Category Archives: Chemistry

NIH Manditory Open Access

According to C&EN, the NIH has issued a rule that publications resulting from NIH funded research be submitted to PubMed Central for posting.  Naturally, organizations with copyright interest in published research is  less than enthused by this ruling.

What has happened over the last century is that a sizeable publishing industry has grown up around the publication of periodicals specializing in scientific research.  In exchange for release of copyrights, authors get free or nominally priced access to publishing and distribution of their work. For their part, publishers tap into a continuous stream of refreshed content that is virtually free of charge. 

Counterbalancing the low cost of content are the sad facts of subscriptions.  Many (most) journals suffer from low distribution numbers, so the zero cost of content helps to keep overhead down, but publishing and distribution costs cannot benefit from the economy of scale.

The special interests seem to be sitting in watchful waiting, but they have raised the issue of copyright. Their concern is that they are being forced to distribute their property by the strong arm of NIH without the chance for reimbursement.  This could resolve to a property rights battle and as such, I can’t imagine that the NIH would prevail in the courts.

Descriptive Inorganic Chemistry

Now that I am doing a fair amount of inorganic synthesis and preparation of metal coordination complexes, I look back to my undergraduate education and wish that it had been somewhat different.

In my undergrad time in the early 80’s, inorganic texts were heavy in theoretical concepts- molecular spectroscopy, ligand field theory, and group theory. It made for a tidy textbook package and coursework was constructed around it.  I cannot speak for other institutions, but in my experience the inorganic curriculum is (was) somewhat leaner in course options than is organic or biochemistry. In particular, the inorganic lab experience was somewhat less endowed with resources than the more popular biochemistry lab.

In graduate school, our graduate level inorganic coursework was even more theoretical than was the undergrad coursework. Obviously, there is a good argument for this and I am not actually complaining about it. But I will say that, in my experience, descriptive inorganic chemistry in the lecture section was sacrificed by the professors apparent preference for the elegance and tidiness of theoretical inorganic chemistry.

To his credit, my undergrad inorganic professor did try to give us the best lab experience possible. We had a vacuum line and did have the chance to use it. We did a prepn of AlI3 a tube furnace. We prepared Cu2(OAc)4 and a few other complexes.  He was also a glass blower  and did his best to teach us a bit about glass.

But in the end, the department was much more highly invested in organic and biochemistry. I was enchanted by synthetic organic chemistry and continued down that track.

With the benefit of hindsight, I now see that the curriculum that I was channeled through was too lean with respect to the rest of the periodic table.  Decriptive and  preparative inorganic chemistry was wedged in only by virtue of the strength of the professors interests and personality. Theoretical inorganic chemistry does not require expensive laboratory facilities.

So, I have come out to speak in favor of more descriptive inorganic chemistry in the curriculum.  More reaction chemistry. More preparation of materials in the lab. More characterization of or reaction products. More experience with setting up reactions and isolations.  More experience with hazardous materials!!

The notion that laboratory experiences for chemistry majors must be constrained by the need for Green consideration is nonsense.

I believe that microscale equipment for chemistry majors should be banned. Students should minimally prepare a few grams of materials so that they can be handled for subsequent purification and characterization. Forcing inexperienced students to prepare a spatula tip of product is unfair and needlessly harsh.

The idea that constraining a junior or senior to preparing less than 100 mg of product in a reaction is somehow green and worthy of merit is absolutely ridiculous. This is chemistry lab, not church camp.  The savings in environmental insult is minimal. There are much bigger fish to fry than this anyway. 

I suspect that equipment expenses and waste costs for university chemistry departments are drivers in what is chosen for the lab experience. If indeed efforts are being thrown on better instrumental experiences rather than better preparatory experiences, then I would say that we are missing the point. Given the creeping featurism in computer controlled instrumentation, I would suggest that monies be spent on better synthetic experiences than on the latest hyphenated instrument. 

Perhaps someone could comment on this.

Herr Doktor Professor

According to the March 10, 2008 issue of C&EN, a number of US PhD scientists working at Max Planck are facing charges for illegal use of the title “Dr.” According to the article, the title Dr is reserved for graduates of EU universities. From C&EN-

According to German criminal law, the title “Dr.” is reserved only for individuals who received a doctoral degree from a European Union institution, explains Erik Kraatz, a criminal lawyer at the Free University, Berlin. Kraatz notes that the law also prohibits masquerading as a police officer, medical doctor, or professor.

Indeed, to legally use the title “Dr.” in Germany, foreign-trained scientists must request permission from their local German state government. With this state-level consent, they can use the title “Dr.” anywhere in the country. But without the state’s permission to use the title, a scientist breaks two laws: the state law requiring approval to use the “Dr.” title and the federal impersonation law, Kraatz says.

Breaking the state law is punishable with a fine akin to that associated with a traffic ticket. However, breaking the federal law is punishable by a larger fine or up to one year in jail, Kraatz adds.

This is a very hard-core, nanny-state policy to apply to an honorific. Golly. To avoid trouble with Interpol, I’ll make sure to change my business cards and my email lest I be mistaken for a physician wannabe.  Heavens.  We don’t want that. \;-)

Hopefully someone in the German legislature will propose a reform for this ridiculous law.

Scattered Bits and Bobs

No rest for the wicked. I have been requested and required by the boss to attend the ACS meeting in NOLA.  Lots to get done before departure.  I’ll have to get my liver conditioned for a visit to the French Quarter.

I have been using the thermogravimetric analyzer (TGA) for fun and profit lately. It is quite useful in solving certain kinds of problems in process development.  Of course, if we attached a chain it might make a dandy boat anchor too.  Just kidding … mostly.

Lots of chemistry is presently under development in the USA. It is premature to concede the future of technology development to Asia just yet.  There are lots of companies struggling to get their new technologies to market- I see this every day. This is in stark contrast to news of the tragic comedy on Wall Street. It is important to remember that the stock market is only one of many indicators of economic vitality.  It seems to me that the current maelstrom is based on negligent banking practices, not industrial weakness.

Back to the hood. Gotta ice the trap on the vac line.

Platinum Group Metals Update

14 March, 2008. As the deepening US gravity well continues to tug at the recession asteriod that is looming ever larger in the sky, we see a steady line of investors boarding Platinum Group Metal (PGM) investment vehicles for immediate launch off this doomed planet. 

Monday and friday opening EIB prices over the week of 3/10/08 thru 3/14/08.

Silver–  US$19.70/toz;  US$20.77/toz.

Gold–  US$971.55/toz;  US$1,0005.86/toz

Palladium–  US$470.00/toz;  US$516.00/toz

Platinum–  US$1,960.00/toz;  US$2,110.00/toz

The geology of PGM deposits is quite interesting. There are numerous resources detailing the Bushveld Igneous Province (or Complex) in South Africa. Check it out.

Green Innovation Lag

It is not unusual for a long time to elapse between an initial customer inquiry and when commercial quantities of product are loaded on the truck and driven out the gate. I have seen it happen over 1 to 10 years, with 3 years being quite common. The chemical industry is not like the semiconductor business. The paradigm shift period seems much longer. In fact, any given chemical processing technology can last for a large part of a career or more. The last big chemical paradigm shift I have noticed is high throughput experimentation (HTE).  Maybe others have a more recent example.

Green chemistry is considered by many to be a new frontier of opportunity. To its detriment, many of us are unsure of what green chemistry really is and how to implement it in manufacturing. Realistically, for green chemistry to find wide acceptance, it needs to turn a profit or offer some kind of concrete advantage. Pollution avoidance is too abstract. For any new method or technology, there must be a payoff.

It seems simple. Reduce VOC emissions by using aqueous solvent compositions. Increase atom efficiency in transformations. Minimize persistant pollutants, organic or metal. Increase space yields, reduce consumables.  Green chemistry is not so easily demonstrated to the public and it may not be in the public domain. Your green technology may be proprietary, so the ballyhoo factor will collapse to zero. The processor may have to labor down the green path in silence.   

A process changeover to a green process may require many people in several companies to align to the change like compass needles to the north pole. A chemical process change must offer some kind of improvement that, by consensus, is meritorious. There is a good chance that the change will require notification of the customer and possibly even their permission. Customers often want a price concession when there is a process change so they can capture some of the value, so this may mean reduced sales volume and profits for the processor.

The customer may require that the proposed process change will be cause for a new validation of their customers product, in which case, the final user will also have to perform a validation.   In all likelihood, you are proposing a green change to a process that previously offered no problem to the downstream users.

Obviously, the time for green process implementation is at the very beginning of process development. The development chemist must have an existing toolbag of techniques, transformations, and reagents to choose from to go forward with implementation. The best way to get to this point is with curriculum change at the university level. Chemists need to have green chemistry awareness from the beginning of their training. Converting souls when they are already within industry is the hard way to do it.

Microscale labs in the undergrad experience maybe green for the university, but it is hard to see how it translates to the implementation of green technology in industry. The green revolution must come from textbooks that use green transformations in chemistry and engineering coursework. It must come from professors who weave it into their lectures and provide examples of such transformations and practices in the lab experience.

Chemists and engineers from such backgrounds must move into industry and become group leaders and managers. Only at this point will green chemistry become “normal” and expected.

And then I woke up

And it came to pass that a Being appeared to Th’ Gaussling one afternoon in the laboratory. But this was not a Being in the league of the Angel Michael or Gabriel. This was a somewhat lesser Being. Call him “Ed”. 

While Th’ Gaussling was tending to some matter in the lab, the Being Ed made his presence known by speaking through the vacuum line.

Gauss-ling“, hissed the disembodied voice through the Buchner filter.

Gaussling startled, dropping a few grams of precious crystals on the benchtop, and looked in full circle around him trying to find the source of the voice.  Puzzled, Gaussling stood still for a few moments listening for more sound and then, with a shrug, began to clean up the mess.

“Gaussling, I’m down here” said the voice, a bit more impatiently. “Set the spatula down and look in the filter”.

Sensing a practical joke, Gaussling replied sarcastically “Bugger off! I’m busy. Buncha NIM-rods …”.

With unmistakable urgency, the voice commanded “Look in the Filter!” At that moment, the vacuum pump changed its sound to a quiet tap-tap-tap, indicating that the pressure had dropped. The mercury column in the manometer collapsed and the pump noise became just a whisper.

Gaussling promptly stopped what he was doing and leaned towards the Buchner filter while scanning sideways for pranksters. But the room was empty and the voice had a decidedly raspy edge to it now. As Gaussling peered into the filter he noticed that a voice appeared to eminate from the vibrating filter paper. As the funnel spoke, crystal fragments danced across the flat paper like rice on a snare drum. Gaussling froze and couldn’t manage a breath.

“What do you want?”, Gaussling gasped.  “How can this be happening? Who are you?”

“You may call me Ed. Some of your kind have referred to my species as ‘Angel’ “, Ed replied matter-of-factly. “I think you’ll find that description to be inaccurate.” 

At that moment Ed apparated beside Gaussling in front of the fume hood. There was a rattling pop and the crackle of static discharge with a brown puff of nitrogen dioxide and ozone. Disconcertingly to the traveler, this type of conveyance caused the accumulation of static charge. Gaussling momentarily wondered how many Coulombs of static an Angel could withstand, but then snapped back to matter at hand. 

Still quite shocked, Th’ Gaussling managed to squeek out a few questions. “How did you do that? Where are you from? What do you mean by Angel?”

Ed was always annoyed with such questions. The gosh-wow-sense-of-wonder reaction from these creatures wore thin after a while. As Ed took a moment to adapt to the atmosphere and the pressure, Gaussling looked up and down at the visitor.  It was apparently a he from the outward mannerisms and dress.  Gaussling wouldn’t push the issue of gender right away.

“Dear fellow” Ed said in an impatient and distinctly British tone, “would you kindly relax and set that bottle down? I need to speak with you.  I’m only able to stay for a moment. This kind of travel causes extreme parity violations in the cosmos and is possible only by rather large energy consumption elsewhere, not to mention great discomfort for me.”

“So, you’re Ed? ” Gaussling said awkwardly. “What are you doing here?”

“I have a gift for you,” Ed replied in a matter of fact tone and reached inside his vest. “In fact, here it is.”

Ed pulled out a small vial that appeared to be of glass construction. At the bottom of the glass vial was a powder. It was unremarkable in every way and initially resembled ten thousand other colorless powders.

Ed held up the small vial and grinned. “See, here it is. Oh, my my my. You are going to be very amused.” He could barely contain his glee. Ed held the vial up toward the light but now the powder appeared somewhat different. Gaussling thought he saw a faint iridescent glint to it. A flash of a shimmer of spectrum against the cold fluorescent lights.

“I have come a long distance to give this to you. It is a substance capable of great wonders for those with the curiosity and wisdom to use it properly. But it is also capable of doing great harm. Soon you will see.”

Gaussling stood there, attentive but unable to utter a single word. After a few moments, Gaussling sputtered “What does it do?” 

Ed stood for a moment and then gushed with great delight, “I though you’d never ask. Get me a flask with some liquid in it, any liquid.”

Gaussling grabbed a 250 mL beaker and splashed a bit of acetone in it- 50 mL or so. Gaussling handed the beaker to Ed.

“Gaussling, I am going to put a single crystal of this substance into your liquid. Watch …” And with that fluorish, Ed expertly shook a single crystal of this substance into the beaker. The result was immediate and spectacular.

As Gaussling watched in amazement, the list of uses washed over his mind like a storm surge over a levee.  “How can this be happening?” Gaussling gasped.

Incident Attenuation in Chemical Plant Design

If you work in a location that handles or processes hazardous materials, eventually you have to come to grips with the matter of risk and accidents. It is possible to design procedures that prevent certain kinds of accidents and casualties.  It is possible to install devices and automated contrivances that can eliminate specific failures and the resulting cascade of multistage calamities that might follow.

Over time and with plenty of thought, a chemical plant can be fool-proofed to a large extent. But in the end, residual margins of safety depend on the man-machine interface. People have to undergo recurrent training and certain staff must be assigned to specialize in safety.

All devices have a failure rate. The rate may be small or large. A device may fail safely or not. Most chemical plants are, to a large extent, hand built. They are fabricated by skilled tradesmen who connect pre-fabricated parts to one-of-a-kind assemblies built on-site. In this way, expertise is captured from the plant designers, contractors, and the manufacturers of the installed equipment.  In the end though, it is up to the designers to assure that there is compatibility and some margin of overdesign in the finished facility.

While it is possible to assemble a facility from the very best equipment, the fascinating question of design for the attenuation of accident propagation is not often discussed, at least openly.  Accidents can usually be reduced to a few characteristic phases. They are initiation, propagation, and termination. 

An incident begins with an initiating event. Some release of hazardous energy is presented to the surroundings that may begin a propagation of undesired events. Events can propagate in series or parallel chains.  Hazardous energy can be electrical, chemical, or mechanical. The initiation is the tipping of a domino as a triggering event that causes the release of other hazardous conditions to ensue. Eventually, the propagation of the hazardous energy release is suppressed, extinguished, or simply exhausted in the termination phase.

One of the best ways of learning about the phenomenon of accidents is reading about them. A website worth visiting is the US Chemical and Hazard Investigation Board. It is useful for chemists and engineers to study the anlyses of the CSB and gain useful insight into the dynamics of chemical plant accidents.

It is possible to configure a chemical plant in such a manner as to attenuate the propagation of hazardous energy during an incident. In general, a large distance between reservoirs of potential energy is the easiest solution. Explosives manufacturers have known this for a long time. One well known German manufacturer of energetic materials has a manufacturing site spread over a large rural area and has built in bunkers with berms and trees to attenuate the propagation of shockwaves and allow flying fragments to land safely in an uninhabited area.  Fortunately, not many manufacturers have processes and products requiring this kind of design consideration.

Situations of “ordinary” risk magnitude do require some thought, however. Consider the storage of drums of flammable materials. Most companies that handle palletized drums of flammable liquids meet the minimal fire and insurance codes for the handling of these materials.

But consider this. What if a forklift driver spears a drum of solvent with his lift, and then in a panic, backs up and pulls the fork out of the drum resulting in a spill? At this point, policy and regulations are irrelevant. The only question is this-  Where does the liquid and the potential fire go?

Indoor storage of flammable materials requires fire suppression. Fire suppression is not the same as fire extinguishment. It is about knocking down the fire to a manageable level for emergency egress, to suppress the spread of the fire, and for firefighters to make some kind of attempt to extinguish the blaze. This is routine firefighter stuff.

What is less than routine, however, is the issue of BLEVE’s. I have written on this phenomenon previously.  Fire suppression is one thing, but BLEVE’s – Boiling Liquid Expanding Vapor Explosions- are quite another matter to deal with.

This is where a well designed facility with passive architectural features to attenuate the spread of hazardous energy can be helpful. An indoor BLEVE is virtually assured to accelerate the pace of a disaster.  So, in the planning phase of a plant, it is important to consider how energy release during an accident may propagate.  Drummed flammable liquids should be isolated from work areas and egress paths. This is pretty obvious to initial designers, but not necessarily years down the road during an expansion.

Consideration should be given to the anticipated direction in which energy is released. Where possible, energy should be released away from populated areas and away from major capital equipment. A fire in a materials storage area shouldn’t lead to an extended plant shutdown due to damaged process equipment. Segregation is key to plant safety and business viability.

Smoke is a potential killer and there are architectural tricks that can add provide slightly greater safety margins. Ceilings designed to collect and channel smoke out of the space could reduce the likelihood of suffocation of stranded workers and suppress the chances of a flashover. Smoke curtains properly placed can channel smoke away from hallways and the resulting spread.

Another concern is the fate of spilled flammable liquids in a storage area. Where should the spill go? Should the spill be concentrated in a small space or channeled to another space where a fire can burn with lower negative consequence? Nobody likes to pay for an overengineered warehouse, but fire resistant partitions in a solvent storage area can go a long way toward the isolation of a fire and attenuation of a larger scale calamity.

One major plant accident I am familiar with has a number of attributes that other operators would do well to consider.  A 750 gallon reactor explosion resulted in the complete fragmentation of the vessel.  A few pieces ejected from the hole in the roof were found lodged in the walls of neighboring structures off-site.  Fortunately, this reactor was in an enclosed space with no other reactors or stored hazardous materials. In one way, this accident was isolated due to passive attributes. However, the building space was interconnected to other spaces by a series of adjacent rooms and hallways. While fragmentation and fire damage were contained due to the happy fortune of isolation, the shockwave was able to follow all of the connected and enclosed pathways.  The connected pathways were a convenience to the workers, but this feature channeled a pressure wave throughout the entire facility, lifting the roof enough to damage large -remote- sections of it as well as badly damaging overhead doors and windows throughout the facility.

Take home lessons? 1) Leave open space walkways between production and storage buildings and the rest of the facility. Collateral damage is likely to be suppressed with this cheap, passive feature. 2) isolate and dedicate certain vessels to hazardous operations. 3) Store hazardous materials well away from processing areas. Storage and processing have their own hazards and a disaster in one area should not be allowed to propagate to the other.

The matter of flammable solvent storage and accident attenuation is only partially solved with enclosed flammable materials lockers. It seems to me that some research should be done to advance the level of best practices in this area.

Ab Initio Chemical Plant Design

So, dear reader. If you were going to design a general/multi-purpose chemical plant capable of doing a wide variety of chemical transformations, what kind of features would you install now that you’ve had some experience in the field? No high pressure vessels, just ambient to 80 or 100 psi. I’m talking about a plant with 50 to 2000 gallon reactors- say, 8 of them. What kind of configurations would be desirable starting from the ground up?

No GMP capacity- too bloody expensive. We don’t want to do API’s.  No gas phase chemistry. No scary oxidation chemistry or energetic materials.  Just the kind of garden variety specialty organic or inorganic compounds and transformations that you might find in the Aldrich catalog.  Synthons, reagents, etc.

One interesting thing to ponder are possibilities with the use of passive architectural features to attenuate the propagation of upset or emergency conditions. 

Literature Swim. The Guo-Liu Catalyst.

Guo & Liu Catalyst

The literature train station is overflowing with diverse catalysts for the large variety of coupling reactions out there, as is the patent literature. Parties scramble to get window seats on the IP Express, the high speed non-stop to that Golden City on the Hill. 

A recent JOC article disclosing an inexpensive catalyst system that struck me as interesting.  The article by Guo and Liu emphasizes economy and so discloses a phosphorus-free bidentate ligand system that affords Heck and Suzuki-type coupled products.  There are pluses and minuses to this system, as is the case for most catalysts.

On the plus side with the Heck and Suzuki reactions, both activated and deactivated aryls gave decent yields. On the minus side, the Heck coupling reaction is a bit slow. A fair amount of energy input was needed- 130 C in DMF over 30 hours. On the Suzuki side, most reported reactions resulted in good yields, except for the aryl chlorides. The relative inertness of chlorides is not particularly unusual, but it may cause this catalyst to be passed over in some applications where the less atom-efficient bromides and iodides have been targeted for replacement.

Finally, the apparent requirement of DMF is rarely happy news. Regardless, I have no doubt that this catalyst will find its way into the future literature and many clever applications will be revealed.  As of this writing, I was unable to find a US patent by inventors Guo and Liu claiming this technology. Since there is a 1 year limit on the filing of a patent application following disclosure, this technology could be in patent prosecution at present. Or not. Wouldn’t it be a happy thing for it to be in the public domain?