Fig. 1: Bacteria isolated from a deep-sea hydrothermal vent accumulating cadmium on the cell wall as cadmium sulfide. Electron micrograph of cells. Fig 2 & 3: (Cd and S) Energy dispersive X-ray images of cadmium or sulfide on cell wall. All images were taken at LBNL. (Clark and Keasling)

"Environmental issues impact us on three levels" says Chemical Engineering Professor Enrique Iglesia, "and as scientists, we need to deal with all three. Locally, we must deal with water pollution and air pollution in densely populated areas; regionally, we must address acid rain and the contamination of large aquifers, and globally we need true international, scientific, and political collaborations to deal with ozone depletion and with anthropogenic greenhouse gases."

Researchers in both the chemistry and chemical engineering departments are working at all three levels. Indeed, the activities are so extensive that we cannot cover them all in one feature. This article focuses on research in the areas of mitigation and prevention of environmental problems by our chemical engineers.

Bacteria Can Do the Job

Professor Jay Keasling has some novel approaches to cleaning up pollution. He works with genetically altered bacteria, modified to remove toxic compounds from aqueous solutions. Keasling uses his metabolic engineering and genetic techniques in collaboration with Professor Douglas Clark, who works with microorganisms that grow around deep-sea hydrothermal vents, at both high temperature and pressure.

One project focuses on removing heavy metals from polluted groundwater. The microorganisms used for this project are found growing near undersea volcanoes, like those found around the Hawaiian islands. "These organisms live naturally in an area highly concentrated with toxic metals, like cadmium, nickel, lead, copper and zinc," says Clark. "But they have adapted tolerance or removal mechanisms in this environment. We hope to enhance and exploit these mechanisms."

Several strains of deep-sea bacteria have been found with unusual tolerances to cadmium and nickel, and one of them can remove the toxic metals in the water around them. "These bacteria have evolved the ability to take in the metal, combine it with other compounds, and excrete it as a precipitate on the outside of the cell, where it is no longer a threat," said Keasling. "Other bacteria have the potential to develop polyphosphate chains within the cell, which then can be broken up and used to bind the metals--a different method, but a similar result," adds Clark. They have some understanding of how this is done, and are genetically engineering other microorganisms to do it for them.

"To bioengineer bacteria, we decide the chemistry we want to select for. We usually want to catalyze degradation or have the bacteria synthesize something," says Keasling. "Then we look for enzymes which catalyze certain reactions, and whether the genes for this reaction have been cloned by other researchers."

The most difficult part of the process, he says, is assembling the genes. It is time consuming and, he says, "Even just getting this to work is hard." First he takes an organism, extracts its DNA, amplifies a specific gene with the desired characteristics, and clones it using the polymerase chain reaction. Then he assembles the genes in a new host organism. The gene is transcribed into mRNA, which is translated into an enzyme (protein) that catalyzes the desired reactions.

Keasling and Clark's efforts have met with some success. "We have been able to take naturally occurring organisms, and through metabolic engineering improve their growth rates in high metal concentrations and improve their ability to remove metal from the environment," said Clark. "We hope to engineer 'superbugs' with unprecedented tolerances and capacities for metal removal."

There are several unanswered questions. Why can the organism exist at all in such a toxic environment? How does it take the metal and turn it into a less toxic, insoluble material? And if it can tolerate the metal enough to grow and remove it, why does it have to remove it at all? "These organisms provide an opportunity to test mechanisms that evolution has devised to solve problems," said Clark. Next steps are to design sampling systems to get more microorganisms in their natural environmental conditions.

Regardless of the remaining questions, the research looks promising. One day bacteria may be used by industry to remove dangerous metal toxins from solutions, and to create insoluble metal sulfides or metal hydroxides that can be removed by other traditional filtration methods. Once they find the right organism, Clark says, they are "particularly interested in taking this to the next level--designing a system that can remove metals from an effluent stream."

Keasling uses similar methods on a project to remove trichloroethene from groundwater. TCE and its byproducts are carcinogenic compounds used in dry cleaning, among other processes. "We've found that certain microorganisms in groundwater can degrade the TCE to ethene, which is non-toxic," says Keasling. "By pumping nutrients into the groundwater, you encourage growth of the microorganisms that break down TCE."

"We are also using genetic engineering to modify bacteria used to combat phosphate contamination," says Keasling. Phosphates, which come from fertilizers and detergents, are removed in wastewater treatment plants. If untreated, phosphates cause algal blooms, like red tide, which kills fish and can poison water sources. He also designs bacteria to degrade organophosphates, like parathion, a pesticide, and Sarin, a deadly nerve agent. "We design [the bacteria] so that they use all parts of the toxic molecule as nutrients for growth, so they will go after, scavenge for these compounds," says Keasling.

One daunting challenge is developing bacteria that can survive in both high concentrations of metals and organic pollutants. Polluted sites owned by the U.S. government and by several manufacturing facilities often involve mixtures of these chemicals. "Organisms may degrade metals but not organics, or may be intolerant to one. We are co-culturing bacteria and manufacturing symbiotic relationships so they survive better together than living singly," says Keasling.

Solid Waste Recycling and Cleanup

Professors Jeff Reimer, Mort Denn and Susan Muller work on a small recycling demonstration project with a grant from Alameda County. Working with the MBA recycling company in Richmond, CA, they are attempting to develop methods to characterize the purity of plastics after separation. "They can take a refrigerator, mechanically separate plastics, non-plastics, metals, and grind all of it up [so the pieces are] not much bigger than a grain of rice," says Reimer. "Plastics are then separated by density [using flotation], but [the company doesn't] have a way to establish the purity of their product, which they would like to resell as pure plastic."

The grant provided equipment to help develop routine tests to detect impurities and the types of plastics in a sample. "Different types of plastics don't mix under normal conditions," says Professor Muller. "So, you need different temperatures, pressures, etc., to reprocess each type. It is very difficult to get pure materials from recycled. The question is, if it is 99% pure, can it be processed as new polymers would?" Muller thinks they have developed these testing methods, but they haven't had the personnel to test them.

"Will a recycled plastic grocery bag, which contains trace amounts of other plastics or impurities, have the same strength and structure as one made from virgin material?" asks Muller. "We've developed useful guidelines for testing so processors could identify the composition of a blend, to predict performance." They hope the information that they have developed so far can help persuade polymer users to buy recycled materials. Unfortunately, producing plastics from virgin stock costs about the same as using recycled plastic. Since there isn't much of a profit margin, and there isn't a steady feed stream of recycled product, Reimer and Muller agree it is unlikely such recycling will be implemented on a wide scale in the near future.

A project with more immediate impact is Reimer's work with the pulp and paper industry. Working with Lawrence Berkeley National Lab researchers and Weyerhaeuser, students in Reimer's group are developing NMR sensors to improve the efficiency of one of the world's messiest industries. "The paper industry doesn't know much about the composition of their effluent, or how much water is in the wood fibers that come into the process. Our sensors enable them to refine the amount of energy used to make paper," said Reimer.

Reimer's group has developed three sensors that measure the water content of wood chips, determine the composition of the effluent (which is burned to generate energy) once the wood fibers are removed, and last, measure the thickness of paper. "Since there is no monitoring going on at all in the industry, this is a great step forward," says Reimer.

Muller and Denn also have a mitigation project that could have dramatic results. A recent grant involves radioactive waste stored at DOE's notorious Hanford nuclear waste facility. "Apparently, the radioactive waste is stored in large tanks as a slurry, with a consistency something like wet sand," says Muller. "The problem is that hydrogen gas trapped in small bubbles in the slurry could cause a dangerous, explosive situation," with even more serious health hazards. Muller and Denn have begun to study bubble dynamics in similar types of fluids, trying to find ways to mitigate this problem.

Grad student Eric Tonnis and Prof. David Graves hook up the device that removes PFCs from their plasma etcher.

Greenhouse Gases and Air Pollution

Even better than cleaning up pollution is preventing it in the first place. Professor David Graves works with a different sort of pollution: that from perfluorinated compounds (PFCs) used in the semiconductor industry. They are global-warming and ozone-depleting gases, and while emissions are relatively small, the industry is under pressure to discontinue their use. "PFCs have incredibly long half-lives and in some cases they break down, making other harmful gasses as a result of reactions in the atmosphere," says Graves. "The semiconductor industry wants to be seen as a green industry, and while there are still no specific EPA regulations requiring PFC reduction, every semiconductor manufacturer worldwide is looking for ways to reduce their use."

This project is part of the Engineering Research Center, funded by a joint National Science Foundation (NSF) - Semiconductor Research Center (SRC) grant, which researches environmentally benign semiconductor manufacturing. The SRC is funded by companies in the industry. Research is being done at the University of Arizona at Tuscon, Stanford, MIT and Berkeley. As part of this national consortium, Graves and his students have had their hands in improving a technology and proving it works in commercial conditions.

In the plasma etching and chamber cleaning processes used to make semiconductors, PFCs become mixed with the effluent gases, and traditional scrubbers don't capture them. At one stage of the production process, the technology Graves and coworkers have perfected adds O2 and H2O vapor to the effluent, which helps to convert up to 90% of the PFCs to products that can be scrubbed. The prototype project has had great success, and has been identified by industrial collaborators as the most cost-effective method currently available to reduce PFC emissions in the plasma-etching process in semiconductor manufacturing.

Professor John Newman is doing the opposite of Graves--some of his research focuses on replacing ozone-depleting CFCs with slightly more desireable PFCs for refrigeration and cooling devices. His newer refrigerants are made by converting anhydrous hydrochloric acid to chlorine, and eliminating the HCL waste produced in the process. "The process currently requires HF to remove the [ozone-reactive] chlorine from CFCs which means you end up with waste HCL. We use a fuel cell to take it and recycle it into chlorine, and have demonstrated that this will make cost-effective refrigerants," says Newman. Unfortunately, the black market for illegal refrigerants has meant this process has not been used widely by industry.

Prevention Can Be Electrifying

Electric vehicles will also prevent air pollution. Professor Elton Cairns is one of this country's leading experts on fuel cells and high performance batteries for electric vehicles. An affordable zero emissions automobile has been in development a long time, but practical electric cars are still several years away. "It is difficult to develop an environmentally clean vehicle without some size and performance compromises," says Cairns.

He notes that today's electric cars are still not economical. General Motors, Ford and Honda have produced electric cars for lease in the United States, but they will only lease them to certain kinds of consumers. Limited battery range, long recharge periods, and higher production costs have made their utility on a large scale doubtful. The race continues, fueled by regulations mandating zero emissions vehicles on the market in California by the year 2003. For now, existing electric cars are more specialty vehicles than a real solution for air pollution.

Fuel cells are a better source of energy for an electric vehicle than batteries, since they generate electrical energy from a tank of fuel, rather than store a relatively small amount of electrical energy. In a hydrogen fuel cell, hydrogen and oxygen react over a platinum electrocatalyst to produce electricity and water. They are twice as efficient as regular combustion engines per unit of fuel consumed, and produce half the CO2, with no particulate, hydrocarbon, SOx or NOx pollution. "Fuel cells will provide large-scale power generation with minimum pollution, and in the distant future will be able to power vehicles," says Cairns. His work developing the fuel cell is related to the"Partnership for a New Generation of Vehicles," which is funded through a consortium with the three American auto manufacturers and the U.S. government.

Prof. Elton Cairns and grad student Ken Lux, who is holding a fuel cell. The cylinder between them is the pressure chamber where the cell is tested.

There are, however, several problems preventing the commercial use of fuel cells. "The use of organic fuels in fuel cell systems now requires that the organic fuel be converted into hydrogen through such reactions as steam reforming, which adds significant cost and complexity to the system" says Cairns. His research is developing a fuel cell using more active catalysts as part of the electrode that will permit the use of organic fuel directly in the cell, without first converting it to hydrogen. "We want to have fuels adsorbed on the electrocatalyst, which will catalyze the electrochemical oxidation of fuels to form carbon dioxide and water," says Cairns, "using a readily available fuel like methanol or ethanol." The problem with this approach, adds Reimer, is that it works briefly, but deactivates. He works with Cairns using NMR spectroscopy to figure out which molecules adsorb onto the catalyst and get in the way of the reaction. It is the only chemical technique available to study this material because it is disordered, opaque, and a conductor, all of which disrupt other scanning devices.

Reimer has had some success with his screening. "We've detected three species that remain on the catalyst, and now we are trying systematic variations of platinum which might affect adsorption," says Reimer.

John Newman's modelling of batteries and fuel cell performance has heavily influenced this research, "giving us clues about power, capability and battery limitations," says Cairns. Newman's group measures the properties of materials in both batteries and methanol fuel cells, where they focus on the transport and thermodynamic properties of water and methane. "We're trying to keep methanol reacting on first electrode. Methanol leaks and reacts on the wrong electrode, which is an issue of efficiency," says Newman.

Until fuel cells are more efficient, Cairns and Reimer's work in extending the lives of batteries will be more relevant to putting electric vehicles on the roads. The main problems with electric car batteries are weight, range, and recharge time. The constant discharge while driving requires massive banks of batteries. Cairns' and Reimer's work with long life lithium batteries focuses on developing new electrode materials.

Lithium is a preferred material because it gives more energy per unit weight than standard battery materials. "We try to reduce the weight and increase range of vehicles by using oxides of metals such as cobalt (CoO2), and nickel (NiO2), but they are relatively expensive to produce," says Cairns. Manganese oxides are less expensive materials that he is experimenting with as well.

Unfortunately, lithium batteries can only be recharged a limited number of times. Reimer explains "Lithium is pushed from a metallic compound to its ionic form when it discharges, and in reverse on recharge. But like a house guest that never leaves, it leaves a little dirty laundry each time." Eventually, it bonds with the graphite and oxide electrode materials and the compound degrades.

So far, there has been some improvement in performance, but Cairns estimates we are at least five years away from a second generation electric vehicle that will be affordable for the consumer. "A big problem is consumer attitude," says Cairns. "With range limitations, battery-powered electric cars will not be for cross-country driving. It will be a commuting car, with range of about 100 miles per day." He says that consumers are reluctant to buy a car with that restriction, even though "ninety-five percent of all the driving you do is within this limit."

While some research is focusing on improving catalysts in fuel cells, Newman says "you can never improve a catalyst enough. Instead, I'd rather engineer around the problem." He talked about the potential for the lithium battery, combined with a fuel cell, as having several advantages over a battery powered car. While more complex, he suggested it would provide a low emissions vehicle with the equivalent of 80 miles per gallon of fuel, and would eliminate the short range and recharge problems with electric vehicles. "The electric vehicle lost to the internal combustion engine in the 1920s because it wasn't the most efficient engine," says Newman. "I won't say that the hybrid is the answer, but the research that we are working on will eventually produce new lightweight materials, efficient fuel cells, efficient diesel engines, lower emissions, and we can take what is good and implement it."

The Road to Clean Air

Other air pollution problems are more commonplace, and their solutions more critical. Dean Alex Bell and Professor Jeff Reimer's work to remove oxides of nitrogen from power plant and automobile emissions may one day prove critical. NOx is a greenhouse gas and causes acid rain, among other problems. Catalytic converters on automobiles and scrubbers at power plants remove NOx by catalyzing reactions and bonding the compounds in non-polluting forms.

The research studies catalysts already used in this process, but places them inside zeolites--crystalline, porous structures made of aluminum, silicon and oxygen, where metal cations can be placed to react with the nitrogen and remove it from the exhaust. "We use different kinds of spectroscopy to characterize the state of cations, usually copper, nickel, cobalt and iron, and what's attached to them, while the reaction proceeds," says Bell. Removing NOx is increasingly important as the automobile becomes more efficient.

"Normally, cars operate so that exhaust produced is a balance of reducing and oxygenating agents in the combustion process," says Bell. "In the future, gas or diesel will have excess oxygen in the mix to improve auto performance, so we need to find a catalyst to reduce NO2 to N2, in the presence of O2. Not many materials enable this," says Bell. Zeolite catalysts may in the end prove impractical for automobiles because they are unstable in the presence of water vapor, and because the metal cations eventually are used up, and must be replaced. Nevertheless, understanding how these cations induce nitrogen removal may be the key for improved emissions controls.

Professor Enrique Iglesia works on another type of green technology--replacing current processes and catalysts with safer and more selective ones. Chemical companies need to produce the products that customers need, but, says Iglesia, "the path does not always have to use toxic chemicals or wasteful reagents that are risky to handle and produce significant waste." In one project, he has been developing metal oxides with acid sites stronger than those in concentrated sulfuric acid. Sulfuric and hydrofluoric acids are widely used in refining and petrochemical processes, but they are very toxic, corrosive, and difficult to contain. "These acids are used to produce highly-branched hydrocarbons with high octane values and less-branched versions useful as lubricants. We are trying to understand the rules by which one assembles solid acid catalysts and how they work to carry out the reactions that we want, without catalyzing unwanted side reactions."

Iglesia collaborates with Bell on several projects involving catalysis. One involves combustion catalysts to remove volatile organic compounds from the exhaust of natural gas-fueled vehicles. In another joint project, they are tackling the difficult problem of how to avoid combustion, and to limit oxidation processes to selective desired pathways that form valuable olefins from less reactive paraffins. Such conversions are currently carried out by energy-intensive thermal processes, such as steam cracking. Their approach involves oxidative dehydrogenation, in which the hydrogen released during paraffin conversion is selectively combusted to provide the heat required to carry out the reaction. This way, the combustion of hydrocarbons and the generation of CO2 are minimized. "We want to avoid totally useless or toxic products, avoid throwing away reactant and waste products which cost money to separate," said Bell. To do this, they test different catalysts, use cheap starting materials and convert them to a higher value product. "We can also make oxygenated compounds, such as alcohols, aldehydes and carboxylic acids." They have learned how to relate the structure of the catalysts, at an atomic level, to the performance of such catalysts at the macroscopic level of practical chemical reactors.

Sara Yu and Eric Lu, graduate students in the Iglesia group, testing sulfur removal from gasoline-range hydrocarbons using zeolite-based catalysts in a laboratory microreactor.

Another way to address local environmental problems resulting from energy use, for example, the smog in many cities throughout the world, is to modify the fuels used for transportation so that they burn more cleanly. The recent shift from aromatics to highly branched paraffins as octane enhancers in gasoline has led to increased interest in the solid acids described earlier. Another trend is to decrease the sulfur content in fuels, because sulfur compounds contribute to acid rain and cause significant deterioration in the performance of automobile exhaust catalysts. Iglesia's group recent entry into sulfur removal catalysis has led to very exciting initial results, he says. Sulfur is currently removed from hydrocarbons by reacting it with H2, an energy-intensive and expensive process. "We are trying to transfer the hydrogen atoms directly from a paraffin to a sulfur-compound in one step, in one pot, using one catalyst," he says.

One can produce fuels that are low in both sulfur and aromatics by replacing petroleum with natural gas, because the sulfur is easier to remove. Of course, the current refining and distribution systems make direct use of natural gas difficult. "But what if we could convert natural gas to liquids, not by condensation at very low temperatures, but by reacting it to form sulfur-free gasoline and diesel free of sulfur and aromatics?" asks Iglesia. One method he uses creates diesel fuel out of natural gas by converting it to H2 and CO, and reacting the two to form linear hydrocarbons without any aromatics or sulfur. This area has become very important in the oil industry. Several companies have shown that "the performance of such fuels is remarkable, with unprecedented levels of soot and NOx emissions from diesel engines," says Iglesia.

On a more philosophical note, Iglesia remarked: "One positive evolution in environmental awareness within industry," says Iglesia, "is that the profits and cost-risk analyses of processes now include a price on unreliable or risky operations, costs that have been largely imposed by legislation or by litigation."

The Bacteria Are At It Again

On another air pollution front, Keasling and Department Chair Harvey Blanch have a joint project to prevent sulfur emissions by removing sulfur from fossil fuels. Again, microorganisms are enlisted to remove the sulfur, a component of acid rain, and a destroyer of catalytic converters in cars. New regulations in Europe--which are being considered in the United States--establishing very low tolerances for sulfur in fuels have created a strong interest by oil companies in this technology.

"It turns out that organic sulfurs are harder to remove than inorganic sulfur compounds, and of course, fuel values are higher with higher amounts of organic sulfur," says Keasling, "so you need to selectively remove sulfur compounds. Microorganisms do this best, so we are working on improving rates to make them commercially viable."

His main problem is transporting the hydrophobic sulfur compounds, which won't dissolve, to the organism. His solution has been to engineer the metabolism of the cells to secrete surfactants on the surface of the cell. "These act like soap bubbles, which capture the sulfur-containing organics and transfer them into the cell," says Keasling.

Keasling's bacteria also naturally accumulate polymers that can be harvested as biodegradable plastic. The plastic is a storage compound that microorganisms make naturally for starvation conditions, and requires the addition of two precursor chemicals. This is a well known, but expensive process, with little demand because regular plastics cost little to produce. But that could change if Keasling could force the bacteria to create both precursor chemicals as well as the plastic itself. In fact, Keasling says, we may "one day make biodegradable plastics from wastewater. All the right compounds are in it, it is renewable, and it's free!"

While it is evident that there are many areas where academic researchers do create new technologies that have significant impact on industry, Professor Iglesia reminds us that "few of us in academia develop and commercialize industrial processes. As scientists, we generate knowledge that can be recycled by industries; as teachers, we train the next generation. The value, in my view, comes from the recyclable nature of the fundamental concepts that we advance and from the potential of the students that we produce, and less so from any technology that we develop as a useful by-product of our central mission to create knowledge and to form scientists and engineers." There are obviously creative solutions just waiting to be discovered, and many areas where scientists and engineers can suggest chemical solutions to environmental problems.