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 Flavins keep a handy helper in their pocket
25.04.2018 | University of Freiburg

nachricht Complete skin regeneration system of fish unraveled
24.04.2018 | Tokyo Institute of Technology

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: BAM@Hannover Messe: innovative 3D printing method for space flight

At the Hannover Messe 2018, the Bundesanstalt für Materialforschung und-prüfung (BAM) will show how, in the future, astronauts could produce their own tools or spare parts in zero gravity using 3D printing. This will reduce, weight and transport costs for space missions. Visitors can experience the innovative additive manufacturing process live at the fair.

Powder-based additive manufacturing in zero gravity is the name of the project in which a component is produced by applying metallic powder layers and then...

Im Focus: Molecules Brilliantly Illuminated

Physicists at the Laboratory for Attosecond Physics, which is jointly run by Ludwig-Maximilians-Universität and the Max Planck Institute of Quantum Optics, have developed a high-power laser system that generates ultrashort pulses of light covering a large share of the mid-infrared spectrum. The researchers envisage a wide range of applications for the technology – in the early diagnosis of cancer, for instance.

Molecules are the building blocks of life. Like all other organisms, we are made of them. They control our biorhythm, and they can also reflect our state of...

Im Focus: Spider silk key to new bone-fixing composite

University of Connecticut researchers have created a biodegradable composite made of silk fibers that can be used to repair broken load-bearing bones without the complications sometimes presented by other materials.

Repairing major load-bearing bones such as those in the leg can be a long and uncomfortable process.

Im Focus: Writing and deleting magnets with lasers

Study published in the journal ACS Applied Materials & Interfaces is the outcome of an international effort that included teams from Dresden and Berlin in Germany, and the US.

Scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) together with colleagues from the Helmholtz-Zentrum Berlin (HZB) and the University of Virginia...

Im Focus: Gamma-ray flashes from plasma filaments

Novel highly efficient and brilliant gamma-ray source: Based on model calculations, physicists of the Max PIanck Institute for Nuclear Physics in Heidelberg propose a novel method for an efficient high-brilliance gamma-ray source. A giant collimated gamma-ray pulse is generated from the interaction of a dense ultra-relativistic electron beam with a thin solid conductor. Energetic gamma-rays are copiously produced as the electron beam splits into filaments while propagating across the conductor. The resulting gamma-ray energy and flux enable novel experiments in nuclear and fundamental physics.

The typical wavelength of light interacting with an object of the microcosm scales with the size of this object. For atoms, this ranges from visible light to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Invitation to the upcoming "Current Topics in Bioinformatics: Big Data in Genomics and Medicine"

13.04.2018 | Event News

Unique scope of UV LED technologies and applications presented in Berlin: ICULTA-2018

12.04.2018 | Event News

IWOLIA: A conference bringing together German Industrie 4.0 and French Industrie du Futur

09.04.2018 | Event News

 
Latest News

Getting electrons to move in a semiconductor

25.04.2018 | Physics and Astronomy

Reconstructing what makes us tick

25.04.2018 | Physics and Astronomy

Cheap 3-D printer can produce self-folding materials

25.04.2018 | Information Technology

VideoLinks
Science & Research
Overview of more VideoLinks >>>