UV/Vis Spectrum of Bromine in Water

We have a Cecil CE 2041 UV/Vis spectrometer.  Data is collected by the DataStream CE2000 software package. The instrument has 4 nm of resolution, not the best, but still quite usable. To quote the famous British philosopher- “You can’t always get what you want!” (M. Jagger).

This posting is an experiment on how to upload data to the web. The graphic below is a jpeg conversion of a pdf conversion of an Excel chart. Seems like an awkward way to do this. Undoubtedly someone out there can offer a suggestion of how to upload an Excel graphic to the blogosphere.

 uv-vis-of-br2-in-water-rev-2.jpg

It looks like prior to an upload the graphic has to be beefed up a bit.   I’m gonna have to monkey with it some more. Maybe someone has a suggestion.

Pissin’ and a moanin’

On occasion I am overcome with episodes of extreme clarity. It can happen anywhere- driving to work or standing in the 104 degree Fahrenheit shower water.  One such episode has recently come and gone. The realization was that for as much as I dearly love my chosen field of chemistry for the employment and multitude of Aha! moments it has given me, I am faced with the stark reality: Some of the most profound and pernicious a**h***s I have ever known have been fellow chemists. Shocking, isn’t it?

For the love of God, man, can it be true? Is this too dark of a subject to blog about? Can we talk about this? Maybe it is a dirty little professional secret that should be kept under wraps.  Maybe I am some sort of chaotic attractor that funnels these people into my local space?  Seems unlikely.  It’s probably just a proximity effect.  If I took up grocery bagging, the same realization would probably happen. 

How did people deal with a**h***s like this 40,000 years ago? If the troublesome Neanderthal who lived a few klicks up Olduvai Creek got out of control, we’d settle it the caveman way. With a club or that newfangled imported Folsom point. Today we are expected to use our words.  Well, here are some words- Damn and blast!

Some lab jerks are petulant turds who, if it weren’t for a wealthy grandmother, might be managing a Denny’s on the interstate. Others are true alpha males- tall, articulate, athletic, and sycophantic. These characters are especially loathesome.  It has been my experience that many sycophants have no immunity to the enchantments of other sycophants. Some cluster and form cells. Others collect clients or something like courtiers– grinning, pasty-faced trolls who lock onto the teat.  It is most distasteful.

(*End of Scorn Routine*)

Organic Qualitative Analysis. RIP.

One of the chemistry classes I took as an undergrad continues to assist me in my synthetic endeavors mid-career.  The class was organic qual.  It was designed to take the student through the determination of an unknown organic compound , or mixture, with the aid of qualitative tests and derivitization to figure out the compound. We did small visual tests to guage acidity, basicity, water solubility, etc. We did sodium fusions to look for halides, 2,4-DNP hydrazones for carbonyls, picrates of amines, and flame tests to make a guess at saturation. We were given just so many grams of unknown and we had to perform several tests to support a claim of identity. It was an excellent experience because an organic prof taught the actual lab section.  We had access to the lab during the week to work on the unknowns. 

We used derivitization to determine some of the more difficult unknowns. CRC Press had a book of physical properties of a large range of known compounds that were derivatized, so you’d compare mp’s, color, bp, solubility, etc., to make a case for identity.

I would be interested to hear if this is still in the curriculum out there. I fear that it has passed along into history in the face of the hyphenated cryptozoology of todays analytical instruments.  That’s a pity.  Organic qual gave me the chance to handle chemicals, perform reactions, deal with ambiguity,  and do tests that might be hard to work into the rest of the curriculum.   Part of being a good organic chemist is racking up lots of time in the lab doing stuff, polishing up the physical intuition and mechanical skills.

I am embarrassed to admit that at one time I embraced the idea that the organic microlab experience was good pedagogy.  I now see it as more of a phenomenon meant to stretch department budgets. The idea of giving students barely enough reagents to make 100 mg of something is pretty dubious.  If the student goofs and spills something or makes a mismeasure, they might end up with 25 mg of product. The isolation of this amount of mass is problematic for fresh learners.  I miss the days when the organic lab kit had 25, 50, 100, and 250 mL flasks in it (19/22 ST joints, of course). 

The argument goes something like this: Our conversion to microlab equipment is justified because of the cost saving gained by going to a lower scale. We buy fewer grams of expensive reagents and we lower waste generation for the department. Well, this is a bunch of self-serving crap. I can just see the department chair’s pointed head nodding in agreement as some tenured Poindexter drones on about minimizing the negative impact on the environment.  

For Christ’s sake, we’re talking about chemistry, not church camp.  Minimally, chem majors should not be cheated by limiting them to the microscale experiments.

If you want to save the environment, stop driving your SUV down to 7-11 to get cigarettes.  Or, don’t bring home so much cheap plastic crap from Big Box Mart.

Colleges should be giving their chemistry majors more synthesis experience, not less.  In industry it can be a real problem finding fresh BS/BA graduates that have lab experience beyond sophomore organic lab.  Schools that promote lab-based synthesis research for undergrads (as opposed to computation) are doing their students a bigger favor than they may realize. 

The Road to Reconstructionism

There is a web site that has been keeping track of a movement in America. It is a quiet movement. It’s purpose is to implement a reconstruction of American values to suit their world view.  The website is the Yurica Report.  It is a movement that seeks nothing less than the establishment of a theocratic form of government in America.  It is also called Theocratic Dominionism or Christian Reconstructionism.  But see for yourself.  Google these terms and browse the websites.

For myself, I have been watching Christian fundamentalism since the early 1970’s.  I recall stopping at a booth at the county fair as a high school student and listening to members of the John Birch Society. I thought at the time that they were Looney Toons, or just a Christian libertarian group.  I guessed that they were mostly harmless.   Well, I was wrong.

Frederick Clarkson at PublicEye.org writes-

“Reconstructionist leaders seem to have two consistent characteristics: a background in conservative Presbyterianism, and connections to the John Birch Society (JBS).”

He goes on to say-

“In 1973, R. J. Rushdoony compared the structure of the JBS to the “early church.” He wrote in Institutes: “The key to the John Birch Society’s effectiveness has been a plan of operation which has a strong resemblance to the early church; have meetings, local `lay’ leaders, area supervisors or `bishops.'”

The JBS connection does not stop there. Most leading Reconstructionists have either been JBS members or have close ties to the organization. Reconstructionist literature can be found in JBS-affiliated American Opinion bookstores. “

But what is reconstructionism about? Again, Clarkson puts it succinctly-

“Reconstructionism is a theology that arose out of conservative Presbyterianism (Reformed and Orthodox), which proposes that contemporary application of the laws of Old Testament Israel, or “Biblical Law,” is the basis for reconstructing society toward the Kingdom of God on earth. “

“Reconstructionism argues that the Bible is to be the governing text for all areas of life–such as government, education, law, and the arts, not merely “social” or “moral” issues like pornography, homosexuality, and abortion. Reconstructionists have formulated a “Biblical world view” and “Biblical principles” by which to examine contemporary matters. Reconstructionist theologian David Chilton succinctly describes this view: “The Christian goal for the world is the universal development of Biblical theocratic republics, in which every area of life is redeemed and placed under the Lordship of Jesus Christ and the rule of God’s law.”

I agree. It is easy to dismiss this as a bunch of paranoid ranting. But if you’re paying attention to things, you might also conclude that we have been in the midst of this movement for some time.  How do you think GW Bush got elected in Tejas? His boyish charm or war record?

I don’t want to give it all away. The reader should see for her/himself.  Let my friend, Mr. Google be your guide on this disturbing journey.

(*fade to black*)

GWII- Gulf War II

To say that there is a lot of antipathy for the Bush regime would be an understatement. I was vaguely aware of similar dissent during the 1960’s, but I was too young to understand it then.  I do recall family elders dismissing Viet Nam war protesters and “hippies” as communists.  In those days, the word “communist” was an epithet that was used with genuine scorn and derision.  Like the pixelated photo of Lincoln, with distance the image begins to form.  Vague similarities between the times are gradually being recognized. Today you hear Bush conservatives spitting the word “liberal”, often with the phrase “cut and run”.  The allusion, of course, is that liberals will spontaneously take “French Leave” when in power, abandoning the Iraqi people and thereby soiling the memories of soldiers who have fallen in Iraq.  So the theory goes.

There is some interesting content at VDARE.com concerning Gulf War II (GWII).  The author is Paul Craig Roberts.  He was Assistant Secretary of the Treasury in the Reagan Administration.  Mr. Roberts apparently had some sort of epiphany as a political insider and has come out against how the Bush cabal has prosecuted GWII.  Anyway, he makes some interesting points-

“To date more than 100,000 US troops who are veterans of these wars have been granted disability compensation. Although the US cannot put on the ground in Iraq more than 150,000 troops at one time, 1.5 million troops have served so far and 567,000 have been discharged of which 100,000 are receiving disability payments.

Paul Sullivan, director of programs for Veterans for America, says that the current rate of injuries will produce 400,000 American veterans suffering 30% to 100% disability. Apparently, one of the severe forms of disability is post-traumatic stress, which does not count as a physical wound.”

As a news junkie, I’m at least average in attentiveness to such things and I’ve heard precious little about US casualties. If the above is true, then it needs to be announced morfrom every hill top.

Or, consider this unsavory comparison-

Americans are too inattentive and distracted to be aware of the grave danger that the neoconservative Bush regime presents to American liberty and to world stability. The neoconservative drive to achieve hegemony over the American people and the entire world is similar to Hitler’s drive for hegemony. Hitler used racial superiority to justify Germany’s right to ride roughshod over other peoples and the right of the Nazi elite to rule over the German people. Neoconservatives use “American exceptionalism” and “the war on terror.” There is no practical difference. Hitler cared no more about the peoples he mowed down in his drive for supremacy than the neoconservatives care about 655,000 dead Iraqis, 100,000 disabled American soldiers and 2,747 dead ones.

When Bush, the Decider, claims unconstitutional powers and uses “signing statements” to negate US law whenever he feels the rule of law is in the way of his leadership, he is remarkably similar to Hitler, the Fuhrer, who told the Reichstag on February 20, 1938: “A man who feels it his duty at such an hour to assume the leadership of his people is not responsible to the laws of parliamentary usage or to a particular democratic conception, but solely to the mission placed upon him. And anyone who interferes with this mission is an enemy of the people.”

“You are with us or against us.”

Here, Roberts may be going a bit non-linear on us.  Read “Rise and Fall of the Third Reich” by William Shirer.  While Bush II is clearly not on the same philosophical or moral plane as Adolph Hitler, nor as cunning for that matter, the fact is that his handlers are using rhetorical tools from an age-old playbook.  That is, whipping up public fear as a means to concentrate power.  Really, the Bush cabal is mythologizing a foe to achieve an unprecedented concentration of power for the executive branch.  The point of the Hitler comparison is that this kind of consolidation of power has precedent. 

Finally, I’ll agree with those who say that Bush II isn’t smart enough to do this on his own. I’ve seen nothing to indicate that this fellow is much more than a frat boy with a golden name.  Bush and his merry men have managed to make a mess of things and it will take generations of other people to smooth it out.  Recall that we still have troops in Japan and Korea and the veterans of those wars are now passing of old age.

A mote in the eye of Schrodingers Cat

I have made some adjustments to the blogroll. It turns out that physicists, to a greater extent than chemists, have taken up the craft of blogging.  Why chemists seem less inclined to blog remains unclear.  This tendency is seen on the shelves of book stores as well.  Whereas, bookstore science shelves are clogged with treatises on Quantum _____ (fill in the blank), works on chemistry are often limited to chemical dictionaries or Schaums Outlines.  Here in Colorado, where the per capita college education is reasonably high, in certain counties at least, urban bookstores may have chemistry titles that go ever so slightly beyond the study guides and dictionaries. 

It seems to me that many of the popular quantum mechanics books on the market are peddling to people looking for a mystical experience.  Fred Alan Wolf and a few others have made a career of feeding this need.  I recall the quote by Niels Bohr-

‘There is only an abstract quantum physical description. It is wrong to think that the task of physics is to find out how nature is. Physics concerns what we can say about nature.“. 

 Bohr and Einstein

But I’ve ventured out on a limb. I am but a lowly synthetic organic chemist, a plebian scribbler in the scientific pecking order, who has not used a Hamiltonian operator or a Kroniker delta since grad school. My fragmented knowledge of quantum mechanical formalism is but a mote in the eye of Schrodingers cat.

Note: I’ve deleted The Volokh Conspiracy from the blogroll. They have developed an unfortunate neocon twitch that I find distasteful. 

S. 3930: Always certain but frequently wrong.

For those who may scoff at the possibility of the DoJ or other agencies abusing secrecy in the courts, have a look at this disturbing story.

http://balkin.blogspot.com/#116119665216036725

The author of this is now a law school prof. It is a chilling account of gaming the system to intimidate opposing attorneys in litigation involving evidence designated as secret. Tamanaha makes the following point-

“A thread that runs through this story is that the government actors involved were not necessarily bad people—they were simply doing what they thought was necessary to defend their country, and they used this end to justify their extreme conduct. That’s the problem. When combined with power and with an unwavering conviction in the correctness of one’s conduct, this mindset—which the Bush Administration oozes—can lead to terrible abuses.”

After you have digested this tale, think about the general case. Granting the executive branch the authority to take actions that are not subject to checks and balances, i.e., rendition, is a step in the direction of autocracy. Our elected legislative branch has abdicated their responsibility to apply checks and balances. It is an astounding development. What is to prevent other nations from adopting the same posture? Pull a suspect out of line at customs at the airport and call them an enemy combatant. Now they have no right of habeas corpus. No court can demand that the person be accounted for. They have no right to inspect the evidence used against them. They quietly go to an undisclosed location. Is this America we are talking about? It is now, thanks to the US Senate.

All of this is being administered by people who are cut from a certain kind of cloth. I know a few of them and they tend to be the bane of my life. They are always certain in their judgements. But when they finally cycle out of your life, you see that they were just as prone to error as anyone. There has to be some metaphor for this, some mythic character or an archetype who exemplifies this flaw.

Fabulous 2-Methyltetrahydrofuran

Some predict a bright future for 2-methyltetrahydrofuran.  At least one company is patenting MeTHF products.  For process chemists, MeTHF offers at least one advantage over THF, i.e., MeTHF is immiscible with water.  Well, mostly.  Your water phase is going to have some MeTHF in it and some water in the MeTHF phase.  You don’t have to salt up your water to get a phase boundary or worse, do a solvent exchange for an extraction. An aqueous quench of a MeTHF reaction mixture should phase separate with the aqueous wash and allow aqueous extraction. This is certainly convenient for the chemist, but at a price. 

Last time I looked, MeTHF is about twice as expensive as THF. For small scale bench work, the cost differential isn’t too onerous. If you’re talking about filling a 5,000 liter reactor with it, the costs do add up.  So, a defensible process improvement/change would have to yield at least the differential solvent cost and probably another 10-25 % to justify the cost of process validation and change management. 

Some process changes will require customer approval and product validation on their side.  Then, they’ll want a price concession for all of the trouble you put them through. So a switch to MeTHF over, say, THF will have to yield some bottom-line value to the manufacturer and the customer. It is always better to fold in your innovations before you submit your process to the plant people.  

The other issue with MeTHF has to do with it’s chirality.  For instance, MeTHF-metal complexes will be solvated by either or both enantiomers. The presence of diastereomeric complexes will only complicate in-process NMR checks of such processes.  Though certainly not a show-stopper, it is a complication that the analytical crew will have to contend with.

Romans, Greeks, and HR 5695

Congress inched us further along toward the security state with the passage of the HR 5695, the Chemical Facility Anti-Terrorism Act (Lungren, R-Calif) (source- the “Capitol Connection”). Though the bill was supposedly watered down, it still provides DHS with latitude to impose regulations.

Nobody wants an act of terror involving a chemical facility. Obviously. But we must be careful not to dismantle the chemical industry with hand-waving mandates that will choke innovation and US competitiveness. I predict that the only people who will benefit from this law are the security consultants who will peddle their PowerPoint deliverables to frightened management MBA’s like flu shots to the Wal-Mart elderly. Maybe Halliburton is in this business already? Ya Think?

We Americans need to ask ourselves- do we want to be like the Romans or the Greeks? Both are extinct cultures, so perhaps it is a funny comparison (or prescient). Do we spend our resources to advance the cause of empire or enlightenment? Do we automatically relent to incursions into our civil liberties because the Executive Branch says that it is required for them to do their job? When you’re a hammer, everything looks like a nail. I’m guessing that once you experience the thrill of commanding the most advanced forces in the history of the world, you are a changed person. It must influence your perception of conflict. I know it would for me. The fact of power is the act of power.

Stalin’s little buddy, that Gilligan of the communist world, Kim Jung Il, has the power thing figured out. Wave it around & watch everybody scatter. Nobody has to know that your nuke was a dud. Strut around like a rooster and state your case. He must watch the poker channel.

Here is a threat for you. What about the opium crop in Afganistan? You know, if Monsanto had made bigger contributions to the RNC, they’d be shipping tankers of Roundup(R) to Afganistan right now for the “War on the Poppy”! Somebody wasn’t thinkin’.

And, what about Afganistan? Weren’t we on a bug-hunt to find that Saudi guy, what’s his name, O’Laden? No, Bin Laden. C’mon, George, keep your eye on the ball. Good lord.

(*End Rant*)