Category Archives: Chemistry

Bloggenvolk

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It would could be fun to meet other bloggers at the ACS meeting in Chicago.  Eventually we’re going to have to have some kind of official (ACS sanctioned) function where bloggers can get together at these meetings.  We’re all driven to write about chemistry in one way or other and I’d say, for the most part, we’re all smitten with this science.  Chemistry bloggers are science writers.  We write because we are driven to do it.

It would have to be done in a way that is not threatening to anyone.  Basically we’re all anonymous writers.  I suppose that fact could be viewed as kind of creepy in some way- I don’t want to run into some wacko either.  But wouldn’t it be fun to sit with other bloggenvolk at the convention hall and chat?  I think it could be lots of fun. The pseudonym stuff wears thin. 

Eventually it’ll happen. This mode of communication isn’t going to disappear anytime soon.

New Failure Modes

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Chemistry can be very humbling.  A person can be absolutely sure of how a new reaction or process will turn out and yet be absolutely dead wrong.  Process research is an engine that consumes dollars and churns out new failure modes in one big pile and positive results in a smaller, steaming heap. 

I have been working with ionic compounds that have weakly coordinating anions.  I’m finding that my finely honed intuition built from years of shame, suffering, and cruel humiliation is turning up flat wrong more times than I care to admit. A house of cards.

More than a few of these compounds seem to participate in the formation of a liquid phase in the right combination of solvents.  If I were keen on monkeying with ionic liquids, this would be just dandy.  But the product is a solid and I want to purify it by xtallization.  I’m tempted to categorize these liquid phases as clathrates, but I’m unclear if the definition will acommodate such a thing. In each case, a normally miscible solvent pair is required to split out the new phase when the weakly coordinating ion pair is dissolved in the more polar solvent. 

There is a happy ending to this.  I was able to isolate solid product from a 2-solvent system, but sadly, I would be hunted down and shot like an egg-sucking dog if I disclosed it.  Bummer.

UV-Vis Spectrum of POM Pomegranate Juice

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Below is a link to a UV-Vis spectrum of POM brand Pomegranate Juice.  The graph shows two spectra- one is a simple dilution of POM-brand pomegranate juice. The other, lower extinction, spectrum was a simple dichloromethane (DCM) extraction of undiluted pomegranate juice as it comes out of the bottle. The extraction was done with a 1:1 v/v ratio of DCM to juice. Notably, the DCM extract contained no visible color. The layers emulsified and had to sit for ~10 minutes to separate. The DCM extract was dried over a bit of magnesium sulfate and filtered.  The undiluted extract was submitted directly to analysis. The dashed curve is the spectrum of the extract.

What is interesting about the extract is that the absorption maxima do not align with the maxima of the whole juice.  The DCM soluble fraction is quite different electronically from the balance of the components. Indeed, the extinction drops off to 0.026 by 350 nm and drops to near zero thereafter.  It is important to note that the absorbance of the extract is based on a much more concentrated solution, so a direct comparison of absorbances with the highly diluted whole juice is not valid. Focus instead on the wavelength of the maxima.

I ran the spectrum of the whole juice as a 500 to 1 dilution in distilled water.  No attempt was made to buffer the pH of the water or to filter the juice. I fully realize that there are experimental control issues to contend with here- i.e., pH dependence, turbidity, oxidative degradation due to air exposure, etc. 

POM Pomegranate Juice UV-Vis

According to the literature, pomegranate juices contain varying amounts of polyphenolic, tannin-type species not just from the juice, but also material that is released from the rind in the pressing process.  So further experiments should try to obtain juice that is pressed in a way to discourage the inclusion of materials from other plant tissues.

According to one source, the components of pomegranate juice can stabilize the level of PSA in men who have prostate cancer.  Whether it works via the anti-oxidant properties or some other more specific interaction is unclear.

Just what is the point of running these spectra?  My original interest related to the visible part of the spectrum. I wanted to know what the visible spectrum of this intensely colored juice looked like.  What is evident is that for all of the extinction in the visible part of the spectrum (>350 nm), the UV band is much more intensely “colored”. That is, the extinction is much higher in the UV range (<350 nm). Why UV-Vis spectra?  Because, silly, I don’t have an NMR. But I do have a UV-Vis spectrometer.

Well, that’s not quite true. I can run a proton NMR of the crude material, but given that pomegranate juice is a plant fluid, all I’m going to see is a forest of peaks.  Actually, more to the point, others have isolated components from this fruit.  My interest is in the reduction capacity of the pigments.

Extracting structural data from a UV-Vis spectrum is not really possible. UV-Vis spectroscopy is about electronic transitions and a wide variety of species overlap appreciably, so structural determinations of components in complex mixtures is out of the question.  Furthermore, pomegranate juice is sensitive to oxidative degradation and is likely to be quite sensitive to pH (next on the agenda), so it’s thermal and O2 exposure history may be important (i.e., has it been Pasteurized, etc).  So it’s back to the drawing board.  

Lanthanide Contractions and a Dog’s Lunch

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The rare earths are a curious group of elements from the commercial point of view.  There are a variety of lanthanide products available from a handfull of vendors, most of whom cater to a small group of users. Some of the catalog houses have respectable collections of them.  My friends at GFS offer lanthanides- specializing somewhat in cerium products.  Aldrich, Gelest, and Strem, of course, offer a variety of rare earths (RE). Hard to say if they are big sellers-I’m guessing they are on the slow side of the 80/20 rule.  I’m aware of a single American company that actually refines Scandium Oxide and manufactures Scandium Triflate as well. They are one of the few, if not the only, companys in North America that refines any RE’s. Most everyone else imports from Estonia, Russia, or China.

From my perusal of the literature it seems that the field partitions roughly into reagents for chemical transformations and oxides for material science.  The material science side is way beyond my reach, so I’ll pass on that segment.

The least expensive and most basic RE products are the oxides. If you spend some time shopping around for various RE’s, what you’ll find is a sliding scale of purity specs, 99%, 99.9%, 99.99%, 99.999%, etc.  If you look even closer to the specs, what you’ll find is some sleight of hand in regard to what the number of nines actually represents.  Most vendors will offer a number of 9’s that are TREO, Total Rare Earth Oxides. So if you are keen on Scandium Oxide, 99.99 % (or 4N), chances are that the 4 nines really represents the total of all of the RE oxides present.  In reality, 99.99 % TREO Sc2O3 will be 99.9 % in Scandium and the balance of the 4 nines is a dogs lunch of Ln Oxides. 

As we all know, when you analyze for more and more 9’s, you eventually find most of the periodic table present in your material.  But if you really want 99.99% in Scandium, it can be relatively hard to sort from the TREO products.  You are forced to swim through spec sheets to find material that meets your need. BSC offers 4N in Scandium, and some others do as well.

One of the interesting applications of RE triflates is as a water tolerant acid catalyst.  Essentially all of the RE triflates have been reported, with the possible exception of Promethium. The lanthanides show a general decrease of ionic radius as one increases atomic number. This is the lanthanide contraction. It has been shown that the catalytic activity in certain acid catalyzed reactions (i.e., with a Ln(III) triflate) correlates with the charge-to-radius ratio in this group.  Not surprising, I suppose. 

So, for an ambitious person with designs of bringing rare earth reagents to the marrket, this is a classic “technology push” situation.  In order to convince people to buy RE triflates as acid catalysts, you first have to offer a value proposition.  They can use conc H2SO4 or they can use Yb(OTf)3 as an acid catalyst. Hmmm.  So which is cheaper in my application?  Given the sparse literature on Ytterbium Triflate chemistry, for instance, it could be hard to convince a customer to adopt your RE product beyond R&D use.

So, whaddaya hafta do to sell a boat load of this stuff? You probably have to come up with a killer application for the RE Triflate to convince people to buy it and try it. If you as the purveyor lack this application, they you have to rely on the customer to do it for you.  In the mean time, you could get very hungry.

Halogenate with extreme prejudice

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Reacting one element with another to make a compound. How much more “elemental” can it get? No solvent and no waste, just element on element at Venusian temperatures. But, an organikker doing inorganic synthesis?  Is this a Coen brothers movie? What strange overlap of events lead to this redox redux?

Paracelsus would have been pleased at this transformation, though his interests with this compound might have diverged from mine. Whereas I as a modern chemyst would add a nucleophile to my blessed conjugation of elements, Philippus Theophrastus Aureolus Bombastus von Hohenheim (Paracelsus) would probably have more mundane applications like the treatment of consumption or perhaps an indelicate medicament for that tell-tale abscess.

After a career of conducting elaborate procedures for the preparation of strange organic compounds, it is refreshing to spend a month performing a non-incandescent combustion of elements.  There is joy in doing a thing well, taking the elements to their endpoint as fast as the equipment will allow. Squeezing maximum performance from the system and myself. It is a kind of poetry in motion. 

Frequently wrong, but never in doubt

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More and more I find myself afflicted with fellow travellers along the timeline who are never in doubt of their judgement, but they are frequently wrong nonetheless.  There has to be some archetype from literature or Greek mythology that symbolizes this. Maybe there is some character from a Greek tragedy who, as a leader, was destined for a fall as a result of such a trait. Perhaps someone out there has a nominee for this position.

One sees examples of this in business organizations not infrequently. Some openly discuss their views, but often with the presumption of making a disclosure of “what we’re going to do”.  Others sit quietly, rarely contributing to open discussions where ideas are put on the table for dissection.  These fellows might listen to others debate, but they prefer to sit quietly and observe while others reveal the content of their thinking. Rather than adopt or synthesize new concepts openly, they will tend to note commentary that aligns with their pre-existing view. This is where that most loathsome of characters, the yes-man, can gain a strong foothold in an organization. 

Howard be thy name

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A few posts ago I wrote about buying chemicals from Asia. I mentioned the weakness with shipping. But there are other snags in the system to contend with.  Recently I received a parcel of non-hazardous material that I bought from China. I have been trying to source this stuff for years and I finally found a candidate vendor. We already make the stuff, but we’re short on capacity.  The qual sample was a white granular product and was packed in thin plastic zip-lock sandwich baggies jammed into a used stereo speaker box (!!@#*!). Hell, the foam part for protecting the speaker was still in the box. OK, not smart. And it was mislabeled as some other product. That was the really dumb part.

Torqued about this, I fired off a grim and terse torpedo-gram expressing my shock and dismay at their poor judgement in these matters.  The vendor rapidly replied, exclaiming in much poorer English this time, that since it was a colorless solid product, they believed there would be “problems” shipping it to the USA.  Well, let’s see … hmmm.  It is TSCA listed, it is non-hazardous, no conceivable abuse issues, it is a salt so it won’t burn, but if you dropped a 200 kg drum of it on a cockroach, the cockroach might die.  Yeah, they thought it would be suspected as an illegal substance so they would be clever and ship it under another name. But it is ACS grade material completely innocent of any conceivable abuse potential.  So by being “clever” about it, they revealed their facility with underhandedness.  How can I go forward with a vendor willing to do this crap?

So, you might be tempted to think “Golly, they’re some pretty dishonest chaps”. Well, I’m not sure yet. They may be redeemable. Thank Howard, I myself have been given many second chances. It’s a karma thing. So we’ll inch along and see how they do on the next round. I suspect they’re just naieve in these matters.  Never attribute to malice what you can first explain by ignorance.

Moral of the story- just be honest and above board in all of your business dealings. Ya can’t fall off the floor.

Update:  It was suggested that this is actually a ploy by the exporter to get around import duties.  Well, I’ll happily pay the duties rather than monkey with this sort of thing. Crimony.

Chemical Logistics

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Any chemical company manager will have to admit that order fulfillment isn’t over until the product is in the hands of the customer.  Chemical manufacturing isn’t just about running reactions in big pots.  It’s about attracting a skilled, reliable, and safe work force. It is about building a supply chain for the timely delivery of raw materials. It is about executing the manufacture of products in spec the first time through. It is about warehousing raw mats and products and keeping the stream of wastes moving through the system.

Chemical manufacturing requires the careful management of cash flow by minimizing costs and maximizing profits. The business office must attend to receivables and collect payments in the most expeditious way that customers will tolerate. This is no different that any other manufacturing arena- sprockets, fur caps, or rocket motors.

One of the key jobs required of any chemical company is the matter of managing logistics.  That is, managing the timely transport of raw materials onto the site and the transport of products off the site. So how does this affect the chemist??

The tender shoot studying chemistry in their junior year of college may not know it yet, but if their path is in the fabulous world of business, then some aspect of logistics may be in their future.  What kind of chemist would need some knowledge of shipping? Well, project managers, sales managers, business development managers, plant managers, procurement managers, etc.  All these positions are often filled with chemists and all have to have some knowledge of this topic.  And how does one get this knowledge? Why, on-the-job training, of course.

If you have read many of my posts, you know that I tend to prattle on about this. There is a reason. It is not uncommon for a sales person or a business development manager to spend no small amount of time with a customer trying to work out how the product will be delivered.  The transport of materials is complicated in proportion to the hazard and the chemical sensitivity to decomposition. 

Let’s say that you are in the chemical business and you are just starting the custom mfg of a trialkylphosphine.  The customer will state that they want say, 100 kg, of their R3P with a list of specifications (e.g., 99% in R3P, oxides < 0.1 %, etc, Karl Fisher water 200 ppm) for their new product. The customer has accepted the quoted price and the delivery date. Hmmm. Price, delivery, and specs. Sounds like everything is in place.

So, the question then arises: How are you going to ship it? Glass bottles? Drums? Polyethylene totes? Whoops, the material is excruciatingly air sensitive, so charging and discharging the product will have to be done airlessly. Sounds like a cylinder is just the thing. But what are the materials of construction? I seem to recall that phosphines are ligands, so can we really use a steel cylinder? Soft steel? Stainless steel?

But there is yet another question.  Do we offer the phosphine neat or as a solution? If the neat R3P is a liquid, we can move it around airlessly and charge a cylinder with it. If it is a solid, then it could be a serious problem to transfer it from a filter to a shipping container. How will you or the customer actually handle it? This is the kind of detail that chemists might find themselves groping with. If it is a solid, the customer might have to consider receiving it as a solution in a non-interfering solvent.

Then the matter of transporting it arises. In the present epoch of security theatre, air transport of any quantity might be banned. So, surface shipment will be needed. The matter of heated shipment may arise if freezing or precipitation is an issue. The last thing anybody needs is a cylinder full of precipitated solids in it.  Remember, if you are shipping product in a heated trailer in the winter, you may have stiff competition from other customers who need to ship their lettuce or strawberrys. In some locations, reefer trucks as they are sometimes called may be in short supply.

OK. So you’ve specified a reefer trailer for heated transport of the goods. Let’s say that the product solution will crash out precipitate at 15 C. In the trailer everything is just fine. Fine that is until the shipper reaches a transfer point and moves the product out onto the loading dock where it sits in the freezing weather for a few hours waiting to be put into another trailer. Or it sits in unheated warehouse space for a while.

Eventually, the cylinder of R3P solution arrives and, sadly, has precipitated and won’t come out of the cylinder. So there you are. The customer is unhappy and you now face having to haul it back and recover the product. These are the kinds of problems that chemists on the business side (the plow horses) can find themselves dealing with. Of course, the R&D chemists (the show horses) are rarely bothered with such things.

On Extracting Abstractions from the Abstracts

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One of the chores that must be done when developing a new technology is “Due Diligence” as applied to intellectual property.  In the fabulous world of industrial chemistry, there is an overlapping of the three great magisteria- Business, Chemical Science, and Law.  In order to get a new product or process on stream, we must find a line of sight through the many hoops and past the many gatekeepers of those magisteria that can obstruct our path the fame and fortune. 

First, allow me to pay homage to two great and wondrous database services- the United States Patent and Trademark Office (USPTO) and Chemical Abstracts Service (CAS).  They are the custodians of data generated by some of the most cantankerous and unruly people on earth- lawyers and chemists.  Their task is complex and effectively endless. 

In actually trying to do a reliable due diligence analysis, a searcher must ascertain that a proposed bit of IP does not conflict with claims in valid patents owned by others.  In a chemical IP search, one can divide the claim universe into 2 domains- composition of matter claims and process claims.  In the patent, the first sentence will state whether a composition is being claimed or that a process is being claimed. Some patents have both composition claims and process claims.

So here is the problem.  Let’s say that you are trying to determine whether or not you have the right to manufacture a particular molecule. This apparently simple question actually deconvolutes to two fundamental questions: 1) Is the composition of matter in the public domain? And, 2) are there claimed processes for it’s manufacture? 

There is a third domain and that relates to the use of the composition.  However, this does not impinge on the right to manufacture the material, just it’s use.

If the material is claimed as a 1) composition of matter in a valid patent, then you cannot lawfully make it or possess it (for commercial use, though precendence is being set for a bar on R&D use as well) without the permission of the assignee of the patent. Note that the owner of the patent is the assignee, not the inventor(s). If the composition of matter is not claimed, then it is in the public domain, assuming that you did not learn of it under trade secrecy. 

So, let’s say then that your target material is in the public domain. Now the question is 2); does your proposed method for its manufacture infringe on claimed methods? This may be a hard or expensive question to answer, and the reason is plain.  When you execute a search for IP issues related to a substance, you search path is limited to fields, key words, structures, CASRN’s, etc. that are flagged in the major databases. 

A CAS search on a given compound will lead to patent families that mention the compound, its preparation, or its use. But you have no way of knowing whether the patent reference claims the composition, its preparation, or its use.  It could very well be that there are no claims pertaining to the compound of interest- it was just cited as an example of some sort.

A CAS search is highly accurate in terms of the focus on a particular compound.  However, a USPTO search is not. A chemical search of the USPTO public database (USPTO.gov) is pretty much limited to a search for specific character strings.  It is possible to narrow down the scope of a search by concentrating on classification numbers, but I have never been convinced of its thoroughness.

After all of this set up, here is my point.  The problem we all face in doing our IP due diligence is that there is no direct means for determining from an indication in a database search report whether or not a composition is in the public domain. A CAS search will not yield a clear yes or no, and the USPTO database search only retrieves hits that have the requested strings.  Despite the advances in database technology, the user still has to collect all of the patent citations pertaining to the material and sift through them and interpret the claim language. 

Wouldn’t it be useful to the public if an applicant for a US patent were required to collate the claimed compositions for uplink into a database?  With such a “field” in a CAS or Beilstein search, you could tell in an instant if the composition was claimed. The same argument holds true for processes.  At present, the “retrievability” of claimed art is poor.

Patent attorneys are likely to object along the following arguments: not all patents that you retrieve from a search on CAS or USPTO will be valid.  Some patents will have expired naturally, others will have expired for non-payment of fees, and still others will have serious weaknesses that will only be apparent from an examination of the prosecution history as revealed in the file wrapper.  Abandonment may be difficult to detect for abstracting services, as would flaws in the prosecution as documented by the wrapper.

Another objection that is unlikely to be openly identified is the matter of clarity.  There is may be advantage conferred to assignees when a claim is a bit fuzzy.  This may afford some manuevering room during an infringement action, though it might be hard to say who the beneficiary would really be. I would estimate that whomever had the most persuasive attorneys would prevail.

It would be interesting to hear from others about this matter.