, but far from good," said Mundy. When it comes to the movement of the electrons and where electrons from different atoms overlap, the expansions don't provide the precise answers scientists need.

This study took advantage of the synergy between computational and experimental science. "Our result would not mean anything without the experimental results," said Baer, a Linus Pauling Distinguished Postdoctoral Fellow at PNNL. "It would just be another number with no weight."

The researchers continue to combine electronic structure, statistical mechanics, and leadership-class computing to assist in understanding the effects of iodide and other . This research will be continued by Mundy at PNNL and by Baer for the rest of his stay at PNNL and when he returns to Europe.

More information: Baer MD and CJ Mundy. 2011. "Toward an Understanding of the Specific Ion Effect Using Density Functional Theory." Journal of Physical Chemistry Letters 2, 1088-1093. DOI: 10.1021/jz200333b

Provided by Pacific Northwest National Laboratory (news : web)

Chemistry never sounded this good

( -- By now, the word is out at UCLA that undergraduates in Neil Garg's organic chemistry course produce clever, creative music videos as an extra-credit assignment. The bigger secret may be just how much chemistry they learn by doing so, as none of them are chemistry majors and most admit they didn't like chemistry when the class started.

It's a little too soon to say which will be this year's sensation. A strong candidate is "We're Yours" by the Gargonauts — Rachel Stafford-Lewis, Myan Pham, Ali Lanewala and Jordan Halfman — which achieves the desired trifecta of excellent in a video that sounds and looks great. But unlike last year, when one video, "Chemistry Jock" — which has become the gold standard of the genre, with 38,000 YouTube views and many fans — ran away from the competition, this year's field is much deeper.

This video is not supported by your browser at this time.

This video is not supported by your browser at this time.

This quarter, 250 produced 87 videos. The most notable ones also include "Let It Be" by John Boles and Edgar Gonzalez and "Forget That" by Alex Jaksha, Sean Nguyen, Kevin Nishida and Nakia Sarad. This video is not supported by your browser at this time.

This video is not supported by your browser at this time.

"When I am doing the problem sets or taking a test, I find myself singing the various chemistry songs that people wrote and it helps me remember all the details," said Stafford-Lewis, a sophomore majoring in microbiology, immunology and molecular genetics. Rewriting lyrics helped her to learn the chemistry, she added.

"I catch myself randomly singing the lyrics while I'm walking through the halls and just kind of laugh," said Gonzalez, a sophomore physiological science major. "It's crazy, because up until this point, I had hated chem. I remember when I first signed up for the class I was afraid, but I soon realized I had a great professor. I can honestly say that professor Neil Garg has not only made it a fun class, but he made me care about learning chemistry. You can tell how much he cares about his students by the time and effort he puts into his lectures. He always had a dozen or so pieces of computer paper on which he wrote his lecture notes.

"Making the music video was really fun, and a great way to get out of my comfort zone and at the same time learn some chemistry. I would recommend this course as long as professor Neil Garg is teaching it."

Pham, a second-year pre-med history major, agreed, saying, "Making this video motivated me to do better in the class. This is my favorite chemistry course by far. It's a lot of thinking and solving problems; I've learned a lot. Sometimes we forget that learning should be a fun experience."

Pham added that she's "never been superbly great in chemistry" and "it's always been a little hard" for her, although you'd never suspect that watching her sing "We're Yours."

The lyrics to "We're Yours" include:

Well, I got this chem equation and it's getting pretty hazy
Palladium on carbon and ethanol, that's crazy
With hydrogen molecules, I don't know what to do
But then Garg showed me cat. hydrogenation
Breaking alkenes, what a sensation
Syn addition of hydrogens, it's reduction ...

I've been spendin' way too long on this one chem equation
Ozone and DMS, I'm filled with frustration
Alkenes and double bonded O's, please get rid of my woes
I looked at Garg's answer and it all made sense somehow
You split the alkene and add oxygen to each now
You've got two molecules, with carbonyls, wow!

Boles and Gonzalez turned for inspiration to the Beatles, whose "Let It Be" was, of course, a huge hit long before they were born. One of their verses is:

SN2 electrophiles: primary carbon not tertiary
Lone pairs show nucleophilicity
Use polar aprotic solvent
Tosylates and halides, they will leave
Inversion of stereochemistry

Boles, a life sciences major, like many of Garg's students, said, "I looked forward to class with Professor Garg. He turned a class of potential hours of memorization and confusion into a series of intricate logic games with organic molecules. I had a great time with my buddy Edgar making the movie. As I studied for the final, at least twice in my head I've sung a part of our song or a part of another song from last year. Putting the exceptions and rules of thumb to music helps me remember concepts like solvation and which solvent causes which reaction."

Halfman, a second-year psychobiology major, called the course "an awesome experience" and said, "I've never had a professor so qualified in all aspects to teach a class." He added, "After spending so much time learning so many different reactions, a chance to use that knowledge creatively was a very welcome break."

The students uniformly agreed that making the videos was great fun.

"We had a great time shooting our video," Stafford-Lewis said, adding that she and her creative partners knew early on that "we were going for a different feel" from the rap music videos that dominated Garg's class last year.

"Organic chemistry is as difficult as you make it," she said, noting that Garg "does help to make it more interesting and entertaining than I ever thought possible."

Most of the students who take this course "come in with little or no interest in organic chemistry," Garg admitted. They don't end the course that way, though. Last year, only 5 percent started the course with a high interest in organic chemistry, but by the end of the 10 weeks, most of the students said they had a high interest.

Why does Garg offer students this optional extra-credit assignment?

"The majority of the Chem 14D students are hooked on technology, such as the Internet and YouTube," Garg said. "Rather than fighting this, I designed the assignment to take advantage of the students' strengths and interests. I didn't realize at the outset that so many students would create spectacular videos. When you consider the clever lyrics about and the high quality of the video editing and the audio, the TA's and I were extremely impressed by how amazingly creative UCLA's south campus students are.

"Don't believe anyone who says creativity is mostly in the humanities and arts; the evidence otherwise is right in these videos. And for all the time the students put into creating these videos, we give them some extra credit, but not much."

Yannick Goeb and Kimberly Bui, who starred with Justin Banaga in "Chemistry Jock," are fans of "O-Chem Toolbox," sung with stellar vocals by Michelle Azurin, joined by Daniel Brenners, Frank Choe and Mike Dai.

This video is not supported by your browser at this time.

This video is not supported by your browser at this time.

If your musical taste runs more to Lady Gaga, you might enjoy "Bond This Way," starring Natalie Green, Storm Hagen, Megan Johnson and Kylie Wilson and directed by Brian Tan.

Garg's course website has all these and more. Garg called this year's class "Chem 14D Jedi," and many of the videos picked up this "Star Wars" theme, in which the students strive to become "Chemistry Jedis."

Provided by University of California

Spotlight on dynamic operation of enzymes

 Our world is unique in that living organisms can undergo complex chemical reactions quickly and precisely, and sequence them together. But how can proteins integral to life effectively hasten these reactions? Researchers from France provide new insight into how enzymes actually work. The study is presented in the journal PLoS Biology.

Scientists from the Institut des Sciences du Végétal (IVS) at the Centre National de la Recherche Scientifique (CNRS) in France, in cooperation with colleagues from the Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), the Institut de Biochimie et Biophysique Moléculaire et Cellulaire (IBBMC) and the Laboratoire de Cristallographie et RMN Biologique, investigated the binding of a compound with therapeutic properties to its biological target.

Experts say specific macromolecules catalyse biochemical reactions and can be reused many times. The question, however, is if these proteins can speed up the reactions. What researchers know is that the enzyme must first recognise the substrate, which then comes into contact with certain chemical groups specific to it and is later transformed. The substrate is then favoured by the chemical environment that is established, and is linked to the deformations of molecular groups physically close to each other in space, according to the researchers.

So the macromolecular assembly reaches an ephemeral state that is highly reactive. Experts define this as the 'transition state'. What results is that the biochemical reaction is accelerated by a factor of several hundred billion.

Research from the 1950s unveiled the 'induced adjustment' model that had the substrate involved in changing the enzyme's form. Here, the small compound initially interacts with the enzyme, and this interaction triggers the conformational change of the macromolecule, which in turn enables the substrate's transformation.

In this latest study, the researchers used a therapeutic target enzyme, investigating a small compound mimicking the substrate that could bind strongly to the enzyme, and blocking its activity and exhibiting antibiotic, antineoplastic and herbicidal properties.

The team says an 'induced adjustment' stage is required to ensure the efficient binding of the compound to the target enzyme. In a nutshell, it is the tiny compound that brings about the conformational modification once attached to the enzyme.

By deriving the resolution of the fine structure of this enzyme from the Arabidopsis thaliana plant, the researchers effectively illustrated the interactions and conformations of each of the enzyme and substrate, at each stage of the reaction.

A hydrogen bond is formed, stabilising the enzyme-substrate complex in the transition state. This enables the enzymatic hydrolysis reaction to be carried out efficiently.

Thanks to their results, the researchers say this model can be used on all forms of the , especially those found in bacteria, which are targeted by antibiotics. The data also show the mechanism of how a therapeutic molecule can bind to its target, making it 'unbind' from it, and thus extending the drug's effect beyond the actual treatment, they say.

The results of this study can contribute to researchers' efforts to develop or improve the pharmacological properties of drug candidates.

More information: Fieulaine, S., et al. (2011) Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis. PLoS Biology. DOI:10.1371/journal.pbio.1001066

Provided by CORDIS

New insights on an old polymer material, Nafion, will enable design of better batteries

Designing new materials depends upon understanding the properties of today's materials. One such material, Nafion, is a polymer that efficiently conducts ions (a polymer electrolyte) and water through its nanostructure, making it important for many energy-related industrial applications, including in fuel cells, organic batteries, and reverse-osmosis water purification. But since Nafion was invented 50 years ago, scientists have only been able to speculate about how to build new materials because they have not been able to see details on how the molecules come together and work within Nafion.

Now, two Virginia Tech research groups have combined forces to devise a way to measure Nafion's internal structure and, in the process, have discovered how to manipulate this structure to enhance the material's applications.

The research is published in the June 19 issue of in the Letters article, "Linear coupling of alignment with transport in a electrolyte membrane," by Jing Li, Jong Keun Park, Robert B. Moore, and Louis A. Madsen, all with the chemistry department in the College of Science and the Macromolecules and Interfaces Institute at Virginia Tech.

Nafion is made up of that combine the non-stick and tough nature of Teflon with the conductive properties of an acid, such as battery acid. A network of tiny channels, nanometers in size, carries water or ions quickly through the polymer. "But, due to the irregular structure of Nafion, scientists have not been able to get reliable information about its properties using most standard analysis tools, such as ," said Madsen, assistant professor of physical, polymer, and .

Madsen and Moore, professor of physical and polymer chemistry; Madsen's post-doctoral associate Jing Li; and Moore's Ph.D. student Jong Keun Park, of Korea, were able to use (NMR)to measure , and a combination of NMR and X-ray scattering to measure molecular alignment within Nafion. "We were looking at water molecules inside Nafion as internal reporters of structure and efficiency of conduction," said Madsen. "The new feature we discovered is the locally aligned aggregates of polymer molecules in the material. The molecules align like strands of dry spaghetti lined up in a box. We can measure the speed (diffusion) of the water molecules and the direction they travel within those structures, which relates strongly to the alignment of the polymer molecule strands."

The researchers observed that the alignment of the channels influenced the speed and preferential direction of water motion. And a startlingly clear picture presented itself when the scientists stretched the Nafion and measured its structure and water motion.

"Stretching drastically influences the degree of alignment," said Madsen. "So the molecules move faster along the direction of the stretch, and in a very predictable way. These materials actually share some properties with liquid crystals -- molecules that line up with each other and are used in every LCD television, projector, and screen."

These relationships have not been previously recognized in a , Madsen said.

The ability to observe motion and direction, and understand what is happening within Nafion, has implications for using the material in new ways, and for designing new materials, the researchers write in the Nature Materials article. Ion-based applications could include actuator devices such as artificial muscles, organic batteries, and more energy efficient fuel cells. A water-based application would be improved reverse osmosis membranes for water purification.

Madsen and Moore started this collaborative project shortly after they arrived at Virginia Tech (Madsen in 2006, Moore in 2007), and they are furthering their work together by investigating new polymeric materials using their unique combination of analysis techniques.

"Alignment provides for a better flow of the molecules through the polymer," Madsen said.

Provided by Virginia Tech (news : web)