Category Archives: Science

Homestake Mine Visit

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The town of Lead, SD, pronounced “leed”, is home to the Homestake gold mine. The mine was purchased and subsequently developed by George Hearst, father of William Randolph Hearst, and partners ca 1876.

Homestake Open Cut from Yates Hoist House

 The photo above shows one ground view of the large open cut found on the north end of town. The pit is approximately 1/2 mile across and 1200 ft in depth from the highest elevation.

The pit exposes the ore body which is comprised of inhomogeneous igneous rock with gold bearing veins. In the photo below the vein structure can be seen. The buff colored rhyolite bands seen below are not associated with value.

Homestake Open Cut, Lead, SD.

Gold was discovered at a surface exposure, called a “lead”, which became the namesake for the town of Lead. Mining activity was halted in 2002, in part due to the low price of gold at the time. By that time the underground workings had reached a depth of 8000 ft, which puts it at ca 3000 ft below sea level. The rock temperature at the 8000 ft level was reported to be 130 degrees F, requiring substantial air conditioning for the workers and equipment.

Hoist Cable

The (poor quality) photo above shows the hoist equipment in the Yates head works. Of interest is the conical cable spool used to provide lift for hoisting operations at the Homestake mine. The purpose of the variable diameter feature of the hoist was to provide maximum mechanical advantage when the cable was at the end of its reach, presumably when it was ready to lift a heavy load of ore from the bottom of the shaft.

Homestake Honey Wagon

The “ore cart” in the photo above was the toilet facility for the miners. It featured a seat on top which could be sealed, a thoughtfully placed foot platform, and railings so the user could hang on for those rough rides.

The surface tour of the mine consists of a trolly ride around town with a stop at the Yates hoist. Warning: It is quite superficial in content, but is the only type of tour available. Our tour guide was student on summer break with near-zero knowledge of the geology or the engineering. He was accustomed to entertaining the barely interested.  If you are keen on the particulars of Homestake history, I recommend Nuggets to Neutrinos, by Steven T. Mitchell.

Homestake was one of the very richest loads of gold in the western hemisphere. Reportedly, some 40 million oz of gold were extracted from the mine.

Today, the Homestake mine is being converted to an underground nuclear physics lab facility under a program called DUSEL. On a side note, it is interesting to listen to the townsfolk talk about the new labs. I could tell they are trying to be enthusiastic, but the reality of neutrinos is very hard to get your arms around.

On the road

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Th’ Gaussling is off-site for a few days of happy motoring in the mysterious Black Hills of South Dakota, or Paha Sapa in Lakota. 

The discovery of Black Hills gold in 1874 by an expedition led by General Custer and the 7th Cavalry ultimately triggered another bout of  hostilities with the Lakota as the land deeded to them by the Fort Laramie Treaty of 1868 was pushed aside by miners and settler. Government agents were not able to prevent mining and settlment of the Black hills area. 

The blowback to Custer’s discovery of mineral wealth in the Black Hills was in the form of his defeat by Sitting Bull at the Little Bighorn River in Montana in late June of 1876.

The locals now mine tourists rather than gold.  The homestake mine has workings at 8000 ft below the surface! Over 1 billion dollars worth of gold was extracted between 1877 and 2004. Presently in the process of being set up for underground labs, the Homestake Mine in Lead, SD, will reopen in the coming years as a center of particle physics and dark matter research as the Sanford Underground Laboratory. Part of a program known as DUSEL, the new labs will exploit the great depth of the Homestake mine for the inherent radiation shielding at the lower levels of the site.  

Snow

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June 15th, 2010. Colorado Front Range.  After a week of rain the clouds have parted to reveal severely clear azure skies and a fresh layer of snow above ~ 11,000′.  The grass is growing so fast you can hear it if you listen carefully. The lagomorphs are frolicking in the dewy turf and the adjacent prairie dog colony is overflowing with barking rodentia. The landscaper’s lawnmower releases a refreshing bouquet of terpenes into the air from freshly severed plant tissues. 

As I wave my card in front of the security card reader, the electromagnetic door release mechanism clicks and I leave behind the flora and fauna of the great outdoors and enter the world of mass selective detectors, nmr, and exotic molecules.  It is a transition from the macro to the micro, from the kilo to the nano. The world on the other side of the wall is immediately concerned with turf management and burrows. In this tiny space we’re concerned with nuclephiles and kinetics, exotherms and yields.  Interesting, yes. But in the end, where is it taking us?

Needlessly invoking clathrates. BP’s underwater ice machine.

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In the news reporting on the BP oil spill, there is talk of methane/water forming a special ice composition that defeated the previous attempt to channel oil to the surface.  I think folks are referring to clathrate formation. This ice blocked the flow of petroleum from the concrete structure that was lowered over the well head.

But, here is the deal. Wouldn’t you expect cooling of a compressed gas as it exits the well pipe and into the sea water? Isn’t this just an example of the Joule-Thompson effect?  As the natural gas component of the petroleum discharge exits the pipe, it is going to expand somewhat, even at a one mile depth, and cool the surrounding water. If this occurs in unconfined, open water, the jet of petroleum will entrain water in the flow and be warmed by the continuous flow of heat from the water.

But, if the gas/oil mixture of petroleum is ejected in a confined space that interferes with heat transfer, then one would expect the expansion cooling of the gas phase to predominate and cool the water in the confining space, possibly to the freezing point. Clathrates may be formed, but the simplest explanation is from good old thermodynamics.

BP oil spill. What are the merits of using dispersants?

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BP Oil Spill Image, May 4, 2010 (NASA Earth Observatory)

Oil Spill near Mississippi delta. Vegetation, red; Oil, silver. MA 24, 2010. (NASA Earth Observatory photo)

Eventually, BP will find a way to block the discharge of petroleum into the Gulf of Mexico.  And, eventually, the effectiveness of how the relevant parties responded to the incident will be analyzed and findings posted.

I hope that some effort will be put into an analysis of the merits of using dispersants in general and Corexit in particular. What sparks my comment is the finding that considerable subsurface petroleum has been found. This material is evidently close to neutral buoyancy and is drifting with the currents.

Question 1: Is there a connection between the dispersant use and the presence of this subsurface body of petroleum?  

Question 2: What is the desired outcome of dispersant use?  Where did the planners think the petroleum would go?

Question 3: Is there any advantage in encouraging petroleum to remain below the surface, if that is even possible?

At some point, a decision was made to use dispersants on this massive discharge. Is there a scientifically supported rationale for this, or was it palliative treatment intended to mask the surface effects of the release?

Field Trip Report. Finding Faults.

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Th’ Gaussling, traveling with a 3-van convoy of local geologists, participated in a field trip on May 22, 2010. The purpose of the trip was to get an appreciation of the kinds of faults to be found in and around the IRSZ and get some insight into the phenomena of faulting. The trip was organized by the Colorado Scientific Society, an earth science oriented organization. This was my second field trip with CSS.

GPS coordinates and elevations were acquired with a Garmin eTrex handheld receiver. Waypoints (WP’s) are just the latitude and longitude of physical locations of interest.  Elevations generally aren’t required to find the formations, but are provided as a matter of general interest.  The photographs are my own and if copied, I would appreciate a citation and/or link.

The trip leader was Jonathan S. Caine, a USGS research geologist who has done more than a bit of work relating fault and fracture networks and fluid flow in the earths crust. A feature called the Idaho Springs-Ralston Shear Zone (IRSZ) was part of the topic of this trip. As Caine says in the abstract on the previous link, the IRSZ is thought to be a persistant weakness in the continental crust. There is interest in the relationship between the IRSZ and the Colorado Mineral Belt. 

Geologists discuss Junction Ranch fault (WP003)

  WP003-  N 39° 44.700′, W 105° 17.485′ elevation 6266′. 

Closeup of Junction Ranch fault. Note white calcite vein (WP003).

 The Junction Ranch fault which had an exposure at waypoint 003 was an example of a fault in a formation that has seen considerable hydrothermal alteration. The orange iron stains on the rock are a clue that fluid transport of minerals has taken place. Calcite veins within the foliated clay filling the fault are an indication that the clay was deposited first. There is no evidence, however, that the fault predates the hydrothermal alteration. 

In a roadcut along the Central City Parkway is an exposure of a brittle fault at location WP005-  N 39° 44.990′, W 105° 28.233′, elevation 7571′. 

Roadcut exposing a brittle fault along Central City Parkway (WP005).

 The formation exposed at WP005 was part of a very old structure with multiple faults and igneous intrusions. In the photo above, the edge of the fault is enhanced with a black line drawn in during editing. The surface above the black line is an example of a slickenside, or one surface of the fault. Some members of the trip said they could see slickenlines, but they are so subtle that it is hard to be certain. A large igneous intrusion 100 m away showed signs of dislocation, presumably due to a fault. Boudins were observed at this location and are shown in the photo below. 

Central City Parkway road cut, boudins visible in foliated rock (WP005).

We visited the location of a fault in Coal Creek Canyon. This is a NNW trending distributed deformation zone which is part of the Boulder Batholith. This location is designated WP008- N 39° 54.268′, N 105° 20.795′, elevation 7771′.  

This fault was discovered filled with clay and dips 35 to 45 degrees. It was further exposed by excavation by Caine and another geologist. Again, the approximate boundary of the fault was enhanced with black lines in editing. There was considerable alteration of the rock on the hanging face side of the fault with iron staining associated with hydrothermal alteration.

Coal Creek fault at WP008 May 22, 2010.

We visited a ductile shear zone with suspected mylonite features. It was located at WP007- N 39° 51.026′, N 105° 21.155′, elevation 7634.  Mylonite zones are evidence of ductile shear in response to a stress field.  Near the mylonite zone was a fault with exposed slickensides. While faulting and ductile deformation may seem incompatible, it should be remembered that over time many kinds of phenomena can be overprinted on the rock formations. Rock may deform in a ductile manner and sometime later undergo brittle fracture.

Suspected myolinite feature (WP007).

 The field trip leader was very enthusiastic and because of his background, was able to provide many important insights into the local geology. It was a very worthwhile day in the mountains.

Whither Diethyl Ether?

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Diethyl ether seems to be in short supply in North America these days. Suppliers have customers under allocation constraints.  Yes Virginia, people still use Et2O in certain kinds of chemical processing. Sometimes Et2O is prized for its solvent effects and sometimes for its volatility. Sometimes the only way to solubilize some  inorganic compounds is as the metal etherate.  Solvent residues in fine chemicals are often a problem and volatile process solvents can be a big help in ameliorating that issue.  You can purchase 5,000 gallon tanker loads of Et2O if the supplier has qualified you. Another reason not to swerve in front of trucks on the highway. 

Part of the problem with Et2O availability is the considerable reduced demand for it these days.  Many companies have banned the use of Et2O on their site for any purpose. It is easy to understand why. The insane vapor pressure and low autodecomposition temperature are problematic for plant safety. The low boiling point of Et2O means that plant utilities can heat a vessel of ethereal soln rapidly and blow a rupture disk at reasonably low pot temps.  Naturally, the safetly department gets surly about this kind of thing.

Tetrahydrofuran is not always a suitable process stand-in for Et2O. Reactivity behaviors may be quite different from Et2O solns.  THF’s sensitivity to butyllithium, for instance, forces one to keep the processing conditions at low temp with a chiller. Lower pot temperatures increase the thermal margin of safety, but may have a deleterious effect on activation of a transformation once BuLi has done its job. 

I have studied the decomposition of methyl tetrahydrofuran with BuLi and have determined that it decomposes in the low 30’s °C range, somewhat higher than THF. MeTHF is not an exact stand-in for THF or Et2O either.  But it is definitely worth having in the stockroom for development work. It will surprise you in regard to how different it can be from THF.

While MeTHF is touted for its ability to phase separate with water, it will hold appreciable amounts of water.

Chemistry Field Trip!

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So I decided to kick up my interest in the local metalliferous deposits and get more folks involved. As a member of the executive cmte of the ACS local section I’ve organized a seminar at a local university and arranged to have the lead exploration geologist from CC&V come to talk about the their gold mine in Cripple Creek.

The seminar is thursday night. Friday morning a few of us will board a van and drive the 5 h round trip to visit the open pit operation. We’ll stop at the nearby Molly Kathleen mine as well. I’m hoping we’ll be 1000 ft down the hole when the mine next door begins blasting. That’s an unforgettable experience.

Enthusiasm is contagious.  Especially with regard to gold colored precious metals. Unfortunately, bench chemists have few opportunities to take field trips. So the thinking here is that we’ll find a way to get members out and about to look at heavy industry. And gold mining is definitely a chemically related industry. Email blast notifications to rouse attendance are surprisingly ineffective- 1 or 2 % response at most. It is hard to get folks to participate in local section activities because everyone has a life.

The next day I’ll be on a field trip with geologists to visit various sites showing ductile and brittle deformation as well as hydrothermal alteration of formations in the central front range. I’ll be a chemical science interloper, as usual. The key to many of the metalliferous features in the world is hydrothermal transport. Shallow magma intrusions energize a kind of heat engine that pumps water through metal-bearing rock and transports hot, pressurized mineral laden fluids through a large and cooler network of fissures and faults where minerals precipitate according to their solubility.  Hydrothermal alteration is an important feature to look for when prospecting for metals.

Phosphate the Wonder Anion

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I thought it would be good to start the week by highlighting a particularly praiseworthy anion. That anion is phosphate, sometimes called orthophosphate, (PO4)3-.

So, you ask, what is so bloody interesting about phosphate? Isn’t every atom, ion, and molecule special in some way?  Well, yes, but phosphate is uniquely constituted to provide services in the critical area of genetic information keeping and functional group transformation (without Pd and boronic acids).

Here is the curious thing: Biochemical systems use phosphorylation and hydrolysis as a means of executing molecular transformation. Remember oxidative phosphorylation?  So, how is it that a phosphate moiety that is so useful as a leaving group or activator is also able to hold together DNA with such high fidelity?

Phosphate Backbone on RNA and DNA

In his much-referenced 1987 paper entitled “Why Nature Chose Phosphates” (1), Frank Westheimer observed that phosphate diesters have a very useful property as a linking group for nucleic acids. The charged oxygen on (RO)2P(=O)O- serves several purposes.  The presence of a charged linker renders DNA and RNA compatible with the hydrophilic environment inside the cell. The charge prevents the nucleic acid polymers from migrating to more hydrophobic environments found inside of cell membranes. And equally important, the monobasic anion serves as a kinetic barrier protecting the millions of phosphate linkages in a DNA strand from cleavage under neutral or basic hydrolytic conditions over the lifetime of the organism.

The hydrolytic stability of phosphate diesters is not to be underestimated. Westheimer points out that dimethylphosphate anion has a half-life of 1 day at 110 C in 1 N base. He cites the rate constants at 35 C for the saponification of (CH3O)2PO2- is 2.0 E-9 (1/mol sec);  (CH3O)3P=O is 3.4 E-4 (1/mol sec); and for ethyl acetate 1.0 E-2 (1/mol sec).

However, the very simplicity and current prevalence of phosphate ion in the environment does not go far in explaining how phosphate might have found its way into metabolic and structural use.  In prebiotic times, the occurence of phosphate is in doubt (2).  But not just the occurrence of phosphate is in doubt. The relative abiotic inertness of phosphate towards esterification and the formation of other metabolically useful species raises the question of the original oxidation state of phosphorus during the onset of early life.

While phosphate is found in certain meteorites, Pasek suggests that a more ubiquitous meteoric phosphide mineral species such as schreibersite, (Fe, Ni)3P, found in iron meteorites may have provided the necessary reactive precursors for metabolic evolution (2). Pasek cites growing evidence of a late meteoric bombardment period at 3.8-3.9 GA.

Schreibersite hydrolyzes to a variety of oxidized species including phosphite. Phosphite has the advantage of being substantially more water soluble than phosphate, providing a larger molar concentration in seawater.  Schreibersite reacts with acetate to form acetylphosphonate. In fact, a variety of organophosphorus compounds may be formed on exposure of schreibersite and its hydrolysis products with organic materials.

Lowly phosphate isn’t sexy like the newer anions triflate and BArF. But its seemingly mundane properties are key to the function of metabolism and genetics.

(1)  F.H. Westheimer, Science, 1987, 235(4793), 1173-1178.  (2) Pasek, M.A. PNAS, January 22, 2008, vol 105, no. 3, 853-858.

Antimatter Storage

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We had an ACS local section meeting recently in the clubhouse of the Air Force Academy golf course.  The featured speaker, a DoD chemist, gave an interesting talk on his work on some of the basic issues relating to the storage of positrons or anti-electrons. In the interest of fairness, since I am writing under a pseudonym, I’ll not wave his name about.

The speakers background is P-Chem and in particular, spectroscopy of isolated species in cryogenic matrices. He pointed out that an atom or molecule or cluster in an inert cryogenic matrix is in a dissipative environment and thus isolated from solvent interactions that might otherwise mask other kinds of phenomena.  So it is possible to spectroscopically examine the solid phase environment of the cryo matrix. In other words, an imbedded subject  molecule might find itself in an isotropic or ansiotropic environment, depending on the matrix. Infrared spectroscopy could give clues as to the symmetry of the local environment.

It turns out that ortho-hydrogen is an interesting matrix in which to study an important aspect of antimatter storage technology.  In order to collect positrons, one has to first find a source of them. While they can be supplied by some kind of nucleosynthesis, an easier route experimentally is to find a radioisotope that emits positrons.

It does not take too long for the would-be keeper of antimatter to move to the problem of storage. If you’re going to have anti-matter, you must think carefully about where you’re going to store it.  But there is another issue.  The challenge in collecting positrons from nuclear decay begins with slowing them down. As they are emitted they are travelling at relativistic velocities. Positrons, like “regular” beta particles are emitted in a fairly broad band of energies, so slowing them down via some kind of electromagnetic trap would result in very high losses. Instead, a moderator is envisioned to bleed off speed.

Positrons do not automatically annhilate with the first electron cloud they encounter. In fact, positrons were observed early on by the tracks of ionization they left in bubble and cloud chambers. So positrons can move through matter some distance without annhilation.

Electrons and positrons can pair up to give a transient neutral form of matter called positronium. There are two forms of positronium- singlet and triplet- with the difference being the relative alignment of their spins in either a parallel (triplet) or an antiparallel (singlet) arrangement.  Singlet positronium has the shortest lifetime at 125 picoseconds and triplet at a relatively long lived 145 nanoseconds.

Back to ortho-hydrogen. Positrons can interact with lattice defects in a solid, resulting in early annhilation losses. It turns out that ortho-hydrogen at 2.3 K can be warmed to 5 K and be annealed to a single crystal structure, largely free of defects. Therefore it is possible to prepare a solid moderator free of positron quenching defects.

This is where the speakers research stands at present. The have uncovered a potential positron moderator that would be part of a collection and storage system.  The speaker freely admitted that practical antimatter storage in a container is 100 years in the future. But given the high energy densities available from antimatter, the Air Force is committing modest funds to exploring the issues.

There is work being done to study the positronium Bose-Einstein condensate. It is complicated by the short lifetime of positronium. But fortunately there are ways of storing positrons in storage rings. The annhilation of positronium as a BE condensate would afford coherent 511 keV gamma rays. This would be the basis of a gamma ray laser.