George Whitesides: "Chemists - we change the way you live or die"

I don't know if I have highlighted this eminently readable quote from a review on the future of chemistry by the always interesting George Whitesides before, but it's quite memorable, not just because it dramatically illustrates how chemistry contributes to our world but also because it accurately does so.

Whitesides is talking about an old and thorny problem: how to pitch the wonders of chemistry to a public which often thinks that while physics is about the universe and biology is about life, chemistry is about glue and vitamins. How do we convince people not just of the practical utility of chemistry but also about its vast reach as the "central science". Whitesides's advice is to try out the line at the end of the following exchange on your next trans-Atlantic flight fellow passenger.

To me, the beauty of that statement is not just that it encompasses the ubiquitous and deep role that chemistry plays in human life and death but that it also satisfies a key constraint from the philosophy of chemistry: that of representing the discipline at the right emergent level. What I mean is that it would be trivial to say that the statement "We change the way you live or die" could encapsulate physics and biology even better; after all there would not be life or death without evolution, and even less so without the second law of thermodynamics. 

Yet not only does chemistry serve as the major workhorse for both evolution and the Second Law but it also contributes to life and death at a very direct level, as opposed to an abstract if very general one. The ATP, glucose and water molecules coursing through your body can put a chokehold on your very ability to live right away if their number dwindled. So can the molecules in your food supply or your environment. They are life-giving and life-depriving in a very real sense unlike the laws of physics and biology which, although they may be more generally encompassing, don't describe the system at the right explanatory level.

It is the combination of pleasing philosophical applicability and damning practical applicability that make that quote feel as satisfying to me as a Bruce Willis quote on living and dying from "Die Hard".

Enthalpy-entropy compensation and water networks

Enthalpy-entropy compensation (EEC) is an endlessly interesting phenomenon; it's the kind of topic that makes scientists either roll up their sleeves for a good fight or slowly walk away from the table. The basic idea is simple; when you are building new chemical functionality into a drug molecule to interact better with a protein (improving ∆H) you are also tying down the molecule (worsening ∆S) and constraining its movement. However since the two variables oppose each other this won't be reflected in the overall ∆G of binding which will stay the same.

Scientists have been going back and forth over the causes of EEC and now there's a new paper from George Whitesides's group at Harvard, Schrodinger and Brookhaven which sheds some light on one possible, usually neglected factor: the subtle changes in the thermodynamics of the network of water molecules surrounding a ligand. These are not the water molecules displaced by the ligand from the protein pocket (which have received considerable attention over the last decade or so) but the ones on the surface that contact the ligand on the outside.

The paper is based on a workhorse protein system that Whitesides's group has been working on for a while now - carbonic anhydrase. The protein is stable, relatively rigid, biochemically well-studied, amply expressed and easily crystallized by itself and with several ligands; all features which make it a good model system to look at the thermodynamics of binding. Whitesides's group has found out that you can have ligands with different fluorination patterns that bind to the protein and show very similar ∆Gs of binding. This is unexpected, since you expect additional fluorines to give you better entropy from the hydrophobic effect.

To explore the phenomenon the authors use two techniques; x-ray crystallography and molecular dynamics simulations. The former provides information on intermolecular interactions while the latter provides information on the thermodynamics of surrounding water molecules, more specifically about their enthalpy and entropy. The MD and thermodynamic calculations are done using the WaterMap tool from Schrodinger.

From the crystal structures the authors find that the enthalpy of binding can actually get unfavorable from the added fluorines as a result of repulsive interactions with a few oxygens in the protein. Since ∆G stays the same this means that the unfavorable ∆H in the active site might be compensated for by ∆H changes in the water network surrounding the ligand along with corresponding ∆S adjustments. In the picture above, water molecules with more favorable ∆H values are colored green while the unfavorable ones are colored red. 

Notice the difference between the three difluorinated analogs: the 4,6 analog has the most green waters, the 5,6 analog has the most red waters (and an extra red water compared to the others) and the 6,7 analog is somewhere in between. The gradation of unfavorable water molecules around the three compounds tracks well with enthalpies extracted from ITC. The entropies duly compensate. The thermodynamics of surface water molecules therefore certainly seem to be one possible reason for the EEC. It's also worth noting that the behavior of the water molecules corresponds to what you would call an "enthalpy-driven hydrophobic effect".

While we are neglecting second-order effects and while it's still hard to get quantitative agreement down to a kcal or so, I like the fact that we can eyeball such figures and at least qualitatively rank cases by favorable and unfavorable enthalpies. I also find it promising that we can actually do this kind of thing for surface water molecules which are part of a network; ten years ago most people might have thrown up their hands when asked to do this. Of course not every drug-protein binding case is going to be dictated by surface water behavior but the fact that we can at least get a semi-quantitative look at this important factor is, in my opinion, a valuable stepping stone toward the future.

Reference: 

Memo to chemists: Move away from the molecule

Megacities of the future - with their heterogeneous population and large-scale problems - will challenges the imagination of chemists (Image: Bldg Blog)

Harvard chemist George Whitesides probably does not consider himself a philosopher of chemistry, but he is rapidly turning into one with his thought-provoking pronouncements on the future of the field and its practitioners. His latest rumination is a piece in the Annual Reviews of Analytical Chemistry provocatively titled "Is the Focus on Molecules Obsolete?" where he uses analytical chemistry as an excuse to really pontificate on the state and progress of chemical science. Along the way he also has some valuable words of advice for aspiring chemists.

Whitesides's main message to young chemists is to stop focusing on molecules. Given the nature of chemistry this advice may seem strange, even blasphemous. After all it's the molecule that has always been the heart and soul of chemical science. And for chemists, the focus on molecules has manifested itself through two important activities - structure determination and synthesis. The history of chemistry is essentially the history of finding out the structure of molecules and of developing new and efficient methods of making them. Putting these molecules to new uses is what underpins our modern world, but it was really a secondary goal for most of chemistry's history. Whitesides tells us that the focus of the world's foremost scientific problems is moving away from composition to use, from molecules to properties. Thus the new breed of chemists should really focus on creating properties rather on creating molecules. The vehicle for Whitesides's message is the science and art of analytical chemistry which has traditionally dealt with developing new instrumentation and methods for analyzing the structure and properties of molecules.

Of course, since properties depend on structures, Whitesides is not telling us to abandon our search for better, cleaner and more efficient techniques of synthesis. Rather, I see what he is saying as a kind of "platform independence". Let's take a minute to talk about platform independence. As the physicist Leo Kadanoff has demonstrated, you can build a computer by moving around 1s and 0s or by moving around buckets of water, with full buckets essentially representing 1s and empty ones representing 0s. Both models can give rise to computing. Just like 1s and 0s simply turn out to be convenient abstract moving parts for building computers, similarly a certain kind of molecule should be seen as no more than a convenient vehicle for creating a particular property. That property can be anything from "better stability in whole blood" to "efficient capture of solar energy" to "tensile strength". The synthesis of whatever molecular material gives rise to particular properties is important, but it should be secondary; a convenient means to an end that can be easily replaced with another means. As an example from his own childhood, Whitesides describes a project carried out in his father's company in which his job was to determine the viscosities of different coal-tar blacks. The exact kind of coal-tar black was important, but what really counted was the property - viscosity - and not the molecular composition.

A focus on properties is accompanied by one on molecular systems, since often it's a collection of different, diverse molecules rather than of a single type that gives rise to a desired property. What kind of problems will benefit from a molecular systems approach? Whitesides identifies four critical ones; health care, environmental management, national security and megacity management. We have already been living with the first three challenges, and the fourth one looms large on the horizon.

Firstly, health care. Right now most of the expenditure on health care, especially in the United States, is on end-of-life care. Preventative medicine and diagnostics are still relegated to the sidelines. One of the most important measures to drive down the cost of healthcare will be to focus on prevention, thus avoiding the expensive, all-out war that is often waged - and lost - on diseases like cancer during their end stages. Prevention and diagnostics are areas where chemistry can play key roles. We still lack methods that can quickly and comprehensively analyze disease markers in whole blood, and this is an area where analytical and other kinds of chemists can have a huge impact. And no method of diagnostics is going to be useful if it's not cheap, so it's obvious that chemistry will also have to struggle to minimize material cost, another goal which it has traditionally been good at addressing, especially in industry.

Secondly, the environment. We live in an age when the potentially devastating effects of climate change and biodiversity loss demand quick and comprehensive action. Included in this response will be the ability to monitor the environment, and to relate local monitoring parameters to global ones. Just like we still lack methods to analyze the composition of complex whole blood, we also lack methods to quickly analyze and compare the composition of the atmosphere, soil and seawater in different areas of the world. Analyzing heterogeneous systems with different phases like the atmosphere is a tricky and quintessentially chemical problem, and chemists have their work cut out in front of them to make such routine analysis a reality.

Thirdly, national security. Here chemists will face even greater challenges, since the solutions are as much political and social as they are scientific. Nonetheless, science will play an important role in the resolution of scores of challenges that have to be met to make the world more secure; these include quickly analyzing the composition of a suspicious liquid, solid or gas, unintrusively finding out whether a particular individual has spent time in certain volatile parts of the world or has been handling certain materials, and using techniques to track the movements of suspicious individuals in diverse locations. Chemistry will undoubtedly have to interface with other disciplines in addressing these problems and questions of privacy will be paramount, but there is little doubt that chemists have traditionally not participated much in such endeavors and need to step up to the plate in order to address what are obviously important security issues.

Fourthly, megacities. As we pick up speed and move into the second decade of the twenty-first century, one of the greatest social challenges confronting us is how to have very large, heterogeneous populations ranging across diverse levels of income and standards of living co-existing in peace over vast stretches of land. This is the vision of the megacity whose first stirrings we are already witnessing around the world. Among the problems that megacities will encounter will be monitoring air, water and food quality (vida supra). A task like analyzing the multiple complex components of waste effluent, preferably with a readout that quantifies each component and assesses basic qualities like carcinogenicity would be invaluable. There is no doubt that chemists could play an indispensable role in meeting such challenges.

The above discussion of major challenges makes Whitesides's words about moving away from the molecule clear. The problems encompassing health care, national security and environmental and megacity management involve molecules, but what they really are are collages resulting from the interaction of molecules with other scientific entities, and with the interaction of chemists with many other kinds of professional scientists and policy makers. In one sense Whitesides is simply asking chemists to leave the familiar environment of their provincial roots and diversify. What chemists really need to think of is molecules embedded in a broad context involving other disciplines and human problems.

Part of the challenge of addressing the above issues will be the proper training of chemists. The intersection of chemistry with social issues and public policy demands interdisciplinary and general skills, and Whitesides urges chemists to be trained in general areas rather than specialized subfields. Courses in applied mathematics and statistics, public policy, urban planning, healthcare management and environmental engineering are traditionally missing from chemistry curricula, and chemists should branch out and take as many of these as is possible within a demanding academic environment. It is no longer sufficient for chemists to limit themselves to analysis and synthesis if they want to address society's most pressing problems. And at the end of it they need not feel that a movement away from the molecule is tantamount to abandoning the molecule; rather it is an opportunity to press the molecule into interacting with the human world on a canvas bigger than ever before.

First published on the Scientific American Blog Network.

George Whitesides on the responsibility of chemists and the future of chemistry

Catching up on a few articles I had missed, I came across a characteristically deep and wide-ranging essay called "Assumptions" by George Whitesides about science, its future and our responsibility as scientists. It's a very general and kaleidoscopic essay not restricted to chemistry, but the bits about chemistry, its role in understanding the major problems confronting humanity and chemists' responsibility in extending the scope of chemical science are quite thought-provoking:

Chemistry, by its culture, has been almost blindly reductionist. I am repeatedly reminded that “Chemists work on molecules”, as if to do anything else was suspect. Chemists do and should work on molecules, but also on the uses of molecules, and on problems of which molecules may be only a part of the solution. If chemists move beyond molecules to learn the entire problem—from design of surfactants, to synthesis of colloids, to MRI contrast agents, to the trajectories of cells in the embryo, to the applications of  regenerative medicine—then the flow of ideas, problems, and solutions between chemistry and society will animate both. 

Whitesides is clearly making a plea for chemists to become even more interdisciplinary than what they already are, to pursue not just the development of the solution but its application and integration; his own group provides a remarkable example of chemists, physicists, biologists and engineers working together on highly multidisciplinary problems. It's quite clear that to achieve this interdisciplinary expertise we have to completely break down the traditional barriers between synthesis, structure determination, biology and materials (in this world the professor who rejected my biochemical literature seminar topic because it "did not include any synthesis" would be an anachronism). The next paragraph makes clear the role of the "central science"

As a technology, chemistry has built the foundation from which many of the discoveries of “biology” or “microelectronics” or “brain science” (or “planetary exploration”, for that matter) have grown. There would be no genomics without chemical methods for separating fragments of DNA, and for synthesizing primers and probes, and for separating restriction endonucleases into pure activities. There would be no nuclear ICBMs without methods of refining plutonium, and making explosive lenses. There would be no drugs without synthesis and mass spectroscopy. There would be no interplanetary probes without fuels, and carbon/carbon rocket throat nozzles, and silicon single crystals. 

And here's something about what the future of chemistry should be:

Those are the past. What about the future? Chemistry is, still, everywhere: It must be! It is the science of the real world. But to remain a star in the play rather than a stagehand, it must open its eyes to new problems. It is impossible that the human life span will increase dramatically without manipulation of the molecules of the human organism, but understanding this problem will require more than manipulating molecules. Communication between the living and non-living will require engineering a molecular interface between them, but designing this interface will require understanding the nature of “information” in organisms and in computers, and how to translate between them. A society that uses information technology to interweave all its parts requires new systems for generating, distributing, and storing power, but batteries will be only one part of these systems.  

Chemistry has always been the invisible hand that builds and operates the tools, and sustains the infrastructure. It can be more. We think of ourselves as experts in quarrying blocks from granite; we have not thought it our job to build cathedrals from them. Whether we choose to focus on the molecules, materials, and tools that are at the beginnings of discovery, or bring our particular, unique understanding of the world to bear on unraveling the problems at the end, is for us to decide.  I believe that everything from methane to sentience is chemistry, and that we should reexamine our own assumptions concerning the boundaries of our field. Examining the broader assumptions that follow may provide some stimulus to do so.  

Indeed, examining the "broader assumptions" of their field in the broadest sense of the term is what chemists should do. The first paragraph presents a fair sampling of the myriad problems in which chemistry can play a central role. They involve everything from engineering interfaces between computers or electronics and human brains to harnessing the power of chemistry in generating, storing, interconverting and deploying energy in all its forms. I strongly think that the future of chemistry lies in recasting itself as an informational science in the broadest sense. At the level of biology chemistry has already manipulated information in the form of sequencing and genomics; synthetic biology will take this capability to a whole new level. But there are other areas in which chemistry can serve to manipulate information, and part of what Whitesides is doing is challenging chemists to become informational scientists in hitherto unexplored areas like energy and transportation.

The essay ends with a systems-level view of chemistry that every chemist should keep in mind, even as she works in her narrow world of natural products, zeolites, ROMP or kinases.

Because chemistry contributes broadly to the foundations of technology, it is particularly difficult to guess its future impact: a new chemical reaction might be used to make a cancer therapeutic, or a chemical weapon. Some of the opportunities that seem within the reach of investigation, if not within the reach of solution—technologies that might substantially prolong life, or develop new forms of life, or lead to sentient systems that rival us in intelligence—will do both good and harm. At minimum, those of us whopursue these problems should accept an obligation to explain to our fellow citizens fully and clearly what we are doing, and why, and (to the limited extent we can) with what possible outcomes. Humankind will do what it will do, but at least everyone should understand—in so far as is possible—what the choices are, and what the consequences might be. Chemistry, if it takes more interest in (and responsibility for) the full scope of programs—from molecules, to applications, and to influence on society—may be able to use the very breadth of its connections to technology to help in this explanation.

Whitesides Image: Boston.com

The strange case of entropy-enthalpy compensation

My original intention was to read about the role water molecules play in active sites, one thing led to another, and I ended up actually spending more time on the fascinating topic of entropy-enthalpy compensation. I drfited from water molecules to this topic primarily because of a 1995 paper by Jack Dunitz, in which he derives the conclusion that for a typical hydrogen bond, ~5 kcal/mol, there is entropy-enthalpy compensation, which means that that typical free energy of transfer of a hydrogen bond from bulk water to a protein active site can be close to zero. There were some assumptions in this paper, but the concept mostly seems to hold.

Entropy-enthalpy compensation (EEC) is actually a pretty logical concept. Let's say you are designing a ligand to bind a protein, and want to increase the binding affinity by adding hydrophobic groups on it. As you add these groups, the ligand will (usually) bind tighter because of increased vdW contacts as well as the hydrophobic effect, but the word "tighter" already indicates that it will do so with a loss in entropy. Thus, the gain in enthalpy of binding is offset by a loss in entropy. So even if you modify the ligand this, the resulting free energy of binding may be close to zero, or at least will stay constant because of these two opposing quantitites.

However, there are some pretty striking exceptions, and this came to light when I read a paper by George Whitesides in which his group was doing studies of ligand binding to carbonic anhydrase (CA). The authors observed that surprisingly, as they were adding more hydrophobic groups to some sulfonamide ligands by extending the side chain, they observed almost no change in the free energy of binding. In fact, they even observed this effect with different classes of side chains. Clearly, EEC was taking place. But remarkably, they observed that the effect was due to exactly the opposite of what usually happens; namely that the enthalpy was become more unfavourable and the entropy was becoming more favourable. Needless to say, this is not what one expects. The authors have proposed a nice model in which they believe there is some sort of negative cooperativity; as you add more atoms to the side chain, it somehow weakens the binding of the initial atoms that were previously binding better. This worsens the enthalpy of binding, and improves the entropy because the ligand becomes free to wiggle around more. Even though this model supports what is happening, the exact details of how it happens are not clear.

Clearly, EEC is an important concept in rational ligand and drug design. Formerly, it was thought to be a "phantom phenomenon", an artifact of experimental measurements and errors. But Whitesides contends that with the advent of Isothermal Titration Calorimetry (ITC), it has become known as a very real phenomenon. Practically, it means that small moelcules with relatively rigid structures could have the best potency and binding affinity, because we would then get a good and favourable increase in binding enthalpy, without having to pay the corresponding cost in entropy.

However, as I was reading this, I realised that while the chemist would aim to design such rigid high-binding ligands, nature already seems to have solved the EEC problem. Consider the various kinds of protein-protein interactions, where highly flexible loops are seen as recognition elements. Would a chemist ever design a loop for molecular reecognition? Yes and No. Yes, because designing such a loop would build in versatility and flexibility to explore conformational space. No because of the above-noted reasons, of attaining favourable entropy. So how does nature circumvent this problem? Clearly, there must be a way in which nature pays the cost of unfavourable entropy. A couple of ways come to mind:

1. Through the very existence of the protein! Consider how much penalty nature pays in synthesizing and compactly folding the protein in the first place. This entropy cost paves the way to a future, entropically less favourable situation.

2. Through 'steric confinment'. Loops are only a small part of a giant protein surface. The coming together of these surfaces is hydrophobically driven by the expulsion of water. Then it is relatively easy for loops to be recognised, as they are already close to the other surface. Again, the entropic cost has been paid by the rest of the protein surface.

3. Through optimizing the binding enthalpy so much, that unfavourable entropy is not so much of an issue. This is of course what chemists try to do all the time, but nature does it elegantly. Think of the umpteen number of cyclic peptides and macrocycles that nature uses for molecular recognition. Admittedly, one of the ways nature solves the EEC problem is by designing through evolution, ultra potent ligands, where a favourable ∆H compensates for an unfavourable ∆S

Once again, nature rules by striking the right balance through relentless optimization, and we have much to learn from it for tackling EEC