September 12, 2011
Running a molecular dynamics simulation with atomistic details is like directing a vast crowd shot in a movie. So says Berkeley chemical and biomolecular engineering professor Jhih-Wei Chu. His crowd shots consist of thousands of molecular actors and take months to run even on the world’s best supercomputers. Although the action occurs at a scale invisible to the human eye, the outcome could have a dramatic impact on biofuel production.
On the left a strand of cellulose is peeling off from the crystalline structure. On the right the table documents the attractive forces between various components of cellulose and the ionic liquid.
In a July 28 article in the Journal of the American Chemical Society (http://pubs.acs.org/doi/abs/10.1021/ja2046155), Chu explains his simulation that shows how ionic liquids dissolve crystalline cellulose. His simulation model, which contains approximately 100,000 clusters of atoms, required around one million CPU hours at DOE’s National Energy Research Scientific Computing Center. This story of a strand of cellulose deconstructing in an ionic liquid is made up of subsections that play out in nanosecond timescales (one nanosecond is one billionth of a second).
Dissolving cellulose in ionic liquids might seem like an obscure topic, but it is at the heart of efforts to create a liquid transportation fuel from renewable plant sources. An ionic liquid is just a salt in its liquid state. Sodium chloride, common table salt, has a very compact crystalline structure and as a consequence it doesn’t melt until about 800 degrees Centigrade. If you replace the sodium cation (positively charged ion) with a bulkier organic cation, the result is a salt with unique properties that is liquid at lower temperatures.
For his simulations, Chu used 1-butyl-3-methylimidazolium chloride (BmimCl), a ionic liquid that dissolves crystalline cellulose. “We know this ionic liquid will dissolve cellulose, but we are really not sure why,” says Chu. “Along with my co-authors, I wanted to understand how the molecular forces provided by ionic liquids help deconstruct crystalline cellulose. That knowledge could allow us to design better solvents and engineering processes.”
In the lab there are many, many ionic liquids to choose from. That’s the good news. The bad news is that there are so many ionic liquids to choose from, that it is impractical for researchers to experiment with all possible candidates in a trial-and-error fashion. Says Chu, “If there are N cations and N anions to choose from, then there can be up to N2 possible ionic liquids. That’s a lot to sort through. To rationally design solvents for cellulose, you have to know what properties you are after, and how the ionic liquid interacts with cellulose. Therefore, a powerful ‘microscope’ with the ability to resolve molecular structures and also sense their interaction forces is needed. That is where computer simulation comes in.”
Chu’s model breaks down the cellulose polymer into four different sections — the hexagonal ring (Rng), the linker oxygen (LO), the side chain (SC) and the hydroxol groups (OH). In turn, the interactions of these groups are tested against water, the anion (Cl-), the charged portion of the cation (Mim+) and the neutral tail portion of the cation (Tail). An elegant table (above) summarizes the interactions between all these groups for a strand of cellulose before and after it has been peeled off by the solvent.
If the various components of cellulose are more attracted to each other than to the solvent, cellulose won’t dissolve. This was the case with water, a poor solvent for cellulose. However, in BmimCl the components of cellulose are more attracted to the components of the ionic liquid than they are to each other, and the cellulose dissolves.
Although this procedure is straightforward, resolving how BmimCl targets cellulose is difficult. Chu and his co-authors were able to demonstrate the versatility of the ionic liquid. Says Chu, “BmimCl has versatility because the Cl anions have strong attraction to hydroxol groups and weak attraction to side chains and sugar rings, while the cations have strong attractions to side chains and linker oxygens. We’ve learned that this versatility is the desired property in a pretreatment solvent to deconstruct cellulose. This versatility can potentially be employed as the basis for molecular design and engineering.”
Chu concludes, “Computer simulation of molecular dynamics and interactions really is like a huge crowd shot in a movie. As the director, there is so much detail at your disposal that you can lose sight of the plot. Knowing where to zoom in requires some judgment and intuition. With this simulation, I think we were able to distill the essential plot elements that we hope biofuel researchers will be able to develop further.”
The authors thank the Energy Biosciences Institute and the University of California, Berkeley, for supporting this research.
Cellulose is the most common organic molecule in the world and is a major component of all plant matter. You may be wearing a garment made from cellulose right now. Cotton is about 90 percent cellulose and contains both the tightly structured crystalline form and the unstructured amorphous form of the molecule.
Cellulose is a polymer of the sugar glucose, the most important energy source for living things. Plants make glucose from sunlight, water and carbon dioxide through the process of photosynthesis. At night, plants burn glucose for energy just as members of the animal kingdom do.
A strand of cellulose passes the the active site of a Trichoderma reesei cellulase.
Plants can also turn this simple sugar into a building material. They link glucose molecules together with oxygen, forming long chains. Then the chains are aligned into sheets that are bound together with hydrogen bonds to form microfibrils of cellulose. These hydrogen bonds are similar to those that link water molecules together and bring about its unique properties.
A plant takes energy and converts it to a building material. Humans now want to take that same building material and convert it back into energy. The problem is that cellulose is a very tough material. Millions of years of evolution created a structure for cellulose that is highly resistant to degradation. If you toss an old cotton rag in your garden, it will eventually degrade like other plant material, but it can take months or years. Scientists and engineers who work with biofuels need the process to go much faster.
Fortunately, evolution also endowed many organisms with cellulases, enzymes that can break down cellulose. Cow and termites digest cellulose, although they rely on cellulases of symbiotic bacteria living in the acidic environment of their digestive tracts. Humans can’t digest cellulose in our food, so we call it fiber.
One of the best sources of cellulases is the fungus Trichoderma reesei. During WWII in the South Pacific, the U.S. Army discovered that its canvas tents were dissolving in the heat and humidity. Army researchers isolated the fungus, and it has been an important source of cellulases ever since.
In a separate paper accepted for publication in the Journal of the American Chemical Society, Chu is using simulation techniques to better understand how T. reesei cellulases work.
Chu Research Group: http://www.cchem.berkeley.edu/chugrp/Welcome.html
Chu Faculty webpage: http://cheme.berkeley.edu/faculty/chu/