Natural Inspiration

Around the world, about $1.5 trillion is spent on fuel for transportation every year. America’s dependence on oil alone sums up to more than 140 billion gallons per year, at a cost of more than $1 billion per day. Relying on fossil fuels like coal, petroleum, and natural gas for about 85 percent of our energy supply influences our foreign policy decisions, drains billions of dollars from the economy, and raises environmental concerns like climate change. It is no wonder that scientists have been looking for alternative sources of energy. Renewable energy–energy that can be naturally replenished––in the form of biofuels has become a topic of increasing interest.

Wood, for example, is one form of biomass that can be converted into biofuel. Wood is clearly combustible; it has been burned as a source of fuel for centuries. However, combustion of a liquid fuel like gasoline is far more efficient than the burning of wood because it has a much higher energy density, the amount of chemical energy stored by the fuel per unit volume. Scientists are therefore looking for ways to efficiently convert low-energy-density solid biomass, like wood and plants, into useful high-energy-density liquid biofuel, like gasoline and ethanol.

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Credit: Helene Moorman

Converting plant matter into fuel requires that individual sugar molecules within the plant first be isolated and then fermented. Biomass is comprised of a mixture of three polymer molecules (lignin, hemicellulose, and cellulose), forming a robust structural substance all together known as lignocellulose. The desired sugars are found in cellulose, an un-branched polymer of several hundred to ten thousand glucose sugar units. Cellulose is the most abundant and renewable organic compound on earth and a major component of most plant cell walls. However, extracting cellulose required for biofuel production is not simple, as it is trapped within lignocellulose, and  vigorous chemical methods are required to break bonds and release this polymer. Next, through a process called depolymerization, the chemical bonds that link each of the glucose molecules together, called glycosidic bonds, can be broken to produce individual sugars from a cellulose molecule. This crucial process is the most expensive step in the production of biofuels and has recently become the major challenge for scientists to overcome as they search for an economical, efficient, and renewable source of energy to replace fossil fuels.

Biomimicry for biomass depolymerization

The necessary chemical reaction to derive glucose from biomass is hydrolysis of the glycosidic bonds that link the sugar molecules together within the cellulose polymer. Hydrolysis is addition of the atoms derived from one water molecule, H2O, to separate the sugars, wherein one sugar ends up with an extra hydrogen atom and the other receives the remaining OH atoms. However, hydrolysis does not occur at an appreciable rate under mild conditions of neutral pH and low temperature, and a substance known as a catalyst is required to increase the reaction rate. A good catalyst for this reaction is acid because it will add a proton, H+, to the sugar molecules, which facilitates bond breakage. One process uses very harsh conditions of concentrated sulfuric acid. Another more conveniently uses dilute acid, but requires high temperature (100 ºC) and, unfortunately, is less selective.

Dr. Alexandre Charmot and Professor Alexander Katz examine a culture of Gluconacetobacter xylinus, a bacterium that naturally produces cellulose. Growing the microbe in the presence of an isotopically-labeled carbon source results in the production of 13Clabeled cellulose at an abundance of 95% compared to the naturally-occuring 12C isotope. This labeling allows them to identify and quantify the amount of glucose and cellulose within the different steps of separation and reaction processes the group is developing. This is achieved by observing the 13C signal in nuclear magnetic resonance (NMR) experiments, a useful technique for research in the field of biomass depolymerization.
Credit: Valerie O’Shea

A group of researchers led by Professor Alexander Katz from the Department of Chemical and Biomolecular Engineering  at UC Berkeley look to nature for inspiration to find better catalysts for cellulose depolymerization. Naturally occurring catalysts found within some microorganisms, mainly fungi, can break up glycosidic bonds under much milder conditions than what can be achieved with strong acid. Nature’s catalysts for cellulose depolymerization are known as cellulase enzymes. On the molecular scale, reactions occur when an enzyme encounters its target, in this case, cellulose. A molecular feature of the enzyme, such as a carboxylic acid group, can donate a hydrogen bond to the glycosidic oxygen atom of glucose, which activates the bond for hydrolysis. Professor Katz remarks, “We don’t really know how to do that. We don’t know how to catch a piece of biomass or have a receptor on the surface of biomass and donate a hydrogen bond just in that position where it needs to be to activate that particular oxygen.” Professor Katz explains that nature works wonders “through intricate molecular-scale control of the enzyme active site––the precise placement of atoms in certain positions to activate molecules. Enzymes don’t use specific acid catalysis. They don’t use sulfuric acid to break the same kinds of bonds, and they are able to do that under much milder conditions: near neutral pH and room temperature.”

However, isolated enzymes have their drawbacks, too. They are costly to produce and cannot be re-used. To develop depolymerization methods which are more economical and have greater selectivity and efficiency compared to current commercial processes, the Katz group is developing enzyme-inspired catalytic surfaces that can promote separation of glucose units under mild conditions. A key advantage of using catalytic surfaces is that they can be easily regenerated, an important factor to consider when designing an industrial-scale process.

Catalytic surfaces

Drawing inspiration from biological catalysts, the Katz group realized in 2006 that a solid silica surface, which presents an ensemble of reactive groups known as silanols, mimics the essential active groups within an enzyme. By having this “pseudo-continuum of active sites on a surface,” the group was able to do reactions similar to those done in nature, without complex and intricate positioning of atoms that enzymes facilitate. Essentially, if a strand of cellulose can get close to the silica surface, then activation and hydrolysis of the glycosidic bonds will occur. Postdoctoral Scholar in the Katz Group, Oz Gazit, determined a method to get the cellulose strands close enough for the reaction to take place. His project involved synthesis of a new class of materials that were the first composites between molecular strands of cellulose chemisorbed on the surface of silica. He saw that as the interaction between the silica surface and the cellulose strands increased, the rate of hydrolysis of the glycosidic bonds increased because those bonds by the surface were being activated. The observed hydrolysis rate was over a hundred times more reactive than cellulose conventionally pretreated. As Professor Katz explained, “This presented a new mechanism by which we could breakup biomass under very mild conditions––using pH of 4 which is very very mild compared to concentrated sulfuric acid breaking up the same bonds.”

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Credit: Helene Moorman

One problem to this initial approach is that it requires high temperature of 100 ºC, which they determined also breaks the bonds that comprise the silica, thus degrades the catalyst. Currently, the group is looking towards other types of materials that function similar to silica, but are less prone to degradation, such as carbon. Professor Katz explained, “Carbon materials also adsorb these long cellulose chains, and by decorating the carbon materials with acid groups you can actually make glucose by just having water as the medium.” Despite this drawback when using silica for biomass depolymerization, the Katz group is continuing to develop and commercialize their cellulose-coated silica surface technology, as it is a convenient way to make the silica (i.e. glass) surface repel water with many potential applications.

Not a quick fix

Understanding the essential chemistry in nature can lead us closer to finding solutions to some of our most complicated problems. Professor Katz commented that biomimicry “doesn’t mean that I’m trying to make an artificial dog, because that’s too much of a challenge. But if we take some aspects of what nature does and try to incorporate them into synthetic systems then we might not be able to get all of the way or even a large fraction, but maybe we will be able to enhance what we already know how to do and be able to do things under milder conditions, under lower temperatures, with less cost or less capital by using the principles that nature incorporates.” Professor Katz stressed that these developments are only steps in the renewable biofuels field, which is dynamically evolving and which has the potential to provide significant benefit to the environment. One such benefit is that biofuels address the carbon dioxide (CO2) problem. “We get to recapture a significant fraction of the CO2 generated by growing the biomass from the CO2 that came from burning the fuel. This addresses a problem in a way that is scalable,” explained Katz, and “could make biofuels much more practical than some people think they are.” Of course, many challenges still remain. Professor Katz remarked, “There is no kit for solving the problems that are facing our society in energy, but through sustained science, it is possible to do. And that also, for a lot of us, is what makes it fun science.”

The Energy Biosciences Institute (EBI)

Professor Katz is one of more than 100 principal investigators who receive funding from the Energy Biosciences Institute (EBI) for biofuels research. The idea for EBI began in the summer of 2006, when the global oil and gas company BP announced an international competition for resources to create an institute in the area of bioenergy. BP initially approached 20 universities that expressed interest in hosting such an institute, and soon narrowed down the list to five finalists, of which UC Berkeley was one. A team representing UC Berkeley, including US Secretary of Energy Steven Chu, Philomathia Professor of Alternative Energy Chris Somerville, Distinguished Professor and CEO of the Joint BioEnergy Institute Jay Keasling, Chancellor Robert Birgeneau, and Vice Chancellor of Research Graham Fleming drew up a proposal to BP and flew to London to defend it against the other four finalists: MIT, UCSD, Imperial College, and Cambridge. In 2007, BP chose the proposal from UC Berkeley and entered into a partnership with the university to tackle one of the greatest challenges of the 21st century: to develop new sources of fuel and reduce the impact of energy consumption on the environment.

Professor Somerville, who serves as the current EBI director, believes they had the winning proposal because they evaluated what BP’s needs were and focused on addressing them. “My personal opinion was they could simply acquire the best technology by just going to whichever group in the world seemed to have a good piece of technology, and get a license to it. That would be the normal path. So we thought, ‘What could we possibly do to justify 350 million dollars of research––why shouldn’t they just go and purchase innovation wherever it occurs?’ And it seemed to us that one thing that they could not just go and purchase was expertise––the coherent expertise, not just bits and pieces, but all in one place.” Importantly, they also recognized essential areas where UC Berkeley was lacking needed expertise, and in the course of the process, Lawrence Berkeley Lab (LBL) was invited to join the Institute. Somerville and Paul Ludden, Dean of UC Berkeley’s College of Natural Resources, also interviewed presidents of many other universities in the search for one that could partner with UC Berkeley and LBL to provide know-how in areas that were then deficient. The University of Illinois was chosen, as Somerville explained, because “when we evaluated the range of expertise within Berkeley, we realized we needed some additional expertise to see all the pieces. For example, Illinois is a distinguished school for agriculture. We knew that we were going to need that capability.” Altogether, there are 127 professors at the three institutions that comprise EBI, with 77 at UC Berkeley and LBL and 50 from Illinois. Including graduate students, postdocs, and staff members, there are nearly 500 individuals within the Institute. To date, these researchers have published more than 300 peer-reviewed articles on EBI-funded projects.

Each year, faculty from the three academic partners submit research proposals to earn a portion of the $350 million annual budget. The proposals are sent out for peer review and among those funded each year, about 25 percent are new, whereas another one fourth of applicants are not renewed. Sommerville explained, “If they add something new to the field and new to the Institute, then we give those the priority for funding. Each year we try to retire some things that are finished and start some new things.”

A multidisciplinary mindset

Arabidopsis plants in growth chambers at the EBI’s Calvin Laboratory location. These plants will be surrogates for future biofuel source plants used in deconstructing biomass. They are being studied for use in feedstock and biomass research to improve yield and separate sugars from cellulose.
Credit: PEG Skorpinsky

EBI hopes to address all parts of the global energy challenge with a multidisciplinary approach. Bringing industry and science together, EBI is composed of specialists from all areas––ecologists, environmental scientists, economists, agronomists, mechanical engineers, chemical engineers, chemists, biochemists, and microbiologists––who all work together to develop new sources of renewable energy. Professor Somerville explains that, although challenging, there are benefits of this approach: “One of the interesting challenges in the Institute is that we try to put in place practices that allow us to get the economists and the ecologists talking with the chemical engineers, so that everybody can see the various pieces, and so that we don’t get narrowly focused on something that might have some shortcomings in another area. I think one of the things we know about technical innovation is that if we get too narrowly focused, we may miss some downsides.” Likewise, Professor Katz believes the multidisciplinary nature of EBI is a definite benefit. “Having all these different perspectives in one place is very special and allows progress to happen much faster than it otherwise would and could, and it is a very stimulating environment because of that. It’s really a wonderful thing to be a part of.”

To ensure this multidisciplinary aspect of EBI persists, the $350 million of funding that is received every year is allocated about equally across five disciplines: environmental, social, and economic––stressing the efficiencies and economics of renewable energy; feedstock development––examining the fuel production capabilities of plants using less land, water, and energy; bioethanol production––the efficient conversion of plant sugars into fuels; fossil fuel bioprocessing––creating more environmentally friendly extraction processes; and biomass depolymerization––the breakdown of plants for energy.

A multidisciplinary education for EBI students

Christy Roche, a graduate student in the Department of Chemical and Biomolecular Engineering and a member of EBI, working in the Clark lab.
Credit: PEG Skorpinsky

Christy Roche, a graduate student in Professor Douglas Clark’s laboratory in the Department of Chemical Engineering and a member of EBI, is currently working on a project involving lipid production in Neurospora crassa, a type of red bread mold. The goal of her research is to use this fungus, which is naturally capable of degrading cellulose and producing lipid, to make larger amounts of lipid, which could then be used to make biodiesel. Ms. Roche commented on her positive experiences as an EBI graduate student: “It’s wonderful. We are never supply limited or resources limited here. We have all kinds of equipment to do pretty much anything we could imagine we would like to do with our research.” She also recognizes the advantage of working with others from many disciplines. “It’s really nice from the research standpoint that we work with all kinds of labs. I’m from chemical engineering, and on our floor, we have plant biologists, and we have microbiologists and chemists––all kinds of people. It is very multidisciplinary; we think about our project from many aspects because we have a lot of people that help us critique our work.”

EBI has played an important role in attracting new researchers to the field of bioenergy and to UC Berkeley. Meera Atreya, another graduate student in the Clark Lab, explained how she chose her field of study and became a part of the EBI: “I consider myself an environmentalist, and I love science. I wanted a way to combine the two that would have an impact on global climate change, which I see as the most important issue of our time. I decided bioenergy was the intersection of my environmental interests to do energy research, plus my scientific interests to do chemistry and biology. I was really motivated to come to Berkeley because of the Energy Biosciences Institute specifically.” Among the many benefits of being an EBI graduate student, Ms. Atreya agrees that the multidisciplinary aspect is key. One way this is played out is through joint lab meetings. She explains, “People from different fields all working towards the same end goal can present their research. You can learn a lot of ways to approach the same problem, so that is really unique about this environment. I like the intersection of all of the different disciples here, especially economics. You are never going to compete with fossil fuels and commodity chemicals if you do not have a competitive price and the proper policies.” This insight into the challenges of competing with fossil fuels is evident in her research, which focuses on improving cellulase enzymes with the end goal of making biofuel production cost competitive with fossil fuels, and thus a greener alternative.

The future of biofuels

Professor Sommerville agrees that biofuels must be able to compete with fossil fuels in order to be implemented as an effective alternative. “Right now there are no commercial cellulosic biofuels refineries operating out there. There are some small ones––BP has a small one, and number of others have small demo pilot plants––but during the next two years I think we are going to see the first commercial-scale facilities being built to make cellulosic fuels.” In the long run, these processes ideally must operate without subsidies to be successful. Biofuels must be able to compete directly with fossil fuels, and many of the innovations made at EBI are going into commercialization. “Our goal is to contribute to getting our best possible process into those refineries and make innovations that will bring the cost of cellulosic fuels below the cost of petroleum,” explained Sommerville. Indeed, the future of biofuels sounds promising. Perhaps one day we will use “grassoline” to power our vehicles.

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