Category Archives: Science

ChemSpider Magic with LASSO

Of late I have been concerned with R&D information and various homebrew means of storing it and retrieving it. Institutionalizing R&D results into easily accessed knowledge can roll into a real hairball if you’re not careful. More on that another time.

My adventures with CHETAH 9.0 have caused me to look deeply into SMILES strings and what utility might be found there. This lead me to rediscover ChemSpider and the many services it provides for free to the user.

Consider the following: if you generate a SMILES structure of acetylsalicylic acid, say, from Chemdraw, O=C(O)C1=C(OC(C)=O)C=CC=C1, and use this character string as a search term in ChemSpider, it will take you to the entry for aspirin. What you get is a treasure trove of information on this substance. Go to ChemSpider, cut and paste the above SMILES string into the search box, and let her rip. I’m not your Momma. Just try it.

The breadth of references is encyclopedic.  But the truly amazing part is found when you scroll to the end of the page. There is a drop down window for SimBioSys LASSO. ChemSpider is working to provide LASSO data on its large database of compounds.  LASSO generates a structure and grinds it through a neural net processor module and produces a score between zero and one. The closer the score is to 1.00, the greater the surface conformity or compatibility of the ligand to a target receptor site.  As you would expect, there is a high score associated with aspirin and the COX-1 receptor. From what I can tell, the software is self-learning in some fashion.

The uses are many. Substances can be screened for drug-like attributes within the 40 receptor types provided.  I would like to hear from someone who might have something to say about the use of LASSO for the estimation of possible toxic effects of substances that have not been biologically tested. I fully realize the hazards of this, but perhaps LASSO scores might help flag particular substances for closer examination by testing.

CT Scans. Who is monitoring a patient’s radiation dose?

The matter of medical x-radiation dosing is surfacing again. I wrote a post about this in 2009.

Let’s get to the core of the matter. Physicians need to take charge of this since only they have any real control. It’s a pretty goddamned simple concept. Doc’s who are calling for x-ray’s need to begin recording calculated dosing from this hazardous energy. If it is too troublesome for them, then the x-ray techs should record the information.

CT scanning seems to be problematic. There is no business incentive to hold back on CT use in for-profit settings. I suppose that documentation would only reveal the extent and magnitude of x-ray use. It would be fodder for malpractice law firms.

I can just see the billboards- Have you or a loved one ever gotten a tan from x-rays? If you have, call Dooleysquat, Schwartz and Schmuck for a free consultation. Do it Now!

Comments on the history of oxidants

Today we know that the chemical elements are capable of showing a range of behaviors in the category of reduction and oxidation (redox). Unlike our predecessors who attempted to wrap their arms around redox phenomena without the benefit of data or atomic theory, we are able to refer to tables of information which give details on the magnitude of redox phenomena and allow us to predict outcomes of transformations.

Reduction and oxidation has always been with us and for most of human history we were blissfully unaware of it as a distinct and complementary phenomenon. Beyond the conduct of redox in biology, for most of human history the major use of redox as a tool was combustion.  I would argue that humans began to do chemistry in earnest when we learned to generate fire and use it at will.  The introduction of fire allowed humans to apply significant thermal energy to materials in contrast to mechanical energy. Thermal energy changed the composition of materials in a way that was visible to us. With fire we could boil, dry, pyrolyze, combust, sinter, fracture and melt materials.  Food once cooked was forever changed. The combustion of wood produced much heat, charcoal, and ash.

Fire could provide warmth and destruction. It could be used as a weapon of war. The Chinese would become renowned for their command of deflagrations, explosions, rocketry, as would the Greeks for their Greek fire.  Chinese adepts learned to produce deflagration and explosions with energetic redox compositions centuries before the Europeans. With the spread of gunpowder formulation around the world, the problem of finding it’s components would plague adopters of this technology.

The basic rules of controlling fire were determined very early in human history. Some things burned and other things didn’t. The effects of air might have been inferred by the simple act of lighting kindling and blowing on it. Blowing on an ember can sustain it for a time and gives rise to increased heat. Fire can be accelerated by blowing air on it but may also be extinguished by too much wind. Clues to the basic nature of fire were there all along, but we lacked vocabulary, theory, and analysis.

The color of a wood fire can range from yellow/orange to bright yellow and it can warm you from a distance. Smoke was something that issued from fire and was perhaps troublesome. Fire and smoke always seem to rise upwards. More clues to to the behavior of matter, but as before, we lacked the tools of science until only in the last few centuries.

Today we can use atomic and quantum theory, thermodynamics, and the physics of radiation and buoyancy to explain and quantify fire and its many attributes. Today we can confidently state that a fire requires an initiation (the energy source), a reductant (the fuel), and an oxidizer (air). I think early man would have had a fairly concrete understanding of heat source and fuel. But the need for an oxidizer may have been less obvious. After all, air is all around us and is invisible. Nobody knew about the fire triangle or Smokey the Bear.

The development of oxidizers as a class of substances whose participation in chemical change was held back owing to the obscurity of the concept and the lack of a good theoretical basis like atomic theory.  Humans had been perishing by suffocation forever. Everyone has experienced the effects of oxygen deprivation whether it was by running from a sabretooth tiger or holding ones breath on a dare. But without the knowledge of oxygen and its function in respiration or in combustion, oxidation was the answer waiting for the right question.

Reducing materials as fuels for combustion or for the reduction of metal ores to the metal was common knowledge for a very long time. The introduction of oxidizing materials beyond the ever present air around us was a much harder nut to crack.  If we set the oxygen in air aside and focus on strongly oxidizing substances, we can begin to see the development of oxidizers as a class of materials.

One of the earliest oxidizers to find use was nitrate, commonly called saltpeter or nitre. Nitre was found in some damp locations that were rich in decaying organic materials. Nitre beds were often observed as having a white crust that migrated to the surface of the ground.  Early references of these nitre beds come from China and India. Nitre was capable of having multiple counter-ions. The early users of nitre were unaware of this of course. Later in history, makers of gunpowder would come to prefer potassium nitrate over the sodium salt owing to it’s lower aptitude for hydration. Hydrated saltpeter will passivate gunowder.  The story of gunpowder is well documented and the reader can pursue that trail on their own.

The discovery of oxygen in 1772 by Scheele could be considered a major step in the development of oxidation technology. While chemists were misguided by the theory of phlogiston, the isolation of a substance that supported combustion was a crucial conceptual leap.  Scheele and later Priestly would show that this new “air” would support combustion. In 1774 the discovery of chlorine by Scheele was the next major oxidizer to be identified. Chlorine was produced by the action of HCl on MnO2 (pyrolusite).  The bleaching effect of Cl2 gas was soon discovered by Scheele. The discovery of Cl2 soon lead to the discovery of bleaching powders. The earliest bleaching powder composition comprised of lime and chlorine was patented in 1798 by Charles Tennant in England. By the close of the 18th century, three important oxidizing compositions were produced: oxygen, chlorine, and calcium hypochlorite.  Chlorine and lime bleaching powder went into mass production at the beginning of the 19th century.

In a real sense, the development of oxidizers is very much like the invention of the lever. A level is used to amplify mechanical force. An oxidizing agent is used to amplify the extractive force on valence electrons. A strong oxidizing agent is able to bring energy to bare on select transformations that might not be otherwise available.  With the advent of this kind of transformation, new possibilities unfolded in history. By the middle of the 19th century, molecules with pendant oxidizing groups would be capable of self reaction to produce tremendous outbursts of energy. Nitroglycerine is one such molecule containing both reducing groups and oxidizing groups in one molecule. Oxidizers and oxidizing functional groups would change how we dig tunnels, extract minerals, carve canals, wage war, and eventually, compress uranium or plutonium into a critical mass for a nuclear explosion.

Transit of Venus

I hope folks out there had a chance to view the transit of Venus across the solar disk yesterday.  I was lucky enough to see it through a 6 inch refractor and a Coronado H-alpha solar telescope. It’s always fun to see celestial mechanics in operation.

NASA has a video of the transit acrosst the sun taken at various wavelengths. Evidence of sunspot activity is much more pronounced at these wavelengths.

Research Squatters. When Universities and Corporate Behemoths Collaborate.

Recently I had the good fortune to get to meet for a consultation with a young and talented chemistry professor (Prof X) from a state university elsewhere in the US. Prof X has an outstanding pedigree and reached tenure rather rapidly at a young age. This young prof has won a very large number of awards already and I think could well rise to the level of a Trost or a Bergman in time.

Not long ago this prof was approached by one of the top chemical companies in the world to collaborate on some applied research. What is interesting about this is that the company has begun to explore outsourcing basic research in the labs of promising academic researchers. I am not aware that this company has done this to such an extent previously.  They do have an impressive corporate research center of their own and the gigabucks to set up shop wherever they want. Why would they want to collaborate like this?

R&D has a component of risk to it. Goals may not be met or may be much more expensive that anticipated.  Over the long term there may be a tangible payoff, but over the short term, it is just overhead.

The boards and officers of public corporations have a fiduciary obligation to maximize the return on investment of their shareholders. They are not chartered to spread their wealth to public institutions. They have a responsibility to minimize their tax liability while maximizing their profitability. Maximizing profit means increasing volume and margins. Increasing margins means getting the best prices at the lowest operating expense possible.

Corporate research is a form of overhead expense. Yes, you can look at it as an investment of resources for the production of profitable goods and services of the future. This is what organic growth is about. But that is not the only way to plan for future growth. Very often it is faster and easier to buy patent portfolios or whole corporations in order to achieve a more prompt growth and increase in market share.

The thing to realize is that this is not a pollenization exercise. The company is not looking to just fertilize research here and there and hope for advances in the field. They are a sort of research squatter that is setting up camp in existing national R&D infrastructure in order to produce return on investment. Academic faculty, students, post-docs, and university infractructure become contract workers who perform R&D for hire.

In this scheme, research groups become isolated in the intellectual environment of the university by the demands of secrecy agreements. Even within groups, there is a silo effect in that a student working on a commercial product or process must be isolated from the group to contain IP from inadvertant disclosure. The matter of inventorship is a serious matter that can get very sticky in a group situation. Confidential notebooks, reports, and theses will be required.  Surrender of IP ownership, long term silence on ones thesis work, and probably secret defense of their thesis will have to occur as well.

While a big cash infusion to Prof X may seem to be a good thing for the professor’s group, let’s consider other practical problems that will develop. The professor will have to allocate labor and time to the needs of the benefactor. The professor will not be able to publish the results of this work, nor will the university website be a place to display such research. In academia, ones progress is measured by the volume and quality of publications. In a real sense, the collaboration will result in work that will be invisible on the professors vitae.

Then there is the matter of IP contamination. If Prof X inadvertantly uses proprietary chemistry for the professor’s own publishable scholarly work, the professor may be subject to civil liability. Indeed, the prof may have to avoid a large swath of chemistry that was previously their own area.

This privatization of the academic research environment is a model contrary to what has been a very successful national R&D complex for generations. Just have a look in Chemical Abstracts. It is full of patent information, to be sure, but it is full of technology and knowledge that is in the public domain. Chemical Abstracts is a catalog and bibliography that organizes our national treasure. Our existing government-university R&D complex has been a very productive system overall and every one of us benefits from it in ways most do not perceive. We should be careful with it.

ReactIR. Infrared spectroscopy revives in the age of NMR.

We have a brand new Mettler-Toledo ReactIR 15 sitting in my lab. It is rather simple to use- just dip the probe in your reaction mixture. It needs a little LN2 to chill the detector. The software is reasonable, bearing some resemblance to iControl of the RC1 sitting a few meters away.

The instrument is used to follow the progress of a reaction by monitoring the growth or extinction of IR absorptions. What is interesting for the user is that it is not necessary to identify any of the peaks in the course of an experiment. The software can integrate absorptions and plot their change over time. The fingerprint region of the IR spectrum is put to good use in that it is a fruitful region for numerous absorptions to appear.

The thing is still new to us, so we’re early in the learning curve. The probe in use has a wave number range from 2500 to  about 650 reciprocal centimeters. It is possible to detect up to 3000 wave numbers with a different probe. The probe is connected to the interferometer by a fibre optic cable comprised of a silver bromide optical pathway.

The thing is the size of a coffee maker and costs as much as a used helicopter. The ATR probe tip is small enough to be immersed in experiments at the scale of a scintillation vial or a 5 liter flask.

What it brings to the table is the ability to follow the progress of reactions in real time for process optimization. Pulling samples and trudging over to the NMR for in-process checks is tiresome and time consuming.

One limitation is the electrical classification. As with other electrical devices you have pay attention to the NFPA classification of the space it sits in. The ReactIR 15 is class 1, but not division 1. If the instrument must be used in this space, there are ways to fashion an enclosure to get around this, according to Mettler. Have a look at your computer as well. If your computer throws sparks and coal cinders, you may want to keep it away from that pool of pet ether on the floor.

Tempest in a Teapot. Philosophy-v-Physics.

A minor snit has broken out between outspoken physicist Lawrence Krauss of Arizona State University and, well, the philosophers of the world. Krauss has become a darling of the cable TV world of NatGeo and the Science Channel. It seems that you can’t swing a dead cat without knocking over the same dozen television astronomer/cosmologists and quantum physicists. This rotating crew of scientists are filmed on various locations straining to explain the universe in terms of string theory, dark matter, and quantum wierdness using language with a Fog Index of 8 or less.

I’m not slighting these folks in the least. Using the English language to convey the essence of these concepts is difficult, as is preventing the reflexive use of the remote control by viewers with the attention span of a house cat.

Anyway, Krauss has managed to inflame those philosophers who pay attention to popular science.  His latest book, A Universe from Nothing: Why there is Something Rather than Nothing, has precipitated this argument. I don’t care about the merits of his argument here. The reader is invited to dive in.

What I am writing about is the social and intellectual mistake Krauss made. Like all physical scientists, he is a reductionist. The drive for a ToE, Theory of Everything, is the ultimate act of reductionism. His assertion that philosophy is obsolete in the face of discoveries in physics and the emergence of big subassemblies of a ToE has been received with dismay by philosophers.  A large fraction of people (adults, anyway) are hardwired to be receptive to mysticism and no amount of handwaving, no matter how logical and crisp, is going to cause the bell curve to skew substantially away from cherished mystical beliefs.

Krauss has fallen into the same trap as those in the 19th century who may have declared that physics was pretty much complete with Newtonian mechanics. While quantum mechanics provides a template for the description of how particles behave constrained to a region of space, it fails as a replacement for philosophy. That is, quantum mechanics and cosmology do not provide any concise analysis on how people should treat each other, how to conduct a worthwhile life, or how to interpret what the meaning of quantum mechanics is in your life.

This is the realm of philosophy and religion and these kinds of questions must be freshly examined by each generation born into this strange universe. The meaning of existence is not yet settled science.

The degree symbol- Do we really need to keep using it?

I had an evil thought just now as I attempt to write 2 reports simultaneously. Why do we keep using that superscripted circle in front of C (i.e., ºC) that designates “degree”?

What the hell? We don’t use it for the Kelvin temperature scale. And, who knows if the engineers use it for Rankine? The thing is useless like an appendix or a titular chairman. Get rid of it!

What do you think?

Plasma

Today I found myself peering at the lovely lavender glow of opaque argon plasma through the viewing screen of a gleaming new instrument. The light-emitting 8000 K plasma sits apparently still alongside the conical metal skimmer. Somewhere a Dewar was quietly releasing a stream of argon into a steel tube that was bent in crisp military angles into and through walls and across the busy spaces above the suspended ceiling. Another cylinder quietly blows a faint draught of helium into the collision cell. A chiller courses cooled water through the zones heated by the quiet but savage plasma. Inside a turbo pump labors to rush the sparse gases out of the mass analyzer and into the inlet of the rough pump and up the exhaust stack.

Up on the roof, the heavy and invisible argon spills along the cobbles of roofing stones until it rolls off the roof onto the ground where the rabbits scamper and prairie dogs yap. The helium atoms begin their random walk into space. The argon shuffles anonymously into the breeze and becomes part of the weather.

All of the delicate arrangements; all of the contrivances and computer controls in place to tune and play this 21st century marvel. And a wonderment it is. The ICPMS obliterates solutes into a plasma state and then taps a miniscule stream of the heavy incandescent argon breath that trickles into the vacuous electronic salsa dance hall of the quadrapole.  All the heat and rhythm for the sake of screening and counting atomic ions. What a exotic artifact of anthropology it is. And it all began in a rift zone in Africa millions of years ago.

Respecting liquid hydrocarbons as a natural wonder

I just had a conversation with a colleague who is somewhat mainstream in his/her thinking. The question came up as to why can’t we be energy independent.  What is taking so long with the electric cars and natural gas powered … everything? When can we break away from middle eastern petroleum?

In the public sphere, all I hear are the questioners seeking reassurance that there are energy forms out there that will allow us to maintain our current level of consumption. They rarely put it exactly that way, but that is the heart of the issue.

I think multiple generations of people have failed to appreciate the natural wonder of liquid hydrocarbons. The C7-C10 fractions of petroleum, whether directly from the ground or from a cat cracker or reformer, are the motive basis for most of our ground transportation. These liquid hydrocarbons are of a reasonably low vapor pressure and high enough boiling point to allow their use in everything from go-carts and lawn mowers to automobiles and caterpillars.  Teenagers and grandmothers can pump hydrocarbons into an inexpensive and simple tank for use at ambient pressure and temperature. This liquid has a melting point low enough to make it flowable under nearly all earthly conditions.

The high energy density and the liquid state of gasoline is what makes it nearly perfect for propulsion. The energy density of gasoline is 34.8 mega-Joules per liter (MJ/L), as opposed to 21.2 MJ/L for ethanol.

Yeah, gasoline is cheaper per liter than the bottled water inside the convenience store. That perversion is just a temporary historical aberration. This will change.

Cosmically, hydrocarbons in the C7-C10 range suitable for automotive use are quite scarce in the local stellar neighborhood.  Some small hydrocarbon molecules like methane have been spotted in the gas giant planets and on Titan. But for the most part, the only supply of hydrocarbons we have are found in porous deposits below the surface of the only place we can get to- Earth.

We should appreciate our hydrocarbon resources for the true natural wonder that it is and be a bit more reluctant to squander it.  I doubt we’ll ever find a source of energy that is as cheap and convenient to use with such a high energy density.  Battery technology may get close, but innovation there is a highly specialized art that is beyond the scope of most shade tree mechanics. Common lead acid batteries require material and energy inputs, like everything else, and have somewhat low energy density and a high weight penalty.

Lithium batteries, with their higher energy density require a variety of manufactured and relatively exotic substances. And, they require lithium which is fairly scarce, both cosmically and on earth. We really should be recycling lithium scrap.  Seriously, we need to have great respect and appreciation for lithium as well. There really isn’t enough lithium to support everyone’s high energy density lifestyle.