Category Archives: Chemical Industry

Gaussling’s 12th Epistle to the Bohemians. Elements Rock.

Some acquaintances have asked about my new interest in geology. What’s the deal with rocks and mining? 

What interests me is not so much the economic value and extravagant production of certain minerals and precious metals. What is of interest is the question of how it came about that there is such a thing as an ore body.  An ore body is a geological formation which is defined by a localized concentration of certain substances. How does it happen that chemical elements can become concentrated from a more distributed condition?

Celebrity astronomers are often seen on cable channels pedantically nattering on about “Star Stuff”.  OK, Dr. Skippy, what is star stuff and what does it do? What are the particulars about the local star stuff, ie., the earth? This is the realm of cosmochemistry and geochemistry- elective classes the TV glamour boys apparently skipped.

The nucleosynthesis of the heavy elements (C to U) and their subsequent ejection from exploding stars is an inherently dispersive process. Eventually, here and there, some heavy matter will aggregate to form a protoplanetary cloud which can then produce planetary bodies. Inevitably, some of the heavy matter is pulled into massive bodies dominated by the presence of thermonuclear fuels- that is, hydrogen and helium. Sufficiently large accumulations of these two highly abundant elements will compress and initiate a self-sustaining fusion reaction of hydrogen to form the (n+1)th generation of stars. All told, some heavy matter accumulates to form of planetary bodies while some of it siphons into the next generation of stars.

It is within the ability of gravity to concentrate matter into smaller volumes of space as a dense, bulk phase. The geometric shape that allows all of the mass to be as near the center of mass as possible is the sphere.  This is why we don’t see planets shaped like cubes, pyramids, or ponies. 

Once cooled well below incandescence, the matter in a sufficiently constituted and situated planet may begin to self-organize into chemical phases. Along the lines of the Three Bears allegory, Earth is parked in an orbit that is just right for the presence of liquid water. Irrespective of the needs of life, liquid water is critical for the eventual concentration of some elements into ore bodies.

Earth has a gas phase blanketing a liquid phase which wets much of the bulk rocky phase of the planet. A generous portion of water circulates in the maze of fractured recesses of the planetary crust. In the case of Earth, we know that our planet has a fluid core within a solid shell. This molten phase in the core energizes a kind of convective heat engine that will drive the shuffling motion of tectonic plates and episodic volcanic mass transfer on the surface. 

Matter has gravitationally self-organized at the planetary scale on the basis of density. But what is perhaps most interesting to a chemist is the phase composition of the planetary solid matter. On cooling, a body of magma will sequentially produce precipitates representing different chemical substances. Over geological time this igneous rock may experience modification by the hydrothermal action of hot water under high pressure. Depending on its circumstances, parts of the formation may be depleted of soluble constituents or it may receive a deposit of new mineral species.

On the scale of planets, the earth has self-organized into bulk phases of matter- Solid, liquid, and gas. But at a much smaller scale, the earth self-organizes into domains of chemical substances. This is evident by simple inspection of a piece of granite. A piece of pink granite shows macroscopic chemical domains of potassium feldspar, quartz, and mica. While these three mineral components of granite are compounds and not pure elements, they nonetheless represent self-organization of species based on chemical properties.

The forces that drive chemical differentiation in mineral formation are ultimately thermochemical in nature. Large differences in Ksp lead to partitioning and phase separation of distinct substances. Subsurface formations may be approximately adiabatic on a short time scale, but over deep time they can slowly cool and equilibrate to yield a sequence of fractional crystallizations of metal carbonates, oxides, silicates, and aluminates giving rise to a complex bulk composition.

Speaking only for myself, coming to an understanding of how mineral deposits form is a kind of hobby.  If I wanted immediate answers to specific questions, I suppose the most expedient thing would be to consult a geochemist. But where is the adventure in that? The answers are not the fun part. The real adventure is in the struggle to find the best questions. As it often happens, once you can frame the problem sufficiently, the answer falls out in front of you. Whoever dies with the greatest insight wins.

Hillbilly Engineering- A Homebuilt Kugelrohr

In the mid 1990’s I had the good fortune to do a 1-year sabbatical replacement teaching gig at Ft Lewis College in Durango, Colorado. Of the several colleges in which I was lucky enough to be a faculty member, this school was absolutely the best. The chemistry department had a vitality that I had not experienced elsewhere, and sadly, would not be fortunate enough to repeat.

From my office high up on the mesa next to town I could hear the whistle of the steam locomotives of the Durango-Silverton Narrow Gauge Railroad. On friday afternoons a campus Native American group would sit around a single drum outside of Berndt Hall, each striking a hypnotic beat on the preserved skin while chanting and singing in the Ute language. While they were chanting the steam locomotives in the town below would blow their whistles, announcing their arrival for the tourists. The sound of it was an otherworldly experience I have not forgotten.

A prof I got to know at Ft Lewis, Dr. Irwin “Ike” Klundt, was a retired VP from Aldrich. He was to become a mentor and friend. It turns out that Ike was the inventor of the coffee pot kugelrohr that Aldrich offered in its catalog. West Bend, the appliance company, had a coffee pot manufacturing operation in Milwaukee, WI, where Aldrich was then headquartered. Ike learned that they would always have a few off-spec units coming from their mfg line, so he arranged to snag a few of these units. He recognized that these pots were built to contain heat and would be dandy ovens for his application. The large metal coffee pots were delivered to a one man shop somewhere in Milwaukee where the they would be converted to ovens for the Aldrich kugelrohr still, or “bulb-tube” short path distillation device to be more precise.

To provide agitation around the axis of the distillation train, an automotive pneumatic windshield wiper motor provided the needed reciprocating motion. It had a built-in tube that would serve to couple the bulb tube train to the vacuum line. The reciprocating motion of the motor removed the need for a sealed bearing as in the case of a rotary evaporator.

Aldrich sold a geat many of these units. In later years the kugelrohr was modified to enhance safety and ease of use. Aldrich has never been shy about pricing, so the price went way up as well.

I was thinking about this bit of history yesterday as I was operating my home-built kugelrohr. Sometimes shortpath distillation is needed and yesterday was the day for it. Using Ike as my inspiration, I horizontally configured a Buchi rotovap into a kugelrohr distillation unit with a still pot and a bulb tube receiver.

On a hotplate with a temperature indicator, I placed an 8 inch diameter sheet metal 90 degree elbow from Home Depot. The elbow, modified with a bit of aluminum foil, would serve as my hot air bath. The elbow and hotplate assembly is scooted over to the rotovap so that the still pot bulb is isolated in the “oven”.  A dry ice/acetone cooling bath for the receiver bulb was made from the bottom of a plastic jar. It was notched on opposite ends to accomodate the receiver joints.

The setup works just like a Buchi-brand kugelrohr, but doesn’t carry the price of a luxury ocean cruise. I know that larger companies would not allow this kind of thing. They would frown on a chemist using his time to kludge together a piece of improvised equipment. Their safety people would not allow the operation of a device that was not purpose manufactured. But when you work for a small company this is one of the things you have to do, and I enjoy every minute of it.

Handy Chart for the 2008 Top 200 Drugs

I ran across this handy pdf file from the website of Prof. Njardason at Cornell. It is a graphic compilation of the top selling drugs (in the USA?). Just click on the image and a pdf will download.  The site has compilations for the last several years as well.

A few of the drugs on the list are protected under patents that will expire in the next few years- Lipitor, Crestor, Lexapro, Advair, Singulair, Plavix, etc. Hours after the license to print money expires, the generic barbarians and visigoths will storm the gates and unceremoniously slaughter these cash cows. The horror, the horror.

Bruker’s New 1 Gigahertz NMR Spectrometer

June 1, 2009, Bruker announced the release of the AVANCE 1000 NMR Spectrometer. This 1000 MHz (1 GHz) instrument features a standard 54 mm bore within a 23.5 Tesla superconducting magnet. The magnet technology offers subcooling (below the bp of He) in the magnet, which Bruker claims to be necessary for the stability of the magnetic field. Bruker also offers nitrogen-free magnets that are able to keep the helium boil-off rates to a minimum. While it would be nice to avoid having to manage two cryogenic liquids, I wonder what the pay-back time is for the chiller equipment?

Imagine the hassles, begging, and incredulous stares that the users will have to contend with to to get some 1 GHz NMR time? I wonder if anyone will do 1-D experiments with it?

The AVANCE  1 GHz instrument is priced at a cryogenic ~$16,000,000 per copy with an 18-24 month lead time. I’ll have to stick with Anasazi Instruments for a while at least.

Separately, a link at the Bruker website will take you to the University of York where a site dedicated to one groups NMR work with parahydrogen is detailed. A technique called SABRE, Signal Amplification by Reversable Exchange, is described. The exposure of an NMR sample to parahydrogen (singlet H2) results in the transfer of polarization to the sample and subsequent increase in sensitivity.

The workers describe the operation of a device used for the conversion of triplet orthohydrogen to singlet parahydrogen as a ready source of this peculiar “isomer” of dihydrogen. Parahydrogen is the dominant form at 20 K, but drops to 25 % abundance at room temperature. Exposure of a mixture of ortho and parahydrogen to a paramagnetic catalyst does the conversion to achieve enriched singlet H2.

According to one on-line source, the conversion of ortho- to parahydrogen evolves 527 kJ/kg. I’d watch out.

HR 2868- Good intentions gone sour

There is a fine line between good sense and paranoia and HR 2868 has definitely crossed over into deep paranoia. This resolution, sponsored by Rep. Thompson (Mississippi), Rep. Waxman of CA, Rep. Jackson-Lee of TX, Rep. Markey of CA, and reps Clarke and Pascrell, is an amendment to the Homeland Security Act of 2002.  Its purpose is

“to extend, modify, and recodify the authority of the Secretary of Homeland Security to enhance security and protect against acts of terrorism against chemical facilities, and for other purposes.”

Well, how could anyone be against such a noble sounding piece of code? The sponsors are struggling to protect the homeland against attack on chemical facilities. Facilities whose hazardous material inventories could be maliciously released to cause harm to the surrounding neighborhoods of innocent and helpless citizens.

Sec. 2102 (a) (1) allows the Secretary to designate any chemical substance as a “substance of concern” and establish a threshold quantity for each substance of concern.

There are many goodies and zingers in this bill. Sec. 2115 (a) (1) (A) requires that the Secretary issue regulations for substantial background checks to establish personnel surety in covered chemical facilities. The security check will be deep and will serve as a reservoir of information collected by company on citizen employees and subject to inspection on demand by the Secretary.

Sec. 2116 (a) (1) states that any person may commence a civil suit against any person “who is alleged to be in violation of any standard, regulation, condition, requirement, prohibition, or order which has become effective pursuant to this title; or … “.  This citizen lawsuit provision will open the floodgates to lawsuits on companies running chemical plants and in so doing, under the rules of discovery, break through the IP protection afforded by trade secrecy.

This proposed law also provides for close oversight by the Secretary of Homeland Security as well as civil penalties (Sec. 2107 (b) (1)) of up to $50,000 per day of violation.

OK. Nobody wants acts of terrorism to happen and especially not on the site of a chemical plant. But to legislate the transformation of chemical plants into a “Fort Apache” scenario in the absence of a history of attacks on US plants is to invite needless cost and complication to an industry that is already heavily regulated. This is plainly the result of irrational fearfulness on the part of congressional sponsors. And Congressmen are in a position to convert their fears into law.

Compliance with this law will require considerable effort and expense to be carried by industry. The downside to being out of compliance is too expensive. Over time companies may opt out of processes that use chemicals of concern simply to reduce the risk of noncompliance as determined by government audit.

The chemical industry uses hazardous chemicals of many varieties. Hazardous chemicals are often reactive chemicals. And reactive chemicals are useful chemicals.

The entire chemical industry is built around the exploitation of reactive attributes in order to cause a desired change in chemical composition. The unintended consequence of this legislation is that useful but reactive chemicals may be inherently prone to identification as chemicals of concern. The effect would then be that key substances at the core of a given technology platform would be regulated on the basis of what a terrorist could do with it rather than its value to technology and to civilization.

What constitutes adequate security? Who is to say what security measures are satisfactory? The security industry seems to attract the paranoid who see threats behind every shrub. To have such people deciding what chemical is acceptable for use in manufacturing is unacceptable.

Robustness Challenge Tests

I and my assistant have spent the last month devising experiments that are meant to chart out the stability or robustness of a small set of compounds whose manufacture has been problematic. This has been a kind of a process development activity wherein we are trying to understand what the specific sensitivities of this molecule are and how they might impact process stability.

My job these days is reactive hazards analysis and process safety. We have been trying to dream up experiments that tease out particular weaknesses a compound may have in normal or plausible off-normal conditions. While the compounds in question do not have apparent issues with reactive hazards, the skill set needed to find reactive hazards is useful in finding economic hazards as well.

An economic hazard would be something that threatens the profitability of a process. A production instability is simply a low threshold for a transition to off-normal processing conditions. Sometimes a process instability is physically dangerous and sometimes it is only an economic threat.

I have to say that this has been very enlightening so far.

National Organic Symposium. Wender Wednesday.

My final attendance at the National Organic Symposium was Wednesday evening. An award was presented to editor-in-chief, Scott Denmark, on behalf of the monograph series Organic Reactions. The original editor was none other than Roger Adams. Denmark presented a retrospective slide show on the history of Organic Reations.

The speaker for the evening was Prof. Paul Wender from Stanford.  Wender presented a long but fascinating talk on his work with several complex molecules including bryostatin. I have to say that I was rather blown away by this work. I guess I’ve been living on a desert island.

Wender has the great fortune of having access to facilities and people who can do complex chemical synthesis and biological assays and all of the other wondrous things that are necessary to rapidly expose a valuable biopharmaceuticals. The payoff is that questions relating to the biological activity of particular derivatives can be answered rapidly and productive leads can be isolated and further cultivated.

This confederation of resources is perhaps as important to Wender’s productivity as anything. My point is that to be a Wender, you need more than just smarts and money. You need a network of like-minded coworkers whose particular strengths can mesh with yours to produce these kinds of results.  I think that his ability to pull together these kinds of resources is just as impressive as his native ability with chemistry.

National Organic Symposium. Tuesday Morning.

Bad day for Th’ Gaussling to be away. The hounds are snapping at my heels at work.

I managed only to see Eric Jacobsen‘s talk on catalytic urea chemistry. Jacobsen’s system is pretty much a chiral proton ligand that can carry along a nucleophilic counter anion. Configured differently, urea’s and thiourea’s with BARF groups on the nitrogen can coordinate with chloride. This can lead to the abstraction of chloride to give a carbenium ion that can then participate in a enantioselective Pictet-Spengler type reaction. 

Jacobsen’s system resembles a radically stripped down enzyme in terms of 3-point binding interactions by hydrogen bonding.  Where Jacobsen went askew is the use of calculations to justify his mechanistic model. The models did not include solvent interactions when affording only 0-2 kcal/mol (!!) differences in energy. Naturally this did not set well with certain distinguished members of the Audience.  The ΔΔG’s did not correlate with the ee’s at all either.

A certain J.D. Roberts took great exception to Jacobsen’s molecular modeling results, resulting in the spectacle of a Harvard Professor frantically qualifying his slides and words as he back pedalled for all he was worth. There was some actual contrition there on the stage. It was quite a thing to see. There but for the grace of God go I.

National Organic Symposium. Monday Morning.

The speakers for the morning of June 8th were Bob Grubbs and Magid Abou-Gharbia. As usual, Bobby Grubbs’ talk was concerned with the latest wonders of olefin metathesis. We saw ATM’s of molecular Cheerios. Pretty cool, actually. Grubbs got the trip to Stockholm for a reason and the work of his group continues to produce molecular wonders.  He was able to demonstrate the production of rings with degrees of polymerization in excess of 5000.  Using NMR and a carefully chosen ring monomer, they could sort out linear polymers from cyclic polymers. Linear polymers will thread a crown ether while the cyclic form will not. By attaching a crown ether (24-crown-8 ??) to polystyrene beads, they could collect and physically separate the linear from the cyclic forms. They were also producing brush polymers.

Prof. Magid Abou-Gharbia, Temple University, gave a talk with lots of fascinating insights into some current thinking on industrial drug discovery. At least from the point of view of a former Wyeth guy. I have been away from the pharma-related work for a number of years now and haven’t really missed it. But his talk has revived enthusiasms in me that have been in a long slumber. 

Anyway, he described the development of the anti-depressant Effexor and their efforts to keep the molecule simple and free of excessive stereocenters. Studies of the metabolism of Effexor lead to the discovery of the des-methyl analog, now called Pristiq.

Concerning High Throughput Synthesis (HTS)-

“… you’re going to get a lot of decorated molecules, but they are not going to be biopharmaceutically useful.”

Abou-Gharbia lamented the languishing of natural products chemistry. He gave some examples of Rapamycin work, which according to his presentation, was originally isolated from a soil sample from Easter Island.  Much productive work apparently has been derived from the modification of this macrocycle. It’s all in the literature.

One of the main take-away lessons from Abou-Gharbia is that workers shouldn’t get too focused on SAR. His advice was that structure-property relationships need an early examination as well. Dual optimization. If the bioavailability is low, then the in vivo activity will not match the in vitro activity- an expensive and time consuming realization.

Organic Symposium

Despite my previous gritching about it and despite trying to stay below the radar at work, the boss has requested and required that I attend the Organic Symposium at CU Boulder. I’ll bop over there later today to register and walk the poster session. Maybe there will be some useful grist for the blogmill.

No better reminder of the scientific pecking order than to skuttle around in the shadows of the great grant writers of our time. A certain speaker with a Nobel Prize casts a shadow so large that it is reported to weigh nearly 5 kilograms. Fancy that!