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 A new technique isolates neuronal activity during memory consolidation
22.06.2017 | Spanish National Research Council (CSIC)

nachricht CWRU researchers find a chemical solution to shrink digital data storage
22.06.2017 | Case Western Reserve University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

Im Focus: Optoelectronic Inline Measurement – Accurate to the Nanometer

Germany counts high-precision manufacturing processes among its advantages as a location. It’s not just the aerospace and automotive industries that require almost waste-free, high-precision manufacturing to provide an efficient way of testing the shape and orientation tolerances of products. Since current inline measurement technology not yet provides the required accuracy, the Fraunhofer Institute for Laser Technology ILT is collaborating with four renowned industry partners in the INSPIRE project to develop inline sensors with a new accuracy class. Funded by the German Federal Ministry of Education and Research (BMBF), the project is scheduled to run until the end of 2019.

New Manufacturing Technologies for New Products

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

A new technique isolates neuronal activity during memory consolidation

22.06.2017 | Life Sciences

Plant inspiration could lead to flexible electronics

22.06.2017 | Materials Sciences

A rhodium-based catalyst for making organosilicon using less precious metal

22.06.2017 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>