Category Archives: Chemistry

Amine Question of the Day

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Here is an interesting question. What fraction of the organic nitrogen in your body is ultimately from the Haber-Bosch Process?  Any guesses?  This question arose during dinner discussion following a rousing seminar on frustrated Lewis pairs. There is no connection to frustrated Lewis pairs, but the speaker raised the question.

Oh, I don’t have an answer. This happens in science.  I’m guessing ~50 %, depending on the extent of protein containing corn products consumed. Any meat science people out there?

Thorium

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A short drive from my office is the Fort St Vrain power plant. The present electrical generating facility is powered by natural gas. But a generation ago it was a nuclear plant powered by a high temperature gas cooled reactor (HTGR). What’s more, the reactor used fissile uranium with fertile thorium.  The output of the plant was ca 330 MW electric and it operated from 1976 to 1989.

The utility eventually decommissioned the helium cooled reactor and converted to natural gas. Today, as before, the plant looks like a planetary humidifier, billowing great clouds of steam condensate into the thin dessicated air of the high plains. The link above outlines the trials and tribulations the utility experienced with some of the auxillary hardware. They had to learn the principle of KISS the hard way.

A thorium-based nuclear reactor uses a fissile element like U-235 to provide a source of neutron flux from which to jumpstart in-situ breeding of U-233. The absorption of a neutron by Th-232 gives Th-233 which beta decays to Pa-233 which decays again to U-233.  Remember, beta decay causes the atomic number to increase by one, but the atomic weight stays the same.  The resulting U-233 is fissile and serves as a fuel.

Thorium as a fuel has pluses and minuses. On the plus side, thorium is more abundant than uranium. And Th-232, the predominant isotope, is the desired fertile material. This is in contrast to natural uranium which offers less than 1 % abundance of fissile isotope U-235. A large part of our nuclear infrastructure involves separation of this isotope to a more concentrated form. After isotopic separation the uranium must then be converted to a suitable chemical form.

The refractory nature of thorium oxide reportedly makes fuel element manufacture somewhat problematic. Interestingly, it is the refractory nature of thorium oxide that makes it valuable for use in thoria lantern mantles. The high melting point of thoria allows a gossamer web of glowing thoria (and ceria) to sit in place in the lantern burner and radiate bright white light.

On the minus side, there is no established fuel supply infrastructure to provide thorium oxide to industry. In fact, there is virtually no thorium trade in the United States today, with the latest annual US sales volume amounting to a paultry $350,000 according to the USGS. Some of the nuclear chemistry is of the thorium cycle is problematic as well.

The natural history of thorium mineral placement is rather different than that of uranium. Uranium migrates fairly readily, depending on its oxidation state and pH of mobilized hydrothermal fluids. As a result, uranium can be found in porous or fractured formations that have a history of water migration.  From what I can tell in the geological literature, thorium concentration results largely from magmatic differentiation in the distant past. There is considerable diversity in the details of each occurrence of thorium, so one should be careful of generalizations.

There is a notable monazite (a common thorium mineral) placer district across the central North and South Carolina border region. These monazite placer deposits sit in ancient stream channels and are the result of alluvial dispersion.

Colorado has two notable thorium mineral deposits. The Wet Mountains SW of Canon City and the Powderhorn district near Gunnison have substantial deposits of thorium as well as lanthanide elements. In fact, rare earths are commonly associated in monazite. Monazite is a phosphate mineral with a variety of thorium and lanthanide cations present. It is useful to recall that the rare earth elements include Sc, Y, the lanthanides, and the actinides. In Colorado, the significant uranium deposits are not coincident with thorium deposits. Uranium is found in sedimentary deposits of the Colorado Plateau, in the tuffaceous sediments of the Thirty-Nine Mile volcanic field, and in vein lodes along parts of the Colorado mineral belt.

There is considerable variability in the elemental associations found in rare earth deposits. Monazite seems to be fairly consistant in regard to the presence of Th and lanthanides. Scandium, however, is often absent or quite scarce in monazites from the assays I have seen in the literature. 

Perhaps the richest thorium district in the lower 48 states is in the Lemhi Pass district along the lower Idaho-Montana border. A company called Thorium Energy reportedly holds substantial claims of thorium rich deposits at Lemhi.

The Passive Aggressive Opera. Act I. Reverse Delegation.

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Supervision of people is one of the things that a chemist can look forward to on the way up the ladder. The people who report to you may be called staff or report-to’s. The term “my employee” should be reserved for use by those who sign paychecks. What ever you call them, they’re your group.

I’m not going to write about how to manage people. After many years of doing it I’m not sure I really understand it yet. All I can say is that every day some people show up and expect you to keep them busy.

Okay, I’m just kidding. But I am serious about the mysteries of management of people. I think most would agree that the best way to lead people- the way most of us would prefer to be lead- is by setting a good example. It’s pulling instead of pushing. Inspired leadership by a charismatic and talented individual is preferable but, unfortunately, rather unusual. 

There are many theories of management and more management consultants than you can count out there urgently interested in telling you how to manage your staff.  All you have to do to sample the many management theories is to stroll through the business section of the local bokstore. Every one of the authors will trot out a set of polished anecdotes that outline the path to their own professional enlightenment.

Chemists on the  management track may move in many directions in a business organization. Most obvious is management of a technical activity like R&D. But there is also management opportunity in scale-up, pilot plant, production, QA/QC, and analytical services activity. Management of the production side is sure to include inventory and warehouse control, regulatory affairs, personnel issues, engineering, and maintenance. Itis not uncommon for engineers to head the production unit.

On the less technical side is sales, procurement management, and business development.  While perhaps less technical, the chemical industry needs (requires, really) chemically savvy people to handle purchasing and sales activity. It is not uncommon for sales oriented people to ascend into the upper reaches of management generally and the chemical industry is no different.

What is perhaps different in the chemical industry is that chemists are often disfavored in the track to the CEO’s office by their lack of economic training. The ability to deliver big projects on time and on budget is a key attribute and engineers are especially well positioned to do this very thing. The bigger the scale of operations the greater the likelihood that an engineer will be in charge. Or so my experience has been.

Among those I have observed, managers who have exemplary experience in controlling the big money are often the ones groomed for executive leadership. And the big money is in big projects with lots of sales volume. It is the source of life giving cash. That which makes the corporate world go ’round. The elusive spondulix.

But back to management. One of the most vexing aspects of managing people is that you have to manage people. People are complex and prone to nonlinear behavior. Everybody knows this. But the manager is tasked with using human resources to provide some kind of work product on time and on spec. How do you compel people to do this every day?

The threat of termination is a good though heavy handed tool to compel folks to do their job. But this is a tool that can also backfire. Frequent termination of people is stressful and puts the manager in the position of having to be in a more or less constant training mode. Best to hire hard working people who are self-starters.

I have not found a simple formula for management. All I can do is to support down and fight up. I fight for resources and reasonable expectations. I treat people in the most hospitable manner I can muster and in return I expect the same.

One of the most annoying behaviors is the phenomenon of “reverse delegation”. You ask your report-to to do a particular thing. In reply you are told that they can only do the thing if you first make some arrangements. You have to get this or that ready, or perhaps you have to write an SOP or work instruction, or maybe even they will need to fly to a hotel in Vegas or Orlando to take some training course. It is all push-back: a kind of passive aggressive behavior meant to deflect your attention.

What I have found is that these reverse delegators may be very concrete in their approach to the unfamiliar. They will assert that they must possess a good deal of skill to even begin some new task. Sometimes this is true. But often it is only a matter of time on task to make some good progress.  The hard part for some of us is dealing with the simple truth of the matter. Not everyone desires being collegial and operating on the give and take level of colleague. A lot of folks only respect the brusque barking of orders by a Captain Bly figure and the sight of a**holes and elbows hustling in the plant. I would have been Captain Kangaroo, not Bly. It’s just a fact.

Old Knowledge and New Problems in Chemistry

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I’ll admit to having a bit of a book fetish. I love everything about books except moving them. I collect new and old books. I have a professional chemistry library that is consuming quite a bit of wall space. And that doesn’t include the boxes of JOC, Organometallics, and JACS. It’s getting out of control.

My amateur geology library has gone from one book last summer to about 50 books and USGS circulars today, and more are enroute this very minute thanks to Amazon.com, Paleopublications, and many more booksellers.

What I’m beginning to see is that university libraries across the country are withdrawing older chemistry books from their shelves. I do not refer to textbooks. I am referring to the valuable secondary literature that has accumulated descriptive chemistry knowledge.  These books are snatched up by specialty book sellers and are placed on the internets for sale where odd characters such as myself will gratefully buy them.

Recently my fetish for old books is helping me solve a thorny contemporary inorganic analysis/synthesis problem. You see, the older texts are rich in wet chemical methods. While a book like Chemistry of the Elements by Greenwood and Earnshaw is fantastically broad in its scope, it is not meant to transfer the pargmatics of procedure. The older chemistry and ore refining texts are full of practical information that seems to be fading away. While the primary literature may be available on SciFinder, books that cover accumulated descriptive chemistries are becoming scarce.

I can’t reveal the details of my revelation. But I can say that a process development person can learn quite a bit about materials processing from the late 19th and early 20th century literature. Our predecessors couldn’t depend on ICP or GDMS or XRD to help them follow the process. The wet chemical methods they developed also give us insights into the transformations necessary to produce purified products.

The unit operations of calcining, comminution, reduction, oxidation, flotation, dissolution, drying, etc., have not changed much in a fundamental way since the days of Agricola. But they are better quantified by virtue of a century of research.

Our collective drift from wet chemical methods to instrumental and computational approaches to analysis are also taking many of us away from the pragmatics of chemistry. The hyphenated instruments of today are leading large numbers of chemists away from the art of chemical transformation and isolation in favor of chemist-as-software-expert. Certainly this computational intensive investigation is not lost in our university curricula. Our hypnotic embrace of technological triumphalism meshes with the perceived need to minimize hazardous material inventories in the chemistry department stockroom. And with the perceived need to minimize chemistry students to exposure to chemicals.

Chemical industry is centered on the art of making things. In the end, somebody has to figure out how to make chemical substances and somebody else has to do the actual work. We chemists have to make sure that university curricula meets the needs of society and that the librarians of the world understand the importance of older chemistry books.

On the pitfalls of process intensification

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As any process development chemist knows, there is motivation to optimize a chemical process to produce maximum output in the minimum of reaction space. In the context of this essay, I’m referring to batch or semi-batch processes. Most multipurpose fine chemical production batch reactors have a capacity somewhere between 25 and 5000 gallons. These reactors are connected to utilities that supply heat transfer fluids for heating and cooling. These vessels are connected to inerting gases- nitrogen is typical- and to vacuum systems as well.

Maximum reactor pressure can be set as a matter of policy or by the vessel rating. Organizations can, as a matter of policy, set the maximum vessel pressure by the selection of the appropriate rupture disk rating. Vessel pressure rating and emergency venting considerations are a specialist art best left to chemical engineers.

Reactor temperatures are determined by the limits of the vessel materials and by the heat/chiller source. Batch reactors are typically heated or chilled with a heat transfer fluid. On heating, pressurized steam may be applied to the vessel jacket to provide even and controlled heating.  Or a heat transfer fluid like Dowtherm may be used in a heating or chilling circuit.

Process intensification is about getting the maximum space yield (kg product per liter of reaction volume) and involves several parameters in process design. Concentration, temperature, and pressure are three of the handles the process chemist can pull to increase the reaction velocity generally, but concentration is the important variable in high space yield processes.  Increasing reaction temperatures or pressures might increase the number of batches per week, but if more product per batch is desired and reactor choices are limited, then eventually the matter of higher concentration must be addressed.

The principle of the economy of scale says that on scale-up of a process, not all costs scale continuously or at the same rate. That is, if you double the scale, you double the raw material costs but not necessarily the labor costs. While there may be some beneficial economy of scale in the raw materials, most of the economy will be had in the labor component of the process cost. The labor and overhead costs in operating a full reactor are only slightly greater than a quarter full reactor. So, the labor component is diluted over a greater number of kg of product in a full reactor.

The same effect operates in higher space yield processes. The labor cost dilution effect can be considerable. This is especially important for the profitable production of commoditized products where there are many competitors and the customer makes the decision solely on price and delivery. Low margin products where raw material costs are large and relatively fixed and labor is the only cost that can be shaved are good candiates for larger scale and higher space yield.

But the chemist must be wary of certain effects when attempting process intensification. In general, process intensification involves increasing some kind of energy in the vessel. Process intensification through increased concentration will have the effect of increasing the amount of energy evolution per kilogram of reaction mixture.

Energy accumulation in a reactor is one of the most important things to consider when attempting to increase space yield. It is crucial to assure that process changes do not result in the accumulation of hazardous energy.

Energy accumulation in a reactor occurs in several ways. The accumulation of unreacted reagents is a form of stored energy. The danger here is in the potential for a runaway reaction. Accumulated reagents can react to evolve heat leading to an accelerated rates and eventually may open further exothermic pathways of decomposition. As the event ensues, the temperature rises, overwhelming the cooling capacity of the reactor. The reactor pressure rises, accelerating the event further. At some point the rupture disk bursts venting some of the reactor contents. Hopefully the pressure venting will result in cooling of the vessel contents and depressurizing the vessel. But it may not. If the pressure acceleration is greater than the deceleration afforded by the vent system, then the reactor pressure will continue to a pressure spike. This is where the weak components may fail. Hopefully, nobody is standing nearby. Survivors will report a bang followed by a rushing sound followed by a bigger bang and BLEVE-type flare if the system suffers a structural failure.

Energy accumulation can manifest in less obvious ways. Here is an example. Assume a spherical reaction volume. As the radius of the sphere increases, the surface area of the sphere increases as the square of the radius. The volume increases as the cube of the radius. So, on scale-up the volume of reaction mixture (and heat generation potential) will increase faster than the heat transfer surface area. The ratios are different for cylindrical volumes, but the principle is the same. Generally the adjustment of feed rates will take care of this matter in semi-batch reactions. Batch reactions where all of the reagents are added at once are where the unwary and unlucky can get into big trouble.

Process intensification via increased concentration may have deleterious effects on viscosity and mixing. This is especially true if slurries are produced and is even worse if a low boiling solvent is used. Slurries result in poor mixing and poor heat transfer. Low boiling solvents may be prone to cavitation with strong agitation, exacerbating the heat transfer problem. Slurry solids provide nucleation sites for the initiation of cavitation.  Cavitation is difficult to detect as well. The instinct to increase agitator speed to “help” the mixing may only make matters worse by increasing the shear and thus the onset of cavitation.

Denser slurries resulting from process intensification are more problematic to transfer and filter as well. Ground gained from higher concentrations may be lost in subsequent materials handling problems. Filtration is where the whole thing can hang up. It is important for the process development chemist to pay attention to materials handling issues before commiting to increased slurry densities. Crow is best eaten while it is still warm.

PETN in his BVD’s

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History will record an underwear bomber and a shoe bomber. Luckily for the passengers of one transatlantic flight, the anonymous martyr on board was incompetent. Like the shoe bomber before him, this murderous buffoon failed to plan for a reliable means of triggering his bomb.

PETN, or pentaerythritoltetranitrate, was found to be the explosive agent used in the attempted inflight bombing of  Northwest Flight 253. This is a relatively common and powerful explosive in the category of aliphatic nitrate esters. It is a colorless powder that can be used in mixed and cast explosives or as the pure material. Like many detonable materials, it does not need to be placed in confinement to produce an explosion. PETN becomes unstable above 71 C, a fact that limits its suitability for some applications. My references do not clarify what is meant by unstable, but the material could be prone to chemical degradation above this temperature which would adversely affect its quality.

Other aliphatic nitrate esters include nitroglycerin, BTTN or 1,2,4-butanetriol trinitrate, EGDN or ethylene glycol dinitrate, and PETRIN, the trinitrate analog of PETN. A nitrate ester has a C-O-NO2 linkage and differs from aliphatic or aromatic nitro compounds which have C-NO2 linkages instead.

Nitrate esters are made from an alcohol or polyol and nitric acid. Nitro aromatics like TNT are made by acid catalyzed nitration of reasonably electron rich aromatic compounds like toluene or phenolics. The oxygen in the C-O-NO2 ester linkage confers some extra measure of instability to the molecule.

PETN is commonly used in Primacord, an explosive cord comprised of a PETN core inside a thin fabric or plastic sleeve. Primacord can be used as a blasting agent itself or it can be used as a fuse or delay line to trigger other explosives from a central point.

PETN is an explosive with a high brisance value. That is, it produces a shock that has a shattering effect on materials. In fact, brisance is quantified by the “sand test” which measures the production of fines from the shattering of 200 g of 30 mesh Ottawa sand. After the test, the sand is re-screened and the finer material that later passes through the screen is weighed. The greater the mass of fines, the greater the brisance.

Explosive         Sand Crush (g)   Heat of Explosion (cal/g) 
Black powder         8                                    684
Lead Azide            19                                  367
Comp C-4             55.7                            1590
TNT                      48                                1080
RDX                  60.2                        1280
Nitroglycerin         51.5                           1600
AN                               nil                                346
Picric Acid              48.5                           1000
PETN                         62.7                            1385
Source:  Cooper & Kurowski, Introduction to the Technology of Explosives, 1996, Wiley-VCH, p76-77. ISBN 0-471-18635-X

Pentolite is a composition prepared from a 50/50 blend of trinitrotoluene (TNT) and PETN with wax as a bonding agent and plasticizer. There are many blends of explosive materials. The composition is adjusted for the application.

The job of an explosive is to do PV work on objects. It does this by generating an abrupt pulse of heat and a large number of small gas molecules like N2 and CO2. The detonation velocity of PETN is ~ 8 km/s, so that a relatively small number of PETN molecules in a small volume are converted rapidly into a larger number of  gas phase molecules, all seeking to occupy the molar volume of 22.4 L/mol. 

The prompt generation of many moles of hot, small molecules results in the expansion of decomposition gases which forcefully press against the surroundings. The gases resulting from the 8 km/s detonation wave in the bulk solid explosive expand and compress the nearby air into a shock front that expands approximately spherically. As it does this the gases cool and the shock dissipates.

Explosive Power is a measure of an explosives ability to do work. Explosive power = Q x V,  Q = heat of explosion and V = volume of gas generated. The Power Index of a material is the ratio of explosive power to that of picric acid times 100 %. The power index of PETN is 167, TNT is 119, and RDX is 169.

Mercury Mining

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One of the least appreciated aspects of the 19th Century gold mining boom in North America was the necessary and parallel boom in quicksilver, or mercury. Numerous mercury bearing minerals are known, but by far the bulk of historical mercury production has come from cinnabar, or HgS. For clarity, cinnabar is distinct from vermillion which is a pigment derived from cinnabar. 

Recovery of gold can be performed by methods as simple as plucking nuggets from a pan or by gravity separation in the form of sluicing. Unfortunately, in many areas placer gold is quickly exhausted by eager miners. Where there is placer gold there is often a lode formation to be found. Gold in a lode can be much more problematic in its recovery.  

Gold from a lode may be found comingled with quartz in bulk form, partitioned in a vein, or dispersed at high dilution in a host rock at a large scale. Lode gold very often has to be extracted from a problematic matrix. In this circumstance, chemical means are necessary to extract and concentrate the value from the rock.

A chemical solution to gold isolation is limited to only a few economically viable possibilities. Beyond macroscopic placer gold there is amalgamation with mercury, borax, cyanidation with NaCN, and chlorination with Cl2 or NaClO. 

Amalgamation has been attractive historically because of its great simplicity. First, cinnabar is readily coerced to liberate mercury by simple roasting and condensation. Dispersed gold is contacted with mercury and selectively extracted. The resulting solution of Au-Hg is relatively easy to isolate by natural phase separation. Finally, gold is easily recovered from the amalgam by heating in a retort. Chemists would call this a simple distillation.

Some silver will also be amalgamated, but it is separated by roasting to silver oxide followed by amalgamation of the residuals. Unfortunately, gold tellurides are problematic for direct gold amalgamation. Gold tellurides must be roasted first to liberate volatile tellurium oxides and native gold residues. Energy becomes a major cost driver at this stage.

Cinnabar ore (Image from Mineral Information Institute)

US cinnabar ore deposits are found predominantly  in California and to a lesser extent in Nevada, Oregon, Arizona, Texas, and Arkansas. The geology of cinnabar ore bodies share a few general features. Cinnabar ore is found in zones historically associated with volcanic activity and alkaline hydrothermal flows.  Ascending flows of metal sulfide saturated water infiltrated faults and fractures and deposited HgS rich mineral.  This is a common ore forming mechanism and is responsible for diverse metalliferous deposits, including mercury. 

Figure 1. Franciscan Quicksilver Ore Body Structure (C.N. Schuette, The Geology of Quicksilver Ore Deposits, Report XXXIII of the State Mineralogist, January 1937.)

According to Schuette, a common feature to economically viable cinnabar occurrences was the presence of a cap rock formation over the ore body. The infiltration of cinnabar laden hydrothermal fluids into fissures and shrinkage cracks in basalt intrusions as well as deposition in brecciated rock in the fault zones lead to enrichment of the mineral.  An impermeable layer above caused a pooling accumulation of mineral and a barrier to oxidation. 

Figure 2. Diagram of Sulphur Bank Mine (C.N. Schuette, The Geology of Quicksilver Ore Deposits, Report XXXIII, of the State Mineralogist, January 1937.)

In these California formations cinnabar is regarded as a primary mineral, meaning that it is the direct result of transfer from deeper source rock. An example of secondary rock would be serpentine (Fig 1) which is formed as a result of aqueous alteration of another mineral. Serpentine is a group of minerals comprised of hydrated silicate which may contain some combination of  Mg, Fe, Al, Mn, Ni, Ca, Li, or Zn. According to Schuette, serpentine is often found associated with cinnabar formations. 

The Sulphur Bank Mine near Clearlake Oaks in Northern California offers an interesting example of cinnabar mineralization. Figure 2 shows a fault that provided a channel for fluid flow to upper level rock formations. Over time oxygen and water caused the oxidation of sulfur to sulfuric acid which aided the decomposition of cinnabar and the host rock. 

Note that the uppermost layer is said to be white silica which resulted from extensive demineralization of solubles from a silicate matrix. Further down, native sulfur was discovered in more reducing conditions and was actually recovered in early mining operations. Cinnabar was located below the layers of oxidized mineral. 

This phenomenon of surface oxidation of an exposed ore body is observed in gold and silver mines as well. Miners often lamented that the nature of the lode changed as the mine operations got deeper. Of course, what was happening was that oxidized formations are encountered near the surface and as the mine gets deeper, progressively greater reducing conditions are found with a corresponding change in mineral species present. 

Air oxidation or infiltration of meteoric water with dissolved air and CO2 would cause the alteration of sulfide minerals to more water soluble H2S and sulfates, leaving native gold behind. But at greater depths, the composition of the ore changes to afford heavier sulfide loading and therefore a requirement for a different kind of milling. 

As it happens, the recovery of mercury from cinnabar is quite simple and has been done since Roman times. Typically, the ore was crushed and roasted in the combustion gases of a reverberatory furnace. This kind of furnace was constructed to isolate the fuel from the ore by a partition and rebound or reflect the hot gases off the ceiling of the furnace onto a heap of ore. Despite the name there is no acoustic aspect to the process. 

The hot gases would produce HgO and sulfides which would oxidize in the gas stream to volatile sulfur oxides. Thermal decomposition of HgO at ca 500 C produced mercury which was condensed out of the exhaust gas stream and collected as the liquid. 

Keeping up with the data stream

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After many years of immersion in technical work I still marvel at how an organization can become mired in raw data. Smart people can easily succumb to the notion that data equals knowledge. Especially in circumstances where data is accumulated faster than it can be assimilated.

It is relatively easy to collect data in a chemical lab. You take a set of samples and prep them for testing, load the sample vials into the sample tray, and let the automated sampling widget move through its paces. In a few minutes or hours the software has accumulated files bulging with data points.  It is even possible to construct graphs with all sorts of statistical manipulations on the data, but still not morph the data into usable knowledge. I’ve been to meetings where graphs are presented but were not backed up with interpretation. What was the presenters point in showing the graph?

Computerized chromatography stations will spew data all day long onto hard drives based on selections from a cafeteria-style menu. With hyphenated instrumentation, an innocent looking 2-dimensional chromatogram is actually just a part of a higher dimensional data set with corresponding mass spectra or UV/Vis spectra.

The task for the technical manager is to get control of this stream of data and render some of it into higher level knowledge that will help people run the organization and get product or research out the door. This is the true work product of the experimental scientist: knowledge woven from a data cross-fire and supported by accepted theory.

I do not know what others do when confronted by a data tsunami. I can only speak for myself on this. When the data flow gets ahead of me, it usually means that I am spread too thin. It indicates that I am not taking enough time to properly devise experiments for maximum impact and am skimping on the analysis in favor of other duties.

Another issue relating to managing diverse data output is the matter of storing accumulated data and knowledge for easy retrieval. It is easy to throw things into folders and file away. But in a few months, the taxonomy used for filing a given bundle of data becomes murky. Soon, one is forced to rummage through many files to find data because you’ve forgotten details on how you organized the filing system.

There are ways around this problem. Laboratory Information Systems (LIMS) are offered by numerous vendors. A good LIMS package goes a long way towards managing data and distributing knowledge. We have a homebrew LIMS system (built in MS Access) that seems to work rather well for analytcial data. However, it was not constructed with process safety information in mind.

What I have constructed for my process safety work is an Access-based application that structures various kinds of information graphically into regions on a form. Within each region is a set of data fields that are subordinate to a given heading or context. The form is devised to prompt the user to consider many types of thermokinetic experiments and provides fields that are links to specific documents. The form provides both actual data and links to source documents. It can be used to enter data or to retrieve it.

This is what Access is designed to do, so I have described absolutely nothing conceptually new. Access allows me to aggregate related kinds of experimental results, reports (the knowledge part), and source documents in one field of view so as to allow the users visual processing capability the chance to browse more efficiently.

An example of “related kinds of experimental data” would be DSC, TGA, ARC, and RC1 reports. What connects these fields is the domain of thermal sensitivity of a compound or reaction mixture.

Another aggregation of fields would be the conditions related to an incident. I like to select key descriptors to an incident so as to aid in incident type studies at a  later date. It is useful to be able to sort incidents resulting from a blown rupture disk or a spill, fire, triangulated drum, etc.

A database is rather like a garden. In order to be useful it must be planted and then cultivated. Ignore it and it will lose its comprehensiveness, casting into doubt its continued use.

Next up is the development of an in-house Wikipedia style browser application for aggregating product, process, and safety information. This offers the best opportunity yet for making information and diverse data available to employees. It can be written in narrative form so as to impart knowledge and history. Why was a particular vendor chosen or how did we decide on that specification? What was the rationale for the process change in step 4.2?  The ability to explain and link to in-house source documents from a familiar and single point of access is key to potential success.

Phase Change for Chemistry?

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Disclaimer: Combichem or HTE is definitely not my area of expertise. It is, therefore, inevitable that I’ll say something blindingly ignorant about it. Despite my admitted ignorance, is appears to me that there is something happening, some kind of phase shift, in the small molecule discovery marketplace that is of general interest to the chemical R&D community. In fact, it may just be part of an overall change in how we do chemistry in general.

I’ve been hearing no small amount of buzz from chemists in the job market about the flattening or even downturn of US pharma R&D in general and of combichem or High Throughput Experimentation (HTE) in particular.  It is not that HTE is in any particular danger of extinction, but rather certain companies who offer the equipment platforms and tech packages seem to be evolving away from supplying equipment as a core business activity. Many of the big customers who could afford the initial cash outlay for HTE technology are doing their work in-house, dampening the demand for discovery services by HTE players at their aggressive prices.

One company I know has evidently shifted emphasis into the drug discovery field rather than try to continue marketing HTE equipment.  Near as I can tell, they are betting that having their own drug candidates in the pipeline is a better strategy than being strictly a technology or R&D services supplier. Time will tell the tale.

What the honchos in the board rooms of America’s big corporations forget is that the art they export so profitably was in all likelihood developed by people educated in US taxpayer subsidized institutions with US government grants. American citizens subsidize the university research complex in this country and by extension, supply a brain subsidy to industry. To export chemical R&D is to subsidize the establishment of a similar R&D capacity in other nations.  I think if you poll most US citizens, they’ll say that this is not the outcome they expected.

Software for HTE has become a derivative product that, for at least one HTE player, is proving to be rather successful. It isn’t enough to have the wet chemical equipment to make hundreds and thousands of compounds. You must be able to deal with the data storm that follows.

The business of HTE technology is evolving to a mature stage as the market comes to understand how to make and lose money with it.  There is always a tension between “technology push” and “market pull”.  It is often easier to respond to concrete demand with existing tools that to get new adopters to invest in leading edge tools to discover risky drug or catalyst candidates.

The extent to which the US chemical industry (all areas, including pharma and specialties) is outsourcing its R&D or simply moving it offshore is distressing. R&D is our magic. And promoting its execution offshore is to accelerate the de-industrialization of the USA.  It is folly to train the workers of authoritarian nations like China to execute your high art. American companies must learn to perform R&D in an economically accessible way and keep the art in-house. 

What makes R&D so expensive in the USA? Well, labor for one thing. In the end, our dependence on expensive PhD’s to do synthesis lab work may be a big part of our undoing. But there is much more to it than that. Look at the kinds of facilities that are built for chemical R&D. In the US and EU they are usually very expensive to build and maintain. Regulations and litigation avoidance are trending industry in the direction of ever more complex and high-overhead facilities in which to handle chemicals and conduct research. 

Then there is the cost of every widget and substance associated with chemistry. Look at the pricing in the Aldrich catalog or get a quote from Agilent. Have a look at the actual invoice from your latest Aldrich order and look at the shipping cost. High isn’t it? We’ve accelerated our demand for ready-made raw materials and hyphenated instrumentation. To what extent are we gladly buying excess capacity? Who doesn’t have an instrument with functions and capabilities that have never been understood or used?

It is possible to conduct R&D under lean conditions. But it can’t be done cheaply in existing industrial R&D campuses. Cost effective R&D will require a recalibration for most chemists in terms of the kinds of working conditions and administrative services they expect. But business leaders will have to recalibrate as well. Prestige can be manifested in product quality and a sense of adventure and conviviality rather than in an edifice. There are companies all over the world doing this every day. They set up shop in a commercial condo or old industrial building with used office furniture and grubby floors. What matters in chemistry is what is happening (safely) in the reactor. Everything else is secondary.

Pitchblende in the Wood Vein, Central City District

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Recently I came upon a copy of Geological Survey Circular 186, 1952, F.B. Moore and C.R. Butler, Pitchblende Deposits at the Wood and Calhoun Mines, Central City Mining District, Gilpin County, Colorado. Like many Geological Survey documents, it contains a pocket with neatly folded scale drawings of the mine workings. These drawings chart the location and elevation of the shafts and drifts and give a best estimate as to the extent of the formation.

Vein Structure in the Central City District. (From Geologic Survey Circular 186, 1952.)

What is interesting about the map above is not so much the minute detail of the locations, but rather the obvious trend of the veins (solid lines with dots).  They are all east-northeast trending.  The country rock is largely precambrian granite gneiss and quartz biotite schist according to the survey. It doesn’t take long to figure out that the mine locations correlate with the veins.

Geological Survey maps of 3 levels of the Wood Mine, Gilpin County, Colorado (Geological Survey Circular 186, 1952).

The second figure was generated by Moore and Butler in 1950 and shows the locations of pitchblende occurrences in three levels of the Wood Mine near Central City, Colorado. The red dots indicate the location of pitchblende along the three drifts at the 135, 197, and 275 foot levels of the mine.

Profile of the Wood Mine, Central City District, Illustration from Geological Survey Professional Paper 371, 1963.

 The Wood Mine was an early and prolific source of pitchblende, though presumably it began as a gold /silver operation. The workings reportedly reached a depth of 600 ft.  The Wood vein is in a fault fissure that shows extensive alteration from hydrothermal action. The width of the vein varies with the type of country rock in which it is found, but ranges from from 1 to 18 inches and has been followed for a lateral distance of nearly 1000 ft.

The productivity of uranium mines is commonly expressed in terms of equivalent weight of U3O8 rather than weight of ore, given the large variety of mineral forms uranium is found to occur in. The figure above is from Geological Survey Professional Paper 371, P.K. Sims and collaborators, Geology of Uranium and associated Ore Deposits, Central Part of the Front Range Mineral Belt, Colorado. Extensive stoping has been done in an attempt to vertically intercept the vein. This was a common practice in hard rock mining- let gravity bring the muck to you.

Pitchblende was discovered on the dump of the old Wood shaft in 1871. Circular 186 reports that by the end of 1872, 6,200 lbs of ore containing 3,720 lbs of U3O8 had been removed. By 1916, 102,600 lbs of ore bearing 30,040 lbs of U3O8 equivalent had been recovered.  The high grade pitchblende was hand sorted and that below ca 10 % was discarded or lost in gold and silver processing.

In Circular 371, Sims observes that “Pitchblende occurs as small, discontinuous lenses and streaks on the footwall of the Wood Vein, which are separated by nonuraniferous vein material.”

What is intriguing is that pitchblende was apparently an item of commerce in the early 1870’s. Radium, extracted from pitchblende, was not discovered until 1898 by the Curies.  A procedure for the preparation of sodium diuranate, Na2U2O7 6H2O, was reported as early as 1849 (Patera, J. pr Chem. 1849, [i] 46, 182. Early uses of uranium yellow were in paints and stains for glass and porcelain. This pigment has also been used for the production of fluorescent uranium glass.