The Curious Wavefunction

I am full of piety

2008-07-03T14:42:00.000-07:00

Or so the Blog Cuss-o-Meter says. Only 0.1% of pages on my blog have "cuss words", less than the average of 10%. I wonder how they are defining these though. Does "creationist" count? How did you do?

OnePlusYou Quizzes and Widgets

Why is body temperature 36 degrees celsius?

2008-06-30T07:50:00.000-07:00

While I was doing an unrelated search on the Nature website, I came across this intriguing debate about why body temperature is maintained around 36 degrees and not some other value. (Nature, Vol 324, December 4, 1986, p. 418)

The discussion was initiated by a letter from John Paul, a scientist in Australia who contended that the specific heat capacity of water is lowest at 36 degrees, and therefore heat loss would be minimal at that temperature

But he neglected a fundamental principle of physical chemistry; the rate of heat loss is proportional to the difference between the temperature of the body and that of the surroundings and is independent of the specific heat capacity (remember high school and Newton's Law of Cooling?). More importantly, the specific heat capacity of a body can be thought of as a measure of how well the body offers "resistance" to fluctuations in temperature. The reason why water works so well as an essential life fluid for example is because its specific heat is so high; there is minimal fluctuation in the temperature of water when heat is injected or taken away from it.

Thus, an optimal substance for maintaining a given temperature would be one whose specific heat capacity is as high as possible under the given circumstances, not one whose specific heat capacity is minimum at the given temperature.

These facts were pointed out by William Calder from the University of Arizona and by Steven Benner and Jack Dunitz at the ETH, Zurich. Dunitz as is known is an extremely versatile scientist, a veteran researcher and one of the greatest structural chemists and technical writers of the last century.

Dunitz and Benner make their objections to Paul's explanation clear and offer an alternative partial explanation; that 36 degrees is the optimum compromise between viscosity and hydrophobicity. It's high enough for the viscosity to not become so low as to impede diffusion-limited processes, and low enough that hydrophobic molecules do not "dissolve" too easily.

Natural selection must have taken a remarkable number of factors into account in optimizing this property.

R.I.P

2008-06-24T12:41:00.001-07:00

A man who epitomized one of those essential qualities of sound science; eternal skepticism, and a congenital aversion to sacred cows

Aß Dimers- The Long-Sought Minimal Culprit in Alzheimer's Disease?

2008-06-22T15:24:00.001-07:00

Following on the heels of the headline-making Nature publication that demonstrated that NSAIDs (Non-steroidal AntiInflammatory Drugs) uniquely targeted a substrate (APP) rather than an active site of the gamma-secretase complex involved in plague formation in Alzheimer's (see Discount Thoughts for a great summary) comes a paper that may turn out to be one of the important papers in the history of Alzheimer's disease (AD) research.

Since 1905 when Alois Alzheimer first detected the symptoms of what we today call AD and identified the characteristic plaques that form in the brains of AD patients, the "amyloid hypothesis" has become almost synonymous with AD. For decades now, insoluble amyloid plaques, later found to consist of 40 (Aß 1-40) and 42 (Aß 1-42) residue oligopeptides, have been thought to be the hallmark of AD. Indeed, amyloid has become the poster boy for diseases caused by protein misfolding. Say "protein misfolding", and college students will pipe up and say "Alzheimer's"

However, the truth as usual has been complicated. In the last few years, attention has been shifting from the insoluble Aß to soluble forms of the peptide that are apparently in equilibrium with the aggegated beasts. Many oligomers have been isolated through antibody labeling and their toxicity has been demonstrated to various extents under various conditions. The "amyloid hypothesis" has become much more complex than before, and one of the original questions- whether these insoluble plaques are really the cause or just a manifestation of AD- has raised its head even more.

Recently exciting progress has been made in the field, with everything from metals to free radicals being implicated in the dementia and neuronal death that AD causes. On a wall in my room I have a Sigma Aldrich poster displaying a huge schematic of the principal species and pathways involved in AD, and one look at the poster clearly indicates how convoluted the whole scenario is. One of the continuing main reasons for slow progress has been the lack of structural information, with amyloid itself not being crystallizable and soluble species by definition being hard to structurally nail down.

But in light of the connection to soluble oligomers unearthed for AD, one lingering question has been foremost on everyone's minds- What is the minimal soluble species responsible for the symptoms of AD? Now it seems that a paper might go a long way in answering this question.

The short answer is "dimers dimers dimers". For the long answer, read the Nature Medicine paper. Charles Selkoe, Ganesh Shankar and others at Harvard separated different Aß species, insoluble and soluble, from the brains of AD patients. They then performed detailed characterization through immunoprecipitation, Western blots and other techniques, and then injected these fractions into rats, documenting which species can be identified as being the minimal as well as dominant contributors to the pathophysiology of AD.

I am no neurologist (paging Retread) but the researchers seem to have focused on three indicators of "brain damage"- an adverse effect on LTP (long-term potentiation); Wikipedia defines this as "the persistent increase in synaptic strength following high-frequency stimulation of a chemical synapse" which seems to indicate the fidelity of synaptic communication and a contributor to memory, LTD (long-term depression) which is the weakening of a synapse, and a decrease in dendritic spine density.

The researchers clearly find that dimers displaying a mass band of 8kD (confirmed by mass spectrometry) provide the greatest effect on these three parameters. Monomers and other soluble oligomers were not just less toxic but inactive. They also performed the interesting experiment of treating insoluble Aß cores with formic acid, this causing some of it to dissociate into dimers. This concoction proved deadly for rat brains, while the original untreated assembly did not prove as toxic. To make sure that the dimers were pure, they also used synthetic Aß dimers and obtained the same results. These set of results are pretty conclusive in demonstrating the toxicity of dimers.

As an interesting sidepoint, the authors also demonstrate the role of the metabotropic glutamate and NMDA receptors in facilitating the symptoms.

The significance of these results are clear. The authors themselves say "Our findings fulfill an essential requirement for establishing disease causation in Alzheimer’s disease". Many questions still remain though. We still don't know the molecular mechanism through which these dimers finally lead to neuronal death. Do they exert their effects by binding to metals like copper or iron? Do they slide into neuronal membranes and cause them to disintegrate? What other species do they actually go through before they cause harm? All these effects have been suggested as part of the list of effects responsible for neuronal damage. Which effects do Aß dimers fit into?

But all this is later. For now it's a significant achievement that we seem to have a handle on the minimal species responsible for AD. It's a staggeringly simple (or not...) structure involved in the progression of a set of maddeningly complex events. This finding seems to open a whole new window of experiments, conjectures and principles related to Aß dimers and AD in general.

My compliments to the team.

1. Shankar, G.M., Li, S., Mehta, T.H., Garcia-Munoz, A., Shepardson, N.E., Smith, I., Brett, F.M., Farrell, M.A., Rowan, M.J., Lemere, C.A., Regan, C.M., Walsh, D.M., Sabatini, B.L., Selkoe, D.J. (2008). Amyloid-ß protein dimers isolated directly from Alzheimer's brains impair synaptic plasticity and memory. Nature Medicine DOI: 10.1038/nm1782

2. Halliwell, B. (2006). Oxidative stress and neurodegeneration: where are we now?. Journal of Neurochemistry, 97(6), 1634-1658. DOI: 10.1111/j.1471-4159.2006.03907.x

3. Bush, A.I. (2003). Copper, ß -amyloid, and Alzheimer's disease: Tapping a sensitive connection. Proceedings of the National Academy of Sciences, 100(20), 11193-11194. DOI: 10.1073/pnas.2135061100

4. Kukar, T.L., Ladd, T.B., Bann, M.A., Fraering, P.C., Narlawar, R., Maharvi, G.M., Healy, B., Chapman, R., Welzel, A.T., Price, R.W., Moore, B., Rangachari, V., Cusack, B., Eriksen, J., Jansen-West, K., Verbeeck, C., Yager, D., Eckman, C., Ye, W., Sagi, S., Cottrell, B.A., Torpey, J., Rosenberry, T.L., Fauq, A., Wolfe, M.S., Schmidt, B., Walsh, D.M., Koo, E.H., Golde, T.E. (2008). Substrate-targeting gamma-secretase modulators. Nature, 453(7197), 925-929. DOI: 10.1038/nature07055

ADMET@TheSpeedOfThought

2008-06-20T13:34:00.000-07:00

Accurate estimation of ADMET effects still remains the Waterloo of drug development, with up-to 40% of promising candidates failing in clinical trials because of unfavorable pharmacological properties. Over the last few years many algorithms and descriptors have been developed and implemented into programs- many of them proprietary- to predict ADMET. However at some point these programs become far from intuitive, being of no real help to medicinal chemists engaged with actual lead design.

Paul Gleeson from GSK has come up with a set of rules of thumb for remembering the different properties of drugs that influence their ADMET behavior. He has used large databases of molecules, sound statistics and confidence intervals and GSK's internal studies to derive these rules. In my opinion he has done us all a service, because most pharmaceutical companies would want to and in fact do keep such data proprietary. He narrows down these properties to three important ones which medicinal chemists are comfortable and familiar with- molecular weight, clogP (lipophilicity) and ionization state (+ve, -ve or neutral). The major ADMET parameters he looks at are:

1. For Absorption:solubility, permeability and bioavailability
2. For Distribution: volume of distribution, blood-brain barrier penetration and plasma protein binding
3. For Metabolism: clearance, half life, P450 metabolism, hERG inhibition, P-glycoprotein efflux

While some of the rules are what they are supposed to be- intuitive- there are also some revelations. I will let the reader muse over the details of how the three aforementioned properties affect the ADME parameters. The author also interestingly considered the effect of changes in clogP- important for medicinal chemists- on the properties. For now I will list a few effects I personally found most interesting:

1. Basic compounds have a larger volume of distribution (which means a larger half-life for a given clearance rate) than acidic compounds. That's because basic compounds can interact with the negatively charged head groups of phospholipid membranes and get distributed easily throughout the body. Acidic compounds in contrast bind to positively charged residues on ubiquitous albumin, which limits their volume of distribution. Thus acidics show greater plasma protein binding.
2. Because of the same property basics also can pass more easily through the gut wall membrane (permeability). However, lesser plasma protein binding can also increase the clearance rate for basics. Thus there's a balance between volume of distribution and clearance, and since half life is given by

half-life = 0.693 * Volume of distribution/Clearance

one often has to face a compromise. In general having basic side-chains can be advantageous (also see effects on CNS penetration below), notwithstanding higher clearance rates. There is an instructive example that comes to my mind; the anti-TB antibiotic rifamycin has an unfavorable Vd which can be improved by adding a basic side chain, thus converting it to rifampicin with a radically better Vd and half-life.

3. As for CNS penetration, it's well-known that small, non-polar molecules easily make their way across the blood brain barrier (ask any druggie). However the study shows that again, basic molecules are on average more CNS permeable than neutrals, followed by acidics. This trend mirrors the permeability trend above. CNS penetration may also be complicated by active transport mechanisms that are hard to predict. For non-CNS drugs, preventing CNS penetration is what's most important. In general I would stay away from making predictions about CNS effects of drugs.

4. hERG inhibition: The human-ether-a-go-go-related-gene ion channel is notorious for flagging toxic molecules in studies. Excessive hERG inhibition leading to QT interval prolongation of heartbeat can assuredly be a death warrant for your molecule, not to mention for yourself. For some years now people have been trying to figure out pharmacophores for hERG inhibition that would enable them to find common features among hERG-unfriendly molecules. To my knowledge nobody has been spectacularly successful although there are have been some interesting results. It is generally accepted now that basic molecules tend to block hERG more than neutrals or acidics. Interestingly as this study shows, effects of clogP on hERG inhibition are also the greatest for basic molecules.

5. Finally, there is no meaningful relationship between molecular weight and many of these factors. Parameters like permeability will naturally be greatly influenced by Mol. Wt. I think it's more accurate to say that relationships between MW and these parameters will be masked by factors like clogP and ionization state.

Readers are urged to go through the article for more details. The sections on PgP and P450 inhibition are interesting and these properties are extremely important (Taxol for example is pumped out by PgP in resistant cells) but it's also difficult as of now to come up with predictive models for these. It's still very difficult to predict ADMET for budding clinical candidates, mainly simply because the body is still too complex a creature for us mortals to ponder. But medicinal chemists will greatly benefit from intuitive rules, which even if they break down in certain scenarios, do provide a rough and ready guide for checking off factors from your list of adverse ADMET effects. Such studies would help.

Gleeson, M.P. (2008). Generation of a Set of Simple, Interpretable ADMET Rules of Thumb. Journal of Medicinal Chemistry, 51(4), 817-834. DOI: 10.1021/jm701122q

Multiconformational MMGBSA Rescoring; Advancing On Mount Free Energy

2008-06-13T12:05:00.000-07:00

Blogging has been a little slow lately mainly because there have been exciting new developments with one of the projects I have been involved in and I was in meetings related to this. One of the topics that was discussed at the conference I was at last week was the accurate prediction of free energies of binding, one of the holy grails of drug discovery. Free-energy perturbation (FEP) still remains the gold standard to get relative free energies of binding, but the procedure is very computer intensive and therefore can be carried out only with small changes in congeneric series of inhibitors. The goal remains elusive and extremely challenging.

A poor man's way of quickly obtaining such ∆Gs is MMGBSA (Molecular Mechanics Generalized Born Surface Area). The GBSA model is well-established as a continuum solvation model for taking solvation into account. What MMGBSA does is take a docked ligand structure and then calculate the free energy of binding as the difference between the bound and unbound states using a force field, including implicit solvation.

Therefore, it calculates

∆G (binding) = ∆G (protein-ligand complex) - ∆G (protein) - ∆G (ligand)

Clearly it has to calculate the energies of the free ligand and free protein. Much of the challenge lies in these two terms. For starters, one has to calculate the strain energy penalty that the protein has to pay in order to bind the ligand. The binding energy that we see experimentally emerges after the protein has paid this strain penalty. How much this strain energy can be has been a controversial topic recently and I will get into it in another post. Suffice it to say that it's a challenging calculation that is not always handled well by MMGBSA. This is because in calculating the ligand free energy, MMGBSA essentially uses a force field to relax the ligand from the bound conformation to the nearest local energy minimum. However, a complex ligand exists in several local energy minima in solution and this force field local minimum may not correspond to any of them. Thus, one has to consider the global strain penalty that the protein has to pay. For this the method also has to consider the multiple conformations that a ligand adopts in solution. Sadly there are very few techniques that will deconvolute the Boltzmann population of a ligand's real conformations in solution and give us the global minimum. This problem in calculating strain energies remains an important drawback of the method.

Calculating ∆G (protein) is also not a trivial matter. We need to consider the entropy of the protein. One can get this from time-consuming MD simulations but it's not certain if the force field is parametrized well and if conformational space has been sampled comprehensively. Another uncertain factor is the induced fit effects involved in binding. A lot of these effects can be subtle and may extend to second shell amino acid residues.

Given these drawbacks, MMGBSA has nonetheless been quite successful in improving agreement with experiment. One of the reasons it works so well is that when you are dealing with congeneric series of ligands for a given target, many of the terms like conformational entropy and protein reorganization energy are the same or very similar and cancel, although there can be surprises. It seems now that at least one of the problems in MMGBSA- not considering the multiple conformations of the ligand in solution- can be tackled. A simple way to get multiple conformations of a ligand in solution is to do a conformational search. Assuming that the search is "complete", one can then calculate the conformational entropy penalty that the ligand has to pay in order to sacrifice all conformations except one in which it binds to the protein. There has been an implicit way to take this into account- many docking programs include a penalty of 0.65 kcal/mol per frozen rotatable bond. But clearly this penalty may be quite less if there are hundreds of conformations in solution that would lead to a large conformational penalty.

Now a group from Amgen has done such multi-conformational MMGBSA rescoring for four important targets and their ligands- CDK2, Thrombin, Factor Xa and HIV-RT. They compare scores obtained with Schrodinger's GlideXP routine with experimental binding affinities. Then they compare scores obtained with MMGBSA rescoring either with a single ligand conformer representation or with a multiple conformer representation that takes ligand conformational entropy into account. The comparison between single and multiple conformers gives somewhat mixed results and sometimes the single conformer representation also does fairly well; however, one thing is strikingly clear, that MMGBSA rescoring can radically improve correlation with experimental affinities compared to simple GlideXP scoring. In some cases the correlation coefficient jumps from essentially 0.00 to a whopping (by current standards) 0.75. There is a lot of interesting methodology described in the paper worth taking a look at. But it's quite clear how including some of the explicit physical effects involved in protein-ligand binding can substantially improve correlation with experiment. In this case the extra effort expended is a fraction of the cost involved in FEP calculations and the methods can also tackle more diverse ligands.

Even if we are not close to conquering the free energy fort, at least we seem to be getting concrete footholds on it.

Guimaraes, C.R., Cardozo, M. (2008). MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization. Journal of Chemical Information and Modeling, 48(5), 958-970. DOI: 10.1021/ci800004w

Glad to be away from home

2008-06-09T14:41:00.001-07:00

I am lounging around in Seattle, WA after a fantastic excursion to Portland, OR. This is one of those moments when I am truly glad to be away from Atlanta. Simple reason- Right now, Seattle is 54 degrees. Atlanta, 97 degrees. Even if this place is cloudy, I prefer it any day to that monstrous heat. This is the first time in 5 years that I am seeing so many 90 degree+ days back home. Hello to my friends there. Hope you had fun playing volleyball at the department picnic...

Portland, Powell's

2008-06-02T14:58:00.000-07:00

I am off to a conference in Portland, OR and while I have heard many tales of its beauty, about the only thing I am looking forward to even more than the conference and place is the delicious-looking and famous Powell's Books store, supposed to be the largest in the world. Unfortunately and sadly it seems I will miss Fup the technical store cat who passed away at the ripe old age of 19 last year.

Right now I am licking my lips reading the store description, and later in the evening will be on my way to buy an extra duffel bag that can hold at least a dozen books. Although this does not bode well for moving time after my PhD.; the last time I counted I had three hundred something books stashed in bookshelves, on the carpet and on chairs in my little rented bedroom. Well.

Myths about disrupting protein-protein interactions with small molecules

2008-05-23T07:53:00.000-07:00

The first era of medicinal chemistry was finding small molecules to target proteins. It's still going strong and will continue to do so. The second era that promises a treasure trove at least in principle is finding small molecules for disrupting protein-protein (PP) interactions. So many important processes in our body are regulated by these crucial interactions that finding small molecules to modulate them could promise a bonanza of new therapies.

But disrupting PP interactions is fundamentally different from designing a small molecule to bind to a (mostly) well-defined active site on a protein. PP interaction surfaces are rather flat and expansive and depend on subtle interactions between amino acids that add up to provide substantial binding affinity. Designing a small molecule to disrupt such interactions is somewhat like disrupting the sliding of one door hinge against another by lodging a grain of sand between the two. However, the picture has been simplified somewhat in recent years by the identification of "hotspots"- key amino acid epitopes that provide the bulk of binding interaction. If one could design a small molecule that could provide this major contribution to the free energy of binding, one could have an effective drug that could target PP interactions. After all, a grain of sand can indeed inhibit hinge sliding if it's placed in the right position.

One of the big players in investigating small molecule PP interaction agents has been Jim Wells, formerly at Genentech and Sunesis and now at UCSF. He has a nice Nature review that traces recent successful examples of small molecule PP interaction antagonists. Wells considers six or seven successful stories involving important proteins playing key roles in health and disease. For example, disrupting the inhibition of the pro-apoptotic BAD and BAK by the anti-apoptotic Bcl-2 and Bcl-xl, disrupting the binding of interleukin IL-2 to its receptor, and disrupting the binding of HDM2 to the tumour suppressor p53.

But more importantly, Wells then address some widely held myths about PP interactions that seem to drive pessimism in the field. They are worth taking a look at:

Myth 1: It's very difficult to find a small molecule that would lodge between the rather disordered flat surfaces of two proteins.

While this is true, in practice as is exemplified by almost all the examples, the protein surface does not remain flat when a molecule binds to it. Loops and side chain adapt and form shallow pockets and dents to which the molecule can bind. The fallacy in believing the myth is to assume that small-molecule protein surface binding is a rigid body interaction. It's not, and there's a strong element of induced fit in the process. This is probably the single most important thing to keep in mind, that small molecules will form their own small pockets and bind well to initially flat protein surfaces.

Myth 2: Small molecules that disrupt PP interactions are too large to be drugs

This is part of the partly substantiated myth that large molecules usually don't become drugs, because of many factors including ROF problems. But many molecules disrupting PP interactions cited in the review are about 500-700 Da, perhaps a little large but not intractable as drugs. The authors also calculated the ligand efficiency which is the free energy of binding per non-hydrogen (heavy) atom for the ligands, and found that it was comparable to that of kinase or protease inhibitors. Clearly with sound med chem efforts, it won't be too difficult to have such drugs. Interestingly, since the molecules occupy about half the binding site that the parts of the native protein partner do, their ligand efficiency is almost twice.

Myth 3: Small molecules disrupting PP interactions won't be potent

Just not true. Almost all the molecules found in the cited examples had mid to low nanomolar Ki values, almost as good as the binding constants for the partner proteins.

Myth 4: Screening would not help find novel small molecule PP modulators

Again, not true. Most of the cited molecules were found by HTS. Interestingly, there may be even more wealth in HTS than we have now. As the authors explain, HTS hits are fundamentally going to be limited by chemotypes present in the libarries. After all we can do only as well as chemical space in existing libraries. Existing libraries contain many molecules targeted against kinases, GPCRs and other well-known targets for which common privileged structures have been deduced. But because of the diversity of PP interactions, it is improbable that common scaffolds will exist for disrupting them, and libraries will have to contain novel scaffolds to get better hits. Given this fact, it's impressive and encouraging that the existing libraries could come up with such potent structures for disrupting a few PP interactions. Remarkably, even with such different scaffolds, the ligand efficiency remains more or less constant for the cases studied.

Clearly the field of small-molecule-PP interactions is alive and kicking. In the next few years, hopefully computational, screening and NMR approaches will converge to discover novel agents for these important processes.

Wells, J.A., McClendon, C.L. (2007). Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature, 450(7172), 1001-1009. DOI: 10.1038/nature06526

Elegant switches in an E. Coli ion channel

2008-05-21T07:46:00.000-07:00

Molecular dynamics simulations comprise one of the most important tools in the armamentarium of chemists and biologists. Initially a curiosity for theoretical scientists, MD is now an explanatory and predictive tool in chemistry, biology, materials science, engineering and even weather prediction. In the field of biology, some masters such as Martin Karplus have honed this tool to the status of an art. While great leaps have been made in the context of methods, hardware, software and applications in this field, much remains to be still done. One of the reasons is that even now, running microsecond MD is computationally quite expensive. But many important biological events involving biomacromolecules take place on this time scale, thus making the achievement of efficient microsecond MD simulations important.

Writing in Science, scientists from D. E. Shaw company, Columbia and the Hebrew University of Jerusalem have a lovely paper documenting the application of the new and innovative MD program Desmond to the dynamics of a bacterial ion channel that transports Na+ ions using the electromotive force generated by proton transport. Desmond is supposed to enable efficient microsecond MD. It is going to be interfaced with the Maestro interface developed by Schrodinger and is due to be released this year I believe. Currently the fastest MD program on a single processor is GROMACS. While head to head comparisons of GROMACS and Desmond have not been reported to my knowledge, Desmond is supposed to be very fast on multiple processors, a facility that many can now afford to have.

In the Science paper, the researchers apply Desmond to understand the transport mechanism of the Na+/H+ antiport ion channel in E. Coli. This protein is crucial for E. Coli to survive harsh conditions of pH, alkalinity, and ionic lithium environments. The authors basically focus on the protonation state of certain key aspartates and find something pretty interesting- two crucial aspartates essentially act as switches that decide whether Na+ ions would be transported to the cytoplasm or to the periplasm. Using many long MD simulations involving different protonation states, the authors discovered that one of the carboxylates always has to be protonated. This acts like a "master aspartate" switch. Once this switch's state is set, it's the state of the other switch that decides the direction of transport- protonated leads to expulsion of the Na+ into the periplasm, while deprotonated leads to expulsion into the cytoplasm.

The observation reminded me of a high-school "staircase lighting" electricity experiment. A master switch had to be always on for the assembly to work. The On/Off state of another switch would then govern whether current flowed or not.

Using this discovery as the basis for exploring further conformational changes related to it, the authors come up with an elegant stepwise mechanism for the transport of Na+ and H+ ions that accounts for the observed stoichiometry of one Na+ ion for every two H+ transported. Using free energy perturbation binding affinity calculations, the authors also rationalize the channel's observed selectivity for Na+ over K+, and slightly for Li+ over Na+.

There is also a a very intriguing explanation for the pH sensitivity of this ion channel. The crystal structure of the channel is solved at pH 4, and it is inactive at this pH. How does the channel get activated at higher pH? To explore this, the authors do something simple but quite clever. They first identify all the key aspartates lining the channel and determine their pKa values. Perhaps not surprisingly, the pKa values of these are abnormally high- not an uncommon observation for amino acids in the unusual environments in protein interiors. They then selectively deprotonate one aspartate keeping all others protonated and do MD on the resulting structures. If there is a key "pH sensing" aspartate, its protonation state will likely govern a conformational change from inactive-active. Indeed, one aspartate, D133, turns out to modulate a conformational change involving two helices when it is deprotonated. Crucially, this results in the "master aspartate" noted above to move away from the Na+ entry/exit pathways. Thus it can no longer bind the ion, resulting in an inactive channel. Mutagenesis studies also support the observations.

A neat conclusion from a beautiful set of experiments. A fascinating example of how nature essentially and surprisingly uses high-school chemistry to modulate movements in complex proteins. And a highly successful and inspiring example of how efficient, long MD simulations can shed light on these crucial processes.

Arkin, I.T., Xu, H., Jensen, M.O., Arbely, E., Bennett, E.R., Bowers, K.J., Chow, E., Dror, R.O., Eastwood, M.P., Flitman-Tene, R., Gregersen, B.A., Klepeis, J.L., Kolossvary, I., Shan, Y., Shaw, D.E. (2007). Mechanism of Na+/H+ Antiporting. Science, 317(5839), 799-803. DOI: 10.1126/science.1142824

Computational modeling of GPCRs: not too bad

2008-05-12T12:31:00.000-07:00

GPCRs constitute one of the most important family of proteins in our body, both for their innate importance in signal transduction and neurotransmission, and as important targets for drugs. Many of the important drugs on the market today target GPCRs. And yet there is an unusual gap between knowledge and application when it comes to this important family. That's because only two crystal structures of GPCRs are known. And one of them was derived last year, so there's been a real dearth of structural information about GPCRs for a long time.

We do know something about many GPCRs, however. We know that they are 7-TM receptor-spanning proteins. And the two structures we do know about shed valuable insight on GPCR function. One is rhodopsin which has been around for a while. Then there was big news last year about the second important GPCR whose structure was determined- the ß-2 adrenergic receptor.

Given the paucity of structural information and the availability of two structures, a logical question is whether computational modeling can teach us something new about GPCRs whose structure is unknown. To this end, Stefano Costanzi at the NIH did a nice set of experiments which he published in J. Med. Chem. He attempted to build a homology model of the adrenergic receptor based on the sequence and structure of rhodopsin. Since we now have a crystal structure of the adrenergic GPCR, we have something concrete to compare modeled structures and ligand orientations to.

Costanzi was particularly interested in knowing how a small molecule-carazolol- binds to the modeled GPCR. This is important both from a structural and functional drug-discovery point of view. His results indicate that we can do pretty well. In essence, he built two models of the receptor, one of them de novo. While the models were similar to rhodopsin in the conserved regions, the important differences were with respect to a loop that flaps on top of the protein. In one model the loop was buried inside the binding pocket, and in the other one it was open. Docking of carazolol into the buriled-loop model using the Glide program from Schrodinger gave a binding pose in which the ligand was, not surprisingly, buried deeper into the cavity compared to the crystal structure. This was naturally the effect of the loop blocking part of the pocket. The other model in which the loop was not buried gave much better results. Curiously, the ligand was buried a little deep in the pocket even in this model, even though it was much less buried compared to the previous one. It still misaligned considerably with the experimental pose. Inspection revealed that there was a Phe in the pocket which was anti in the model but +gauche in the crystal structure. Since the corresponding residue in rhodopsin was Ala, there was no way this unusual conformation could have been predicted ab initio. Fixing the conformation of this residue to +gauche suddenly gave excellent alignment with the ligand orientation in the crystal structure.

An instructive piece of work that shows that homology modeling and docking of ligands into GPCRs of unknown structure can be fruitful. However, it also indicates caveats like the Phe conformation which are hard to account for de novo. However, since structures of members in this important family of proteins are unavailable anyway, even some predictive ability might be welcome in this area.

Costanzi, S. (2008). On the Applicability of GPCR Homology Models to Computer-Aided Drug Discovery: A Comparison between In Silico and Crystal Structures of the ß2-Adrenergic Receptor. Journal of Medicinal Chemistry DOI: 10.1021/jm800044k

Hexacyclinol as a test case: ab initio C13 chemical shift prediction

2008-05-05T18:55:00.000-07:00

Anybody heard of this natural product called hexacyclinol and how doubts were raised about its synthesis and structure? Kidding obviously. I am going to assume that any organic or related chemist who has not heard of hexacyclinol has not heard of Robert Burns Woodward by default.

Well, in any case, recall that the high point of that deb(acle)ate was Scott Rychnovsky's demonstration by using quantum chemical prediction of C13 chemical shifts that a structure quite different from hexacyclinol fit the C13 NMR data much better compared to JJLC's structure. To do this Rychnovsky used DFT methods and the mpw1pw91 functional which was tried, tested and proven to be a reliable tool for C13 chemical shift prediction by Bifulco and others. (excellent general review here which deals with calculation of both shifts and 2 and 3 bond homo and heteronuclear coupling constants)

The point of value for the organic chemist from the whole exercise was the fact that C13 chemical shift prediction could not just be used to distinguish regioisomers whose identity might be ambiguous but, based on Rychnovsky's analysis, also can be used to correctly assign misassigned C13 peaks. To me this is the greatest benefit of the analysis for the practicing organic chemist.

Henry Rzepa and Christopher Braddock at Imperial College in London have now demonstrated the application of this increasingly valuable method to the correct assignment of some interesting halogenated natural products called obtusallenes. In this case there was ambiguity about the positions of a chlorine and a bromine. The proton chemical shifts were very similar and could not be used to assign the positions. Rzepa and Braddock used the mpw1pw91 functional not just for the chemical shift calculation but also for the optimization. Fast computational power has made this possible now. The bottom line is that average C13 shift deviations are much more for the incorrect regioisomer. Using the method, the authors also re-assigned two ambiguous peaks. In addition, they determine that the 6-31G (d,p) basis set gives some errors for certain functional groups while using the aug-cc-pVDZ basis set (all that's left to say is "warp speed" now) basis set eliminates these errors.

A short, neat demonstration of the increasing value of quantum chemical NMR prediction methods for the practical organic chemist.

Braddock, D.C., Rzepa, H.S. (2008). Structural Reassignment of Obtusallenes V, VI, and VII by GIAO-Based Density Functional Prediction. Journal of Natural Products, 71(4), 728-730. DOI: 10.1021/np0705918

It's Clay Time: The Origins of "Silicon-Based" Life

2008-04-22T19:10:00.000-07:00

Every thinking man or woman seems to have their own favourite theory of origins of life. Like clothes fashions and hairstyles, in this case one is sometimes reduced to mere irrational favoritism at the end, devoid of real substantial logic. The reason is straightforward; origins might be the biggest unsolved problem in chemistry and biology of all time, but it deals with things billions of years backwards in time which we can hardly mimic, let alone observe directly. Modern life with its machinery of DNA, RNA and proteins provides tantalizing clues and yet no answers. Which came first? Genes, protein, or something else?

For many years now, I have placed my own bets on an origins theory about which I first read in mathematician John Casti's sweeping survey of the big problems facing modern science- Paradigms Lost. The theory which Casti says is his favourite is mine too because of a sane reason that Casti provides- the venerable (perhaps too much so) principle in science called Ockham's Razor, which simply says that "entities should not be unnecessarily multiplied" or, "Simple is best". When one is confronted with several explanations that lead to the same conclusion, the simplest one is likely to be the correct one. Well, not really, but if we are going to proceed on hunches anyway, why not choose the simplest one. The premise is simple here; DNA, RNA and proteins are too complicated for us to think about how they could have arose on our primordial planet. Better to start with simple, possibly inorganic substances that were abundant on early earth.

Enter the British biochemist Alexander Graham Cairns-Smith (CS from now on) who came up with a "life from clay" theory. CS conjectured that it makes much more sense to think of life evolving from simple inorganic materials, especially crystals, rather than from organic molecules. His hypothesis was straightforward and dealt with two familiar properties of crystals that are very similar to what we think are essential properties for anything to be called "living"- reproduction and natural selection. Crystals by their very nature are periodic, extending regularly in infinite planes, "reproducing" if you will in three dimensions. Crystals are also subject to defects and impurities. The beauty of crystallization is that impurities or defects always exist. The key principle that CS recognized was that these impurities or defects, if they confer some benefit like better 'stickiness' or mechanical properties, would be propagated in the way that beneficial mutations are propagated through evolution. Gradually, the old, decrepit crystal will be left behind and this impure crystal with its superior properties would take over. Ergo crystal evolution.

Which crystal would be preponderant on primitive earth to possibly do such a job? Why, ordinary clay of course. Silicon dioxide in its myriad manifestations. For one thing, it's always been extremely abundant for billions of years on earth. Secondly, it comes in an amazing variety of polymorphs, allotropes and geometries. Silicon is a wonderful element. It can mix and match with an untold number of cations and anions and form quixotic 3D structures. It can act as a scaffold for many other substances. One can spend a lifetime studying silicates. Science fiction writers have long since fantasized about a silicon-based biosphere. But here silicon has been theorized to be the seed of life in quite another fashion.

According to CS, crystals of silicon easily harbor organic impurities in them. With time, these impurities will grow along with the crystal. At some point as noted above, the organic molecules will have an evolutionary benefit possibly because of their greater flexibility, branching power, stickiness due to hydrophobic interactions and multiple bonding characteristics. Gradually, like a snake shedding its old skin, the organic molecules will simply grow faster and stronger and leave their old siliconian parentage behind. In time, what you will have would be an organic crystal. Now think about DNA, RNA, proteins and suchlike forming from such organic entities. At least it's a little easier than before, where one had to conjure up these biochemical wonders from inorganic gunk.

CS now has an article (cited below) expounding upon his "life from clay" theory. The most compelling hypothesis I found in this article is that if crystals are to serve as a template for making copies, replication should have to be edgewise and not in other directions. CS cites DNA as an example and considers a simplified version of it with the sugar-phosphate backbone removed and hydrogen bonds removed too. Now it's just a stack of colored plates, with each color corresponding to a base. It's pretty obvious that copying can take place only along the edge, as CS's figure shows:

CS then gives some example of silicate minerals which could have such edges acting as templates. Edges could come together because of electrostatic or non-polar interactions. They could be jagged or smooth. Finally, you need not have only one kind of edge. A whole panoply of silicates with their varied kinds of edges could compete for sheet formation and consequent duplication. After that, the aforementioned impurities and defects could ensure natural selection and organic crystal formation. Life could then piggyback on the surfaces of these crystals.

CS also ponders if one could have inorganic enzymes that could possibly speed up the arrival of life. One does not imagine such enzymes to have the flexibility of organic ones. On the other hand as CS says, inorganic enzymes are already used in industry as superior catalysts. Clay crystals could similarly act as catalysts and speed up all kinds of reactions. By the way, CS is of the "genes first" camp as opposed to the "metabolism first" camp. However, CS's idea is one of metabolism facilitated by "inorganic genes" that replicate and improve their stock. I personally find the idea of crystal surfaces very alluring; after all so many reactions are speeded up on surfaces- Haber's ammonia synthesis which partly led to the latest Nobel Prize for Gerhard Ertl immediately comes to mind. If one is looking for simple chemical entities that could kick-start and speed up reactions, inorganic crystal surfaces sure seem to be good candidates.

CS's most tantalizing thoughts are about such clay-based life-inducing reactions happening even today, quietly in the nooks and crannies of nature. While such reactions would be hard to discover and compared to our life spans would be trivial and temporary, it is fascinating to think that the echoes of the origins of life still resonate all around us. Score one for Si.

Cairns-Smith, A. (2008). Chemistry and the Missing Era of Evolution. Chemistry - A European Journal, 14(13), 3830-3839. DOI: 10.1002/chem.200701215

Force field dependence of conformational energies

2008-04-15T06:40:00.000-07:00

This paper explores the fallacy of determining conformational energies for polar organic molecules from molecular mechanics force fields. Using Taxol as a test case, it investigates how different force fields can produce downright contradictory results for energetic rankings of Taxol conformations.

The bottom line is simple; do NOT trust energies from force fields. Trust geometries. In case of energies force fields usually overemphasize electrostatic interactions because of lack of explicit solvent representation. Thus sometimes even geometries can be warped because of electrostatics overwhelming the optimization. The one thing force fields are good at calculating on the other hand is sterics.

Running a "complete" conformational search with multiple force fields will usually give you completely different geometries for the global minimum, or at least slightly different ones (depending on the molecule). Thus, trusting the global minimum conformation from any one force field is a big fallacy. Thinking that that global minimum will be the true global minimum in solution is nothing short of blasphemy. And for a bioactive molecule, thinking that the global minimum from a force field search will be the bioactive conformation is just...well, that just means you have been seduced by the dark side of the force field.

Lakdawala, A., Wang, M., Nevins, N., Liotta, D.C., Rusinska-Roszak, D., Lozynski, M., Snyder, J.P. (2001). . BMC Chemical Biology, 1(1), 2. DOI: 10.1186/1472-6769-1-2

Magic without Magic: John Archibald Wheeler (1911-2008)

2008-04-14T14:37:00.000-07:00

Image copyright: NNDB, Soylent communications (2008)

When I heard from a friend about John Wheeler's death this morning, I grimaced and actually loudly let out an exclamation of pain and sadness. That's because not only was Wheeler one of the most distinguished physicists of the century but with his demise, the golden era of physics- that which gave us relativity, quantum theory and the atomic age- finally passes into history. The one consolation is that he lived a long and satisfying life, passing away at the ripe age of 96. It was just a few weeks ago that I asked a cousin of mine who did his PhD. at the University of Texas at Austin whether he ever ran into Wheeler there. My cousin who himself is in his fifties said that Wheeler arrived just as he was finishing- after retirement from Princeton university.

Wheeler was the last survivor of that heroic age that changed the world and he worked with some true prima donnas. He was an unusually imaginative physicist who made excursions into exotic realms; particles traveling backwards in time, black holes, time travel. A list of his collaborators and friends includes the scientific superstars of the century- Niels Bohr, Albert Einstein, Enrico Fermi, Edward Teller and Richard Feynman to name a few. To the interested lay public, he would be best known as Richard Feynman's PhD. advisor at Princeton.

Wheeler is famous for many things- mentor to brilliant students, originator of outrageous ideas, coiner of the phrase "black hole", outstanding teacher and writer. My most enduring memory about him is from John Gribbin's biography of Feynman. Gribbin recounts how Wheeler in his pinstriped suits used to look like a conservative banker, a look that belied one of the most creative scientific minds of his time. The fond incident is about the playful rogue Feynman being summoned into Wheeler's office for the first time. In order to underscore the importance of his time, Wheeler laid out an expensive pocket watch in front of Feynman. Feynman who had a congenital aversion to perceived or real pomposity took note of this and during their next meeting, laid out a dirt-cheap watch on the table. After a moment of stunned silence, both professor and student burst into loud laughter, laughter that almost always accentuated their discussions on physics and life thereafter. Feynman and Wheeler together derived a novel approach to quantum mechanics that involved particles radiating backwards in time. Wheeler also initiated the discussion of the notorious sprinkler problem described by Feynman in Surely you're joking Mr. Feynman

John Wheeler was born in Florida to strong-willed and working class parents. After obtaining his PhD. from Johns Hopkins at the age of 21, he joined Princeton in 1938 where he remained all his working life. Princeton in 1938 was a mecca of physics, largely because of the Institute for Advanced Study nearby which housed luminaries like Einstein, John von Neumann and Kurt Godel. Wheeler knew Einstein well and later sometimes used to hold seminars with his students in Einstein's home. As was customary for many during those times, Wheeler also studied with Niels Bohr at his famous institute in Copenhagen. In 1939 Bohr and Wheeler made a lasting contribution to physics- the liquid drop model of nuclear fission. According to this, the nucleus of especially heavy atoms behaves like a liquid drop, with opposing electrostatic repulsive forces and attractive surface tension and strong forces. Shoot an appropriately energetic neutron into an unstable uranium nucleus and it wobbles sufficiently for the repulsive forces to become dominant, causing it to split. The liquid drop model explained fission discovered earlier. The mathematics was surprisingly simple yet remarkably accurate. Bohr was one of Wheeler's most important mentors; in his biography he describes how he used to have marathon sessions with Bohr, with the great man often insisting on walking around the department, tossing choice tidbits to Wheeler ambling at his side. Caught up in the recent heated debate about the philosophical implications of quantum theory, Wheeler argued the nature of reality with both Einstein and Bohr.

When World War 2 began, Wheeler like many physicists was recruited into the Manhattan Project. Because of his wide-ranging intellect and versatility, he was put in charge as scientific consultant to Du Pont, who was building plutonium producing reactors at Hanford in Washington state. There Wheeler tackled and solved an unexpected and very serious problem. As the reactors were transforming uranium 238 into the precious plutonium, the process suddenly shut down. After some time it started up again. Nobody knew what was happening. Wheeler who was the resident expert worked out the strange phenomenon in an all-night session. What was happening was that some of the fission products produced had a big appetite for neutrons and were therefore "poisoning" the chain reaction. After some time when these products had decayed to sufficiently low levels, they would stop eating up the neutrons and the reactor would start again. This was one of the most valuable pieces of information gained during plutonium production. Ironically, the omission of this information in a second edition of a government history of atomic energy released just after the war alerted the Soviets to its importance. Working on the Manhattan Project was also a poignantly personal experience for Wheeler; the bomb could not save his brother Joe who was killed in action in Italy in 1944. Wheeler later also worked with Edward Teller on the hydrogen bomb, a decision about which he was fairly neutral because he thought it was necessary at the time to stand up to the Soviets.

After the war Wheeler embarked on a lifelong quest in a completely different field and became a pioneer in it- general relativity. He took up where Robert Oppenheimer had left off in 1939. Oppenheimer had made a key contribution to twentieth century physics by first describing what we now know as black holes. Strangely and somewhat characteristically, he lost all interest in the field after the war. But Wheeler took it up and reinitiated a bona fide revolution in the application of general relativity to astrophysics. As his most enduring mark, he coined the word "black hole" in the 1960s. Wheeler became the scientific godfather of a host of other physicists who became pioneers in exploring exotic phenomena- black holes, wormholes, time travel, multiple universes. His most successful student in this regard has been Kip Thorne whose wonderful book expounds on the golden age of relativity. Hugh Everett, the tragic genius who invented multiple universes and the Lagrange multipliers method for optimization problems before plunging into paranoia and depression, left behind choice fodder not just for science but for science fiction; parallel universes have been a staple of our collective imagination ever since then. In retrospect, Wheeler followed his mentor and did for astrophysics what Bohr had done for quantum theory- he served as friend, philosopher and guide for a brilliant new generation of physicists.

Wheeler also was known as an outstanding teacher. His mentoring of Feynman is well-known, and he devoted a lot of time and care to teaching and writing. Along with his students Kip Thorne and Charles Misner, Wheeler produced what is surely the bible of general relativity, Gravitation, a mammoth book running more than a thousand pages whose only discouraging feature may be its length. The book has served as advanced introduction to Einstein and beyond for generations of students. Wheeler also co-authored Spacetime Physics, an introduction to special relativity which even I have timidly managed to savor a little during my college days. His own autobiography, Geons, Black Holes and Quantum Foam: A Life in Physics is worth reading for its evocation of a unique time of the last century, as well as for fond anecdotes about great physicists.

But many people will remember Wheeler as a magician. Sitting in his office in his pinstriped suits, Wheeler's mind roamed across the universe straddling everything from the smallest to the largest, exploring far-flung concepts and realms of the unknown. He grappled with the interpretation of quantum mechanics and was an early proponent of the anthropic principle- in John L Casti's magnificent book Paradigms Lost, Casti quotes Wheeler analogizing observer-created reality with the game in which a group of people asks someone else to guess an object they have in mind by asking questions, except that in the modified version of this game, they let the object be created during the process of questioning. With his mentor Bohr's enduring principle of complementarity as a guide, Wheeler produced esoteric ideas that nonetheless questioned the bedrock of reality. Wheeler was entirely at home with such bizarre yet profound concepts that still tug at the heartstrings of physicist-philosophers. Only Wheeler could have introduced paradoxical and yet meaningful phrases like "mass without mass". In celebration of his sixtieth birthday, physicists produced a volume dedicated to him with a title that appropriately captured the essence of his thinking- "magic without magic".

John Wheeler was indeed a magician. He made great contributions to physics, served as its guide for half a century and motivated and taught new generations to wonder at the universe's complexities as much as he did. He was the last torch-bearer of a remarkable age when mankind transformed the most esoteric and revolutionary investigations into the universe into forces that changed the world. He will be sorely missed.

Large-scale effects of a nuclear war between India and Pakistan

2008-04-09T17:24:00.000-07:00

Back in the days when the Cold War was simmering, one of the rather depressing activities scientists and other officials used to engage in was to conjure up hypothetical scenarios involving nuclear war between the US and the Soviet Union and try to gauge its effects. Such theorizing was often done behind closed doors in enclaves like the RAND corporation. In the early 1960s, RAND's Herman Kahn wrote an influential and morbid book called On Thermonuclear War. Kahn, a portly, overweight, brilliant Strangelovian character was said to be a possible inspiration for the good doctor in Kubrick's brilliant movie Dr. Strangelove. In fact Kubrick supposedly read Kahn's 600 page book in detail before working on the movie (A recent biography of Kahn sheds light on this fascinating man)

The book ignited a controversy about nuclear conflict because Kahn's thesis was that nuclear war fought with thermonuclear weapons was winnable, thus possibly upping the ante for the nuclear powers. Kahn used many quite rather incomplete arguments to make the not entirely unreasonable point that while such a war would be horrific, it would not mean the end of humanity. The survivors may not necessarily envy the dead. But of course Kahn was speculating based on the then best available scientific data along with his own idiosyncratic biases. One of the biggest effects of a nuclear explosion is to send up debris in the atmosphere, and climate models in the 60s were in a primitive stage to help with predicting any such effects. Also, nuclear effects start wide-ranging fires and, on the rare occasions when the conditions are right, gruesome firestorms; a firestorm is the nearest thing to hell that one can imagine. Fires can account for up to 60% of the damage from a nuclear explosion. While the thermal effects constitute about 35% of the total effects from a typical nuclear air-burst (blast effects constitute about 50%), thermal effects unlike others can naturally sort of self-perpetuate through starting successive fires. According to some analysts, state department officials in the 50s calculating nuclear weapons effects neglected the devastation due to fire, which made their results underestimates. Any realistic simulation of a nuclear explosion has to take into account effects due to fires.

The debate about the effects of a global thermonuclear war was galvanized in the 1980s when Carl Sagan and his colleagues proposed the idea of nuclear winter, in which dimming of sunlight because of the debris from nuclear explosions would lower the average temperature at the surface of the earth. Among other effects, this combined with the resulting darkness would devastate crops, thus bringing about long-term starvation and other catastrophes. Since then, scientists have been arguing about nuclear winter.

What has changed between 1980 and now though is that climate models including general circulation models have vastly improved and computational power to analyze them has exponentially gone up. Although we still cannot predict long-term climate, we now have a reasonably good handle on quantifying the various forcings and factors that affect climate. Thus for the last few years it has seemed worthwhile to predict the effect of nuclear war on our climate. Now scientists working at the University of Colorado and NOAA have come up with a rather disconcerting study in the Proceedings of the National Academy of Sciences indicating the effects of a regional nuclear war on global climate. A typical scenario is a war with 50 warheads of 15 kilotons each (about the yield of the Hiroshima bomb) between India and Pakistan, a conservative estimate. There have been a few such studies published earlier but this one looks at the effects on the ozone layer, the delicate veneer that protects life from UV radiation.

The researchers' main argument is that there is a tremendous mass of soot that is kicked up tens of kilometers into the atmosphere during a nuclear explosion. The study seems to be carefully done, taking into account various factors acting to both reinforce and oppose the effects of this soot. The number they cite for the amount is about 5Tg (teragrams, a teragram being 10^12 grams) which is a huge number. They account for local fallout of the soot through rain as being about 20%. What happens to the remaining 4Tg is the main topic of investigation. According to the model, this enormous plume of soot is intensely heated by sunlight. By this time it has entered the upper layer of the troposphere and snakes up into the lower stratosphere where the ozone layer is situated, it is radiating heat that disrupts the delicate balance of chemical reactions that produce and get rid of ozone, reactions that have now been well-studied for decades. These involve the interaction of radical species of oxygen, nitrogen and halogens with ozone that sap the precious molecule away. The bottom line is that this heat from the hot soot vastly increases the rate of reactions that produce these species and eat up the ozone at that altitude, thus depleting the layer. The soot lingers around since removal mechanisms are slow at that height. The heat also encourages the formation of water vapour and its consequent break up and reaction with ozone, thus further contributing to the breakdown. The researchers also include circulation of water vapour and other gases in the global atmosphere, and how this circulation will be affected by the heat and the flow. Nitrogen oxides generated by natural and human processes have already been shown to deplete ozone, and the heated soot will also intensify the rate of these processes.

The frightening thing about the study is the magnitude of the predicted ozone loss due to these accelerated processes; about 20% globally, 40% at mid latitudes and up to 70% at high latitudes. Also, these losses would last for at least five years or so after the war. These are horrifying numbers. The ozone layer has evolved in a synergistic manner over hundreds of millions of years to wrap up life in a protective blanket and keep it safe. What would the loss of 40% of the ozone layer entail? The steep decline would allow low wavelength UV radiation which is currently almost completely blocked out to penetrate the biosphere. This deadly UV radiation would have large-scale devastating effects including rapid increases in cancer and perhaps irreversible changes in ecosystems, especially aquatic ones. The DNA effects documented by the researchers are appalling- up to 213% increases in DNA damage with respect to normal levels, with plant damage up to 132%. In addition, the increased UV light would hasten the normal decomposition of organic material, further contributing to the natural balance of the biosphere. The phenomenon would indeed be a global phenomenon. Decomposition of the soot is thought to be negligible.

Now I am no atmospheric scientist, but even if we assume that some of these estimates end up a little exaggerated, it still seems to me that effects on the ozone layer could be pretty serious. If I had to guess, I would think that there could be uncertainty in estimating how much soot is produced, how much goes up and to what altitude, and how long it stays there. What seems more certain are the effects on the well-studied radical reactions that deplete ozone. Some elementary facts seem to reinforce this in my mind- carbon has a very high sublimation point and can get heated up to high temperatures, the energy radiated by a hot body goes as the fourth power of the temperature, and from college chemistry I do remember the rule of thumb that on an average, the rate of a reaction doubles with a 10 degrees centigrade temperature rise. The estimates of rate increases made by the authors seem reasonable to me.

What is most disconcerting about the study is that it involves a rather "small" nuclear exchange that takes place in a localized part of a continent, and yet whose effects can affect the entire world. "Globalization" acquires a new and portentous meaning in this context. India and Pakistan can both easily field 50 weapons each of 15 kilotons yield, if not now, in the near future. In addition to this global-scale devastation of the ozone layer, it would be unthinkable to imagine the more than 10 million people dying in such a conflict, as well as total devastation of public systems and the food supply. Herman Kahn might have thought that nuclear war is "survivable". Well, maybe not exactly...

Reference and abstract for those who are interested:
Mills, M.J., Toon, O.B., Turco, R.P., Kinnison, D.E., Garcia, R.R. (2008). Massive global ozone loss predicted following regional nuclear conflict. Proceedings of the National Academy of Sciences, 105(14), 5307-5312. DOI: 10.1073/pnas.0710058105

"We use a chemistry-climate model and new estimates of smoke produced by fires in contemporary cities to calculate the impact on stratospheric ozone of a regional nuclear war between developing nuclear states involving 100 Hiroshima-size bombs exploded in cities in the northern subtropics. We find column ozone losses in excess of 20% globally, 25–45% at midlatitudes, and 50–70% at northern high latitudes persisting for 5 years, with substantial losses continuing for 5 additional years. Column ozone amounts remain near or <220 Dobson units at all latitudes even after three years, constituting an extratropical "ozone hole." The resulting increases in UV radiation could impact the biota significantly, including serious consequences for human health. The primary cause for the dramatic and persistent ozone depletion is heating of the stratosphere by smoke, which strongly absorbs solar radiation. The smoke-laden air rises to the upper stratosphere, where removal mechanisms are slow, so that much of the stratosphere is ultimately heated by the localized smoke injections. Higher stratospheric temperatures accelerate catalytic reaction cycles, particularly those of odd-nitrogen, which destroy ozone. In addition, the strong convection created by rising smoke plumes alters the stratospheric circulation, redistributing ozone and the sources of ozone-depleting gases, including N2O and chlorofluorocarbons. The ozone losses predicted here are significantly greater than previous "nuclear winter/UV spring" calculations, which did not adequately represent stratospheric plume rise. Our results point to previously unrecognized mechanisms for stratospheric ozone depletion.

Profile of a fiend

2008-04-08T06:15:00.001-07:00

Plutonium: A History of the World's Most Dangerous Element- Jeremy Bernstein
Joseph Henry Press, 2007

The making of the atomic bomb was one of the biggest scientific projects in history. Some of the brightest minds of the world worked against exceedingly demanding deadlines to produce a nuclear weapon in record time. To do this, every kind of problem imaginable in physics, chemistry, metallurgy, ordnance and engineering had to be surmounted. Many of the problems had never been encountered before and challenged the ingenuity and perseverance of even the best of the brightest.

To accomplish this feat, human, material and monetary resources were poured in on a scale unsurpassed till then. Factories were constructed at Oak Ridge, Los Alamos and Hanford that were bigger than anything built until then. The resources required were staggering; at one point the Manhattan Project was using 70% of the silver produced in the United States. Steel production in the entire nation had to be ramped up to fulfill the needs of the secret laboratories. Extra electricity on a national scale had to be generated to power the hungry reactors and electromagnetic separators. The factories at Oak Ridge were giant structures; one of them was a whole mile under one roof. The gargantuan factories and the resulting employment increased the population of the small town from 3000 to about 75,000. At the end of the war, hundreds of thousands of people and an estimated 2 billion 1945 dollars had been spent on the biggest technical project in history. The entire country had had to be mobilized for it. In just three years, the scale of the project was consuming about as many resources as the US automobile industry, an astonishing achievement. Only the United States could have done something like that at the time.

Of all the myriad and complex problems involved in the project, two stand out for their formidable complexity and difficulty. One was the separation of uranium-235 from its much more abundant cousin uranium-238. The differences between the masses of the two isotopes is so small that at the beginning, nobody believed that it could be done. Indeed, the atomic bomb effort in Germany largely stalled because its leaders could not think of any way this could be done in any reasonable time. An entire town had to be constructed at Oak Ridge to surmount this problem. Even today this is probably the single-hardest problem for anyone wanting to construct an atomic bomb from scratch.

However, the uranium separation problem was at least anticipated at the very beginning. Compared to this, the second problem was completely unexpected. It involved a material from hell that nobody had seen before. This material was highly unstable and difficult to work with, intensely radioactive, and its discovery was one of the most closely-kept secrets of all time. The material would play a decisive role in the project and in the nuclear arms race that was to ensue. Today, its shadow looms large over the world. This material is plutonium.

Now in a succinct and readable book, well-known physicist and historian of science Jeremy Bernstein tracks the history of a diabolical fiend. Bernstein has earlier written biographies of Oppenheimer and Hans Bethe and a recent book on nuclear weapons. He is an accomplished veteran physicist who has known some of the big names in physics of the century, Oppenheimer and Bethe included. Bernstein is a fine writer who recounts many interesting anecdotes and bits of trivia. But he does have one annoying habit; his constant tendency to digress from the matter under consideration. He could be talking about one event and then suddenly digress into a four page life history of a person involved in that event. One gets the feeling that Bernstein wants to put his opinion of every small and sundry event from the life of every scientist he has met or heard of on record. At times, the connections he unravels are rather tenuous and long-winded. Readers could be forgiven for finding Bernstein's digressions too many in number. But at the same time, those interested in the history of physics and atomic energy will be rewarded if they persevere; most of Bernstein's forays, though exasperating, are also quite interesting. In this particular case, they weave a complex story around a singular element.

Plutonium was discovered by the chemist Glenn Seaborg and his associates at Berkeley in 1940. In a breathtakingly productive career, Seaborg would go on to discover nine more transuranic elements, advise four US presidents, win the Nobel prize, win enough other awards and honors to have an entry in the Guinness Book, and have an element and asteroid named after him while still alive. After fission was discovered, it was hypothesized that elements with atomic numbers 93 and 94 might also behave like uranium. In 1939 Seaborg was a young scientist working at Berkeley when he heard about the discovery of fission. In the next year he performed many experiments on fission at Chicago and Berkeley. In 1940, another future Nobel laureate named Edwin McMillan discovered a radioactive element past uranium with a postdoc, Philip Abelson. In logical sequence they named it neptunium. Abelson and McMillan's June 1940 paper on neptunium was the last paper to come out of the United States on fission and related issues; the need for secrecy in such matters had already been realised by senior scientists. There matters stood until December 1941- a decisive time due to Pearl Harbor- when Seaborg, McMillan and their associates Joseph Kennedy and Arthur Wahl discovered element 94 by using tedious and clever chemical techniques. After uranium and neptunium, Seaborg decided to name the new element after Pluto- the god of fertility but also the god of the underworld.

Concomitantly with the American effort, the Germans were also trying to understand the properties of plutonium and Bernstein devotes a chapter to their efforts and background. A resourceful German physicist named Carl Friedrich von Weiszacker had observantly noticed the dwindling and disappearance of papers from the United States after the paper by McMillan and Abelson appeared in mid 1940. He also realised the advantage of using plutonium in a nuclear weapon. But as the history of the German atomic project makes clear, Weiszacker's report was not taken too seriously, and in any case the Germans were too cash and resources-strapped to seriously pursue the production of plutonium. Notice was also taken by accomplished physicists in the Soviet Union but it was espionage that provided them with information about the real potential and importance of plutonium. The fascinating story of Soviet espionage is superbly narrated in Richard Rhodes's Dark Sun: The Making of the Hydrogen Bomb.

Plutonium was soon isolated in gram quantities by Seaborg's team and its enhanced fissile properties were investigated. After the enormous problems with separating U-235 were realised, the great advantage of plutonium became obvious; plutonium being a different element, it would be relatively easy to separate from its parent uranium, thus avoiding the difficulty of isotope separation. After plutonium was discovered, it was found that it is even more prone to fission than uranium. Compounded with its relative ease of separation, this property of plutonium made it a key material for a nuclear weapon. It was also realised however that many tons of uranium would have to be bombarded with neutrons to produce pounds of the precious element. By 1942, it was known that at least a few kilograms of both uranium and plutonium would be needed for the critical mass of a bomb. To this end enormous factories were constructed at Oak Ridge (for enriching uranium) and reactors at Hanford in Washington state (for producing plutonium) in 1943. The reactors at Hanford would keep on producing the material for thousands of nuclear warheads until the late 1980s. A secret lab at Los Alamos was concurrently established, headed by Robert Oppenheimer. He would bring a group of "luminaries" to the mesa high up in the mountains for working on the actual design of an atomic weapon.

At Los Alamos, initial designs of bombs with both uranium and plutonium involved the "gun method" wherein a plug of fissile material would be shot down at great speed along a large gun barrel into another mould of fissile material. When the two met a critical mass would suddenly materialize and fission would result in an explosive detonation. However, a fatal flaw was unexpectedly encountered in 1944. When the first few grams of plutonium arrived at Los Alamos from Hanford, it was observed that Pu-239 had a very high rate of "spontaneous" fission due to the copious presence of another isotope, Pu-240. Even today, the feature that distinguishes "reactor-grade" plutonium from "weapons-grade" plutonium is the higher presence of Pu-240 in reactor-grade material. Because of the presence of extra neutrons from spontaneous fission, a gun type bomb though it would work for U-235 would be worthless for Pu-239 since by the time the two pieces met, fission would have already started and the result would be a "fizzle", a suboptimal explosion. Because of this difficulty the whole lab was reorganised by Oppenheimer in August 1944 and experts were brought in to investigate new mechanisms for a plutonium bomb.

The result was one of the most ingenious concepts in nuclear weapons history and design- implosion. The idea was to suddenly squeeze a sub-critical ball of plutonium using high explosives into a highly compressed supercritical mass, causing fission and a massive explosion. The problem was that this microsecond compression had to be perfectly symmetrical, otherwise the Pu-239 would simply squirt out along the path of least resistance like dough squeezed within the cupped palms of our hands. To circumvent this problem would require the capabilities of some of the greatest scientists of the day. The Hungarian genius John von Neumann supplied the crucial idea of using "lenses" of explosives of differing densities to direct shock waves that would symmetrically converge onto a point, just like light through glass lenses. The concept required a paradigm shift- nobody had used explosives before as precision tools; they were generally used to blow things out, not in. Even after the idea was floated, the engineering and diagnostics obstacles were formidable. Chemist George Kistiakowsky from Harvard was put in charge of a division that would painstakingly develop the moulds for the lenses; machining had to be accurate to within microns as any air bubbles, cracks or irregularities would immediately impede the symmetrical shock wave. Another challenging device was the "initiator", a tiny ball of radioactive elements in the center of the sphere that would release neutrons right after the implosion, but not a moment before. Its design was so challenging that it is one of the few things that's still almost completely classified. One of the physicists who worked on both shock wave hydrodynamics and on initiator design was Soviet spy Klaus Fuchs. He was ironically brought in as part of a British team to replace Edward Teller, whose reluctance to pursue implosion and obsession with hydrogen bombs tested the patience of theoretical division leader Hans Bethe. Information obtained by Fuchs would prove invaluable to the Russians in building their own implosion bomb.

Compounding all of these difficulties was the hideously diabolical nature of Pu-239 itself. Chemists and metallurgists had never faced the challenge before of working with such an unusual and dangerous material. Pu-239 exists as several allotropes, different physical forms of the same element, depending upon the conditions. When one investigates the use of plutonium in a bomb and then looks at its allotropic behavior, it's almost as if nature had conspired to keep humans from using it. The reason is that at room temperature, Pu-239 exists as an allotrope named the alpha phase allotrope. The problem with this is that while it is dense, it is brittle and won't do at all for an implosion. On the other hand the allotrope of Pu-239 that is suitable for a bomb, the delta phase, exists only at 315 degrees centigrade and above. This is a catch-22 situation; the useful and machinable allotrope exists only at high temperatures while the one at room temperature is worthless. A very clever solution to this was discovered by human ingenuity; Cyril Smith, head of the metallurgy division at Los Alamos found that adding a small amount of the metal gallium to Pu-239 stabilized the valuable delta phase at room temperature. This was found only a few months before the first test of the bomb.

In the end, while the uranium bomb was reliable enough to not require testing, the implosion bomb was too novel to use without testing. On July 16, 1945, the sky thundered and a new force surpassing human ability to contain it was unleashed in the cold desert sands of New Mexico at the Trinity test site. Plutonium tested on that ominous dawn would reincarnate into Fat Man, the bomb that leveled Nagasaki in less than ten seconds.

In addition to Pu-239's unusual chemistry, there were of course its radioactive properties that make its name so dreaded for laypersons. But we have to put things in perspective. I would easily be within a kilometer of Pu-239 than within a kilometer of anthrax or VX nerve gas. Plutonium decays by emitting alpha particles and simple laws of physics dictate that these particles have a very short range. You could hold Pu on a sheet of paper in the palm of your hand and live to talk about it. The real danger from Pu-239 comes from inhaling it; it can cause severe damage to lungs and bone and cause cancer. Its half-life is 24,000 years and another law of physics dictates that half-life and radioactive intensity are inversely related. To help understand Pu-239's true nature, Bernstein narrates a fascinating study of 37 technicians and scientists at Los Alamos who ended up getting Pu-239 into their system. This group was whimsically named the "UPPU" (U Pee Pu) group as Pu-239 could be detected in their urine. The group was tested periodically at Los Alamos for many years. The verdict is clear; none of these people suffered long-term damage from Pu-239. Many of them lived long and healthy lives and some of them are still alive. As with other aspects of nuclear power, the danger from plutonium has to be carefully reasoned and objectively assessed. As with other nuclear material, Pu needs to be handled with the utmost care, but that does not mean that fears about it should outweigh benefits that one could get from its potential for providing power. There is naturally a real proliferation danger with plutonium, but even there, risks are often inflated. Terrorists will have to steal a substantial amount of Pu using special equipment from facilities which are usually heavily guarded. Stealing Pu and using it is not as easy as robbing a bank and laundering the money.

However, there are sites in the former Soviet Union where plutonium is not that heavily guarded and these will have to be secured. 5 kilograms of Pu-239 if efficiently utilised can be used for a weapon that will easily destroy Manhattan. It is very difficult to keep track of such small quantities through inspection. International collaboration will be necessary to keep track of and contain every gram of plutonium at vulnerable facilities. At the same time, power-generating plutonium is indispensable for the future of humanity. Forged on earth by human brilliance, Pu outlived its initial use. Most of the warheads in the US arsenal including thermonuclear warheads use plutonium for the fission assembly. Several hundred tons of both weapons-grade and reactor-grade plutonium have been produced and are being produced. Hundreds more sit in fuel rods immersed in huge water pools, glowing eerily with a bluish light. Plutonium production sites in the United States are facing a heavy and expensive backlog of cleanups.

Plutonium seems to be a classic case of the "careful what you wish for" adage. Glenn Seaborg would not have imagined the consequences of his discovery that hazy morning in December 1941, when after an all-night session the angry element revealed itself to a warring world, kicking and screaming from its fiery radioactive cradle. But as Richard Feynman once so lucidly put it, science is a set of keys that open the gates to heaven. The same keys open the gates to hell. Plutonium constitutes one of the keys to heaven that's given to us. Which gate to approach is entirely our choice.