Direct Optical and Ultrasensitive Probing of Nonequilibrium Dynamics of Carbon Monoxide in an Aqueous Phase during Biochemical Reactions

Detection of trace carbon monoxide (CO) dissolved in an aqueous phase is key for monitoring and optimizing biological and chemical gas conversions. So far, irrespective of the nonequilibrium nature of these conversion processes, because of low water solubility of CO, such detection has been performed indirectly, under the assumption of thermodynamic equilibrium, by the combination of chromatographic measurement of relatively abundant CO in a gas phase and Henry's law. Direct and sensitive detection of dissolved CO under nonequilibrium has not been explored yet. Here, we report the direct, ultrasensitive, and real-time monitoring of nonequilibrium dynamics of CO in an aqueous phase during biochemical conversions by devising miniaturized fluidic reactors with built-in CO-specific optical probes via surface-enhanced Raman spectroscopy. As the sensitive and selective probes, we fabricate ligand-free Au@Pd core-shell nanoparticle monolayers to maximize the Raman signal of single CO in the aqueous phase. We confirm that under equilibrium conditions, aqueous and gaseous CO concentrations estimated by our method are in good agreement with those measured directly and indirectly by gas chromatography (GC). We show that our probe can detect the aqueous CO concentrations as low as ca. 0.01% with high signal reproducibility, which is 200-fold more sensitive than that achieved by infrared spectroscopy. Finally, we successfully observe the nonequilibrium dynamics of the aqueous CO during biochemical reactions, which cannot be sensed by other detection methods including even indirect measurement by GC. We anticipate that our method can be widely applied not only for monitoring of biochemical gas reactions on multiple scales from a large reactor to a single-molecule level but also for molecular imaging of biological systems.

Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy

We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO2), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron-nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe-Nε (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied dσ and dπ - πligand* orbitals. 1s → dπ transitions contribute weakly for MbO2, metMb and deoxyMb. However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s → 4p) moment due to the low symmetry of the heme environment.

L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser

L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming O K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.

State-dependent electron delocalization dynamics at the solute-solvent interface: soft-x-ray absorption spectroscopy and ab initio calculations

Nonradiative decay channels in the L-edge fluorescence yield spectra from transition-metal-aqueous solutions give rise to spectral distortions with respect to x-ray transmission spectra. Their origin is unraveled here using partial and inverse partial fluorescence yields on the microjet combined with multireference ab initio electronic structure calculations. Comparing Fe2+, Fe3+, and Co2+ systems we demonstrate and quantify unequivocally the state-dependent electron delocalization within the manifold of d orbitals as one origin of this observation.