Category Archives: Chemistry

Mercury Mining

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

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?

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

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.

Uranium roll fronts

As a kind of hobby Th’ Gaussling has been surveying the literature on uranium occurrences in North America. Uranium is found in many interesting locations and as a result of several distinct kinds of ore forming processes.

Prospector with Geiger Counter

From Ballard &Conklin, Uranium Prospectors Guide, 1955 Harper & Brothers

For the most part, uranium ore body formation is the result of aqueous transport and deposition.  Uranium is found as a lode in vein formations in precambrian  igneous/metamorphic structures as in the case of the Schwartzwalder mine near Denver. In fact, there are many lode occurrences that contain a variety of uranium minerals in the Colorado mineral belt.

What seemed counterintuitive to me was the extent to which uranium is found in sandstone. Evidently I had developed a bias for connecting heavy metal occurrences with igneous/metamorphic formations.

Uranium occurrences in sandstone take on certain characteristics as a result of ore forming processes. Uranium is often found in concentrated bodies called “roll fronts” or “ore rolls”. A roll front is a body of concentrated mineral with a lenticular cross section and is found in confined strata sandwiched between impermeable clays, shales, or mudstones.

Roll Front Cross Section

Adler & Sharp, Guidebook to the Geology of Utah, No. 21, Utah Geological Society, 1967, p. 59.

The action of oxygenated meteoric water (i.e., rain and surface water) migrating through a porous sandstone stratum will selectively mobilize mineral species that are soluble. In the case of uranium, the relatively insoluble U4+ compounds are oxidized to more soluble U6+ species which are then mobilized and flow in the formation.

Eventually, as the water flow encounters reducing conditions, U6+ gets reduced to U4+ and deposition occurs. Sandstone with organic material may be a net reducing environment and provide the necessary carbonaceous reductants to do the deed.

As the U6+ enriched aqueous flows encounter reducing conditions, deposition of U4+ insolubles occurs in a manner determined by fluid mechanical forces. The result is an elongated and tapered ore body confined to a narrow stratum.

Uranium roll fronts are common in many uranium districts. The Uravan uranium belt in the Colorado Plateau is a good example. Uranium is found concentrated in tuffaceous formations as well. An example of this is the uranium occurrence found in the 39 Mile Volcanic Field in the central Colorado mountains.

What is interesting to ponder is the geological effect of plant metabolic byproducts like oxygen. Oxygen directly contributes to a natural process that lead to the concentration of a scarce element like uranium. Plant life facilitating nuclear power. Hmmm.

The Passing of Irwin “Ike” Klundt

I just received the sad news that my friend, boss, and mentor, Dr. Irwin “Ike” Klundt died in Tucson, AZ, of cancer. Ike retired in the early 1990’s as VP of Sigma-Aldrich. He was an organic chemist from eastern Washington state. He joined Alfred Bader in the 1960’s (?) and helped build Aldrich into what is is today. He started the Aldrichimica Acta and appeared in it many times in the capacity of awarding a prize to honor prominent chemists. Ike also managed the publication of the catalog and invented the Aldrich “Coffeepot” Kugelrohr.

I first met Ike when I taught for a year at Ft Lewis College in Durango, CO. He was an adjunct prof and I was a visiting prof. Ike was loved by all and was a useful hand to have around for the department.

Ike was a good hearted soul who enjoyed the company of others and actively worked to help younger chemists develop their careers. He loved the science and business of chemistry and the people who worked in this field of ours. Ike was forced out of Aldrich soon after Bader was given the boot as the once entrepreneurial company began to behave like a normal publicly traded company- you know, the ones that eat their young.

The chemical field is poorer for the loss of Ike Klundt. He was one of the human beings of the trade and he will be missed.

The joy of logistics

It is amazing how complicated and labor intensive logistics can be for manufacturers. Customers often have strict requirements on how materials are to arrive at their facilities. Some customers have preferred shipping companies and will require that you use them. Others don’t care. Some want you to pre-pay and add the freight to the invoice. Some will accept FOB shipping point terms and pay the shipper themselves. 

International shipments are even more complex. Multimodal freight forwarding companies will take charge of the shipment and get it on a boat or plane. Once across the pond, they’ll get the shipment through customs and plugged into the local ground transport.

If you’re shipping internationally, unless the customer is a known quantity, you’d better get prepayment or a letter of credit from their bank.  Cash is king.

It becomes complex if you allow yourself to be a custom shipper. Some companies simplify things by offering a one size fits all shipping policy. This is best if you can get away with it, but more often than not, custom service means custom shipping.

There is much more to chemical business than just the chemical part. Chemistry students planning to enter the fabulous world of chemical industry should be advised that if they are going to step out of the lab, then the full spectrum of business related problems and challenges will be available to them. It is a great opportunity for some and a gigantic nuisance for others.

Mole Day Thoughts on Lab Life

I have come to the realization that, after a career of avoiding it, I really dig physical organic chemistry. While I do have the synthetikkers love for developing a synthesis, I really enjoy taking the rare opportunity to do a focused study on a single transformation or compound.  It is a stylized form of play that any developmental psychologist would recognize. Discovery is about learning, just like play, and many of the exploratory behaviors observed in play apply just as well to discovery (well, except for hitting and crying).

One way a scientist learns is by doing a search for boundary conditions. Where or how in parameter space does a thing change? What is the best solvent for the desired outcome? What effect does stoichiometry have? Does dry, inert atmosphere really make a difference? What are the best leaving groups? Yes, it’s just research. But there is more.

In order to claim that you have expertise with a substance or process, you must have an understanding of how a process or substance behaves under a variety of conditions. If faced with a product that is off spec and the prospect of having to rework or remake, it is very helpful to understand what conditions lead to the off-normal outcome. Either the chemist sleuths each upset for a cause, or the chemist goes in the lab and purposely exposes the process to off-normal parameters and analyzes the outcome, or both. After a while, patterns begin to arise and trends become apparent. This is play.

Seems bloody obvious. But in a production environment the opportunity to explore  parameter space is often not possible. Favor almost always finds the more practical, though short term, fixes. Production managers are not always chosen for their focus on the long term. They are short term oriented- a necessary predilection for timely delivery of product on a tight timeline.

Part of a good process development program is a study of how the process behaves in various upset conditions. This is important for understanding the thermal safety issues, but it also is a good time to take snapshots of how the composition of the process system behaves when it is out of whack.  A reaction profile under conditions of reagent mischarges or off-temperature can give many clues as to the operating window of the process. It can also tell you something about the best way to do an in-process check and define flags for particular types of upsets.

Many companies do this, but a good many find a way to gloss over such work.

Lowest Common Denominator

What is happening in the chemical world is that the safety people are taking control. Everything is dumbing down to the point where the safety of a facility is being judged on the basis of what the least qualified deem as safe. 

I just received an MSDS for the Buchner funnel (!$#%!!) I recently purchased from Aldrich.  The MSDS lists zero’s for Health, Flammability, and Reactivity both for HMIS and NFPA ratings. Thank heavens for that. It does recommend “suitable storage” and that it be kept “tightly closed”.  It is silent, though, on the matter of repeatedly jabbing the pointy end into your eye.

I gotta get out of the chemical business if this is where it is going. Administrative controls on common laboratory activity requires management by a dedicated staff member in order to maintain a favorable paper trail and stay in compliance with the ever growing web of regulation. OSHA, EPA, Homeland Security, as well as state and local agencies who want to inspect this or that or place tax stamps on your balances.

How did civilization get this far along without the legions of officious ninnies who want to exert control over everything you do? Chemical labs have inherent hazards, depending on the work that is being done in them. The cost of achieving de minimus risk for the lowest common denominator is quite high. Risk ends up being transferred to countries who reside on the other side of the curve- those who have little care for people.

2009 Nobel Prize in Chemistry

Congratulations to the international trio winning the 2009 Nobel Prize in Chemistry-  Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada E. Yonath. The three chemists won the prize for their fundamental work in characterizing the structure and detailed function of the ribosome.

I sat in on a talk at the Organic Symposium this summer where the speaker showed a bit of the work of Yonath.  The ribosome work is simply stunning in its detail and experimental prowess. Hackers like myself can only watch from a distance and admire the work.