Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New algorithm offers fast and accurate X-ray crystal structure identification

03.09.2003


Identifying the structures of certain types of molecular compounds can now take minutes, instead of days, and be performed much more accurately, say scientists who developed a new approach for analyzing key experimental X-ray data.



Knowing the structure of a molecule allows scientists to predict its properties and behavior. While X-ray diffraction measurements have become a powerful tool for determining molecular structure, identifying the three-dimensional structure that best fits the diffraction data can be a major challenge.

As will be reported in the September issue of Acta Crystallographica Section A, researchers at the University of Illinois at Urbana-Champaign have developed an algorithm that provides fast and accurate structure determination for organic compounds and other molecular structures that have a center of symmetry.


In X-ray diffraction, a crystallized version of the target compound is bombarded by a beam of X-rays. Recorded by an X-ray detector, the two-dimensional patterns of diffracted wave intensities can be used to reconstruct the three-dimensional object.

"A big problem, however, is identifying the phases of the diffracted X-rays from measurements of intensities alone," said Nikolaos Sahinidis, an Illinois professor of chemical and biomolecular engineering. "You know how strong the waves are, but you don’t know their phases, which are needed in order to compute the three-dimensional structure. This is known as the ’phase problem’ in crystallography."

Crystallographers usually rely upon various trial-and-error methods to search for a solution that solves the phase problem and identifies the crystal structure. But such methods are time-consuming and do not guarantee a correct solution.

"Most methods for solving the phase problem make use of a merit function to score potential structures based on how well they match the experimental data," Sahinidis said. "In the past, local optimization techniques and advanced computer architectures have been used to solve this problem, which may have a very large number of local optima."

Sahinidis and graduate student Anastasia Vaia developed a new approach: reformulating the problem for the case of centrosymmetric crystal structure into an integer programming problem in terms of the missing phases.

"Integer programming problems have been studied extensively in the optimization literature," Sahinidis said. "A great variety of combinatorial optimization methods have been developed to solve these problems without explicitly trying all possible combinations of the missing phases."

By introducing integer programming into crystallographic computing, "we can use off-the-shelf optimization software to rapidly find the correct solution to the phase problem," Sahinidis said. "We were able to solve many X-ray structures for which popular crystallographic software failed to provide a solution. No trial-and-error is required by our algorithm and there is no ambiguity that the correct three-dimensional structure has been identified."

Sahinidis and Vaia are now working to extend the integer programming approach to the more general case of non-centrosymmetric structures, which includes most proteins.



###
The University of Illinois, National Science Foundation and ExxonMobil Upstream Research Company funded the work.

Jim Kloeppel | EurekAlert!
Further information:
http://www.uiuc.edu/

More articles from Life Sciences:

nachricht Rainbow colors reveal cell history: Uncovering β-cell heterogeneity
22.09.2017 | DFG-Forschungszentrum für Regenerative Therapien TU Dresden

nachricht The pyrenoid is a carbon-fixing liquid droplet
22.09.2017 | Max-Planck-Institut für Biochemie

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: The pyrenoid is a carbon-fixing liquid droplet

Plants and algae use the enzyme Rubisco to fix carbon dioxide, removing it from the atmosphere and converting it into biomass. Algae have figured out a way to increase the efficiency of carbon fixation. They gather most of their Rubisco into a ball-shaped microcompartment called the pyrenoid, which they flood with a high local concentration of carbon dioxide. A team of scientists at Princeton University, the Carnegie Institution for Science, Stanford University and the Max Plank Institute of Biochemistry have unravelled the mysteries of how the pyrenoid is assembled. These insights can help to engineer crops that remove more carbon dioxide from the atmosphere while producing more food.

A warming planet

Im Focus: Highly precise wiring in the Cerebral Cortex

Our brains house extremely complex neuronal circuits, whose detailed structures are still largely unknown. This is especially true for the so-called cerebral cortex of mammals, where among other things vision, thoughts or spatial orientation are being computed. Here the rules by which nerve cells are connected to each other are only partly understood. A team of scientists around Moritz Helmstaedter at the Frankfiurt Max Planck Institute for Brain Research and Helene Schmidt (Humboldt University in Berlin) have now discovered a surprisingly precise nerve cell connectivity pattern in the part of the cerebral cortex that is responsible for orienting the individual animal or human in space.

The researchers report online in Nature (Schmidt et al., 2017. Axonal synapse sorting in medial entorhinal cortex, DOI: 10.1038/nature24005) that synapses in...

Im Focus: Tiny lasers from a gallery of whispers

New technique promises tunable laser devices

Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...

Im Focus: Ultrafast snapshots of relaxing electrons in solids

Using ultrafast flashes of laser and x-ray radiation, scientists at the Max Planck Institute of Quantum Optics (Garching, Germany) took snapshots of the briefest electron motion inside a solid material to date. The electron motion lasted only 750 billionths of the billionth of a second before it fainted, setting a new record of human capability to capture ultrafast processes inside solids!

When x-rays shine onto solid materials or large molecules, an electron is pushed away from its original place near the nucleus of the atom, leaving a hole...

Im Focus: Quantum Sensors Decipher Magnetic Ordering in a New Semiconducting Material

For the first time, physicists have successfully imaged spiral magnetic ordering in a multiferroic material. These materials are considered highly promising candidates for future data storage media. The researchers were able to prove their findings using unique quantum sensors that were developed at Basel University and that can analyze electromagnetic fields on the nanometer scale. The results – obtained by scientists from the University of Basel’s Department of Physics, the Swiss Nanoscience Institute, the University of Montpellier and several laboratories from University Paris-Saclay – were recently published in the journal Nature.

Multiferroics are materials that simultaneously react to electric and magnetic fields. These two properties are rarely found together, and their combined...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

“Lasers in Composites Symposium” in Aachen – from Science to Application

19.09.2017 | Event News

I-ESA 2018 – Call for Papers

12.09.2017 | Event News

EMBO at Basel Life, a new conference on current and emerging life science research

06.09.2017 | Event News

 
Latest News

Rainbow colors reveal cell history: Uncovering β-cell heterogeneity

22.09.2017 | Life Sciences

Penn first in world to treat patient with new radiation technology

22.09.2017 | Medical Engineering

Calculating quietness

22.09.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>