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In-situ X-ray diffraction snapshotting: determination of the kinetics of a photodimerization within a single crystal.

ABSTRACT: In a single-crystal-to-single-crystal (SCSC) transformation, a preformed three-dimensional coordination polymer,[Ni3(oba)2(bpe)2(SO4)(H2O)4]· H2O (H2oba = 4,4'-oxydibenzoic acid; bpe = (E)-1,2-di(pyridin-4-yl)ethane) (1), was shown to undergo a [2+2] cycloaddition reaction upon exposure to UV irradiation. The kinetics of this reaction were followed by taking "snapshots" of the solid state transformation using in situ single crystal X-ray crystallography; a first order process was indicated. The reaction rate was influenced by many factors such as the separation of the sample from the UV light source, the heat produced by the UV irradiation, the light flux of the UV lamp used, the size of the single-crystal and the powder samples. The investigation of the kinetics was complemented by (1)H NMR studies. The results clearly demonstrate that in situ single-crystal X-ray diffraction is able to provide useful insights into the gradual formation of the photoproducts and the reaction processes. The work also offers a clear indication that it is possible to use the technique to study the kinetics of other photocycloaddition reactions and SCSC processes in general.

SUBMITTER: Hu FL

PROVIDER: S-EPMC4212243 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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In-situ X-ray diffraction snapshotting: determination of the kinetics of a photodimerization within a single crystal.

Hu Fei-Long FL Wang Shu-Long SL Lang Jian-Ping JP Abrahams Brendan F BF

Scientific reports 20141029

In a single-crystal-to-single-crystal (SCSC) transformation, a preformed three-dimensional coordination polymer,[Ni3(oba)2(bpe)2(SO4)(H2O)4]· H2O (H2oba = 4,4'-oxydibenzoic acid; bpe = (E)-1,2-di(pyridin-4-yl)ethane) (1), was shown to undergo a [2+2] cycloaddition reaction upon exposure to UV irradiation. The kinetics of this reaction were followed by taking "snapshots" of the solid state transformation using in situ single crystal X-ray crystallography; a first order process was indicated. The ...[more]

PMID: 25351677

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Project description:This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 µm grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.

Dataset Information

In-situ X-ray diffraction snapshotting: determination of the kinetics of a photodimerization within a single crystal.

Publications

In-situ X-ray diffraction snapshotting: determination of the kinetics of a photodimerization within a single crystal.

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