Category Archives: Chemistry

ACS Meetings

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Now that my abstract for a talk at the upcoming ACS meeting in Denver has been accepted, the reality of it has sunk in. I still have lots of data to collect and sense to be made out of it.

I resolved a few years ago that I wouldn’t go to an ACS meeting again unless I had something to present. It is very depressing to go to one of these extravaganzas and not be able to participate. One of the down sides of generating proprietary information is that you rarely get to present it at meetings to the scientific community. A negative side effect is that it appears to students and our academic colleagues that nothing much is being done in industry if the lion’s share of results are being presented by the university research establishment.

XRF Up Close

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Had the chance to visit a lab today with an XRF and a GDMS. It was very interesting. Even though I’m an organikker by training, I have to say that I really dig haunting other parts of the periodic table. Organic chemists are spoiled by the splendid richness of multinuclear, multidimensional NMR.  But when you stray from C,H,N, & O, composition and structure can become much more problematic.

The XRF samples were prepared as a lithium borate fusion in a Pt mold in the muffle furnace. The vitreous buttons were then placed in the instrument sample station. One of the problems with XRF, like any other kind of spectroscopy, is the occasional interfering peak.  But, like the famous British philosopher M. Jagger once said, you can’t always get what you want.

The GDMS was a sight. This instrument is sensitive to sub ppm levels all over the periodic table. At this level, just about everything shows up to some extent. The concept of purity becomes muddied a bit, at least for mining samples. For most things there aren’t good standards at this level. You have to trust in the linearity of the instrument and be happy with 30 % error.

Startup Failures

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Having been a part of several startups that failed, I think I can speak credibly about aspects of the startup phenomenon.  My friend Bill who lives in a state shaped like an oven mit sent a link to a blog written by a venture capitalist (VC). The long and short of it is that, according to this VC, too many discoveries reported in the biotech literature are based on very slender threads of experimental evidence and often have been performed by a limited number of people.  He ges on to lament that the nature of grant funding may contribute to an R&D style that focuses on reporting only the best looking data that supports the hypothesis forming the basis of the grant.  The basis of his commentary is his experience funding biotechstartups.

Based on my life experiences I have no doubt that his comments are reasonable.

The unspoken rule is that at least 50% of the studies published even in top tier academic journals – Science, Nature, Cell, PNAS, etc… – can’t be repeated with the same conclusions by an industrial lab. In particular, key animal models often don’t reproduce.  This 50% failure rate isn’t a data free assertion: it’s backed up by dozens of experienced R&D professionals who’ve participated in the (re)testing of academic findings. This is a huge problem for translational research and one that won’t go away until we address it head on.     –Bruce Booth, Life Sci VC.

The thing is, this phenomenon doesn’t have to be based on dishonesty, though sometimes it is.  It is in the nature of entrepreneurs to be extremely (or rabidly) optimistic about the value of their ideas.  Entrepeneurs who are specialists with some kind of standing in their field, ie., minimally having tenure or a tenure track slot at a reputable institution, can produce very convincing PowerPoint presentations and handwaving arguments to support their assertions. Especially in front of viewers and investors who are desperate to find the “next big thing”.  Finding investors is a numbers game. You simply have to go out in the big, big world and talk to a great many people. Eventually you will find people who want to invest in a startup.  It is a form of enchantment. And charismatic entrepreneurs learn early on that they can do this.

If you thought that this is limited to biotech or to academic entrepreneurs, you’d be wrong.  I’ve seen this kind of thing up close in other areas of technology. I can say that the prospect of riches just over the horizon can move otherwise sober individuals to commit significant resources to the startup wagon train. 

Especially dangerous is the entrepreneur with a patent or even a portfolio of them.  Having a patent amounts to an endorsement by the US government, or so it would appear to the unwary.  I’ve witnessed entrepreneurs collect and spend millions of dollars of investors money on nothing more than a patent based on handwaving. Remember, patent examiners do not require that you trot out a working model and run it for a while.  Before you invest, I would recommend that you demand to be shown a working model or some other hard evidence of proof of concept.

There are several ways to set up shop in the world economy. One is to steal market share. This is the better mousetrap world of “market pull”.  You develop a product or service that is superior in some way and compels customers to abandon their loyalties. You depend on taking someone else’s share of the pie.

The other way to set up shop is a bit harder. And riskier.  It is the “technology push” domain and consists of introducing new capability through goods and services.  It is more than taking a share of the pie- it is baking a new kind of pie.  This is the realm of the paradigm shift. Examples are the introduction of petroleum, electricity, vacuum tube electronics, synthetic chemistry, semiconductors, and the internet to name some of the really big ones. 

But not all technology push history is so grand. Most technology push is incremental.  Marketing products that create new capability requires early  investors and early adopters. And not everyone wants to be an early to the show.  The trick for purveyors of technology push is to get the cash flow going by selling to early adopters.

I would offer this to those who want to be involved in a startup.  Demand results from a marketing study and examine them as closely as you might the technology. If the entrepreneurs are hazy on how the sales part will look, then watch out.  If they have not included money people and marketing people early in their adventure, then the investor or employee should beware. It’s not all about the technology in the startup.  The entrepreneurs should be as focused on sales and marketing as the tech package. This is where academic entrepreneurs can be extremely weak.

Taking the dragon out for a walk

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Plan on working with HF? A friend who was president of an HF manufacturing company once gave me some valuable advice. He said there are several things to do before the plastic bottle of HF arrives. First, have a well ventilated fume hood available. Next, read up on HF first aid. Try to identify a hospital ER that could cope with an HF incident. How do you do that? You call and ask questions. Get some calcium gluconate salve.  Learn what to do with it.  If you have an incident, you will need to get decontaminated before you arrive at the hospital, otherwise there may be delays in getting teatment  by the medical staff.

Here is my personal policy. You follow your own policies. If you handle HF and do not have a specific response plan, get one in place. If you handle this acid, you need to have a plan.

Do not rely on the local fire department to know what to do.  They’ll want to take charge as soon as they arrive. Time will be lost as they ignore the staff of chemical experts standing right there while they confer on a plan. I’ve seen variants of this many times. It might transpire that the firemen will be ordered to stand clear of you until their commander has a plan for dealing with the contamination. So there you’ll sit.

Your main concern in a major splash incident is to get decontaminated.  Your lab buddies who are there with you need to know how help you with this so there is no delay in getting you decontaminated. Do not wait for the fire department to come decontaminate you. Strip off contaminated clothing and get under the shower pronto, even if you have to use your one good arm to drag yourself there.

HF is a weak acid with a pKa of 3.17.  It is somewhat skin permeable and will cause deep tissue injury.  In addition to the general hydrolytic havoc associated with an acid exposure, HF delivers fluoride which scavenges calcium and will precipitate calcium fluoride in your tissues. That is what sets an HF exposure apart. This link to Honeywell Specialty Materials is especially well written and informative.

Avoid inhalation exposure and provide for splash protection.  If you are heating it, consider using a full face respirator with appropriate cartridges when opening the sash of the hood when  handling the reaction mixture.  Wear a long rubber or plastic gloves and apron and make sure that your lab coat is non-absorbant. Be fastidious.

Don’t be afraid of HF. It is a lot like a table saw. You just have to know how to behave around it. And like a table saw, it’ll take body parts or worse from the careless or the complacent. You have to handle it carefully every single time. Be in the moment. Don’t get distracted by talkative bystanders. Pay attention to what you’re doing.

Retorting the Auriferous Spud

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Gold miners of the 19th and early 20th century had a processing advantage over todays gold miners despite all of their modern diesel powered trommels, pumps, and sluices. Some early placer miners had access to mercury or quicksilver. Auriferous fines could be concentrated in a small container with water and a few ounces of mercury would be added to extract the gold as an amalgam. Or, the concentrates could be contacted with mercury-coated copper for the same effect. Mercury coated copper pans or flat plates were often used to scavenge gold and isolate it as the amalgam.

Today, the use of mercury is strictly forbidden in mining operations around the world. But there was a time when mercury was a key part of the miners toolkit.  Many extraction schemes were developed to concentrate gold into a small package.  Panning or the use of a shaker table would provide nuggets and dust as concentrate. But often there was heavy black sand comingled with the gold dust.  Isolation by amalgamation followed by distilling off the mercury (retorting) would provide moderately pure gold.

For example, a simple retort may be made from a pipe nipple with a cap on the bottom and a top connector attached to a long condenser tube that could be cooled with stream water. The retort vessel was set into a campfire and perhaps a cloth was wrapped around the condenser tube and wetted to knock down the mercury vapors so that they could be collected in a receiver.

Curiously, there is lore about the potato retort.  My source is Eldred D. Wilson, Gold Placers and Placering in Arizona, Bulletin 168 (1961), State of Arizona, Bureau of Geology and Mineral Technology, Geological Survey Branch. In the potato retort method, a potato is cut in half and one half is hollowed out enough to accomodate an ounce or so of amalgam. The auriferous spud is wired back together and placed in the ashes of the campfire for 30-60 minutes until done. The potato is then opened to reveal a gold button in the middle. Or, so the story goes.

There were variations. Analogous to the preparation of hoe cake, digging implements were put to use in retorting duty. A potato amalgam package could be placed in a frying pan or in a shovel which would then sit in the campfire.

It’s hard to say just how effective potato retorting was compared to other methods. Admittedly, I have trouble believing that the internal temperature of the potato was high enough to do the job. It’s conceivable, perhaps, that enough Hg was cooked away to leave behind a metallic mass with some gold color.  It would be interesting to try this and then get an assay.

Wilson offers this advice- don’t eat the potato.

XRF Magic

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We’ve been looking at hand held XRF spectrometers.  If you have not been introduced to this, you may be in for a real treat. A variety of companies make them- Bruker, Thermo, and Innov-X to name a few. These things are in the low-end Lexus price category, but are they ever amazing.  It’s straight out of Star Trek.

Clarke’s Third Law states that any sufficiently advanced technology is indistinguishable with magic. I gotta tell ya that these hand held XRF’s are just amazing.  You point at a sample and it gives a tally of the elements present, or most of them at least.  Some even have a built-in GPS you can punch to take a waypoint of the location of the sample you just analyzed out in the field.  It is a great tool for mineral prospecting.  

What is embarrassing is that this is the first I’ve heard of it. Our geologist friends have been using these things for a while now. 

The whole thing depends on a miniature X-ray source.  I’ve been looking into this.  For the curious folks out there, lithium niobate- LiNbO3- is a very interesting material.  Crystals of LiNbO3 have the property of pyroelectric potential. A pyroelectric crystal is one that is able to generate a polarization across the crystal faces in proportion to the temperature.  A pyroelectric xtal placed on a heating/cooling block in a vacuum is able to generate a stream of electrons energetic enough that, when stopped by a copper electrode, will generate x-rays. 

One manufacturer, AmpTek, produces a miniature x-ray unit called the Cool-X that has a photon output equivalent to two milliCuries, with 75 % of the flux less than 10 KeV.  Elsewhere in the product literature, the output is described as 5 milliSieverts per hour.  So, the user has to be a little careful with this thing. But rad safety issues aside, this is quite an amazing source. The product literature doesn’t come out and say what kind of crystals are used, but they may be a tantalate salt.

AmpTek Cool-X

The unit does not operate continuously. It can only generate x-rays durig a thermal cycling period, The xtal starts out cool and as it’s heated, generates the electron flux that is de-accelerated by impacting the copper to produce the x-rays. The lit gives a cycling interval of 2-5 minutes.  It is referred to as a Kharkov X-ray generator.

It’s magic.

Materials of Construction

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One of the things you have to consider when scaling up a chemical process is the composition of the wetted or exposed surfaces in the reaction vessel, associated feed piping, gaskets, and overhead vapor  spaces.  Common materials of construction subject to wetting are steel (various types), glass, Hastelloy(s), tantalum, titanium, PTFE, Viton, and various polymers found in hoses.

Metal batch reactors are subject to erosion over time. Vessel walls can be tested for thickness periodically. Glass coated reactors are very useful for their broad applicability to many kinds of reactions, but have drawbacks of their own.  Glassed vessels are sensitive to very high and very low temperatures as well as thermal gradients across the vessel wall. It is possible to crack the glass coating and have it flake away, exposing the underlying metal to corrosion.

We are all trained to do chemistry in glass reactors, but it should be pointed out that much chemistry can be performed in steel vessels. While you want to give some thought to the use of hydrogen, for the most part metal pots are well suited for reaction under neutral or reducing conditions. That is, metal hydrides, Na, carbanionic species BuLi and RMgX, alkoxides, etc., are well tolerated in wetted-metal pots.

Oxidizing or acid halide producing reaction systems are problematic for metal pots, however.  Acidic corrosive reaction mixtures can attack the wetted metal parts of the reactor system. Acidic chlorides in particular are quite corrosive to various grades of steel. It is especially problematic when you’re talking about shell and tube condensers. The tubes are often very thin for good heat transfer, leading to the possibility of the introduction of chiller fluids into the reactor if corrosion chews through the tubes.  If the chiller fluids are protic and the pot is full of MeLi, then the batch may be lost or an unplanned reactive hazard event may take place.

Condenser surfaces can be subject to more corrosion that you realize. This is the location where hot concentrated corrosive gases will condense, after all. To extend the life of the condenser, special materials of construction may be used. Tantalum and PTFE can be used when the cost is justified. With exotic materials of construction come exotic prices.

There is more to consider than corrosion.  Polymer transfer lines will generate static electric hazards via the isolation of charge on nonconductive surfaces. Tranferring hydrocarbon solvents from a drum or cylinder to a reactor through nonconductive plumbing can generate significant hazardous energy and certainly enough to be incendive. Grounded metal piping can prevent part of this problem.  However, discharging a flammable liquid into an air filled space may lead to an incendive discharge as well. It is important that all atmospheres over flammable liquids be inerted. While you may not be able to stop static discharges, you can certainly keep the fire triangle for being formed.

Operators are often alarmed by the sight of a glassed reactor with stirring toluene in it generating sparks by discharge through the glass coating.  While this may be hard on the glassing by forming pinholes, unless there is an explosive material in solution, the lack of a complete fire triangle means that the sparks cannot lead to ignition of the toluene.

Remember not to take your material to high viscosity or dryness in a large reactor. You might end up rolling your solid material into a giant bowling ball and bending your agitator shaft.  Maybe even slamming it into the reactor wall. A very expensive mistake.

Of Limited Brain Bandwidth

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At some point a person has to decide that he/she is involved in enough activitites in life. This uncomfortable world of overcommitment is where I have been for a while. I’ve come to the realization that my consciousness has limited bandwidth and that intellectual stimulus can overload it in ways that are hard to recognize. 

Having been born with lots of curiosity, I find myself piqued by a great variety of things in the universe.  The sciency stuff is obvious. But there are other things that can consume much of my capacity for attention.  It is much like an addiction to a drug. One soon becomes accustomed to a high baseline level of stimulus.  As boredom sets in,  the brain seeks greater stimulus. I can’t bear to wait 5 minutes without something to read. Cable television and the internet takes full advantage of this.

Last weekend I found myself totally immersed in the Free Electron Gas theory of metals. As I was wrestling with the math my family was out shopping and having fun. I was having fun as well, but it was of a more cloistered form. Was I being selfish? I think the answer is yes.

So, this life of intellectual pursuit can spin into a solitary life.  I like to joke that some days I’m misanthropic and other days I’m very misanthropic. That’s not exactly true, but I will say that my patience for unstimulating conversation is limited.  It comes down to the fuzzy boundary between ambition and obsession.  It is very easy to slip into a condition that is referred to as eccentric.  I can see how it happens. Maybe it is too late.

Extractive Metallurgy as Inorganic Chemistry

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I am involved in an extractive metallurgy project 1 day per week give or take.  So I have been trying to take apart undesirable minerals in an ore to concentrate the desired metal. It’s called beneficiation- a word introduced by Agricola in his book De Re Metallica published in 1556.  I can’t disclose what the desired metal is.  Suffice it to say that it is rather scarce though not a coinage metal. 

What really amazes me is the disconnect between what many of us think of as the field of inorganic chemistry and the field of extractive metallurgy.  In my training as an organikker, I had never been exposed to extractive metallurgy, nor did I even know what it was.  Turns out that it is a field of applied inorganic chemistry. In this field, a metallurgist is the person who figures out how to extract desired metals from ore.  Nobody seems to call them a chemist, at least to their face. They’re the metallurgist.  No doubt there are exceptions.

Well, that clears things up quite a bit. I feel better getting that off my chest.  I’m sure any wayward metallurgist who happens upon this site has already begun to laugh. Extractive metallurgists do synthetic inorganic chemistry. It’s just that they prefer to keep company with a gangue of engineers and geologists rather than those who don’t work with minerals.  I can relate.

On the Digestion of Rock

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A rock consists of one or more minerals that may be held together by a cementitious binder. Or a rock may be a continuous mass of interlocking crystalline domains.

Igneous and metamorphic rocks are comprised of crystalline phases compacted into an inhomogeneous mass. Amorphous phases may be found as well.  Sedimentary rocks are often made of distinct mineral grains or pebbles held into position by cementitious matrix. There is a great deal of variety to be found.

The point is that rocks may have quite complex compositions. If the goal is to use rock for construction, then the composition may not be that important as long as some minimum structural attribute exists.  

But if the goal is to extract specific components from a rock, then the details of composition become very important.  Rock may be made of simple inorganic compounds.  Good examples would be calcium carbonate, sodium chloride, or calcium fluoride.  These substances are often found in crystalline form where the crystal consists of cations and anions which are free to solvate in the right solvent system and dissolve. These kind of minerals may be very weak structurally and subject to easy fracture.  The geological fate of such minerals is often aqueous transport and deposition to some location where a new mineral may precipitate from component ions in solution.

Some rocks may have appreciable fractions of monomers like silicate and aluminate. Monomeric components are able to form polymer networks which have a large effect on many properties of the mineral.  Glass and quartz are silicate network polymers that form rigid matrices. Silicate has 4 attachment points in a tetrahedral array that can form a variety of  linkages.  These matrices have properties like elevated melting point and rigidity that add or detract from the value of a given material. 

Quartz is a pure SiO2 network whereas soda glass contains network terminating additives that alter the connectivity and lower the glass transition temperature and melting point of the material. The additives lend workability to the glass. Chain and network termination no doubt has a major influence on the physical properties of rock.

Most metals are found in nature as an ionic compound in various oxidation states and charge balanced by simple anions like oxide, sulfide, or a halide.  Metal cations may also be associated with complex, polyatomic anions like sulfate, molybdate, tungstate, silicate, aluminate, and a few other oxidized species.  A few of these polyatomic anions, especially silicate, are held together with substantially covalent bonds. So their network polymer compositions may be very high melting and difficult to mill.

Extraction of desired metals from a rock will follow a path depending on the the type of mineral present. Rocks made of an ionic compound and not subject to network connectivity maybe susceptible to chemical attack and dissolution.  Treatment with strong acids or various fluxing agents may cause the digestion of a rock under less than drastic conditions. Such rocks maybe susceptible to weathering as well.

Rocks with substantial polysilicate or polyaluminate compositions are rather more difficult to digest. For the same reason glass resists most chemical attack, so too do silicate and aluminate minerals.  But substances that attack glass and alumina may also be useful in digesting rocks high in silicate and aluminate. In particular, hydrogen fluoride stands out. This acid is well known to attack glass by breaking the Si-O bond and making an Si-F bond due to silicons affinity for fluorine.  Digestion of silicate minerals with HF or ammonium bifluoride (NH4FHF) has been known for a long time.  The use of disulfur dichloride (S2Cl2) has been reported as well.

Silicates and aluminates are also susceptible to attack by hydroxide or carbonate.  This is often taken advantage of in the lab through the use of a muffle furnace and crucible. Digestion of a rock sample is affected at high temperature and the resulting digested material is then treated in a manner as to allow the separation of the metal as, for instance a hydroxide or carbonate that can then be ignited in the muffle furnace. This time a purified metal oxide is formed and weighed to give a yield or wt %. Metal oxides can usually be dissolved in aqueous acid and subjected to a variety of tests thereafter.