Eliminating finite-size effects on the calculation of x-ray scattering from molecular dynamics simulations.

Structural studies using x-ray scattering methods for investigating molecules in solution are shifting focus toward describing the role and effects of the surrounding solvent. However, forward models based on molecular dynamics (MD) simulations to simulate structure factors and x-ray scattering from interatomic distributions such as radial distribution functions (RDFs) face limitations imposed by simulations, particularly at low values of the scattering vector q. In this work, we show how the value of the structure factor at q = 0 calculated from RDFs sampled from finite MD simulations is effectively dependent on the size of the simulation cell. To eliminate this error, we derive a new scheme to renormalize the sampled RDFs based on a model of the excluded volume of the particle-pairs they were sampled from, to emulate sampling from an infinite system. We compare this new correction method to two previous RDF-correction methods, developed for Kirkwood-Buff theory applications. We present a quantitative test to assess the reliability of the simulated low-q scattering signal and show that our RDF-correction successfully recovers the correct q = 0 limit for neat water. We investigate the effect of MD-sampling time on the RDF-corrections, before advancing to a molecular example system, comprised of a transition metal complex solvated in a series of water cells with varying densities. We show that our correction recovers the correct q = 0 behavior for all densities. Furthermore, we employ a simple continuum scattering model to dissect the total scattering signal from the solvent-solvent structural correlations in a solute-solvent model system to find two distinct contributions: a non-local density-contribution from the finite, fixed cell size in NVT simulations, and a local contribution from the solvent shell. We show how the second contribution can be approximated without also including the finite-size contribution. Finally, we provide a "best-practices"-checklist for experimentalists planning to incorporate explicit solvation MD simulations in future work, offering guidance for improving the accuracy and reliability of structural studies using x-ray scattering methods in solution.

Initial metal-metal bond breakage detected by fs X-ray scattering in the photolysis of Ru3(CO)12 in cyclohexane at 400 nm.

Using femtosecond resolution X-ray solution scattering at a free electron laser we were able to directly observe metal-metal bond cleavage upon photolysis at 400 nm of Ru3(CO)12, a prototype for the photochemistry of transition metal carbonyls. This leads to the known single intermediate Ru3(CO)11(µ-CO)*, with a bridging ligand (µCO) and where the asterisk indicates an open Ru3-ring. This loses a CO ligand on a picosecond time scale yielding a newly observed triple bridge intermediate, Ru3(CO)8(µ-CO)3*. This loses another CO ligand to form the previously observed Ru3(CO)10, which returns to Ru3(CO)12via the known single-bridge Ru3(CO)10(µ-CO). These results indicate that contrary to long standing hypotheses, metal-metal bond breakage is the only chemical reaction immediately following the photolysis of Ru3(CO)12 at 400 nm. Combined with previous picosecond resolution X-ray scattering data and time resolved infrared spectroscopy these results yield a new mechanism for the photolysis of Ru3(CO)12.

Guest-host interactions investigated by time-resolved X­ray spectroscopies and scattering at MHz rates: solvation dynamics and photoinduced spin transition in aqueous Fe(bipy)3(2+).

We have studied the photoinduced low spin (LS) to high spin (HS) conversion of [Fe(bipy)(3)](2+) in aqueous solution. In a laser pump/X-ray probe synchrotron setup permitting simultaneous, time-resolved X-ray diffuse scattering (XDS) and X-ray spectroscopic measurements at a 3.26 MHz repetition rate, we observed the interplay between intramolecular dynamics and the intermolecular caging solvent response with better than 100 ps time resolution. On this time scale, the initial ultrafast spin transition and the associated intramolecular geometric structure changes are long completed, as is the solvent heating due to the initial energy dissipation from the excited HS molecule. Combining information from X-ray emission spectroscopy and scattering, the excitation fraction as well as the temperature and density changes of the solvent can be closely followed on the subnanosecond time scale of the HS lifetime, allowing the detection of an ultrafast change in bulk solvent density. An analysis approach directly utilizing the spectroscopic data in the XDS analysis effectively reduces the number of free parameters, and both combined permit extraction of information about the ultrafast structural dynamics of the caging solvent, in particular, a decrease in the number of water molecules in the first solvation shell is inferred, as predicted by recent theoretical work.

Picosecond time-resolved laser pump/X-ray probe experiments using a gated single-photon-counting area detector.

The recent developments in X-ray detectors have opened new possibilities in the area of time-resolved pump/probe X-ray experiments; this article presents the novel use of a PILATUS detector to achieve X-ray pulse duration limited time-resolution at the Advanced Photon Source (APS), USA. The capability of the gated PILATUS detector to selectively detect the signal from a given X-ray pulse in 24 bunch mode at the APS storage ring is demonstrated. A test experiment performed on polycrystalline organic thin films of alpha-perylene illustrates the possibility of reaching an X-ray pulse duration limited time-resolution of 60 ps using the gated PILATUS detector. This is the first demonstration of X-ray pulse duration limited data recorded using an area detector without the use of a mechanical chopper array at the beamline.

A strong steric hindrance effect on ground state, excited state, and charge separated state properties of a Cu(I)-diimine complex captured by X-ray transient absorption spectroscopy.

Photophysical and structural properties of a Cu(I) diimine complex with very strong steric hindrance, [Cu(I)(dppS)2](+) (dppS = 2,9-diphenyl-1,10-phenanthroline disulfonic acid disodium salt), are investigated by optical and X-ray transient absorption (OTA and XTA) spectroscopy. The bulky phenylsulfonic acid groups at 2,9 positions of phenanthroline ligands force the ground state and the metal-to-ligand charge-transfer (MLCT) excited state to adopt a flattened pseudo-tetrahedral coordination geometry in which the solvent access to the copper center is completely blocked. We analyzed the MLCT state dynamics and structures as well as those of the charge separated state resulting from the interfacial electron injection from the MLCT state to TiO2 nanoparticles (NPs). The OTA results show the absence of the sub-picosecond component previously assigned as the time constant for flattening, while the two observed time constants are assigned to a relatively slow intersystem crossing (ISC) rate (∼13.8 ps) and a decay rate (100 ns) of the [Cu(I)(dppS)2](+) MLCT state in water. These results correlate well with the XTA studies that resolved a flattened tetrahedral Cu(i) coordination geometry in the ground state. Probing the (3)MLCT state structure with XTA establishes that the (3)MLCT state has the same oxidation state as the copper center in [Cu(II)(dppS)2](2+) and the Cu-N distance is reduced by 0.06 Šcompared to that of the ground state, accompanied by a rotation of phenyl rings located at 2,9 positions of phenanthroline. The structural dynamics of the photoinduced charge transfer process in the [Cu(I)(dppS)2](+)/TiO2 hybrid is also investigated, which suggests a more restricted environment for the complex upon binding to TiO2 NPs. Moreover, the Cu-N bond length of the oxidized state of [Cu(I)(dppS)2](+) after electron injection to TiO2 NPs shortens by 0.05 Šcompared to that in the ground state. The interpretation of these observed structural changes associated with excited and charge separated states will be discussed. These results not only set an example for applying XTA in capturing the intermediate structure of metal complex/semiconductor NP hybrids but also provide guidance for designing efficient Cu(I) diimine complexes with optimized structures for application in solar-to-electricity conversion.

Inhomogeneous plastic flow investigated by X-ray absorption microtomography of an aluminium alloy containing marker particles.

By combining a synchrotron X-ray source and the microtomography technique, the displacement gradient tensor components can be measured directly throughout the volume of a metal sample containing highly absorbing marker particles to detect material flow. The present article describes application of these techniques to compression of a rectangular Al-W specimen with a central hole. The results show that the externally imposed axial displacement gradient is accommodated mainly in two 45 degrees shear bands passing through the hole. A simple deformation analysis provides insight into shear band formation.