Category Archives: Chemical Industry

ChemSpider Magic with LASSO

Of late I have been concerned with R&D information and various homebrew means of storing it and retrieving it. Institutionalizing R&D results into easily accessed knowledge can roll into a real hairball if you’re not careful. More on that another time.

My adventures with CHETAH 9.0 have caused me to look deeply into SMILES strings and what utility might be found there. This lead me to rediscover ChemSpider and the many services it provides for free to the user.

Consider the following: if you generate a SMILES structure of acetylsalicylic acid, say, from Chemdraw, O=C(O)C1=C(OC(C)=O)C=CC=C1, and use this character string as a search term in ChemSpider, it will take you to the entry for aspirin. What you get is a treasure trove of information on this substance. Go to ChemSpider, cut and paste the above SMILES string into the search box, and let her rip. I’m not your Momma. Just try it.

The breadth of references is encyclopedic.  But the truly amazing part is found when you scroll to the end of the page. There is a drop down window for SimBioSys LASSO. ChemSpider is working to provide LASSO data on its large database of compounds.  LASSO generates a structure and grinds it through a neural net processor module and produces a score between zero and one. The closer the score is to 1.00, the greater the surface conformity or compatibility of the ligand to a target receptor site.  As you would expect, there is a high score associated with aspirin and the COX-1 receptor. From what I can tell, the software is self-learning in some fashion.

The uses are many. Substances can be screened for drug-like attributes within the 40 receptor types provided.  I would like to hear from someone who might have something to say about the use of LASSO for the estimation of possible toxic effects of substances that have not been biologically tested. I fully realize the hazards of this, but perhaps LASSO scores might help flag particular substances for closer examination by testing.

Adrift in Cheminformatics Space. CHETAH 9.0 Fails with Some ChemSketch SMILES Strings.

The ASTM software Chemical Thermodynamic and Energy Release version 9.0, CHETAH 9.0, has many useful features for calculating thermodynamic values of substances.  My interest is in the (gas phase) calculation of ΔHf, limiting oxygen concentration, lower flammability level, Cp, entropy, ΔG, maximum heat of decomposition, net plosive density, ΔHc, and minimum ignition energy. The package claims to have the largest known database of Bensen group values at 965 entries.

I would have supplied links but the WordPress Editor is on the fritz. One more bloody software “issue”. – ‘th Gaussling

I recently upgraded from CHETAH 8.0 to 9.0 because 8.0 is incompatible with Windows 7.  These upgrades are a kilobuck a pop so they can be a budgetary surprise. After I upgraded I noted that 9.0 is not compatible with Windows 7 either!! Luckily I have a couple of lab computers that are still XP systems and therefore compatible with 9.0.  The folks at the University of South Alabama write and support CHETAH.

I understand from private communication that CHETAH 10.0 is in the works in anticipation of the release of Windows 8. Oh joy. I hope that some effort will be put into the user interface and general robustness. My question is this- what about those of us who will be using Windows 7 for the next few years? Will rev 10.0 be compatible? Will it have click and drag features or more of a DOS accent like the current rev?

One of the features that is nice about CHETAH is that it accepts SMILES strings as data input.  It parses the string into known Benson groups and flags unknown groups.  Previously I had been entering smiles strings from ChemDraw 7.0, an ancient but still useful version. Lately I have been evaluating ChemSketch freeware.  And lucky for me, I found another hole to stumble into.

SMILES is not inflexible in its syntax, apparently.  ChemDraw will convert a structure to a SMILES string that is different in its sequence from the identical structure drawn by ChemSketch.  I have found that CHETAH 9.0 will consistently accept SMILEs string entries from ChemDraw, but with only some ChemSketch SMILES strings.

Consider the following SMILES strings of the same structure-  5-Bromo-7-tert-butoxy-3-methyl-3H-isobenzofuran-1-one. The nomenclature is from Chemdraw. I do not use this compound- I dreamed it up as an example.

ChemDraw 7.0–  O=C2OC(C)C1=CC(Br)=CC(OC(C)(C)C)=C12

ChemSketch 12–  CC(C)(C)Oc1cc(Br)cc2c1C(=O)OC2C

The ChemDraw SMILES string is accepted by CHETAH 9.0 and parsed into Benson groups, but when you attempt to process the data it gives a “Run-time error 9” warning and then closes the program. From what I can tell, CHETAH 9.0 will only accept 9 Benson groups because when you clip off functional groups, it will accept the string for the next step. However, it still shuts down and indicates another error saying “subscript out of range”. I don’t know why this happens and the handbook does bnot seem to list errors. The programmer put the error routines in the program, but I guess was too busy to tell anyone what they mean.

The ChemSketch SMILES string above is not accepted at all.

I cannot justify switching to ChemSketch for several reasons and this is one of them.  The ChemSketch editor is generally balky compared to the smooth operation of ChemDraw. However, I must say that ChemSketch is very feature rich and has gotten much better. If I wasn’t already committed to ChemDraw (and Chem3D) I’d strongly consider it.

CHETAH seems to have limitations on the number of Benson groups it will accept for a molecule. It seems to require a particular edition of SMILES syntax. And, the user interface is is balky and antiquated.  I’ll try to uninstall CHETAH and reinstall it. That said, it still seems … brittle.

From what I can piece together by googling SMILES, the system has been evolving. Apparently, chemical graphics software out there has captured particular editions of SMILES at the time when their revision is released.  It would be nice if some international standard were in place to devise an enduring syntactical structure. Seems like something CAS could help with.

Comments on the history of oxidants

Today we know that the chemical elements are capable of showing a range of behaviors in the category of reduction and oxidation (redox). Unlike our predecessors who attempted to wrap their arms around redox phenomena without the benefit of data or atomic theory, we are able to refer to tables of information which give details on the magnitude of redox phenomena and allow us to predict outcomes of transformations.

Reduction and oxidation has always been with us and for most of human history we were blissfully unaware of it as a distinct and complementary phenomenon. Beyond the conduct of redox in biology, for most of human history the major use of redox as a tool was combustion.  I would argue that humans began to do chemistry in earnest when we learned to generate fire and use it at will.  The introduction of fire allowed humans to apply significant thermal energy to materials in contrast to mechanical energy. Thermal energy changed the composition of materials in a way that was visible to us. With fire we could boil, dry, pyrolyze, combust, sinter, fracture and melt materials.  Food once cooked was forever changed. The combustion of wood produced much heat, charcoal, and ash.

Fire could provide warmth and destruction. It could be used as a weapon of war. The Chinese would become renowned for their command of deflagrations, explosions, rocketry, as would the Greeks for their Greek fire.  Chinese adepts learned to produce deflagration and explosions with energetic redox compositions centuries before the Europeans. With the spread of gunpowder formulation around the world, the problem of finding it’s components would plague adopters of this technology.

The basic rules of controlling fire were determined very early in human history. Some things burned and other things didn’t. The effects of air might have been inferred by the simple act of lighting kindling and blowing on it. Blowing on an ember can sustain it for a time and gives rise to increased heat. Fire can be accelerated by blowing air on it but may also be extinguished by too much wind. Clues to the basic nature of fire were there all along, but we lacked vocabulary, theory, and analysis.

The color of a wood fire can range from yellow/orange to bright yellow and it can warm you from a distance. Smoke was something that issued from fire and was perhaps troublesome. Fire and smoke always seem to rise upwards. More clues to to the behavior of matter, but as before, we lacked the tools of science until only in the last few centuries.

Today we can use atomic and quantum theory, thermodynamics, and the physics of radiation and buoyancy to explain and quantify fire and its many attributes. Today we can confidently state that a fire requires an initiation (the energy source), a reductant (the fuel), and an oxidizer (air). I think early man would have had a fairly concrete understanding of heat source and fuel. But the need for an oxidizer may have been less obvious. After all, air is all around us and is invisible. Nobody knew about the fire triangle or Smokey the Bear.

The development of oxidizers as a class of substances whose participation in chemical change was held back owing to the obscurity of the concept and the lack of a good theoretical basis like atomic theory.  Humans had been perishing by suffocation forever. Everyone has experienced the effects of oxygen deprivation whether it was by running from a sabretooth tiger or holding ones breath on a dare. But without the knowledge of oxygen and its function in respiration or in combustion, oxidation was the answer waiting for the right question.

Reducing materials as fuels for combustion or for the reduction of metal ores to the metal was common knowledge for a very long time. The introduction of oxidizing materials beyond the ever present air around us was a much harder nut to crack.  If we set the oxygen in air aside and focus on strongly oxidizing substances, we can begin to see the development of oxidizers as a class of materials.

One of the earliest oxidizers to find use was nitrate, commonly called saltpeter or nitre. Nitre was found in some damp locations that were rich in decaying organic materials. Nitre beds were often observed as having a white crust that migrated to the surface of the ground.  Early references of these nitre beds come from China and India. Nitre was capable of having multiple counter-ions. The early users of nitre were unaware of this of course. Later in history, makers of gunpowder would come to prefer potassium nitrate over the sodium salt owing to it’s lower aptitude for hydration. Hydrated saltpeter will passivate gunowder.  The story of gunpowder is well documented and the reader can pursue that trail on their own.

The discovery of oxygen in 1772 by Scheele could be considered a major step in the development of oxidation technology. While chemists were misguided by the theory of phlogiston, the isolation of a substance that supported combustion was a crucial conceptual leap.  Scheele and later Priestly would show that this new “air” would support combustion. In 1774 the discovery of chlorine by Scheele was the next major oxidizer to be identified. Chlorine was produced by the action of HCl on MnO2 (pyrolusite).  The bleaching effect of Cl2 gas was soon discovered by Scheele. The discovery of Cl2 soon lead to the discovery of bleaching powders. The earliest bleaching powder composition comprised of lime and chlorine was patented in 1798 by Charles Tennant in England. By the close of the 18th century, three important oxidizing compositions were produced: oxygen, chlorine, and calcium hypochlorite.  Chlorine and lime bleaching powder went into mass production at the beginning of the 19th century.

In a real sense, the development of oxidizers is very much like the invention of the lever. A level is used to amplify mechanical force. An oxidizing agent is used to amplify the extractive force on valence electrons. A strong oxidizing agent is able to bring energy to bare on select transformations that might not be otherwise available.  With the advent of this kind of transformation, new possibilities unfolded in history. By the middle of the 19th century, molecules with pendant oxidizing groups would be capable of self reaction to produce tremendous outbursts of energy. Nitroglycerine is one such molecule containing both reducing groups and oxidizing groups in one molecule. Oxidizers and oxidizing functional groups would change how we dig tunnels, extract minerals, carve canals, wage war, and eventually, compress uranium or plutonium into a critical mass for a nuclear explosion.

Some good career advice from Bill Carroll

At our annual ACS Colorado section banquet for local high school students and their teachers, we invited Bill Carroll to be the guest speaker.  Carroll gave a good talk with pertinent advice on starting and grooming ones technical career. I won’t repeat all of it, but a few good points stand out.

Carroll began the talk by highlighting the differences between commodity and specialty products. Then he transitioned into the suggestion that careers can be partitioned into specialty and commodity categories as well. His argument was that jobs can become commoditized just like gasoline and that, like any commodity, choices as to who fills the position may be made from a crowd of indistinguishable candidates. And, like commodities, the salary paid to such workers may be beaten down by excess supply.

However you stretch analogy, the point was that it might be best to have core skills embellished with secondary and diverse abilities.

Research Squatters. When Universities and Corporate Behemoths Collaborate.

Recently I had the good fortune to get to meet for a consultation with a young and talented chemistry professor (Prof X) from a state university elsewhere in the US. Prof X has an outstanding pedigree and reached tenure rather rapidly at a young age. This young prof has won a very large number of awards already and I think could well rise to the level of a Trost or a Bergman in time.

Not long ago this prof was approached by one of the top chemical companies in the world to collaborate on some applied research. What is interesting about this is that the company has begun to explore outsourcing basic research in the labs of promising academic researchers. I am not aware that this company has done this to such an extent previously.  They do have an impressive corporate research center of their own and the gigabucks to set up shop wherever they want. Why would they want to collaborate like this?

R&D has a component of risk to it. Goals may not be met or may be much more expensive that anticipated.  Over the long term there may be a tangible payoff, but over the short term, it is just overhead.

The boards and officers of public corporations have a fiduciary obligation to maximize the return on investment of their shareholders. They are not chartered to spread their wealth to public institutions. They have a responsibility to minimize their tax liability while maximizing their profitability. Maximizing profit means increasing volume and margins. Increasing margins means getting the best prices at the lowest operating expense possible.

Corporate research is a form of overhead expense. Yes, you can look at it as an investment of resources for the production of profitable goods and services of the future. This is what organic growth is about. But that is not the only way to plan for future growth. Very often it is faster and easier to buy patent portfolios or whole corporations in order to achieve a more prompt growth and increase in market share.

The thing to realize is that this is not a pollenization exercise. The company is not looking to just fertilize research here and there and hope for advances in the field. They are a sort of research squatter that is setting up camp in existing national R&D infrastructure in order to produce return on investment. Academic faculty, students, post-docs, and university infractructure become contract workers who perform R&D for hire.

In this scheme, research groups become isolated in the intellectual environment of the university by the demands of secrecy agreements. Even within groups, there is a silo effect in that a student working on a commercial product or process must be isolated from the group to contain IP from inadvertant disclosure. The matter of inventorship is a serious matter that can get very sticky in a group situation. Confidential notebooks, reports, and theses will be required.  Surrender of IP ownership, long term silence on ones thesis work, and probably secret defense of their thesis will have to occur as well.

While a big cash infusion to Prof X may seem to be a good thing for the professor’s group, let’s consider other practical problems that will develop. The professor will have to allocate labor and time to the needs of the benefactor. The professor will not be able to publish the results of this work, nor will the university website be a place to display such research. In academia, ones progress is measured by the volume and quality of publications. In a real sense, the collaboration will result in work that will be invisible on the professors vitae.

Then there is the matter of IP contamination. If Prof X inadvertantly uses proprietary chemistry for the professor’s own publishable scholarly work, the professor may be subject to civil liability. Indeed, the prof may have to avoid a large swath of chemistry that was previously their own area.

This privatization of the academic research environment is a model contrary to what has been a very successful national R&D complex for generations. Just have a look in Chemical Abstracts. It is full of patent information, to be sure, but it is full of technology and knowledge that is in the public domain. Chemical Abstracts is a catalog and bibliography that organizes our national treasure. Our existing government-university R&D complex has been a very productive system overall and every one of us benefits from it in ways most do not perceive. We should be careful with it.

ReactIR. Infrared spectroscopy revives in the age of NMR.

We have a brand new Mettler-Toledo ReactIR 15 sitting in my lab. It is rather simple to use- just dip the probe in your reaction mixture. It needs a little LN2 to chill the detector. The software is reasonable, bearing some resemblance to iControl of the RC1 sitting a few meters away.

The instrument is used to follow the progress of a reaction by monitoring the growth or extinction of IR absorptions. What is interesting for the user is that it is not necessary to identify any of the peaks in the course of an experiment. The software can integrate absorptions and plot their change over time. The fingerprint region of the IR spectrum is put to good use in that it is a fruitful region for numerous absorptions to appear.

The thing is still new to us, so we’re early in the learning curve. The probe in use has a wave number range from 2500 to  about 650 reciprocal centimeters. It is possible to detect up to 3000 wave numbers with a different probe. The probe is connected to the interferometer by a fibre optic cable comprised of a silver bromide optical pathway.

The thing is the size of a coffee maker and costs as much as a used helicopter. The ATR probe tip is small enough to be immersed in experiments at the scale of a scintillation vial or a 5 liter flask.

What it brings to the table is the ability to follow the progress of reactions in real time for process optimization. Pulling samples and trudging over to the NMR for in-process checks is tiresome and time consuming.

One limitation is the electrical classification. As with other electrical devices you have pay attention to the NFPA classification of the space it sits in. The ReactIR 15 is class 1, but not division 1. If the instrument must be used in this space, there are ways to fashion an enclosure to get around this, according to Mettler. Have a look at your computer as well. If your computer throws sparks and coal cinders, you may want to keep it away from that pool of pet ether on the floor.

Mining Asteroids

The founders of the Silicon Valley startup, Planetary Resources, have announced plans for mining asteroids for valuable metals. Peter Diamandis, Eric Anderson and investors including director James Cameron and Google CEO Larry Page are behind this venture.

I’m trying to be positive here. Perhaps these fellows should visit some earthly mines and see what it takes to break actual rock and extract the value from it.

Earth bound ore bodies near the surface are commonly the result of concentration by hydrothermal flows. In the absence of water-based geothermal concentration processes, or recrystallization of PGM’s in magma chambers, the reality of economically viable ore bodies in asteroids is an open question. A lot of survey work needs to be done to answer this question.

Oh, and one more thing. When you blast rock on a largish planet like earth, the fragments fall back to the ground. This won’t happen on an itty bitty asteroid.

The talk about recovering water from asteroids to subsequently crack and make propellant is a large challenge all by itself.

I predict that civilization will slump back to a 19th century Dickensian-style world of robber barons and sharecroppers before any hardware gets to an asteroid.  Children will ask “Momma, what’s an iPad?” as they walk from their rundown subdivision to a quonset where they strip insulation from wire for copper to barter for food. It’s all so clear now …

Thorium power. Will the US get on board?

Everybody knows by now that China is flush with rare earth elements (REE’s), or at least to the uppermost extent that any country can be. And, everybody knows the market hijinks that China has planned with REE’s, namely, buy all the REE’s you want from them, as long it is in a value-added manufactured good.

What most folks are probably not aware of is that the ore bodies that carry the REE’s (Sc, Y, and the Lanthanides) are usually enriched in thorium and/or uranium.  So much so that no little amount of skill and equipment is needed to separate Th & U from the REE’s. The US and USSR developed much of this separations technology post WWII and for decades thereafter. Much of this art is in the US patent literature. The rest of it is buried in dusty, obscure volumes on library shelves.

The art of REE separation is arcane and somewhat isolated from the rest of inorganic chemistry owing to its specialized nature. Most of the separations art relies on leaching and elaborate solvent exchange schemes.  Ion exchange technology is also highly represented in this domain.  Few chemistry students are exposed to this science and most of the cold war era practitioners are retired, ailing, or deceased.

Chemistry students rarely see this art for another reason. It is generally practiced by engineers and metallurgists who seem to be in a perpetual phase separation from the standard chemistry curriculum. I would argue that this distinction is mainly cultural.

Back to the Chinese. While Americans have been busy yammering about drill-baby-drill, or following the escapades of reality show imbeciles or a thousand other idiotic distractions, we have failed to focus pressure on our government to consider technologies like thorium power or molten salt reactor technology.

While a gullible and frankly, cognitively impaired, vocal minority in the US accept that we have a right to $<3.00/gal gasoline, we are being distracted into the warm feather bed of self-congratulation and delusion about our supposed exceptionalism. I sense that our culture is beginning to show a type of exceptionalism that is not very admirable.

While American voters are being spun up into a frenzy again about commodity oil prices, China has been promulgating its national industrial policies. American industrial policy seems to be about lining the citizens up for accelerating consumption. China’s industrial policy emphasis seems to be about putting infrastructure and capacity in place for exports as well as anticipated internal consumption.

China has a substantial presence in mineral rich Africa. China imports copper ore from Peru and Chile. Not finished copper- but copper ore. China keeps the value added steps for its own coffers. Most distressingly, China is busily working on copper mining in Afganistan while our kids fight and die there in an intractable cultural shooting war. Did you get that?

China is mining in Afganistan and Americans are paying to die there.

While the US pays to make the world safe for commerce, China is spreading out over the world looking for scarce resources like copper under the umbrella of stability.  While China mines copper in Afganistan, the USA consumes copper in Afganistan in the form of brass bullet casings ejected over the landscape. Brass is an alloy of copper and zinc.

Is this a diatribe against all things Chinese? Absolutely not. If anything, China has skillfully mastered it’s range of control and made purposeful, long term plans to reach its goals. Like its plans for Thorium-based molten salt reactors. Thorium power is undergoing a bit more examination now, as described in this Forbes article.

Here is a point I’d like to get across. The present boom in REE exploration and mining is in a good place for thorium extraction. If thorium were to be part of the extracted value rather than a costly sidestream in need of segregation and remediation, then the subsequently improved economics of REE extraction and greater availability might translate to lower REE costs for users of rare earth metal technology.

There is a crucial synergy here that the US would do well to exploit. But it requires vision, long term planning, and regulatory flexibility in the handling, accumulation, and processing of thorium.  These attributes the US now lacks. The current lead pipe doctrines of American politics represents a critical systems failure of our culture. We cannot continue to regard middle-ground compromise as total forfeiture.

Chemistry Lab Accidents Reports from the Chemical Safety Board.

Here is a link to a US Chemical Safety Board video summarizing several recent lab accidents.  If you have never visited or heard of the CSB, here is a link to their web site. Have a look around.

This link is to the case CSB case Study of the Texas Tech explosion with nickel hydrazine perchlorate. It has a nice illustration of the Swiss Cheese Model of safety. This model was devised by British Psychologist James T. Reason at the University of Manchester in 1990.

The degree symbol- Do we really need to keep using it?

I had an evil thought just now as I attempt to write 2 reports simultaneously. Why do we keep using that superscripted circle in front of C (i.e., ºC) that designates “degree”?

What the hell? We don’t use it for the Kelvin temperature scale. And, who knows if the engineers use it for Rankine? The thing is useless like an appendix or a titular chairman. Get rid of it!

What do you think?