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17 Posts tagged with the green-chemistry tag

"Necessity is the father of invention," so the saying goes. While I don't personally hold with broad sweeping generalizations, it has to be said that many of the materials innovations that drive and enable our modern world have been driven by demand, need or circumstance. Examples of this range from the glass that protects and allows our phones to have dazzling displays to the batteries that power our mobile computers, pacemakers and surgical implants that enable people to have a good quality of life. Also there are non-stick cooking pans, energy efficient compact fluorescent and led lights, artificial sweeteners, advanced anti-irritant or skin-whitening cosmetics and creams, and new medical treatments.


Sometimes I think that we take for granted all the advanced science and materials that enable us to for example to cross almost half the world with relative comfort and safety. To land in a cold location with appropriate clothing to keep us comfortable and safe. To get there in a reasonable amount of time, and at a reasonable price in safety. To have available a car which starts and continues to function and to be able to call home to our families.


I was musing on this as I drank my cup of coffee and considering instant coffee. I am, and I admit it, a coffee snob. I like my coffee, I like it a certain way and so for many years while travelling I have had a constant vigil and hunt for coffee that is to my liking. With the spread of coffee chains globally, this is an easier problem, however I still I really like taking my coffee with me. This can be done with certain brands, and I remembered how instant coffee was actually invented by Dr. Hans Morgenthaler in 1938 for Nestle, but only became popularised by the American GIs in the Second World War, where weight and space were at a premium. The same issues of space and weight apply to so many things in the modern world, and as I planned my trip to winter-bound Europe, I wondered about these innovations. Of course the fact that now I can have decaffeinated coffee with caramel and that it can come in hot and cold varieties as well as a myriad range of flavors and specialty choices is all due to technical and formulation advances and the advent of new packages, processes and capabilities.


For my journey to Europe, I first needed a warm coat. Historically when people explored cold places they used large bulky coats and large heavy woolen gloves. Now, with the advent of high performance fibers such as those used in GoreTex where the body is maintained dry and sweat free yet the material can breathe and perspire without any snow or rain entering, I can have a lightweight jacket which is wearable, in the color I want and that lasts well when out hiking or mountain biking. So in went my hiking jacket, a smart choice because recently the UK has had one of the wettest periods of weather ever. Next, it was which bag to choose to pack my gear in. Suitcases and rolling bags or carriers have in the last decade changed due to polymers, plastics and composites out of all recognition. They have become lighter, more resistant to abrasion and damage. They have become more colorful and easier to open due to advanced plastic zippers and expandable sections. In addition, the new complex materials allow the wheels to roll more smoothly and to be honest, don't break with the frequency that the older ones did. Again, the materials technology that resists such impacts with flexible deformation and includes a smoothly lubricated bearing is really quite remarkable.


The next stage in my thoughts was about which route to take for my journey. This, as anyone knows in the winter is not a simple choice. It involved juggling which airports get snowed-in or have bad weather. Which (if any) airports can cope? What de-icing equipment and provisioning each has and what the cost might be. The issue of de-icing, which is basically removing the ice and coating the airplane with a complex formulation or mixture to prevent the onset of ice crystals is very complex. This is necessary since the buildup of ice crystals can rob a plane of its lift and control, which is not a desired state. The coating, however, has a whole series of design constraints that govern it. For example, it must be deployed easily and in low temperatures, and it must not damage the plane (for composite modern aircraft such as the Dreamliner this is harder than it would appear). It must be non-toxic, not affect passengers with allergies, be environmentally benign and of low cost. These are not easily balanced requirements for a formulated product that has to remain stable for extended periods of time, and like many advanced chemical products, it must be produced or deployed in many different locations with high frequency.

















Of course I also wondered about the composite materials used in the airplane. Those made by advanced manufacturing and materials companies such as Boeing, have many different and diverse requirements. They need to be able to stand the intense cold at altitude, and function for extended periods of time. Airplanes spend more time flying than they do on the ground. They need to survive lightning strikes, rain, hail, de-icing fluids and the many different sources of external impact. In addition their whole raison d'etre (lighter weight), better fuel per passenger performance needs to be enabled and provided. The fuel for airplanes (Jet A1) needs to be of high purity, consistent quality and not affected by the fluctuation in temperatures from 35,000 feet in the air to ground. This product involves very careful chemical processing design and administration. Companies such as BP Aviation and other aircraft fuel providers spend a lot of time managing the changing feed and input streams to yield consistent and constant products, as well as tracking lot to lot quality. They must also have stringent product safety and testing requirements.


Once I got to my destination, I expected to find a rental car that started and ran, and that would allow me to be transported to my hotel of choice, where I would be warm and safe in my well lit and heated room. Those simple common travel steps I realised are all triumphs of materials science, innovation and design. The fact that my car also has a fuel that can flow and burn consistently in low temperatures is amazing. The petrochemical companies actually adjust the ratios of different chemistries in winter, and summer fuels to aid burning and volatility in low temperatures. In some cases such as for diesel fuel, which can gel or almost freeze in low temperatures, they add specific pour point depressant additives and viscosity improvement additives. The same of course occurs for engine lubricating oil, which due to modern synthetic materials can have such a wide range of viscosities that people do not need to switch from a winter to summer oil and back again.


The battery of my rental has a unit which converts the electrochemical potential of the battery into current that drives my starter motor. It must function at high load when the whole car is probably at it coldest, and so again it’s a complex piece of chemical, materials and electrical engineering. In hybrid or electrical vehicles, this is an even more necessary situation. Finally, I consider the tires, which hopefully would keep me on the road. These materials which have actually a very small area in contact with the ground, whether it be asphalt, slush, snow or gravel, need to function in all seasons and in a whole different range of temperatures, irrespective of load and speed. Tires which are a significant contributor to the vehicles overall energy use, have to be engineered to have the right performance characteristics while maintaining safety and keeping costs, noise and performance within bounds and managed.


At the hotel, I hoped I would find a warm, well-lit room in the evenings with plenty of hot water. This requires ability to insulate the building and manage its heat loss, and to distribute electricity in very cold or warm temperatures for cooling or lighting. The ability to distribute natural gas is a triumph of modern science and materials development – natural gas is hard to find and harder to produce. Another critical development for the growing planet from a sustainability perspective is reducing the energy burden for housing. Building development with advanced materials, such as self-cleaning glass and lightweight insulation removes the need for excessive air conditioning or heating. Other amazing uses of advanced materials technology are low energy bulbs that use less energy, provide excellent light for reading, and can be easily recycled.


As I finished my planning for the trip at the beginning of the year, I wondered what would change in 2013 and how travellers in the future would see things when they too reflect on the things that go unnoticed but make all of their travelling so much easier.

3,459 Views 0 References Permalink Categories: Materials Informatics, Executive Insights, Modeling & Simulation, Electronic Lab Notebook, Data Mining & Knowledge Discovery Tags: materials_studio, materials_visualizer, forcite, dmol3, catalysis, materials, nanotechnology, atomic-scale-modeling, materials-studio, computational-chemistry, green-chemistry, quantum-chemistry

DFT by the Numbers: 2011

Posted by gxf Jan 12, 2012

DFT_2011.pngThis blog post continues my annual tradition of reviewing the DFT literature for the previous year. Most users of Accelrys Materials Studio have at least heard of this method. DFT=Density Functional Theory, a quantum mechanical method for solving the electronic Schroedinger equation of molecules and crystals using a formalism that is based the charge density rather than the wavefunction. You can see the Kohn-Sham equations at a number of sites on the web. These are what have been implemented in a number of software packages such as Accelrys MS DMol3 and MS CASTEP, as well as, in packages developed by other research groups.


In my annual informal survey, the year 2011 saw a 22% increase in the number of publications with the term "DFT" in the text (as determined by full text searches at the ACS and Science Direct web sites). Total count was 12 080. DFT has been outrageously successful since it combines relatively high accuracy with low computational cost - at least low by QM standards. In addition, it works very well for periodic systems, so it has extended routine QM calculations to areas such as heterogeneous catalysis.


This year, I'd like to highlight some applications in one of my favorite areas: alternative energy. I found a total of 2,255 citations that included DFT along with 'fuel cells,' 'batteries,' 'biofuels,' 'solar cell,' or 'photovoltaic'. That's almost 20%: Just about 1 DFT paper in 5 addressed some topic in alternative energy! Let's hear it for green modelers.


Some of my favorite papers from 2011:

  • Gao, et al., Dynamic characterization of Co/TiO2Fischer-Tropsch catalysis with IR spectroscopy and DFT calculations, presentation at North American Catalyst Society meeting Detroit, 5-10 June 2011, available on slidesshare.
  • Castrucci, et al., Light harvesting with multiwall carbon nanotube/silicon heterojunctions Nanotechnology 22 (2011) 115701. doi:10.1088/0957-4484/22/11/115701
  • Shin et al, Effect of the alkyl chain length of C70-PCBX acceptors on the device performance of P3HT : C70-PCBX polymer solar cells, J. Mater. Chem., 2011, 21, 960–967. DOI: 10.1039/C0JM02459G
  • Gaetches, et al., Ab Initio Transition State Searching in Complex Systems: Fatty Acid Decarboxylation in Minerals, J. Phys. Chem. A 2011, 115, 2658–2667.
  • Di Noto et al, Structure–property interplay of proton conducting membranes based on PBI5N, SiO2–Im and H3PO4 for high temperature fuel cells, Phys. Chem. Chem. Phys., 2011, 13, 12146–12154. DOI: 10.1039/c1cp20902g


Full disclosure: my favorites were done with Accelrys tools. You can see all the 2011 scientific publication lists for DMol3 and CASTEP on the Accelrys web site. Be sure to let me know what your favorites are.

1,756 Views 0 References Permalink Categories: Materials Informatics, Modeling & Simulation Tags: materials-studio, alternative-energy, green-chemistry, quantum-chemistry

As many readers know, I have a personal interest in alternative energy research. The past year, 2011, brought good news not just for research but for practical implementation, as well. A comprehensive analysis of the deployment of alternative energy technologies has been collected in the Renewables 2011 Global Status Report. This report covers historical growth in many areas of renewable energy, as well as, year-on-year growth from 2009 to 2010.


PV.pngThe report estimates that 194 gigawatts (GW) of electric generating capacity were added globally in 2010. It’s great to see that about half the new capacity comes from renewables. Including hydroelectricity, renewables account for about a quarter of total capacity: 1320 out of 4940 GW. Photovoltaics, in particular did well, increasing generating capacity by 73% year-on-year!


A lot of research articles were published in 2011. The research that I follow focused on improving the materials and processes used to generate or store energy and fuels. In biomass conversion, for example, people want to convert more of the plant to fuel, convert it to higher energy compounds, and do it cheaper and faster. In the area of batteries, we need materials that store more energy per kg, deliver it more rapidly, and last longer.


These kinds of topics may seem far removed from the practical engineering aspects of building a photovoltaic power station, but fundamental research is critical to improving efficiency and reducing cost. On ScienceDirect one can find for 2011 over 6500 citations on batteries, 5000 on photovoltaics, 6000 on fuel cells, and 3000 on biofuels. That’s about a 30% increase over 2010. Let’s hear it for fundamental research!


As a scientist, I’m thrilled at the technical achievements. As a concerned citizen, I’m pleased to see that alternative energy is making significant inroads in replacing fossil fuels.


What will next year bring? What do you readers think is the most significant alternative energy development we’ll see in 2012?


I’m hoping for a new battery I can swap into my Prius that will double my mileage to 100 mpg (42 km/L).

1,189 Views 0 References Permalink Categories: Materials Informatics, Trend Watch Tags: alternative-energy, green-chemistry

Catalysis is the chemical way that complex reactions which are difficult and costly in terms of energy, are carried out. Catalysts allow the odification of basic materials or feedstocls to they can be made ibnto complex materials or products. Then of course, as in the case of a paint, coating, cosmetic or pharmaceutical, there are a whole series of formulation and modification steps, as well. However, the starting gate for this process is the design and development of the catalyst for the manufacture of the material.


Catalysts can also allow energy-producing reactions to occur in reasonable and economic conditions, possibly holding the key, perhaps, to our energy future and the sustainable use of materials. A recent article on the Visible-Light-Driven Catalytic Properties and First-Principles Study of Fluorine-Doped Ti02 Nanotubes, indicates how the chemistry of these complex systems and the morphology or structure can affect their performance as promising photocatalysts for hydrogen production through water splitting under visible light-irradiation without other modifications.


Nanotubes are a novel and complex species of catalysts and their production, modification and fabrication goes through many steps. As these novel systems progress from test bed ideas into the field of development and production, the needs of quality assurance, raw materials, processing step and treatment step definition and monitoring come to the fore. It is very easy for one slight variation or mis-step in a complex process to affect the whole lot or batch of a production run of materials. Further, in many of the catalyst systems, just like a cake, materials are incorporated in layers, each having a specific function and passing the products of its reaction onto the subsequesnt or lower layers. Again, due to the complexity of the interacting chemistry and species, the ability to track these materials and their samples from inception through processing, complex modification or treatment and engineering steps are essential.


To drive better results with this precarious and prevalent process, a system which enables the planning of experimental programs, i.e., ad hoc or designed experiments, for best material or process coverage and subsequent data mining; or the sequential tracking of step-by-step stages of experiments which gathers the data produced from instrument files, spreadsheets and databases to eliminate manual piecing together of data, is essential. Ideally the system also provides the scientist and catalyst developer with the analysis tools, reporting or data insight tools, and data mining or information and knowledge generation tools such as, neural net or recursive partitioning algorithm analysis of the data.


It is important to note that such catalyst information, if systematically captured, stored and then mined, can provide both key indicators of future directions for development, as well as, point to areas of current formulation and materials space that have not been covered adequately for intellectual property protection. Such information would also provide a clear link to the process, scale-up and historiam types of data so that scientists and chemical engineers can identify good systems in the laboratory earlier, that stand a high probability of working in the pilot plant in a stable and multi-site or multi-feed environment.

564 Views 0 References Permalink Categories: Executive Insights, Lab Operations & Workflows, Data Mining & Knowledge Discovery, Modeling & Simulation, Electronic Lab Notebook Tags: catalysis, green-chemistry, formulations

Natural Gas to the Rescue

Posted by gxf Jan 20, 2011

A recent article in C&E News caught my attention: "Ethylene from Methane." This discusses some very interesting technology that can indirectly help ease the energy crunch.


Here's a little background. We do a lot with petrochemicals beside putting them into our automobiles. Most modern polymers are derived from petroleum, so as the oil wells dry up, there go our Barbie (TM) dolls, cell phone cases, and stretchy polyester trousers. The principle starting material for most of these polymers is ethylene, H2C=CH2. This is commonly formed from petroleum feedstock by steam cracking, which makes smaller molecules out of larger ones like naptha or ethane. How much longer can we keep this up? According to SEPM (Society for Sedimentary Geology) the current world-wide proven reserves are estimated to be over 1,000 billion barrels of crude oil; at the current rate of oil consumption there are only 32 years of reserves left. According the US Energy Information Administration, the reserves of natural gas are 6,609 trillion cubic feet, and the C&EN article claims that we have 'multiple centuries' of this left.


The problem is that natural gas is primarily methane (CH4) and it's been harder to build ethylene up from this small molecule than to crack it from larger ones... until now. According the the C&EN article, a new process of oxidative coupling of methane (OCM) holds the promise of tapping this new source of raw material and making ethylene for a lower energy cost. The approach to this problem was really neat. Based on the work of Angela Belcher of MIT, scientists at Siluria Technologies grow catalysts by mineralizing the surface of a virus. By genetically engineering the viruses, they can generate an almost limitless number of different surfaces and hence explore a huge range of catalysts. An effecient OCM catalyst means that it becomes commercially feasible to use cheap natural gas as a feedstock to create raw materials for sophisticated products.


This sort of creative solution to problems of energy and natural resource utilization are excellent examples of why government must continue funding fundamental research. This work draws on the fields of molecular biology, catalysis, high-throughput screening, and petrochemistry — disciplines that you might not think would play well together. To find the best solutions to our energy challenges, researchers need the freedom to explore lots of alternative solutions; and we need to have many scientist engaged in this. As scientists and citizens, let's make sure that our elected officials know how important fundamental research is to our future.

704 Views 0 References Permalink Categories: Materials Informatics Tags: catalysis, alternative-energy, green-chemistry

Sustainability and green chemistry, are key aspects of the future of cosmetic chemistry, science and products, as well as, for a range of other consumer packaged goods. These aspects or design principals are very important and I suggest worth considering as we witness dramatic growth in the interest and corresponding consumer dollars driving significant demand for them.


The good news is that these principals do not necessarily require a change of product formulation or performance; rather they are about how a product is made, and how from discovery to development and manufacturing, the product moves through “Green Stage Gates” for reaction mass, solvent and catalyst use. As Dr Liliana George, executive director of strategic developments in R&D at the Estee Lauder Companies recently discussed, the ability of green chemistry to reduce the impact of a product, without necessarily changing the product itself is key, and is a challenge faced by many cosmetic formulators. “No one is asking you to change the end product, but how you get there can be altered and improved”.


It is in this light that catalysis and reaction planning and pathway or synthesis step substitution become very important. The EPA green principals can be applied as a very good benchmark to developments like these:


  1. Prevent waste
  2. Design safer chemicals and products
  3. Design less hazardous chemical syntheses
  4. Use renewable feed-stocks
  5. Use catalysts, not stoichiometric reagents
  6. Avoid chemical derivatives
  7. Maximize atom economy, reduce wasted side reactions or mass
  8. Use safer solvents and reaction conditions
  9. Increase energy efficiency
  10. Design chemicals and products to degrade after use
  11. Analyze in real time to prevent adverse reactions, excessive reactions and pollution
  12. Minimize the risk or potential for accidents


The advent of virtual chemistry and formulation design, allow the research and evaluation of alternatives, within optimal boundaries such as cost, performance, processability, as well as, time to market. This always has been the aim of modeling and simulation technologies, i.e. to generate understanding and information. However, the need for novel and improved solutions, as Lillian says and as Dr Steve Collier of Codexis presented in Barcelona, Spain at the Organic Process Research & Development Meeting recently, in his presentation entitled, "The Development of Commercial Biocatalytic Processes to Simvastatin and Other Molecules using Highly Evolved Enzymes", the need for complex understanding of chemical and bio-molecular entities is growing. In many cases the competing needs of discovery or idea generation science are now being filtered or aided by information and knowledge extracted from development processing and assembly so that systems can be brought faster to market as well as more accurately and reproducibly. The new generation of tools where models, data and information are treated on an equal footing enables and supports these workflows, while freeing up time for scientist and engineers to do more high value activities such as product creation and delivery (

868 Views 0 References Permalink Categories: Executive Insights, Modeling & Simulation, Trend Watch Tags: simulation, catalysis, green-chemistry, sustainability, formulations, cpg

Sustainability continues to grow in importance as an issue, both ecologically and sociologically. One source of resistance, I think, is the perceived cost of implementing sustainable practices vs the status quo. A recent article by Rosemary Grabowski in Consumer Goods Technology (CGT) outlines a number of practices and shows - among others things - why cost shouldn't be an issue. Sustainability isn't just good for the environment: it's good for the bottom line. Grabowski lists 10 requirements for sustainable strategies that also serve as drivers of business. I won't repeat them all here since you can read them for yourselves, but I'd like to highlight a couple that fit with the themes that we've already explored on this web site over the past year or so.


We have written a lot on sustainability on this web site, with examples such as Michael Doyle's blogs on sustainability, my own blog on methanol from biomass, or Michael Kopach's entry on incorporating green features into electronic lab notebooks (ELNs).


As a modeler I just love these topics because there's so much that software can contribute - in fact all 10 of Grabowski's requirements can be met this way. Open Collaboration, for example. This is an idea that P&G pioneered some years ago. Of course anyone can dump a new idea into the system, but you need a way to keep track of it, share it, add to it, and feed it back again. This is where software tools like ELNs come in. They also deliver centralized data, data continuity, and tracking, all of which are mentioned in the CGT article.


Another key requirement is Virtual Design. (You guessed it: as a modeler this is my absolute favorite topic.) Software has reached the stage where a lot of work can be done computationally rather than in the lab. No messy chemicals to clean up, no animals to experiment on, no toxic by products. The capabilities include alternative energy, more efficient use of resources, and the prediction of toxicology (see SlideShare for specific examples).


Sustainability shouldn't be a buzz word in 2011: it should be a serious consideration for all corporations and individuals concerned about the future. Software offers  inexpensive and non-pollution solutions. I've touched on only a few here, but I'm really interested to hear from you folks out there. What are your challenges in sustainability and how are you meeting them? Whether with software or otherwise, let me know.

727 Views 1 References Permalink Categories: Electronic Lab Notebook, Modeling & Simulation Tags: alternative-energy, green-chemistry, sustainability

What are critical problems in alternative energy research? How does modeling play a role in bringing us closer to answers?


A recent review article on this topic by long-time associate Prof. Richard Catlow, et. al, caught my attention. Readers of this blog will be familiar with our many posts pertaining to 'green chemistry,' sustainable solutions, and the like. Last month, Dr. Misbah Sarwar of Johnson Matthey was featured in a blog and delivered a webinar on the development of improved fuel cell catalysts. Dr. Michael Doyle has written a series on sustainability. Drs. Subramanian and Goldbeck-Wood have also blogged on these topics, as have I. All of us share a desire to use resources more responsibly and to ensure the long-term viability of our ecosphere. This will require the development of energy sources that are inexpensive, renewable, non-polluting, and CO2 neutral. Prof. Catlow provides an excellent overview on the applications of molecular modeling to R&D in this area. Read the paper for a very comprehensive set of research problems and case studies, but here are a few of the high points.


  • Hydrogen production. We hear a lot about the "hydrogen economy," but where is all this hydrogen going to come from? Catlow's review discusses the generation of hydrogen from water. Research challenges include developing photocatalysts capable of splitting water using sunlight.

  • Hydrogen storage. Once you've created the hydrogen, you need to carry it around. Transporting H2 as a compressed gas is risky, so most solutions involve storing it intercalated in a solid material. LiBH4 is a prototypical example of a material that can reversibly store and release H2, but the process is too slow to be practical.

  • Light absorption and emission. Solar cells hold particular appeal, because they produce electricity while just sitting there (at least in a place like San Diego; I'm not so sure about Seattle). One still needs to improve conversion efficiency and worry about manufacturing cost, ease of deployment, and stability )with respect to weathering, defects, aging, and so forth).

  • Energy storage and conversion. Fuel cells and batteries provide mobile electrical power for items as small as hand-held devices or as large as automobiles. Catlow and co-workers discussed solid oxide fuel cells (SOFC) in their paper.


The basic idea with modeling, remember, is that we can test a lot of materials for less cost and in less time than with experiment alone. Modeling can help you find materials with the optimal band gaps for capture generation of photoelectric energy. It can tell us the thermodynamic stability of these new materials: can we actually make them and will they stick around before decomposing.


Simulation might not hit a home run every time, but if you can screen out, say, 70% of the bad leads, you've saved a lot of time and money. And if you're interested in saving the planet, isn't it great if you can do it using less resources?


Check out some of my favorite resources on alternative energy, green chemistry, and climate change.


513 Views 0 References Permalink Categories: Materials Informatics, Modeling & Simulation Tags: catalysis, materials, atomic-scale-modeling, alternative-energy, green-chemistry, fuel-cells, hydrogen-storage, solar-cells

The ACS GCIPR meets next week in Washington, D.C., and we will be presenting at the meeting a vision for using ELNs to support green chemistry. I asked Todd Clement, our resident expert on green chemistry and ELNs, to respond to the recent entry by Michael Kopach, a member of the ACS GCIPR. We look forward to continuing the conversation with you on this timely topic. 


todd_clement_small.jpgRecently, an increasing number of our customers have expressed internal directives toward incorporating green chemistry principles into their development processes.  Pharmaceutical companies have introduced, via various means, green chemistry reviews that have become a standard operating procedure for taking a chemical process through the different stages of the development lifecycle.  In industry, there is wide agreement on the governing principles and philosophy of green chemistry; however, the difficulty arises in obtaining consensus on what factors deserve the most weight when one actually evaluates the greenness of a chemical process.  As an ELN vendor, we aim to enable the workflow of our customers and need to support important initiatives such as those being implemented to support the development of green processes.


In 2007, the ACS GCIPR endorsed process mass intensity (PMI) as one simple means to capture data on the greenness of a process.  This metric was brought to our attention by Dr. Kopach, with the support of several other customers, as a calculation that could be incorporated into an ELN since the information needed to calculate this metric was readily available in the ELN entry.  Due to the wide support PMI has received, this calculation was implemented in the Symyx ELN.


As Mike pointed out in his write up, the next logical question seems to be what more can be done from the data captured in the ELN? If one looks at the guiding principles of green chemistry, there are many possibilities for additional metrics to be calculated and reported as a component of an overall greenness report.  Some simple additions might be to consider the number of isolated intermediates and the number of chemical transformations in the process as a whole.  Each of these contribute some amount to the overall score, the fewer the better, obviously.  In accordance with the third principle of green chemistry (Less Hazardous Chemical Synthesis), calculations could be incorporated based on the acceptable (or unacceptable) nature of the reagents and solvents used in the process.  The question then becomes what materials are considered in these lists?  One would assume this ought to be configurable.


I’ll reiterate Mike’s question: Are there other metrics (besides PMI) that are important at your sites?

538 Views 1 References Permalink Categories: Electronic Lab Notebook, Trend Watch Tags: green-chemistry, eln, symyx-notebook-by-accelrys, standards

Michael Kopach, research advisor at Eli Lilly and Company, is a member of the American Chemical Society Green Chemistry Institute Pharmaceutical Roundtable (ACS GCIPR), a coalition between the ACS Green Chemistry Institute and several major life science corporations. The group is meeting June 21 in Washington, D.C., and in the run up to the meeting, hopes to collect information on particular challenges in green chemistry and how ELNs could support greener methodologies in pharmaceutical R&D. I’d like to help him out with some discussion here. In this entry, Mike asks about which green chemistry metrics are most important to green chemistry development. We’ll respond with a few entries describing our ideas for handling green chemistry in an ELN.


Mike Kopach small.jpgSignificant efforts are underway within the pharmaceutical industry to develop more efficient processes for manufacturing both small and large molecule drugs. Green chemistry development has been guided by the twelve principles of green chemistry and engineering, which stress atom economy and low yield methodology, less hazardous chemical synthesis, use of safer chemicals, design for energy efficiency, and use of renewable feedstocks. ACS GCIPR’s mission is to integrate the twelve principles into the business of drug discovery, drug development, and production.


Most ACS GCIPR members currently use ELNs to capture and retrieve scientific information within their organizations. This presents an incredible opportunity for ELNs to help scientists develop greener processes from the outset. For example, ELNs could automatically calculate some common metrics of greenness, such as process mass intensity. PMI is a value based on Sheldon’s E-Factor and is defined as the total amount material used per product produced (kg/kg API). The metric includes all solvents, reagents, and water used in chemical processes. In many instances, PMI has been found to be a useful surrogate measurement for process energy. In 2006, the PMI reported for ACS GCIPR member companies averaged 180 kg/kg API for phase 3 processes, with solvent and water constituting 80-90% of the total waste produced.


ACS GCIPR members generally concur that PMI is an important metric of greenness, but other metrics also exist, and organizations rank them differently. Which greenness metrics are most important at your sites? And how do you think ELNs could assist in developing greener processes?

513 Views 3 References Permalink Categories: Electronic Lab Notebook Tags: green-chemistry, eln

Green Chemistry

Posted by lsubramanian May 27, 2010
Green chemistry is a concept best applied right at the beginning of a project; it is hard to change a process once it is set in stone.  Increasingly, companies choose a “benign by design” method to assure the sustainability of new products, taking into account this consideration across the complete lifecycle.  Though product development strives for environmentally acceptable chemical processes and products, the application of green chemistry is fragmented and still represents only a small fraction of actual chemistry.  Series of reductions in water and energy consumptions and reduction of toxic wastes leading to economic, environmental and social benefits can only be attained by a full commitment of all parties involved in the supply chain.

Whether it is in producing cellulose based biopolymer or in redesigning a catalytic reaction with zeolites, the challenge is in maintaining the Price-Performance balance.  The main stream consumers need to change their attitude and be ready to sacrifice either price or performance in order for Green Chemistry to grow.  Since its birth in 1991, Green chemistry has come a long way, growing from a small grassroots idea into a new approach to scientifically-based environmental protection.  Several commercial and government organizations are working to transform the economy into a sustainable enterprise.  Accelrys’ contribution, small but sure in the area of Green Chemistry, is shown in this example.  In our published work, we report on the nitration of toluene, an important precursor used in dyes, pharmaceuticals, perfumes, plastics, etc.

What are your thoughts on the evolution of green chemistry and its effects on the economy?
455 Views 0 References Permalink Categories: Materials Informatics, Trend Watch Tags: chemistry, catalysis, green-chemistry, polymers, sustainability, toluene, zeolites

The recent oil spill in the Gulf of Mexico is a catastrophe whose consequences will be felt for years to come. Prince William Sound, Alaska, still shows the presence of oil from the Valdez oil spill in 1989. Nevertheless, my intent in this blog entry is not to castigate the parties responsible for it or to lament the damage to the environment, but rather to discuss the chemistry that led to the initial explosion and subsequent tragedy. The problems began on 10 PM on April 20 when a surge of gas (apparently CH4) and oil shot up the drill pipe. Much mention has been made of hydrates, which seem to have contributed to this initial surge and which have subsequently impeded several attempts to cap the well.



Molecular model of gas hydrate

Molecular model of gas hydrate, from Leibniz Institut fuer Meereswissenschaften



Hydrates (as explained by the Leibniz Institut fuer Meereswissenschaften) are "non-stoichiometric compounds. Water molecules  form cage-like structures in which gas molecules are enclosed as guest molecules" (see image). These structures occur naturally in many deep ocean sites. Any number of gases can be found in the lattice, but the one of interest here is methane, which is produced by "zymotic decomposition of organic components or by bacterial reduction of CO2 in sediments." These are stable over a specific range of temperatures and pressures as described here, and shown in the image below. There is a limited zone of stability for the hydrates: they extist at high pressures and relatively low temperatures. The weight of the ocean induces a pressure of roughly 1 atm for every 10 meters. Temperature initially drops with ocean depth, but then increases beneath the sea floor. Once you get deep enough - and hot enough - the hydrates are no longer stable. Consequently, their occurrence is limited to a relatively narrow band beneath the ocean floor. The operation was taking place in 1500 m (5,000 ft) of water, and drilling to a depth of 5000 m (18,000 ft).



Stability diagram for gas hydrates

Stability diagram for gas hydrates in marine environment, from Leibniz Institut


As reported in the Financial Times energysource blog, "It has been suggested that they [hydrates] may have been responsible for the leakage of gas into the Deepwater Horizon’s drill riser..." Why did the gas appear then? The crew of Deepwater Horizon was in the process of capping off the well, which involves pumping concrete into the top to seal it (nice graphic of that process in the FT). It is known that this process can destabilize hydrates: a 2009 report by Halliburton, reported again in the FT's energysource blog, warned that "gas flow may occur after a cement job in deep-water environments that contain major hydrate zones." As the FT blog summarizes, gas might stop flowing from the hydrates in a few hours or days, or - if you're unlucky - it might notstop. The chemistry of concrete is explained on this site maintained by WHD Microanalysis Consultants Ltd, who mention that the curing of concrete is an exothermic process, with the period of maximum heat evolution occurring typically between about 10 and 20 hours after mixing. I can't help wondering whether heat released by the setting concrete can contribute to destabilization of the gas hydrates. Anybody got any thoughts on that?

Subsequently, gas hydrates played a role in hindering attempts to stop the flow of oil. Remember the 100-ton steel and concrete box they tried to move on top of the hole? As reported in the FT (again): 'When gas leaks out [from the well], its pressure drops and it cools... In the presence of water, light hydrocarbon liquids can react with water to form a ... hydrate. This happens quite often in gas pipelines, but the circumstances 5000 ft down on the sea bed ... make this very difficult to control.'  This says that the leak from the well is creating even more  hydrates. The hydrates clogged the container and forced a halt to the operation.


Incidentally, methane hydrates would be a great source of energy. Unfortunately, that's not a carbon-neutral process: there's a tremendous amount of CO2 that would be released. Still, it's really fascinating to see ice burn as the CH4 is released.


Fascinating chemistry. As a theoretical chemist, I've been thinking about how modeling could help. Modeling could predict (T,P) phase diagrams for CH4 in H2O lattices. Monte-Carlo simulations can predict loading curves for these structures, while molecular dynamics or DFT could predict thermodynamic and kinetic stability of the methane absorption. Ultimately, you'd like to be able to use such approaches to identify ways to stabilize these structures, or to destabilize them in a controlled manner: imagine pumping in a chemical that causes the CH4 to be released sloooowly. The advantage of computational methods, of course, is that models won't blow up no matter how much pressure you apply to them or how much methane 'escapes.'


Such a study might help prevent future tragedies, but the main focus of scientists & engineers now needs to be on the cleanup. More on that in a future blog.

434 Views 0 References Permalink Categories: Materials Informatics, Trend Watch Tags: green-chemistry, gas-hydrates, oil-spill, petroleum
3D Pareto Surface

3D Pareto surface shows the tradeoffs among target properties: dipole moment, chemical hardness, electron affinity. The optimal leads are colored red, poor leads blue.

How do you search through 106 materials to find just the one you want? In my very first blog post "High-Throughput- What's a Researcher to Do?" I discussed some ideas. The recent ACS had a session devoted to doing just that for materials related to alternative energy, as I wrote here and here.

My own contribution was work done with Dr. Ken Tasaki (of Mitsubishi Chemicals) and Dr. Mat Halls on high-throughput approaches for lithium ion battery electrolytes. This presentation is available now on Slideshare (a really terrific tool for sharing professional presentations).

We used high-throughput computation and semi-empirical quantum mechanical methods to screen a family of compounds for use in lithium ion batteries. I won't repeat the whole story here; you can read the slides foryourselves, but here are a couple take-away points:

  • Automation makes a big difference. Obviously automation tools make it a lot easier to run a few 1000 calculations. But the real payoff comes when you do the analysis. When you can screen this many materials, you can start to perform interesting statistical analyses and observe trends. The 3D Pareto surface in the accompanying image shows that you can't optimize all the properties simultaneously - you need to make tradeoffs. Charts like this one help you to understand the tradeoffs and make recommendations.

  • Don't work any harder than you need to. I'm a QM guy and I like to do calculations as accurately as possible. That isn't always possible when you want to study 1000s of molecules. Simply looking through the literature let us know that we can get away with semi-empirical.

Enjoy the Slideshare, watch for more applications of automation and high-throughput computation, and let me know about your applications, too.

667 Views 0 References Permalink Categories: Materials Informatics, Modeling & Simulation Tags: materials, atomic-scale-modeling, high-throughput, lithium-ion-batteries, materials-studio, alternative-energy, green-chemistry, virtual-screening

Sustainability: Part 1

Posted by mdoyle Mar 16, 2010
Recently I have been flying a lot; its sort of an occupational hazard of being a field scientist during the winter months. Anyway, on one of the flights I was reading an article about the Exxon initiative in green algae based bio-plastics and feedstocks. This brought my mind back to the concept of sustainability and its myriad facets in chemical, pharmaceutical and materials sciences. Sustainability in terms of energy usage and cost of synthesis. Sustainability in terms of sourcing and raw materials and bio processing or germline design and breeding.  Even sustainability in terms of our education. These features fall into a common framework of technology and planning for the future, or using some of the perception and benefits of technology to guide our steps forward.

I remembered my initial feelings as a young scientist working in a refinery. I was overawed by the complexity and size of the cracking, reforming, fractionating, stripping and converting columns and reactors in the refinery and plant. I was there setting up a modelling and near remote sensor, (infra-red) process control system, to help optimize plant throughput and quality using chemical and process optimization, but that is another story.

Anyway, one day after climbing up and down the towers, I was discussing the plant with my manager and he asked me a question. "What is the most interesting or amazing thing about a chemical plant?”  I replied about the size, intricacy and complexity. He said in his view “no;” in his view it was the fact that you could never see, touch or smell the product, unless there was a vent over, or some sort of failure "bad thing" in the process. He continued the comparison; think of a car production line, there you can see all the product as it moves down the line with new wheels and engines being attached. In a chemical plant you cannot see anything of the complex changes that are performed on the materials as they flow through the reactors, stripping columns and condensers. In hind sight, this is a green or sustainable comment.  My view a few years on is that the chemical industry, and yes there have been some very few mistakes, is an amazing industry where very little of the product is exposed to the environment and all the complex and myriad transformations are performed in carefully protected containers. This in terms of efficiency, complexity and microscale materials engineering is a stunning achievement. Now other aspects of sustainability are the fate of the products that come out of these processes, the use of precious energy and fossil fuel reserves in these processes and the impact these materials have on people and their lives.

It is interesting to also note that one of the larger areas of sustainable research is in the pharmaceutical area. Here, there is significant research and development activity in the area of sustainable synthesis, which we will explore later, in Part 2 of this post.  Stay tuned!
427 Views 1 References Permalink Categories: Materials Informatics, Trend Watch Tags: materials, pharmaceuticals, green-chemistry, chemicals, refinery, sustainability

A number of recent (and not so recent) initiatives in Congress are designed to encourage production of ethanol as an alternative fuel, but how much is really feasible and how much is catering to eco-hype? A search of congressional bills for the 111th congress turns up an astonishing 1592 bills relating to “energy” and 150 to “renewable energy.” These bills do everything from providing tax credits for growing corn, to funding development of production facilities, to providing tax credits for consumers. But which options really make sense?

The debate over methanol from corn has been going on for a while, and judging from the available information, there’s plenty to be concerned about. Paztec and Pimantel have published numbers that suggest that such production is a net energy loss. This is supported by an EPA report summarized in Chemical & Engineering News (C&EN) May 11, 2009 [sorry, you’ll need a subscription to read that]. A 2007 energy law set a production target of 36 billion gallons of biofuels by 2022. As reported in C&EN, the law requires a full life-cycle analysis that “reflects a growing concern that ethanol may result in higher CO2 emissions due to land-use practices, such as clearing rain forest…”  And another recent C&EN article discussed the potholes on the road to commercial biofuels. According to the article, of the six cellulosic ethanol projects to receive DoE grants in 2007, none of the projects has been built, although one is under construction.

Yet, optimism abounds. As reported in C&EN, Sean O'Hanlon of the American Biofuels Council is confident that next-generation biofuels will deliver. On top of that, Exxon plans to invest up to $600 million to develop biofuels from algae.  And there’s no shortage of small startups trying to reach similar goals.

Despite the differences between the optimists and pessimists, I think that they agree on one thing: the need for higher efficiency. Given the current efficiencies of biofuel production, internal combustion engines, and fuel cells, biofuels can’t reach the goals that we’ve set for them (e.g., 10% of electricity from renewable sources by 2012, and 25 percent by 2025). What is unquestionably needed is more fundamental research. To underscore some of my favorite, recent high points:

These are just a few examples of the many fundamental advances that will be required to make biofuel sustainable and commercially viable.


Scientists regularly cry out for more fundamental research funding at the start of each federal budget cycle. The American Reinvestment and Recovery Act (ARRA) of 2009 provides for $4.6 billion in DOE grants for basic R&D. The latest congressional omnibus bill provides $151.1 billion in federal R&D, an increase of $6.8 billion or 4.7 percent above the FY 2008 value. This is a real good start. Let’s make sure that we use the money wisely.


Here are the results from the poll attached to this blog post:



444 Views 2 References Permalink Categories: Trend Watch Tags: alternative-energy, green-chemistry, biofuel, biomass, funding, methanol
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