Archive for the ‘Chemistry’ Category
An interesting paper:
A Ishizaki and G R Fleming
The observation of long-lived electronic coherence in a photosynthetic pigment–protein complex, the Fenna–Matthews–Olson (FMO) complex, is suggestive that quantum coherence might play a significant role in achieving the remarkable efficiency of photosynthetic electronic energy transfer (EET), although the data were acquired at cryogenic temperature [Engel GS, et al. (2007) Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 446:782–786]. In this paper, the spatial and temporal dynamics of EET through the FMO complex at physiological temperature are investigated theoretically. The numerical results reveal that quantum wave-like motion persists for several hundred femtoseconds even at physiological temperature, and suggest that the FMO complex may work as a rectifier for unidirectional energy flow from the peripheral light-harvesting antenna to the reaction center complex by taking advantage of quantum coherence and the energy landscape of pigments tuned by the protein scaffold. A potential role of quantum coherence is to overcome local energetic traps and aid efficient trapping of electronic energy by the pigments facing the reaction center complex.
Here is a commentary on the paper:
P G Wolynes
Quantum mechanics seems alien to physiology. Alarm bells go off in our heads when we hear even people of such genius as Sir Roger Penrose (1) invoke the weird coherence of quantum mechanical wave functions to explain biological function. Of course, it is only some of the “weirder” parts of quantum mechanics that bother us. Structural biochemistry is founded on the rigid geometrical relationships involved in chemical bonding that arise from quantum mechanics; the α-helix could only have been discovered by Pauling by acknowledging the power of quantum mechanical resonance to flatten the peptide bonding unit (2). Nevertheless, most modern biomolecular scientists view quantum mechanics much as deists view their God; it merely sets the stage for action and then classically understandable, largely deterministic, pictures take over. In this issue of PNAS Ishizaki and Fleming (3), by combining experimental and theoretical investigations, demonstrate that quantum coherence effects play a big role in light energy transport in photosynthetic green sulfur bacteria under physiological conditions. Quantum coherence allows a nonclassical simultaneous exploration of many paths of energy flow through the many chromophores of a light-harvesting complex, thereby significantly increasing the efficiency of the energy capture process, presumably helping the bacteria to survive in low light.
Single-molecule mechanics, gender, culture and mathematics performance, effect of tubulent driven instabilities on insect flight, and magnetic stabilizationJune 3, 2009
Here are some interesting papers from the latest PNAS.
- Characterizing the resistance generated by a molecular bond as it is forcibly separated — L B Freund
The goal of measurements of the resisting force generated by a molecular bond as it is being forcibly separated under controlled conditions is to determine functional characteristics of the bond. Here, we establish the dependence of force history during unbinding on both those parameters chosen to characterize the bond itself and the controllable loading parameters. This is pursued for the practical range of behavior in which unbinding occurs diffusively rather than ballistically, building on the classic work of Kramers. For a bond represented by a one-dimensional energy landscape, modified by a second time-dependent energy profile representing applied loading, we present a mathematical analysis showing the dependence of the resistance of the bond-on-bond well shape, general time dependence of the imposed loading, and stiffness of the loading apparatus. The quality of the result is established through comparison with full numerical solutions of the underlying Smoluchowski equation.
- Gender, culture, and mathematics performance — J S Hyde and J E Mertz
Using contemporary data from the U.S. and other nations, we address 3 questions: Do gender differences in mathematics performance exist in the general population? Do gender differences exist among the mathematically talented? Do females exist who possess profound mathematical talent? In regard to the first question, contemporary data indicate that girls in the U.S. have reached parity with boys in mathematics performance, a pattern that is found in some other nations as well. Focusing on the second question, studies find more males than females scoring above the 95th or 99th percentile, but this gender gap has significantly narrowed over time in the U.S. and is not found among some ethnic groups and in some nations. Furthermore, data from several studies indicate that greater male variability with respect to mathematics is not ubiquitous. Rather, its presence correlates with several measures of gender inequality. Thus, it is largely an artifact of changeable sociocultural factors, not immutable, innate biological differences between the sexes. Responding to the third question, we document the existence of females who possess profound mathematical talent. Finally, we review mounting evidence that both the magnitude of mean math gender differences and the frequency of identification of gifted and profoundly gifted females significantly correlate with sociocultural factors, including measures of gender equality across nations.
- Turbulence-driven instabilities limit insect flight performance — S A Combes and R Dudley
Environmental turbulence is ubiquitous in natural habitats, but its effect on flying animals remains unknown because most flight studies are performed in still air or artificially smooth flow. Here we show that variability in external airflow limits maximum flight speed in wild orchid bees by causing severe instabilities. Bees flying in front of an outdoor, turbulent air jet become increasingly unstable about their roll axis as airspeed and flow variability increase. Bees extend their hindlegs ventrally at higher speeds, improving roll stability but also increasing body drag and associated power requirements by 30%. Despite the energetic cost, we observed this stability-enhancing behavior in 10 euglossine species from 3 different genera, spanning an order of magnitude in body size. A field experiment in which we altered the level of turbulence demonstrates that flight instability and maximum flight speed are directly related to flow variability. The effect of environmental turbulence on flight stability is thus an important and previously unrecognized determinant of flight performance.
- Magnetic stabilization and vorticity in submillimeter paramagnetic liquid tubes — J M D Coey et al
It is possible to suppress convection and dispersion of a paramagnetic liquid by means of a magnetic field. A tube of paramagnetic liquid can be stabilized in water along a ferromagnetic track in a vertical magnetic field, but not in a horizontal field. Conversely, an “antitube” of water can be stabilized in a paramagnetic liquid along the same track in a transverse horizontal field, but not in a vertical field. The stability arises from the interaction of the induced moment in the solution with the magnetic field gradient in the vicinity of the track. The magnetic force causes the tube of paramagnetic liquid to behave as if it were encased by an elastic membrane whose cross-section is modified by gravitational forces and Maxwell stress. Convection from the tube to its surroundings is inhibited, but not diffusion. Liquid motion within the paramagnetic tube, however, exhibits vorticity in tubes of diameter 1 mm or less—conditions where classical pipe flow would be perfectly streamline, and mixing extremely slow. The liquid tube is found to slide along the track almost without friction. Paramagnetic liquid tubes and antitubes offer appealing new prospects for mass transport, microfluidics, and electrodeposition.
They chemically synthesised many fragments of the DNA, encoding the 582,970-units-long genome of a bacterium called M ycoplasma genitalium. Next, they assembled these fragments in perfect order to generate the genome of the bacterium.
The DNA sequence of the synthetic one was confirmed to be identical to the natural one. Preliminary results were first published in the 24 Jan 2008 issue of Science, and the more detailed successful one in the 5 Dec 2008 issue of PNAS (US).
The task is somewhat akin to writing phrases and sentences first, and then putting them together in proper order to make the meaningful chapter of a book.
While the DNA pieces were synthesised chemically, the stitching together was done using the biochemical machinery of a host cell. About 100 pieces of the genome, each 5000-7000 units long in DNA sequence, were first joined together to produce 25 sub-assemblies, each about 24000 base pairs long.
These were then introduced into the bacterium E. coli to produce sufficient DNA for the next steps. Next, they repeated the procedure to generate large fragments comprising 1/4th of the whole genome of M genitalium.
Now, they used the clever trick of exploiting the process called homologous recombination. This is a basic essential process in every cell, which physically rearranges the two strands of DNA.
It involves the alignment of similar sequences, is used in DNA repair and to restart replication that has been stalled or damaged. And an organism like yeast does this more efficiently, wholesale faster than bacteria like coli.
The JCVI researchers inserted the synthesised DNA fragments into yeast and utilised its homologous recombination ability to generate the whole 580,000 long genome of M genitalium in one step. As one of the authors of the paper remarked: “I am astounded by our team’s progress in assembling large DNA molecules. It remains to be seen how far we can push this yeast assembly platforms to boot up the synthetic chromosome”.
This is clearly a landmark work that leads into the brave new world of synthesising life itself in the laboratory. It was hardly 200 years ago when Friedrich Wohler synthesised urea, an organic molecule, in the chemical laboratory, thus throwing out the notion of “vital forces” involved in the components of living organisms.
Balasubramanian goes on to conclude the piece with some discussion on the ethics and morals of the research after making an exciting prediction:
If only we find a way to insert the bacterial genome into this proto-cell, and somehow trigger it (electric pulse? ionic currents?) to make the bacterium itself!! We would have chemically created life in the lab. This is not a pipedream; JCVI scientists are already on the job, and my bet is they will do it within a few years.
A wonderful piece; don’t miss it.
PS: I think Balasubramanian gets both the references wrong though — there is no 24 January issue in 2008, and no PNAS issue on 5th December; But, I believe the references are to the following two papers:
 Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome,
Daniel G. Gibson, Gwynedd A. Benders, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Holly Baden-Tillson, Jayshree Zaveri, Timothy B. Stockwell, Anushka Brownley, David W. Thomas, Mikkel A. Algire, Chuck Merryman, Lei Young, Vladimir N. Noskov, John I. Glass, J. Craig Venter, Clyde A. Hutchison, III, Hamilton O. Smith, Science, 29 February 2008, Vol. 319. no. 5867, pp. 1215 – 1220.
We have synthesized a 582,970–base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted “watermarks” at intergenic sites known to tolerate transposon insertions. Overlapping “cassettes” of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb (“1/8 genome”), and 144 kb (“1/4 genome”), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.
 One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome,
Daniel G. Gibson, Gwynedd A. Benders,Kevin C. Axelrod, Jayshree Zaveri, Mikkel A. Algire, Monzia Moodie, Michael G. Montague, J. Craig Venter, Hamilton O. Smith, and Clyde A. Hutchison III, PNAS, Published online on 10, December 2008 before print.
We previously reported assembly and cloning of the synthetic Mycoplasma genitalium JCVI-1.0 genome in the yeast Saccharomyces cerevisiae by recombination of six overlapping DNA fragments to produce a 592-kb circle. Here we extend this approach by demonstrating assembly of the synthetic genome from 25 overlapping fragments in a single step. The use of yeast recombination greatly simplifies the assembly of large DNA molecules from both synthetic and natural fragments.
The PNAS piece is an Open Access article too. Have fun!
I finished reading Peter Atkins’ Four laws; I enjoyed it a lot, and I have no hesitations in recommending it. I hope OUP publishes a low priced, paperback edition so that many more students will have access to this wonderful book.
Be it the very first sentence in the book
The zeroth law is an afterthought
which reminded me of some good openings of certain mystery novels, or the interesting pieces of information (as, for example, that in the original Celsius scale, water froze at 100 and bolied at 0 degrees Celcius), or the deep concepts explained in a rather lucid fashion (like the section on Fluctuation-Dissipation theorem on page. 42), or the new aspects of looking at thermodynamics that the book introduces (for example, as to why Boltzmann constant is not to be considered a fundamental constant but a conversion factor), I never found the book dull (though, at times, I did find it to be very engrossing and a bit time-consuming to go through the arguments).
Overall, I also think that the approach used by Atkins, namely
… we consider first the observational aspects of each law, then dive below thhe surface of bulk matter and discover the illumination that comes from the interpretation of the laws in terms of concepts that inhabit the underworld of atoms[.]
is very natural and effective; concepts like energy, entropy, temperature, enthalpy, and Helmholtz and Gibbs free energies are explained by Atkins using this approach; and, by far, these are some of the best explanations that I have seen.
Let me end this post by quoting Paul Davies from the blurb of the book,
Arkins is a master expositor, who combines penetrating insight with simplicity of style and a gentle elegance.
Hunt for the book in your library; or, better still, buy yourself a copy and have fun!
PS: By the way, here is an YouTube video wherein Atkins introduces the book.
Note to self: At least a couple of books from Atkins’ Further Reading list sound interesting: G N Lewis and M Randall, Thermodynamics and B Widom, Statistical Mechanics: a concise introduction for chemists.
PS 2: Thanks to my colleague Rajesh for introducing the book to me, and agreeing to part it for the last one month. I hope to get a personal copy for myself soon.
A dozen or so years ago, I drove my Biochemistry prof to tears with questions – she had 200 people in front of her and she tried hard to make Biochem interesting enough not to get us all bored to tears, and she was pretty good at that, as much as it is possible not to make people bored to tears with Biochem. But my questions exasperated her mainly because she could not answer them, because, as I learned later, the field of biochemistry was not able to answer those questions yet at the time: questions about dynamics – how fast is a reaction, how long it takes for a pathway to go from beginning to end, how many individual molecules are synthesized per unit of time?, etc.
Well, the field is starting to catch up with my questions lately – adding the temporal dimension to the understanding of what is going on inside the cell. In today’s issue of PLoS Biology, there is a new article that is trying to address exactly this concern: Dynamics and Design Principles of a Basic Regulatory Architecture Controlling Metabolic Pathways.
Coturnix also points to an editorial synopsis that accompanies the paper, and goes on to say that the paper is a potential classic:
You should also check out the editorial synopsis for the paper, as it places it nicely into the context – exactly the kind of context I was looking for, in vein, back in my Biochem class: The Fourth Dimension of Biochemical Pathways.
… but perhaps in 10 years we’ll look at it and say “it’s a classic!”
Take a look!
A couple of News stories in the latest issue of Nature by Katherine Sanderson on the use of computations for (a) crystal structure
At present, chemists use X-ray crystallography to determine how atoms are arranged in a molecule and how molecules pack into a crystal. It is a time-consuming method that has remained practically unchanged for almost a century, and it means that experimentalists need to produce a high-quality crystal. …
The problem has been attacked head-on by the Cambridge Crystallographic Data Centre (CCDC) in Britain. Every three years since 1999, the centre has set a challenge for software developers to predict the structure of four molecules, the structure of which was known only to the CCDC. But nobody had been able to predict the correct structures of all four molecules.
This year saw a breakthrough. A team consisting of Frank Leusen and John Kendrick of the University of Bradford, UK, and Marcus Neumann of Avant-garde Materials Simulation in Saint-Germain-en-Laye, France, correctly predicted the structure of all four molecules.
and (b) spectroscopic studies
Theoretical spectroscopy simulates how electrons in molecules behave and can predict what the molecule’s spectra will look like. …
… European Theoretical Spectroscopy Facility (ETSF), a network created earlier this year. The network can investigate anything from how the structure of a protein affects its properties to the likely properties of a new material. Established mainly as a service for academic collaboration, its sponsors hope that it will evolve into a service for sale to industry.
R Ramachandran, in the latest issue of Frontline, profiles Gerhard Ertl, the winner of this year’s Chemistry Nobel and puts his work in perspective:
Surface chemistry, as the term implies, is essentially chemistry in two dimensions. Unlike the chemical reactions in bulk, with substances in test tubes, beakers and glass jars that one normally associates a chemistry laboratory with, surface chemistry has to do with the chemical processes that occur in the few atomic layers that constitute the interface between two phases, such as solid-liquid, solid-gas, solid-vacuum and liquid-gas interfaces. And two dimensions are better suited to probing reactions in greater detail at the atomic level than those in three-dimensional solutions because they are confined to the surface, but it is neither straightforward nor cheap to study how atoms and molecules react on solid surfaces. It involves painstaking and high-precision work, with advanced equipment such as high-vacuum systems, electron microscopes and spectroscopes, and clean rooms. And Ertl put these to innovative use in the past three decades and more. His work has chiefly been concerned with gas-solid interfaces. As Mark Peplow, the editor of Chemistry World, said, “he gave us the tools to understand why [oxygen] atoms do not bounce off [iron surfaces] but rather stick to them and turn into iron oxide”.
The science of surface chemistry has important industrial applications, such as in the manufacture of artificial fertilizers, and the science is also key to understanding such diverse phenomena as the rusting of iron; the working of catalytic converters, which make automobile exhaust less polluting; the functioning of fuel cells; and the depletion of atmospheric ozone, which is owing to reactions on the surface of minute ice crystals in clouds.
In another piece in the same issue, he also profiles the winners of the Medicine prize:
Almost every aspect of mammalian physiology can now be studied by gene targeting. In particular, Capecchi’s later work has revealed the roles of genes involved in mammalian organ development, in the body plan’s blueprint, as it were. His work has also been concerned with causes of several birth-defects and malformations. Likewise, Evans has developed mouse models for the inherited disease cystic fibrosis and used them to study disease mechanisms and gene therapy. Smithies, too, has developed mouse models, for thalassaemia, hypertension and atherosclerosis.