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 Single-stranded DNA and RNA origami go live
15.12.2017 | Wyss Institute for Biologically Inspired Engineering at Harvard

nachricht New antbird species discovered in Peru by LSU ornithologists
15.12.2017 | Louisiana State 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: First-of-its-kind chemical oscillator offers new level of molecular control

DNA molecules that follow specific instructions could offer more precise molecular control of synthetic chemical systems, a discovery that opens the door for engineers to create molecular machines with new and complex behaviors.

Researchers have created chemical amplifiers and a chemical oscillator using a systematic method that has the potential to embed sophisticated circuit...

Im Focus: Long-lived storage of a photonic qubit for worldwide teleportation

MPQ scientists achieve long storage times for photonic quantum bits which break the lower bound for direct teleportation in a global quantum network.

Concerning the development of quantum memories for the realization of global quantum networks, scientists of the Quantum Dynamics Division led by Professor...

Im Focus: Electromagnetic water cloak eliminates drag and wake

Detailed calculations show water cloaks are feasible with today's technology

Researchers have developed a water cloaking concept based on electromagnetic forces that could eliminate an object's wake, greatly reducing its drag while...

Im Focus: Scientists channel graphene to understand filtration and ion transport into cells

Tiny pores at a cell's entryway act as miniature bouncers, letting in some electrically charged atoms--ions--but blocking others. Operating as exquisitely sensitive filters, these "ion channels" play a critical role in biological functions such as muscle contraction and the firing of brain cells.

To rapidly transport the right ions through the cell membrane, the tiny channels rely on a complex interplay between the ions and surrounding molecules,...

Im Focus: Towards data storage at the single molecule level

The miniaturization of the current technology of storage media is hindered by fundamental limits of quantum mechanics. A new approach consists in using so-called spin-crossover molecules as the smallest possible storage unit. Similar to normal hard drives, these special molecules can save information via their magnetic state. A research team from Kiel University has now managed to successfully place a new class of spin-crossover molecules onto a surface and to improve the molecule’s storage capacity. The storage density of conventional hard drives could therefore theoretically be increased by more than one hundred fold. The study has been published in the scientific journal Nano Letters.

Over the past few years, the building blocks of storage media have gotten ever smaller. But further miniaturization of the current technology is hindered by...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

See, understand and experience the work of the future

11.12.2017 | Event News

Innovative strategies to tackle parasitic worms

08.12.2017 | Event News

AKL’18: The opportunities and challenges of digitalization in the laser industry

07.12.2017 | Event News

 
Latest News

Engineers program tiny robots to move, think like insects

15.12.2017 | Power and Electrical Engineering

One in 5 materials chemistry papers may be wrong, study suggests

15.12.2017 | Materials Sciences

New antbird species discovered in Peru by LSU ornithologists

15.12.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>