A model world for chemists

Modelling the details of a chemical reaction has always been a computational nightmare. Once the chemist considers interacting molecules with more than a handful of atoms, the complexity of the equations needed to describe the bonds that hold the atoms together and how they change during a reaction become far too much for even a supercomputer to portray accurately within a reasonable time.

Nobel-prize winning theories have over the years allowed chemists to develop simplifications that allow even proteins with their hundreds of atoms to be modelled to a high degree of accuracy in a matter of days rather than decades. But, even these simplifications don’t allow reactions to be modelled readily. Chemists would like to be able to simulate every atom and every bond and how they react with precision and rapidity. They may now have taken a step closer to this Holy Grail through ongoing work by Daniel Crawford and colleagues at Virginia Tech and Bethel College of St. Paul in Minnesota. There are many chemical reactions that you don’t want to do in the lab, explains Crawford, Perhaps they are too slow or too toxic or too explosive, or there may be micro- or nano-scopic components of reactions you can’t probe experimentally.

Daniel Crawford

Daniel Crawford

Quantum chemistry can unlock the secrets of reactions involving small molecules, such as ozone and a chlorofluorocarbon in atmospheric chemistry, say. But, consider the reaction of a steroidal hormone with an enzyme, or a pheromone with a vomeronasal receptor and the number of atoms involved is simply too high for even the most sophisticated of quantum chemistry computer programs to simulate.

The problem is that even simple-seeming molecules, such as the amino acids that comprise those protein receptors and enzymes, take days to compute. Consider two amino acids and the calculation time expands from days to years. Far too long for even the most patient PhD student!

Rollin King

Rollin King

Crawford and Bethel College’s Rollin King are now applying a technique called local correlation. The basic idea is to describe the electronic interactions in a molecule piece by piece. You shouldn’t have to consider interactions of electrons on parts of the molecule that are far apart, in general, so by breaking the molecule into fragments, we can reduce the cost (time) of the calculation, explains Crawford.

To take advantage of this local correlation approach, Crawford explains that he and his colleagues have had to completely reorganize their quantum chemistry computers programs. In some sense we have to start from scratch, he told Spotlight. We build the electronic wave functions using a set of localized orbitals rather than the usual so-called canonical orbitals, which are smeared across the entire molecular framework.

In this new, more focused set of orbitals, many pieces of the wave function (such as those corresponding to electronic interactions on distant atoms) become negligible. By reorganizing the programs to determine in advance which pieces are small, we can avoid computing and storing them from the beginning, he adds.

One of the most important target applications the team is shooting for is the simulation of optical activity in chiral, or handed, molecules. Many natural products and bioorganic compounds, including drugs, are chiral and in one handed form are safe and effective while in the other can be less effective or even dangerous.

Our goal is the development of a computational technique that will help organic chemists identify the absolute configuration – that is, the handedness — of a newly isolated chiral compound so that it can be synthesized in the laboratory, says Crawford. Such a development could potentially save months or even years of laboratory work. The problem, though, is that natural products are large, at least by quantum chemical standards, explains Crawford, To compute the optical activity, we have to be able to deal with systems containing 30-50 non-hydrogen atoms. This is where the local correlation idea comes in.

The researchers presented their results at the 223rd national meeting of the American Chemical Society, in Florida in April 2002.

Further reading

Daniel Crawford
http://www.chem.vt.edu/people/faculty/crawford-daniel/

Suggested searches

Quantum chemistry
Chemistry modelling
Wavefunctions
Molecular orbitals
Chirality

Do the Bosenova

Desktop astrophysics could be the next event on the horizon thanks to the synthesis of a new form of matter known as a Bose-Einstein condensate.

In 1924, Indian physicist Satyendra Nath Bose came up with an idea about the behaviour of photons. He reckoned they might exist in different energy states and he used his idea to derive Planck’s Law of Radiation without resorting to classical physics. Einstein extended Bose’s work to atoms, particles of matter and predicted that if a gas were cooled enough the atoms would condense into their lowest possible energy state. This weird form of matter, the Bose-Einstein condensate, was first created in a laboratory in 1995 and earned Eric Cornell (of NIST), Carl Wieman (University of Colorado) and Wolfgang Ketterle (MIT) the 2001 Nobel Prize in Physics.

Burst movie

Burst movie

The quantum mechanical blob that is a BEC is not peculiar to the physics laboratory though. Astrophysicists believe that BECs could be at the core of one of the strangest entities in the universe – the neutron star. Ketterle cautions, however, that, while the two have some aspects in common, and it is nice to explore these analogies, I doubt that BEC work will contribute in a major way to advances in astrophysics.

Neutron stars are, as their name suggests, composed of neutrons and form under the enormous pressure as a star collapses. A thimbleful of neutron star would weigh a billion tonnes and the whole thing would sit neatly on Manhattan Island, New York. With a mass about 1.5 million times that of the sun, these iron-encrusted stars spin at hundreds of revolutions per second. The brittle, iron-rich crust of the neutron star hides an interior that is even more mysterious than their enormous density. Inside, they are fluid. In their swirling depths is a vast sea of neutrons – the debris from atoms crushed by a supernova explosion – and within those depths rage quantum storms.

Crab Nebula

Crab Nebula

You might think such an object would be impossible to handle, but physicists would like to take a closer look at such stellar species as neutron stars and their cousins, the white dwarfs and black holes. They all represent extreme forms of matter that could betray the secrets of universe. The discovery of how to make a BEC in the laboratory provided a technical tip on handling the types of extreme matter that exist in a neutron star.

Magnetar

Magnetar

BECs are 100,000 times less dense than air, and are colder than interstellar space. In contrast, neutron stars have a density of up to 100 million tonnes per cubic centimetre, and their internal temperature is 100 times that of the centre of the sun. The link between the two, however, is in that they are both superfluids – they are liquids that flow with zero friction and zero viscosity.

Swiss cheese!

Swiss cheese!

Setting a superfluid in motion is difficult. Try to rotate a container of supercold liquid helium-4, for instance, and the lack of friction between it and the inside wall of the container means it doesn’t budge. But, superfluids can swirl according to Ketterle. And the concept that unifies neutron stars and BECs is that they share this characteristic of superfluids. Ketterle and his colleagues at MIT began experimenting with swirling BECs. At the time, they did not have neutron stars in mind. BECs are a new form of matter, and we wanted to learn more about them, he explains, By rotating BECs, we force them to reveal their properties.

Quantum swirls

Quantum swirls

To set a BEC swirling Ketterle’s team shone a rotating laser beam on it while holding it in place with strong magnets. The experiment is like stroking a ping-pong ball with a feather until it starts spinning, muses Ketterle. The surprising thing was that suddenly, a regular array of whirlpools appeared in the BEC. It was a breathtaking experience when we saw those vortices, recalls Ketterle. Researchers had seen such whirlpools before (in liquid helium and in BECs) but never so many at once. This array of superfluid whirlpools was exactly the kind of storm system astronomers predicted would swirl beneath the iron crust of a neutron star.

Lighthouse? Neutron star

Lighthouse? Neutron star

Evidence for the swirling depths of neutrons stars is based on the fact that some neutron stars are pulsars – the emit a powerful beam of radiation as they spin – like a cosmic lighthouse. The pulses are very regular but occasionally there is a glitch and a pulse might come slightly too early or too late and it is these glitches that are thought to be due to superfluid vortices hammering into the inside of the neutron star’s crust.

Ketterle adds that attractions between atoms in a BEC could parallel the collapse of a neutron star so emulating the distant and massive in the laboratory too. The explosive collapse of a BEC, dubbed a Bosenova (pronounced bose-a-nova) by Wieman releases only a tiny quantity of energy, just enough to raise the temperature of the BEC by 200 billionths of a degree. Supernovae release many times the energy.

Further reading

Nature, 416, 211-218 (2002)
DOI: 10.1038/416211a

Satyendra Nath Bose
http://www.calcuttaweb.com/people/snbose.shtml

Wolfgang Ketterle
http://www.rle.mit.edu/rleonline/People/WolfgangKetterle.html

2001 Nobel Prize in Physics
http://nobelprize.org/nobel_prizes/physics/laureates/2001/

Neutron star
http://www.astro.umd.edu/~miller/nstar.html

Suggested searches

Neutron stars
Bose Einstein condensation
Superfluids

Flowing hot and cold

It is a relatively easy to control the direction of an electric current – use a rectifier – but heat usually flows from hot to cold. Now, Italian and French researchers have devised a rectifier for heat in a computer simulation. They reckon a heat rectifier might be made from DNA or another biological molecule.

Giulio Casati, Michael Peyrard and Marcello Terraneo of Insubria University in Como, Italy, have simulated the vibrations of atoms in a crystal lattice and reckon that given the right arrangement of atoms a device could be built that carried heat energy in one direction only. They looked at one-dimensional solids whose vibrational frequency depends on the size of the vibration. A material such as a long strand of DNA in the solid state might behave in this way for instance.

Thermal transfer Renaissance style (Georges de La Tour, particular of Saint Joseph, Paris, Musée du Louvre)

Thermal transfer Renaissance style (Georges de La Tour, particular of Saint Joseph, Paris, Musée du Louvre)

In such an anharmonic material, energy is transferred less efficiently from one end to the other than in a harmonic material where the vibrational frequency (temperature) is independent of the amplitude of the vibration.

At its simplest level, thermodynamics describes atoms in a solid as vibrating with heat energy flow as though they are connected to each other by springs. Casati believes that computational tools can provide a deeper insight and as such allow interesting and potentially surprising properties, such as allowing heat to travel in only one direction.

Giulio Casati

Giulio Casati

A thermal rectifier might consist of an anharmonic chain molecule tethered by a stiff molecular spring at one end and a loose spring at the other. When the spring is at a higher temperature, the chain molecule will vibrate more slowly because energy is not carried through the chain so effectively. Imagine the effect of plucking a guitar string on to which small pieces of children’s play clay have been stuck. The sound produced would be muffled because of the inefficiency of the string’s vibration. Suppose such a thermal rectifier material as we describe is constructed and you put some object inside this material, then if what is inside is cold then it remains cold; if instead it is warm it will cool down. The heat can flow only in one direction, Casati explained to Spotlight.

Computer simulated rectifier

Computer simulated rectifier

Such a thermal rectifier might have applications in electronics – as a cooling device for computer chips and in biotechnology as a heat flow controller for microscale chemical reactors. As to applications, I feel it is too early to say… much work needs to be done, confesses Casati, but what is important is that we now know that possibility exists.

Further reading

Phys. Rev. Lett. 88, 094302
http://link.aps.org/abstract/PRL/v88/e094302/

DOI: 10.1103/PhysRevLett.88.094302

Michael Peyrard
http://perso.ens-lyon.fr/michel.peyrard/

Suggested searches

Thermal Rectifiers
Thermodynamics