Subscribe free to our newsletters via your
. 24/7 Space News .




TIME AND SPACE
Researchers unmask Janus-faced nature of mechanical forces with the Julich supercomputer
by Staff Writers
Bochum, Germany (SPX) Jun 21, 2013


The Janus nature of mechanochemistry: Mechanical forces normally accelerate chemical reactions. However, in the case of disulfide bonds, which are present in large numbers in proteins, force-induced structural changes result in a relative deceleration above a certain threshold. The force thus shows its Janus-faced nature. Image courtesy P. Dopieralski, D. Marx.

The harder you pull, the quicker it goes. At least, that used to be the rule in mechanochemistry, a method that researchers apply to set chemical reactions in motion by means of mechanical forces. However, as chemists led by Professor Dominik Marx, Chair of Theoretical Chemistry at the Ruhr-Universitat Bochum now report in the journal "Nature Chemistry", more force cannot in fact be translated one to one into a faster reaction.

With complex molecular dynamic simulations on the Julich supercomputer "JUQUEEN" they unmasked the Janus-faced nature of mechanochemistry. Up to a certain force, the reaction rate increases in proportion to the force. If this threshold is exceeded, greater mechanical forces speed up the reaction to a much lesser extent.

Outdated view: mechanical force steadily reduces energy barrier
In order to activate chemical reactions, an energy barrier first has to be overcome. This energy can, for example, be supplied in the form of mechanical forces that "distort" the molecules involved. In order to achieve that experimentally, two long polymer chains are attached to the molecule. These chains serve as ropes to stretch the molecule either using a force microscope or by radiating the solution with ultrasound.

Until now it was assumed that the energy barrier decreases steadily, the more mechanical energy is put into the molecule. This hypothesis has now been refuted by the RUB-chemists. The key to success was a particularly complex form of computer simulation, the so-called ab initio molecular dynamics method, which they could only master on Europe's currently fastest computer at the Julich Supercomputing Centre within the framework of a "Gauss Large Scale" project.

Updated view: more force brings considerably less effect
The RUB team was looking at a small molecule with a disulfide bond, i.e. two sulphur atoms bound to each other, as a computational model in the "virtual laboratory". "This molecule represents - in an extremely simplified fashion - the corresponding chemically reactive centre in proteins", says Dominik Marx. In the course of the reaction, the sulphur bridge is cleaved.

The harder the chemists pull on the molecule, i.e. the more they distort the molecular structure, the faster the cleavage happens - but only up to a mechanical force of approximately 0.5 nanonewtons. Forces above ca. 0.5 nanonewtons accelerate the reaction significantly less than forces below this threshold.

Stressed molecules: too much mechanical force generates unfavourable spatial structure
The Bochum team could explain this effect based on the relative position of the individual molecular building blocks to each other. During the reaction, a negatively charged hydroxide ion (OH-) from the surrounding water attacks the sulphur bridge of the virtual protein.

At forces above approximately 0.5 nanonewtons, however, the protein is already distorted to such an extent that the hydroxide ion can no longer reach the sulphur bridge without difficulties. The application of the force thus blocks the access, which increases the energy barrier for the reaction. This can only be reduced again by an even greater mechanical force.

In the next step, the researchers investigated the blockade mechanism on more complex models, including a large protein fragment, similar to previous experiments. "The Janus mechanism explains puzzling and controversial results of previous force-spectroscopy measurements on the protein titin, which is found in muscles", says Prof. Marx.

Role of the solvent decisive for successful simulation
"Around the world, several theory groups have already tried to explain this experimentally observed phenomenon", says Marx. "It was crucial to correctly take into account the role of the solvent, which is water in the present case."

The hydroxide ion that attacks the sulphur bridge is surrounded by a shell of water molecules, which changes over the course of the attack in a complex way. The experimentally observed effects can only be correctly treated in the "virtual lab" when these so-called de- and re-solvation effects are accounted for included in the simulation as the reaction goes on.

However, theorists usually resort to methods that drastically simplify the effects of the surrounding water (microsolvation and continuum solvation models) in order to reduce the computational cost.

P. Dopieralski, J. Ribas-Arino, P. Anjukandi, M. Krupicka, J. Kiss, D. Marx (2013): The Janus-faced role of external forces in mechanochemical disulfide bond cleavage, Nature Chemistry, DOI: 10.1038/nchem.1676

.


Related Links
Ruhr-University Bochum
Julich Supercomputing Centre at the Research Centre Julich
Understanding Time and Space






Comment on this article via your Facebook, Yahoo, AOL, Hotmail login.

Share this article via these popular social media networks
del.icio.usdel.icio.us DiggDigg RedditReddit GoogleGoogle








TIME AND SPACE
New quantum dot technique combines best of optical and electron microscopy
Washington DC (SPX) Jun 17, 2013
It's not reruns of "The Jetsons", but researchers working at the National Institute of Standards and Technology (NIST) have developed a new microscopy technique that uses a process similar to how an old tube television produces a picture-cathodoluminescence-to image nanoscale features. Combining the best features of optical and scanning electron microscopy, the fast, versatile, and high-resoluti ... read more


TIME AND SPACE
Scientists use gravity, topographic data to find unmapped moon craters

Australian team maps Moon's hidden craters

LADEE Arrives at Wallops for Moon Mission

NASA's GRAIL Mission Solves Mystery of Moon's Surface Gravity

TIME AND SPACE
Study: Mars may have had ancient oxygen-rich atmosphere

Opportunity Recovers From Another Flash-Related Reset

ExoMars 2016 Set To Complete Construction

Mars Water-Ice Clouds Are Key to Odd Thermal Rhythm

TIME AND SPACE
NASA Bill Would 'End Reliance on Russia,' Nix Asteroid Capture Project

Britain shut down UFO desk after finding no threat: files

New Zealand emerges as guinea pig for global tech firms

NASA announces eight new astronauts, half are women

TIME AND SPACE
China's space program less costly

China seeks to boost share of satellite market

Space lotuses to touch down in Shanghai

Half-Time for Shenzhou 10

TIME AND SPACE
Accelerating ISS Science With Upgraded Payload Operations Integration Center

Strange Flames on the ISS

Europe's space truck docks with ISS

Russian cargo supply craft separates from International Space Station

TIME AND SPACE
Plan for modified European rocket gets backing

Peru launches first homemade rocket

The Centaur Upper Stage

INSAT-3D is delivered to French Guiana for Arianespace's next Ariane 5 launch

TIME AND SPACE
NASA's Hubble Uncovers Evidence of Farthest Planet Forming From its Star

Exoplanet formation surprise

Sunny Super-Earth?

Kepler Stars and Planets are Bigger than Previously Thought

TIME AND SPACE
New method to distinguish between neighbouring quantum bits

Working backward: Computer-aided design of zeolite templates

Raytheon extends ballistic missile defense capability through radar modernization effort

An innovative material for the green Earth




The content herein, unless otherwise known to be public domain, are Copyright 1995-2014 - Space Media Network. AFP, UPI and IANS news wire stories are copyright Agence France-Presse, United Press International and Indo-Asia News Service. ESA Portal Reports are copyright European Space Agency. All NASA sourced material is public domain. Additional copyrights may apply in whole or part to other bona fide parties. Advertising does not imply endorsement,agreement or approval of any opinions, statements or information provided by Space Media Network on any Web page published or hosted by Space Media Network. Privacy Statement