A nearly on-axis spectroscopic system for simultaneously measuring UV–visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline

Sakaguchi, Miyuki; Kimura, Tetsunari; Nishida, Takuma; Tosha, Takehiko; Sugimoto, Hiroshi; Yamaguchi, Yoshihiro; Yanagisawa, Sachiko; Ueno, Go; Murakami, Hideo; Ago, Hideo; Yamamoto, Masaki; Ogura, Takashi; Shiro, Yoshitsugu; Kubo, Minoru

doi:10.1107/s1600577515018275

Cited by 4 publications

(5 citation statements)

References 33 publications

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“…A novel portable optical system, coupled to a diffractometer, was used for the pump illumination. The details of the optical system have been reported ( 18 ).…”

Section: Methodsmentioning

confidence: 99%

“…The diffraction images were collected with and without pump laser irradiation at 4°C. The diffractometer with some modifications from its previously reported version was set up in EH4c/BL3 at SACLA (SPring-8 Angstrom Compact free electron LAser) ( 18 ). As the modifications to accommodate the pump-probe experiment at 4°C, the optical system described above was placed in the space surrounding the crystal sample, and the cryostat was replaced with a crystal humidity controller for the HAG (humid air and glue-coating) method described below.…”

Section: Methodsmentioning

confidence: 99%

“…A novel portable optical system, coupled to a diffractometer, was used for the pump illumination. The details of the optical system have been reported (18). The same optical system was also used for on-line visible absorption spectroscopy by introducing a visible white light (from one direction) on-axis with the pump beam using a dichroic mirror.…”

Section: Setup For Time-resolved X-ray Crystallographymentioning

confidence: 99%

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A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase

et al. 2017

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“…A novel portable optical system, coupled to a diffractometer, was used for the pump illumination. The details of the optical system have been reported ( 18 ).…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Setup For Time-resolved X-ray Crystallographymentioning

confidence: 99%

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A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase

et al. 2017

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“…Because the kinetics of a reaction can differ greatly for a protein between the solution and the crystalline state (see Section 4.1), it is of prime importance to perform these spectroscopic experiments directly on the crystals that will be used during the diffraction experiment, and possibly also in solution. A number of instruments and facilities have been built for this purpose, in general close to synchrotron sources, such as the icOS (in crystallo Optical Spectroscopy) Laboratory at the ESRF (von Stetten et al, 2015), the SpectroLab at the SLS (Pompidor et al, 2013) and beamline BL26B1 at SPring-8 (Rose et al, 2022), which took over the online microspectrophotometry capability of BL26B2 (Sakaguchi et al, 2016).…”

Section: How To Monitor the Progress Of A Reaction Within The Crystalmentioning

confidence: 99%

From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons

Caramello,

Royant

2024

Acta Crystallogr D Struct Biol

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Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump–probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.

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“…Examples of in situ cells include those used for UV–vis–NIR absorption in combination with nuclear magnetic resonance (NMR), EPR, various synchrotron measurements, .... − ,,− Also in this category are operando measurements of catalysis; spectrophotometric titration; temperature-programmed desorption, oxidation, and reduction; and kinetic measurement. Alternatively the complementary measurements can be “ ex situ ”, after isolating a sample.…”

Section: Role Of In Situ Uv–vis–nir Absorption Spectroscopiesmentioning

confidence: 99%

In Situ UV–Vis–NIR Absorption Spectroscopy and Catalysis

Bols,

Ma,

Rammal

et al. 2024

Chem. Rev.

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This review highlights in situ UV–vis–NIR range absorption spectroscopy in catalysis. A variety of experimental techniques identifying reaction mechanisms, kinetics, and structural properties are discussed. Stopped flow techniques, use of laser pulses, and use of experimental perturbations are demonstrated for in situ studies of enzymatic, homogeneous, heterogeneous, and photocatalysis. They access different time scales and are applicable to different reaction systems and catalyst types. In photocatalysis, femto- and nanosecond resolved measurements through transient absorption are discussed for tracking excited states. UV–vis–NIR absorption spectroscopies for structural characterization are demonstrated especially for Cu and Fe exchanged zeolites and metalloenzymes. This requires combining different spectroscopies. Combining magnetic circular dichroism and resonance Raman spectroscopy is especially powerful. A multitude of phenomena can be tracked on transition metal catalysts on various supports, including changes in oxidation state, adsorptions, reactions, support interactions, surface plasmon resonances, and band gaps. Measurements of oxidation states, oxygen vacancies, and band gaps are shown on heterogeneous catalysts, especially for electrocatalysis. UV–vis–NIR absorption is burdened by broad absorption bands. Advanced analysis techniques enable the tracking of coking reactions on acid zeolites despite convoluted spectra. The value of UV–vis–NIR absorption spectroscopy to catalyst characterization and mechanistic investigation is clear but could be expanded.

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A nearly on-axis spectroscopic system for simultaneously measuring UV–visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline

Abstract: A nearly on-axis UV–visible absorption spectrometer was developed at SPring-8 that enables spectroscopic analysis of the X-ray-exposed volume of a crystal during X-ray diffraction data collection.

Cited by 4 publications

References 33 publications

A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase

A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase

From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons

In Situ UV–Vis–NIR Absorption Spectroscopy and Catalysis

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