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The interaction of intense light with matter gives rise to competing nonlinear responses that can dynamically change material properties. Prominent examples are saturable absorption (SA) and two-photon absorption (TPA), which dynamically increase and decrease the transmission of a sample depending on pulse intensity, respectively. The availability of intense soft X-ray pulses from free-electron lasers (FEL) has led to observations of SA and TPA in separate experiments, leaving open questions about the possible interplay between and relative strength of the two phenomena. Here, we systematically study both phenomena in one experiment by exposing graphite films to soft X-ray FEL pulses of varying intensity, with the FEL energy tuned to match carbon 1s to $\pi^*$ or 1s to $\sigma^*$ transitions. It is observed for lower intensities that the nonlinear contribution to the absorption is dominated by SA attributed to ground-state depletion; for larger intensities ($>10^{14}$ W/cm$^2$), TPA becomes more dominant. The relative strengths of the two phenomena depend in turn on the specific transition driven by the X-ray pulse. Both observations are consistent with our real-time electronic structure calculations. Our results reveal the competing contributions of distinct nonlinear material responses to spectroscopic signals measured in the X-ray regime, demonstrating an approach of general utility for interpreting FEL spectroscopies.

Solid-state electrolytes overcome many challenges of present-day lithium ion batteries, such as safety hazards and dendrite formation1,2. However, detailed understanding of the involved lithium dynamics is missing due to a lack of in operando measurements with chemical and interfacial specificity. Here we investigate a prototypical solid-state electrolyte using linear and nonlinear extreme-ultraviolet spectroscopies. Leveraging the surface sensitivity of extreme-ultraviolet-second-harmonic-generation spectroscopy, we obtained a direct spectral signature of surface lithium ions, showing a distinct blueshift relative to bulk absorption spectra. First-principles simulations attributed the shift to transitions from the lithium 1 s state to hybridized Li-s/Ti-d orbitals at the surface. Our calculations further suggest a reduction in lithium interfacial mobility due to suppressed low-frequency rattling modes, which is the fundamental origin of the large interfacial resistance in this material. Our findings pave the way for new optimization strategies to develop these electrochemical devices via interfacial engineering of lithium ions.

TcS2 metallizes through interlayer interactions when sufficiently dense and has a high pressure extended 3D phase similar to MnS2.

Charge transport processes at interfaces play a crucial role in many processes. Here, the first soft x-ray second harmonic generation (SXR SHG) interfacial spectrum of a buried interface (boron-Parylene N) is reported. SXR SHG shows distinct spectral features that are not observed in x-ray absorption spectra, demonstrating its extraordinary interfacial sensitivity. Comparison to electronic structure calculations indicates a boron-organic separation distance of 1.9Å, with changes of less than 1Å resulting in easily detectable SXR SHG spectral shifts (ca. hundreds of milli-electron volts).

The coexistence of ferroelectricity and metallicity seems paradoxical, since the itinerant electrons in metals should screen the long-range dipole interactions necessary for dipole ordering. The recent discovery of the polar metal LiOsO3 was therefore surprising [as discussed earlier in Y. Shi et al., Nat. Mater. 2013, 12, 1024]. It is thought that the coordination preferences of the Li play a key role in stabilizing the LiOsO3 polar metal phase, but an investigation from the combined viewpoints of core-state specificity and symmetry has yet to be done. Here, we apply the novel technique of extreme ultraviolet second harmonic generation (XUV-SHG) and find a sensitivity to the broken inversion symmetry in the polar metal phase of LiOsO3 with an enhanced feature above the Li K-edge that reflects the degree of Li atom displacement as corroborated by density functional theory calculations. These results pave the way for time-resolved probing of symmetry-breaking structural phase transitions on femtosecond time scales with element specificity.

Ultrafast time-resolved extreme ultraviolet (EUV) reflectivity measurements of optically pumped amorphous carbon (a-C) have been performed with the FERMI free electron laser (FEL). This work extends the energy range used in previous reflectivity studies and adds polarization dependence. The EUV probe is known to be sensitive to lattice dynamics, since in this range the reflectivity is essentially unaffected by the photo-excited surface plasma. The exploitation of both s- and p-polarized EUV radiation permits variation of the penetration depth of the probe; a significant increase in the characteristic time is observed upon increasing the probing depth (1 vs. 5 ps) due to hydrodynamic expansion and consequent destruction of the excited region, implying that there is only a short window during which the probed region is in the isochoric regime. A weak wavelength dependence of the reflectivity is found, consistent with previous measurements and implying a maximum electronic temperature of 0.8 eV ± 0.4.

We present a high energy resolution x-ray spectrometer for the tender x-ray regime (1.6–5.0 keV) that was designed and operated at Stanford Synchrotron Radiation Lightsource. The instrument is developed on a Rowland geometry (500 mm of radius) using cylindrically bent Johansson analyzers and a position sensitive detector. By placing the sample inside the Rowland circle, the spectrometer operates in an energy-dispersive mode with a subnatural line-width energy resolution (∼0.32 eV at 2400 eV), even when an extended incident x-ray beam is used across a wide range of diffraction angles (∼30° to 65°). The spectrometer is enclosed in a vacuum chamber, and a sample chamber with independent ambient conditions is introduced to enable a versatile and fast-access sample environment (e.g., solid/gas/liquid samples, in situ cells, and radioactive materials). The design, capabilities, and performance are presented and discussed.

The fluorine K-edge of LiF is studied both experimentally and theoretically as a function of temperature. Instantaneous thermal fluctuations in atomic positions are shown in molecular dynamics simulations to increase in amplitude from 0.029 to 0.064 nm in the temperature range from 40 to 298 K. This is sufficient to cause instantaneous deviations from local octahedral atomic symmetry in this rock-salt crystal, resulting in altered electronic structure. The lowered symmetry of the lowest core-excited states of fluorine atoms is evident in X-ray absorption spectra at the F K-edge. In addition, sufficient radiation exposure produces a new X-ray absorption peak, below the F K-edge of LiF, which is assigned to defects in LiF based on both calculations and comparison to previous experiments.

The surface and near surface structure of copper-indium-gallium-selenide (CIGS) absorber layers is integral to the producing a high-quality photovoltaic junction. By using X-ray absorption spectroscopy (XAS) and monitoring multiple elemental absorption edges with both theory and experiment, we are able to identify several features of the surface of CIGS as a function of composition and surface treatments. The XAS data shows trends in the near surface region of oxygen, copper, indium and gallium species as the copper content is varied in the films. The oxygen surface species are also monitored through a series of experiments that systematically investigates the effects of water and various solutions of: ammonium hydroxide, cadmium sulfate, and thiourea. These being components of cadmium sulfide chemical bath deposition (CBD). Characteristics of the CBD are correlated with a restorative effect that produces as normalized, uniform surface chemistry as measured by XAS. This surface chemistry is found in CIGS solar cells with excellent power conversion efficiency (

The phase diagram of water is complex, and interfacial effects can stabilize unusual structures at the nanoscale. Here, we employ bond order accelerated molecular dynamics simulations to show that upon encapsulation within bilayer graphene, water can spontaneously adopt a two-dimensional (monomolecular) layer of "square ice" at ambient conditions, instead of an encapsulated water droplet. Free energy calculations show that this motif is thermodynamically stable up to diameters of approximately 15 nm due to enhanced hydrogen bonding and favorable binding to the graphene sheets. Entropic losses due to solidification and reduced graphene-graphene binding enthalpy are opposing thermodynamic forces that conspire to limit the maximum size, but modification of any of these thermodynamic factors should change the range of stability. Simulated core-level spectroscopy reveals unambiguous orientation dependent signatures of square ice that should be discernable in experiments.

A systematic investigation of the electronic structure of the CdS buffer layer of CIGS solar cells has been undertaken using S K-edge X-ray absorption spectroscopy (XAS), both experimentally and theoretically. We found from XAS that growing CdS films by chemical bath deposition (CBD) exhibits more long-range disorder when compared to single crystal CdS, CdS grown by atomic layer deposition (ALD) and theory. We investigated the significance of a variety of point defects and potential atomic substitutions in first-principles estimates of the differential S K-edge XAS sensitivity. We find that substituting some sulfur atoms with e.g. oxygen or selenium does not introduce significant changes to the partial S(3p) density of states of the conduction band in CdS and we infer that the electronic structure modifications of these defects are spatially localized and do not hybridize strongly with bands with significant sulfur p character. Moreover, by comparison with experimental XAS should be sensitive to CdSO4; however this is not in the CdS layers of CIGS devices studied here. We also find that the CBD of CdS on FTO-glass and separately on CIGS does not produce any significant changes in the local atomic structure of CdS indicating no CIGS-influenced growth.

Controlling the morphology of laser-derived nanomaterials is dependent on developing a better understanding of the particle nucleation dynamics in the ablation plume. Here, we utilize the femtosecond-length pulses from an x-ray free electron laser to perform time-resolved grazing incidence x-ray scattering measurements on a laser-produced silicon plasma plume. At 20 ps we observe a dramatic increase in the scattering amplitude at small scattering vectors, which we attribute to incipient formation of liquid silicon droplets. These results demonstrate the utility of XFELs as a tool for characterizing the formation dynamics of nanomaterials in laser-produced plasma plumes on ultrafast timescales.

© 2018 American Physical Society. Nonlinear optical processes at soft x-ray wavelengths have remained largely unexplored due to the lack of available light sources with the requisite intensity and coherence. Here we report the observation of soft x-ray second harmonic generation near the carbon K edge (∼284 eV) in graphite thin films generated by high intensity, coherent soft x-ray pulses at the FERMI free electron laser. Our experimental results and accompanying first-principles theoretical analysis highlight the effect of resonant enhancement above the carbon K edge and show the technique to be interfacially sensitive in a centrosymmetric sample with second harmonic intensity arising primarily from the first atomic layer at the open surface. This technique and the associated theoretical framework demonstrate the ability to selectively probe interfaces, including those that are buried, with elemental specificity, providing a new tool for a range of scientific problems.

We have examined the transmission of soft X-ray pulses from the FERMI free electron laser through carbon films of varying thickness, quantifying nonlinear effects of pulses above and below the carbon K-edge. At typical of soft X-ray free electron laser intensities, pulses exhibit linear absorption at photon energies above and below the K-edge, ∼308 and ∼260 eV, respectively; whereas two-photon absorption becomes significant slightly below the K-edge, ∼284.2 eV. The measured two-photon absorption cross section at 284.18 eV (∼6 × 10−48 cm4 s) is 7 orders of magnitude above what is expected from a simple theory based on hydrogen-like atoms – a result of resonance effects.

We report measurement of the valence-to-core (VTC) region of the K-shell x-ray emission spectra from several Zn and Fe inorganic compounds, and their critical comparison with several existing theoretical treatments. We find generally good agreement between the respective theories and experiment, and in particular find an important admixture of dipole and quadrupole character for Zn materials that is much weaker in Fe-based systems. These results on materials whose simple crystal structures should not, a prior, pose deep challenges to theory, will prove useful in guiding the further development of DFT and time-dependent DFT methods for VTC-XES predictions and their comparison to experiment.

Semiconductor materials that can be doped both n-type and p-type are desirable for diode-based applications and transistor technology. Copper nitride (Cu3N) is a metastable semiconductor with a solar-relevant bandgap that has been reported to exhibit bipolar doping behavior. However, deeper understanding and better control of the mechanism behind this behavior in Cu3N is currently lacking in the literature. In this work, we use combinatorial growth with a temperature gradient to demonstrate both conduction types of phase-pure, sputter-deposited Cu3N thin films. Room temperature Hall effect and Seebeck effect measurements show n-type Cu3N with 10^17 electrons/cm^3 for low growth temperature (~35 degrees C) and p-type with 10^15-10^16 holes/cm^3 for elevated growth temperatures (50-120 degrees C). Mobility for both types of Cu3N was ~0.1-1 cm^2/Vs. Additionally, temperature- dependent Hall effect measurements indicate that ionized defects are an important scattering mechanism in p-type films. By combining X-ray absorption spectroscopy and first-principles defect theory, we determined that V_Cu defects form preferentially in p-type Cu3N while Cu_i defects form preferentially in n-type Cu3N. Based on these theoretical and experimental results, we propose a kinetic defect formation mechanism for bipolar doping in Cu3N, that is also supported by positron annihilation experiments. Overall, the results of this work highlight the importance of kinetic processes in the defect physics of metastable materials, and provide a framework that can be applied when considering the properties of such materials in general., Comment: 12 pages, 8 figures, accepted manuscript

© 2016 Author(s). Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

The dissolution of carbon dioxide in water and the ensuing hydrolysis reactions are of profound importance for understanding the behavior and control of carbon in the terrestrial environment. The first X-ray absorption spectra of aqueous carbonate have been measured at three different pH values to characterize the evolution of electronic structure of carbonate, bicarbonate, carbonic acid and dissolved CO2. The corresponding carbon K-edge core-level spectra were calculated using a first-principles electronic structure approach which samples molecular dynamics trajectories. Measured and calculated spectra are in excellent agreement. Each species exhibits similar, but distinct, spectral features which are interpreted in terms of the relative C–O bond strengths, molecular configuration, and hydration strength.

Nitrogen K-edge spectra of aqueous triglycine were measured using liquid microjets, and the effects of Hofmeister-active salts on the spectra were observed. Spectra simulated using density functional theory, sampled from room temperature classical molecular dynamics trajectories, capture all major features in the measured spectra. The spectrum of triglycine in water is quite similar to that in the presence of chaotropic sodium bromide (and other halides), which raises the solubility of proteins. However, a new feature is found when kosmotropic Na 2 SO 3 , which lowers solubility, is present; this feature results from excitations of the nitrogen atom in the terminal amino group of triglycine. Both direct interactions between this salt and the protonated amino terminus, as well as corresponding changes in the conformational dynamics of the system, contribute to this new feature. These molecular measurements support a different mechanism for the Hofmeister effect than has previously been suggested based on thermodynamic measurements. It is also shown that near edge X-ray absorption fine structure (NEXAFS) is sensitive to strong direct interaction between certain salts and charged peptides. However, by investigating the sensitivity of NEXAFS to the extreme structural differences between model β-sheets and α-helices, we conclude that this technique is relatively insensitive to secondary structure of peptides and proteins.

A computational approach is presented for prediction and interpretation of core-level spectra of complex molecules. Applications are presented for several isolated organic molecules, sampling a range of chemical bonding and structural motifs. Comparison with gas phase measurements indicates that spectral lineshapes are accurately reproduced both above and below the ionization potential, without resort to ad hoc broadening. Agreement with experiment is significantly improved upon inclusion of vibrations via molecular dynamics sampling. We isolate and characterize spectral features due to particular electronic transitions enabled by vibrations, noting that even zero-point motion is sufficient in some cases.

We describe an approach for characterizing selective binding between oppositely charged ionic functional groups under biologically relevant conditions. Relative shifts in K-shell x-ray absorption spectra of aqueous cations and carboxylate anions indicate the corresponding binding strengths via perturbations of carbonyl antibonding orbitals. XAS spectra measured for aqueous formate and acetate solutions containing lithium, sodium, and potassium cations reveal monotonically stronger binding of the lighter metals, supporting recent results from simulations and other experiments. The carbon K-edge spectra of the acetate carbonyl feature centered near 290 eV clearly indicate a preferential interaction of sodium versus potassium, which was less apparent with formate. These results are in accord with the Law of Matching Water Affinities, relating relative hydration strengths of ions to their respective tendencies to form contact ion pairs. Density functional theory calculations of K-shell spectra support the experimental findings.

Previous measurements of the X-ray absorption spectra of PbCl2 at the chlorine K-edge have shown significant variation between different studies. Herein, using first principles simulations of X-ray absorption spectroscopy, we show that the observed spectral variations are due to the generation of Cl2 gas and depletion of chlorine from PbCl2, consistent with what is observed during ultraviolet absorption for the same compound. We note that Cl2 gas generation can also be initiated using higher resonant X-ray energies, including Pb X-ray absorption edges. While this casts doubt on previous interpretations of certain measurements, it does indicate a means of generating chlorine gas during in situ experiments by passing high energy x-rays through a hard x-ray transparent medium and onto PbCl2.

The nitrogen K-edge spectra of aqueous proline and diglycine solutions have been measured by total electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at neutral and high pH. All observed spectral features have been assigned by comparison to the recently reported spectrum of aqueous glycine and calculated spectra of isolated amino acids and hydrated amino acid clusters. The sharp preedge resonances at 401.3 and 402.6 eV observed in the spectrum of anionic glycine indicate that the nitrogen terminus is in an "acceptor-only" configuration, wherein neither amine proton is involved in hydrogen bonding to the solvent, at high pH. The analogous 1s --sigma(NH) preedge transitions are absent in the NEXAFS spectrum of anionic proline, implying that the acceptor-only conformation observed in anionic glycine arises from steric shielding induced by free rotation of the amine terminus about the glycine CN bond. Anionic diglycine solutions exhibit a broadened 1s --pi(CN) resonance at 401.2 eV and a broad shoulder resonance at 403 eV, also suggesting the presence of an acceptor-only species. Although this assignment is not as unambiguous as for glycine, it implies that the nitrogen terminus of most proteins is capable of existing in an acceptor-only conformation at high pH. The NEXAFS spectrum of zwitterionic lysine solution was also measured, exhibiting features similar to those of both anionic and zwitterionic glycine, and leading us to conclude that the alpha amine group is present in an acceptor-only configuration, while the end of the butylammonium side chain is fully solvated.

By employing redox-active probes, condensed-phase molecular transport through nanoporous thin films can often be measured electrochemically. Certain kinds of electrode materials (e.g. conductive glass) are difficult to fabricate as rotatable disks or as ultramicroelectrodesthe configurations most often used for electrochemical permeation measurements. These limitations point to the need for a more materials-general measurement method. Herein, we report the application of walljet electrochemistry to the study of molecular transport through model metallopolymeric films on indium tin oxide electrodes. A quantitative expression is presented that describes the transport-limited current at the walljet electrode in terms of mass transport through solution and permeation through the film phase. A comparison of the film permeabilities for a series of redox probes measured using the walljet electrode and a rotating disk electrode establishes the accuracy of the walljet method, while also demonstrating similar preci...

X-ray absorption spectra of 1M aqueous solutions of indium (III) chloride, yttrium (III) bromide, lanthanum (III) chloride, tin (IV) chloride and chromium (III) chloride have been measured at the oxygen K-edge. Relatively minor changes are observed in the spectra compared to that of pure water. SnCl{sub 4} and CrCl{sub 3} exhibit a new onset feature which is attributed to formation of hydroxide or other complex molecules in the solution. At higher energy, only relatively minor, but salt-specific changes in the spectra occur. The small magnitude of the observed spectral changes is ascribed to offsetting perturbations by the cations and anions.

We demonstrate the use of electrostatically driven micro-electromechanical systems (MEMS) devices to control and deliver synchrotron x-ray pulses at high repetition rates. Torsional MEMS micromirrors, rotating at duty cycles of 2 kHz and higher, were used to modulate grazing-incidence x rays, producing x-ray bunches shorter than 10 μs. We find that dynamic deformation of the oscillating micromirror is a limiting factor in the duration of the x-ray pulses produced, and we describe plans for reaching higher operating frequencies using mirrors designed for minimal deformation.

Borohydride salts have been considered as good prospects for transportable hydrogen storage materials, with molecular hydrogen released via hydrolysis. We examine details of the hydration of sodium borohydride by the combination of X-ray absorption spectroscopy and first principles' theory. Compared to solid sodium borohydride, the aqueous sample exhibits an uncharacteristically narrow absorption feature that is shifted to lower energy, and ascribed to the formation of dihydrogen bonds between borohydride and water that weaken the boron–hydrogen covalent bonds. Water also acts to localize the highly excited molecular orbitals of borohydride, causing transitions to excited states with p character to become more intense and a sharp feature, uncharacteristic of tetrahedral molecules, to emerge. The simulations indicate that water preferentially associates with borohydride on the tetrahedral corners and edges.

Near edge x-ray absorption fine structure (NEXAFS) spectra at the boron K-edge were measured for aqueous boric acid, borate, and polyborate ions, using liquid microjet technology, and compared with simulated spectra calculated from first principles density functional theory in the excited electron and core hole (XCH) approximation. Thermal motion in both hydrated and isolated molecules was incorporated into the calculations by sampling trajectories from quantum mechanics/molecular mechanics simulations at the experimental temperature. The boron oxide molecules exhibit little spectral change upon hydration, relative to mineral samples. Simulations reveal that water is arranged nearly isotropically around boric acid and sodium borate, but the calculations also indicate that the boron K-edge NEXAFS spectra are insensitive to hydrogen bonding, molecular environment, or salt interactions.

Inspired by recent photoelectron spectroscopy experiments on hydroxide solutions, we have examined the conditions necessary for enhanced (and, in the case of solutions, detectable) inter-Coulombic decay (ICD)--Auger emission from an atomic site other than that originally excited. We present general guidelines, based on energetic and spatial overlap of molecular orbitals, for this enhancement of inter-Coulombic decay-based energy transfer in solutions. These guidelines indicate that this decay process should be exhibited by broad classes of biomolecules and suggest a design criterion for targeted radiooncology protocols. Our findings show that photoelectron spectroscopy cannot resolve the current hydroxide coordination controversy.

Near edge x-ray absorption fine structure (NEXAFS) spectroscopy at the nitrogen and carbon K-edges was used to study the hydration of adenosine triphosphate in liquid microjets. The total electron yield spectra were recorded as a function of concentration, pH, and the presence of sodium, magnesium, and copper ions (Na(+)/Mg(2+)/Cu(2+)). Significant spectral changes were observed upon protonation of the adenine ring, but not under conditions that promote π-stacking, such as high concentration or presence of Mg(2+), indicating that NEXAFS is insensitive to the phenomenon. Intramolecular inner-sphere association of Cu(2+) did create observable broadening of the nitrogen spectrum, whereas outer-sphere association with Mg(2+) did not.

The nitrogen K-edge near edge x-ray absorption fine structure spectrum of alpha-crystalline glycine has been calculated for temperatures ranging from 0 to 450 K. Significant temperature dependent spectral changes are predicted. The calculated room temperature spectrum is in good agreement with the experiment. At high temperatures, molecular motions strongly influence the spectrum, as any unique spectrum from an individual instantaneous configuration does not resemble the experimental result or the average calculated spectrum; complex coupled motions in this prototypical molecular crystal underlie the observed spectral changes.

Despite the obvious significance, the aqueous interactions of peptides remain incompletely understood. Their synthetic analogues called peptoids (poly-N-substituted glycines) have recently emerged as a promising biomimetic material, particularly due to their robust secondary structure and resistance to denaturation. We describe comparative near-edge X-ray absorption fine structure spectroscopy studies of aqueous sarcosine, the simplest peptoid, and alanine, its peptide isomer, interpreted by density functional theory calculations. The sarcosine nitrogen K-edge spectrum is blue shifted with respect to that of alanine, in agreement with our calculations; we conclude that this shift results primarily from the methyl group substitution on the nitrogen of sarcosine. Our calculations indicate that the nitrogen K-edge spectrum of alanine differs significantly between dehydrated and hydrated scenarios, while that of the sarcosine zwitterion is less affected by hydration. In contrast, the computed sarcosine spectrum is greatly impacted by conformational variations, while the alanine spectrum is not. This relates to a predicted solvent dependence for alanine, as compared to sarcosine. Additionally, we show the theoretical nitrogen K-edge spectra to be sensitive to the degree of hydration, indicating that experimental X-ray spectroscopy may be able to distinguish between bulk and partial hydration, such as found in confined environments near proteins and in reverse micelles.

We report the effects of sampling nuclear quantum motion with path integral molecular dynamics (PIMD) on calculations of the nitrogen K-edge spectra of two isolated organic molecules. s-triazine, a prototypical aromatic molecule occupying primarily its vibrational ground state at room temperature, exhibits substantially improved spectral agreement when nuclear quantum effects are included via PIMD, as compared to the spectra obtained from either a single fixed-nuclei based calculation or from a series of configurations extracted from a classical molecular dynamics trajectory. Nuclear quantum dynamics can accurately explain the intrinsic broadening of certain features. Glycine, the simplest amino acid, is problematic due to large spectral variations associated with multiple energetically accessible conformations at the experimental temperature. This work highlights the sensitivity of near edge x-ray absorption fine structure (NEXAFS) to quantum nuclear motions in molecules, and the necessity of accurately sampling such quantum motion when simulating their NEXAFS spectra.

The nanoscale structures of multilayer metal-phosphonate thin films prepared via a layer-by-layer assembly process using Zr(4+) and 1,12-dodecanediylbis(phosphonic acid) (DDBPA) or porphyrin square bis(phosphonic acid) (PSBPA) were studied using specular X-ray reflectivity (XRR), X-ray fluorescence, and long-period X-ray standing wave (XSW) analysis. The films were prepared in 1, 2, 3, 4, 6, and 8 layer series on both Si(001) substrates for XRR and on 18.6 nm period Si/Mo layered-synthetic microstructure X-ray mirrors for XSW. After functionalizing the SiO(2) substrate surfaces with a monolayer film terminated with phosphonate groups, the organic multilayer films were assembled by alternating immersions in (a) aqueous solutions containing Zr(4+)or Hf(4+) (final metal layer only) cations and then (b) organic solvent solutions of PO(3)-R-PO(3)(4-), where R was DDBPA or PSBPA spacer molecule. The Hf(4+) cation served as the marker for the top surface of the films, whereas the Zr(4+) cation was present in all other layers. The PSBPA also contained Zn and Re atoms at its midline which served as heavy-atom markers for each layer. The long-period XSW generated by the 0th- (total external reflection) through 4th-order Bragg diffraction conditions made it possible to examine the Fourier transforms of the fluorescent atom distributions over a much larger q(z) range in reciprocal space which permitted simultaneous analysis of Hf, Zn/Re, and Zr atomic distributions.

By employing redox-active probes, condensed-phase molecular transport through nanoporous thin films can often be measured electrochemically. Certain kinds of electrode materials (e.g. conductive glass) are difficult to fabricate as rotatable disks or as ultramicroelectrodes-the configurations most often used for electrochemical permeation measurements. These limitations point to the need for a more materials-general measurement method. Herein, we report the application of walljet electrochemistry to the study of molecular transport through model metallopolymeric films on indium tin oxide electrodes. A quantitative expression is presented that describes the transport-limited current at the walljet electrode in terms of mass transport through solution and permeation through the film phase. A comparison of the film permeabilities for a series of redox probes measured using the walljet electrode and a rotating disk electrode establishes the accuracy of the walljet method, while also demonstrating similar precision for the two methods. We apply this technique to a system consisting of zirconium phosphonate assembled films of a porphyrinic molecular square. Transport through films comprising three or more layers is free from significant contributions from pinhole defects. Surprisingly, transport through films of this kind is 2-3 orders of magnitude slower than through films constructed via interfacial polymerization of nearly identical supramolecular square building blocks (Keefe; et al. Adv. Mater. 2003, 15, 1936). The zirconium phosphate assembled films show good size exclusion behavior. The details of the observed dependence of permeation rates on probe molecule size can be rationalized with a model that assumes that the walls of the squares are slightly tilted from a strictly vertical geometry, consistent with atomic force microscopy measurements, and assumes that the individual wall geometries are locked by rigid interlayer linkages.

We study the relative ability of several models of x-ray absorption spectra to capture the Franck-Condon structure apparent from an experiment on gaseous nitrogen. In doing so, we adopt the Born-Oppenheimer approximation and a constrained density functional theory method for computing the energies of the x-ray-excited molecule. Starting from an otherwise classical model for the spectrum, we systematically introduce more realistic physics, first by substituting the quantum mechanical nuclear radial density in the bond separation R for the classical radial density, then by adding the effect of zero-point energy and other level shifts, and finally by including explicit rovibrational quantization of both the ground and excited states. The quantization is determined exactly, using a discrete variable representation (DVR). We show that the near-edge x-ray absorption fine structure (NEXAFS) spectrum can be predicted semiquantitatively within this framework. We also address the possibility of non-trivial temperature dependence in the spectrum. By using constrained density functional theory in combination with more accurate potentials, we demonstrate that it is possible to improve the predicted spectrum. Ultimately, we establish the predictive limits of our method with respect to vibrational fine structure in NEXAFS spectra.

Near edge x-ray absorption fine structure spectra have been measured at the carbon and nitrogen K-edges of the prototypical aromatic molecule, pyrrole, both in the gas phase and when solvated in water, and compared with spectra simulated using a combination of classical molecular dynamics and first principles density functional theory in the excited state core hole approximation. The excellent agreement enabled detailed assignments. Pyrrole is highly reactive, particularly in water, and reaction products formed by the auto-oligomerization of pyrrole are identified. The solvated spectra have been measured at two different temperatures, indicating that the final states remain largely unaffected by both hydration and temperature. This is somewhat unexpected, since the nitrogen in pyrrole can donate a hydrogen bond to water.