Category Archives: Chemistry

Reading, searching, researching, and writing. My life as a chemist.

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It turns out that I like Russian fiction. On a lark I picked up a collection of short stories by Nikolai Gogol on Amazon (ISBN 978-0-14-044907-5). It was worthwhile. 

Actually, it wasn’t such a lark. I was looking for a copy of Diary of a Madman.  The idea was to find a cutting for an audition, in case such an opportunity arose.  Gogol’s Diary of a Madman and The Government Inspector have been performed for generations and, as usual, I’m the last of my age cohort to read it.

I spend my days supervising chemical research, doing reactive hazard studies and IP analysis. From the job description point of view, I’m a walking, jabbering freak. How the hell am I going to get a job elsewhere with a resume like that? HR will look at it and, failing to find an exact match in their organization, toss it into the discard folder.  I don’t fear chemicals, but I do fear HR.  HR is the bane of our profession.

Back to the day job, these areas are basically writing activities and occur at a desk. It has occured to me that working at a desk is more dangerous than working with chemicals.  You soon get fat(ter) and stressed. It’s not good. 

It is funny how job descriptions differ. Many colleagues have jobs where they execute some task by bringing something into a predetermined structure. By that I mean, an analyst performs a standard procedure or the QA manager documents data for a product cert. An accountant performs procedures in the general ledger according to rules. Their work is reasonably well defined and they know when they are done.

Not a single thing I do is amenable to this kind of structured performance.  The chemistry stuff is experimental and involves sorting out what the hell happened. That’s just the nature of applied scientific investigation.

The IP work involves searching for information. If you find a relevant patent, well, you might be near the endpoint. Lucky day. But if you don’t find claims on a composition or a process, it’s a negative result. You have to ask if your search strategy was adequate. Anyone who has used a search engine knows what I mean. Sometimes, you don’t pick the best search terms and you come up with junk. Eventually you blunder into the right term and find the mother lode.

Sometimes an information search becomes dendritic. You find yourself bobbing along in the brackish waters of the “merely interesting”. So, you back up and revise the search terms.  Doing an IP search for an exact composition in CAS is very straightforward. A structure search or a CASRN search is very reliable and fast.

Much time can be wasted with patents that use compositions or processes but do not claim them. In particular I mean patents that mention compounds in the description (or specification) but do not claim them in the claim section.  A great many patents may be served up in the list of hits in this way. How you deal with this depends on what you want and what kind of search tool you’re using.

If you are interested in a class of compositions or the range of technology that might be out there, this is a kind of search that is more dendritic and subject to stranding in cul de sacs. If you do not use Chemical Abstracts Service in some way, your options become restricted.  There are many IP services that tap the various patent offices around the world. Some seem to have their own databases. Many seem to focus solely on searching the patent data through clever use of search terms or the patent classification system. For prior art searching, this is inadequate. For the most part, only CAS can provide reliable hits if a compound was reported in Acta Retracta by Professor van Wingenheuk in 1907.

After a day of reading abstracts and patents, it’s nice to read something well written and get lost in it for a little while. Patents are not written to be easily understood. They are often masterful in their obfuscation. I often admire the conciseness with which many are written. But in the end, they are all disclosures written grudgingly and with the intent to obscure.

Memo to Aldrich, or ahem, SAFC

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[Note: The rest of you can go about your business. This memo is to whomever at SAFC will listen. If you’re not SAFC, click here or here.]

Dear Aldrich, or shall I say SAFC?

I have a bone to pick wth you. I’ve noticed that the bottles of reagents I have received from you in the last year have been labeled with a newly formatted design. The Aldrich bottles do indeed stand out on the shelf in resplendent red and white as designed. Well done. The bottles function in the manner in which they are intended. Again, well done. All of that is as expected.

What I’m unhappy with is the fact that the labels all seem to lack the molecular weight of the contents. Having grown accustomed to finding the MW on the bottle, I now have to set the bottle down in the lab and reach for the calculator to do it myself.  After decades of using Aldrich products with the MW printed on the bottle, my addled brain now has to unlearn this and do the calculation myself.

So, what caused this? It was not an accident, was it? Were there complaints about printing errors that twittered your legal people?  Were there a series of meetings in which serious senior managers furrowed their brows and intervened over the possibility of liability? Nothing like the mention of liability to get a VP agitated.  Perhaps ink has gotten expensive.  I just don’t understand.

Was it one of us who complained? Was it some white-coated laboratory fussbudget? Did some crabby pisswink from “out there” write a letter and frighten someone in St Louis or Milwaukee? That would be sad.

One more thing. Why does the font size have to be so small on large labels? 

Th’ Gaussling

Helium

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With uptick of natural gas exploration and “recovery” happening, you have to wonder if anyone is bothering to look for helium in it? And I’m referring to the Marcellus shale formation in particular.  Wouldn’t it be nice for some forethought here and try to recover some of the helium that may be lost.  Helium is a non-renewable resource and is critical to many industrial sectors, including superconductor applications.

The US has held helium in reserve since 1925. Helium extraction has been most fruitful from gas wells in the western states. The Helium Privatization Act of 1996 has resulted in the release of the helium reserve to the private sector at a federally mandated price. The FY2011 price is$75.00 per thousand cubic feet.  

According to the BLM, the agency that manages the strategic reserve, their enrichment facility in Amarillo, TX, can produce 6 million cu ft per day of crude helium at ca 80 % purity. The Amarillo plant provides crude He to refiners who polish it to the necessary level of purity for the end user.

A Homily on Extractive Metallurgy

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In the last 6 months I have learned a bit of what extractive metallurgy is about. One of my projects involves isolating an element from an ore where the desired element is one of many minor constitutents. What is important here is the term “minor constituents”.  When the desired element is a minor constituent, then one necessarily faces the prospect of processing large quantities of mass.

Processing large quantities of mass requires that the material and energy inputs used in the process must be very inexpensive. Except for gold, you have to start thinking of heat as a kind of reagent that can be applied to make things happen. The lucky circumstance with gold is its affinity for cyanide in an oxygenated aqueous environment.

It is a very interesting and worthy challenge to start with rock and contrive to remove purified products from it. Half of the fun is working with the engineers and metallurgists. They have a very different perspective of industry than a stiff like me who has always relied on Aldrich for “raw materials”. I have had to recalibrate a bit. You don’t meet people like this at ACS meetings.

I have spent more than a little time digging into extractive metallurgy from the 19th century.  A good deal of fairly sophisticated technology was worked out long ago for many metals on the periodic table.  Mostly, what has changed between the metallurgy of yesteryear and today is that we now consider fairly low grade ore as economically viable. 

The tailings of yesterday will become the ore of tomorrow. It just depends on the value.  When you drive around the gold and silver mining districts in the Colorado Mineral Belt, the tailings that you see from the road have most likely been worked over at least once.

The View

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I don’t know where others sit in the chemical industry, but the view from my chair seems encouraging. The market is abuzz with activity. The chemical industry and the people who run it are, well, rather stodgy.  So to see lots of rfq’s flying around the ether is encouraging.

Every day I wake up and thank whomever will listen that I did not go into pharmaceuticals. There is a vibrant world outside of pharma and I’m glad to be in it. Those of you in pharma, I’m honestly happy for you. I’m relieved that so many bright people dig that brutal business.  But for me, I’m glad I let that bus go right on by.  The public corporation GMP life is not for me.

I have a PhD and a post doc in asymmetric organic synthesis. It was interesting at the time and admittedly hard to let go of, but I have few regrets today. If I’d have stayed in academics, I be teaching my 18th year of 2nd semester organic or (*gulp*) general chemistry and doing battle over meager and diminishing departmental budgets. That is, if I had survived student evaluations. What dipshit thought of student evaluations as a tenure and promotion metric?  The little punks should be grateful to be sitting in the classroom. Well, ok. That was a bit harsh.

I think the best part of having a background in synthesis is that you become very mechanistically oriented. Latent and blatant functional groups bristle and are pregnant with possibility. The ability to make a good stab at what happens when two molecules interact is a very powerful thing and I’m grateful for what little I can do.  And if you think that is false modesty, just try to go back and make sense again out of ligand field theory or lanthanide chemistry. Chemistry is a big field and much of it remains unfamiliar.

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.