Resonant X-ray emission with a standing wave excitation.

The Borrmann effect is the anomalous transmission of x-rays in perfect crystals under diffraction conditions. It arises from the interference of the incident and diffracted waves, which creates a standing wave with nodes at strongly absorbing atoms. Dipolar absorption of x-rays is thus diminished, which makes the crystal nearly transparent for certain x-ray wave vectors. Indeed, a relative enhancement of electric quadrupole absorption via the Borrmann effect has been demonstrated recently. Here we show that the Borrmann effect has a significantly larger impact on resonant x-ray emission than is observable in x-ray absorption. Emission from a dipole forbidden intermediate state may even dominate the corresponding x-ray spectra. Our work extends the domain of x-ray standing wave methods to resonant x-ray emission spectroscopy and provides means for novel spectroscopic experiments in d- and f-electron systems.

Inelastic x-ray scattering in heterostructures: electronic excitations in LaAlO3/SrTiO3.

We present an investigation of the valence-electron excitation spectra including the collective plasmon modes of SrTiO3, LaAlO3 and their heterostructures with non-resonant inelastic x-ray scattering. We analyse the spectra using calculations based on first principles and atomic multiplet models. We demonstrate the feasibility of performing valence IXS experiments in a total reflection geometry. Surprisingly, we find that the plasmon, interband and semicore excitations in multilayers are well described as a superposition of bulk-compound spectra even in a superstructure composing of layers of only one atomic layer thickness.

The origin and loss of periodic patterning in the turtle shell.

The origin of the turtle shell over 200 million years ago greatly modified the amniote body plan, and the morphological plasticity of the shell has promoted the adaptive radiation of turtles. The shell, comprising a dorsal carapace and a ventral plastron, is a layered structure formed by basal endochondral axial skeletal elements (ribs, vertebrae) and plates of bone, which are overlain by keratinous ectodermal scutes. Studies of turtle development have mostly focused on the bones of the shell; however, the genetic regulation of the epidermal scutes has not been investigated. Here, we show that scutes develop from an array of patterned placodes and that these placodes are absent from a soft-shelled turtle in which scutes were lost secondarily. Experimentally inhibiting Shh, Bmp or Fgf signaling results in the disruption of the placodal pattern. Finally, a computational model is used to show how two coupled reaction-diffusion systems reproduce both natural and abnormal variation in turtle scutes. Taken together, these placodal signaling centers are likely to represent developmental modules that are responsible for the evolution of scutes in turtles, and the regulation of these centers has allowed for the diversification of the turtle shell.

Effect of the hydrophobic alcohol chain length on the hydrogen-bond network of water.

The microscopic structure of the hydrogen-bond network of water-alcohol mixtures was studied using X-ray Raman scattering (XRS). To systematically examine how the hydrogen-bond network of water is affected by an increasing size of the hydrophobic group, small linear alcohols (methanol, ethanol, and propanol) in constant mole fractions were studied. The oxygen K-edge spectra were not altered upon hydration of the alcohols beyond a simple superposition of signals from alcohol and water. The experiment thus indicates that alcohols do not have a substantial effect on the structure of the hydrogen-bond network of water. In particular, no apparent breaking or forming of the hydrogen bonds is observed to take place in the overall structure. In addition, there is no indication of changes in the tetrahedrality of the hydrogen-bond network of water in the vicinity of alcohol molecules.

Molecular-level changes of aqueous poly(N-isopropylacrylamide) in phase transition.

We report a Compton scattering study on the molecular-level structural changes of aqueous poly(N-isopropylacrylamide) (PNIPAM) across the conformational phase transition. PNIPAM is a thermoresponsive polymer that changes its conformation in water from the hydrophilic coil state to the collapsed hydrophobic globule state at 32 °C. Combined with density functional theory calculations, the Compton scattering experiments detect two type of changes in the phase transition. The amount of hydrogen bonds is found to reduce, and an elongation of the internal covalent bond lengths is observed. The elongation of the bonds indicates that not only the hydrogen bonding changes but there are other processes, most likely related to hydrophobic interaction, that should be taken into account in the phase transition.

Interplay between temperature-activated vibrations and nondipolar effects in the valence excitations of the CO2 molecule.

We report a study on the temperature dependence of the valence electron excitation spectrum of CO2 performed using nonresonant inelastic X-ray scattering spectroscopy. The excitation spectra were measured at the temperatures of 300 and 850 K with momentum-transfer values of 0.4-4.8 Å(-1), i.e., from the dipole limit to the higher-multipole regime, and were simulated using high-level coupled cluster calculations on the dipole and quadrupole level. The results demonstrate the emergence of dipole-forbidden excitations owing to temperature-induced bending mode activation and finite momentum transfer.

Saturation behavior in X-ray Raman scattering spectra of aqueous LiCl.

We report a study on the hydrogen-bond network of water in aqueous LiCl solutions using X-ray Raman scattering (XRS) spectroscopy. A wide concentration range of 0-17 mol/kg was covered. We find that the XRS spectral features change systematically at low concentrations and saturate at 11 mol/kg. This behavior suggests a gradual destruction in the hydrogen-bond network until the saturation concentration. The surprisingly large concentration required for the saturation supports an interpretation in which the ions affect the structure of water only within their first hydration shell. The study is complemented by density-functional-theory calculations and molecular dynamics simulations.

Microscopic structure of water at elevated pressures and temperatures.

We report on the microscopic structure of water at sub- and supercritical conditions studied using X-ray Raman spectroscopy, ab initio molecular dynamics simulations, and density functional theory. Systematic changes in the X-ray Raman spectra with increasing pressure and temperature are observed. Throughout the studied thermodynamic range, the experimental spectra can be interpreted with a structural model obtained from the molecular dynamics simulations. A spatial statistical analysis using Ripley's K-function shows that this model is homogeneous on the nanometer length scale. According to the simulations, distortions of the hydrogen-bond network increase dramatically when temperature and pressure increase to the supercritical regime. In particular, the average number of hydrogen bonds per molecule decreases to ≈ 0.6 at 600 °C and p = 134 MPa.

Contraction of completeness-optimized basis sets: application to ground-state electron momentum densities.

Completeness-optimization is a novel method for the formation of one-electron basis sets. Contrary to conventional methods of basis set generation that optimize the basis set with respect to ground-state energy, completeness-optimization is a completely general, black-box method that can be used to form cost-effective basis sets for any wanted property at any level of theory. In our recent work [J. Lehtola, P. Manninen, M. Hakala, and K. Hämäläinen, J. Chem. Phys. 137, 104105 (2012)] we applied the completeness-optimization approach to forming primitive basis sets tuned for calculations of the electron momentum density at the Hartree-Fock (HF) level of theory. The current work extends the discussion to contracted basis sets and to the post-HF level of theory. Contractions are found to yield significant reductions in the amount of functions without compromising the accuracy. We suggest polarization-consistent and correlation-consistent basis sets for the first three rows of the periodic table, which are completeness-optimized for electron momentum density calculations.

Completeness-optimized basis sets: application to ground-state electron momentum densities.

In the current work we apply the completeness-optimization paradigm [P. Manninen and J. Vaara, J. Comput. Chem. 27, 434 (2006)] to investigate the basis set convergence of the moments of the ground-state electron momentum density at the self-consistent field level of theory. We present a black-box completeness-optimization algorithm that can be used to generate computationally efficient basis sets for computing any property at any level of theory. We show that the complete basis set (CBS) limit of the moments of the electron momentum density can be reached more cost effectively using completeness-optimized basis sets than using conventional, energy-optimized Gaussian basis sets. By using the established CBS limits, we generate a series of smaller basis sets which can be used to systematically approach the CBS and to perform calculations on larger, experimentally interesting systems.

ERKALE-A flexible program package for X-ray properties of atoms and molecules.

ERKALE is a novel software program for computing X-ray properties, such as ground-state electron momentum densities, Compton profiles, and core and valence electron excitation spectra of atoms and molecules. The program operates at Hartree-Fock or density-functional level of theory and supports Gaussian basis sets of arbitrary angular momentum and a wide variety of exchange-correlation functionals. ERKALE includes modern convergence accelerators such as Broyden and ADIIS and it is suitable for general use, as calculations with thousands of basis functions can routinely be performed on desktop computers. Furthermore, ERKALE is written in an object oriented manner, making the code easy to understand and to extend to new properties while being ideal also for teaching purposes.

On the difficulty of increasing dental complexity.

One of the fascinating aspects of the history of life is the apparent increase in morphological complexity through time, a well known example being mammalian cheek tooth evolution. In contrast, experimental studies of development more readily show a decrease in complexity, again well exemplified by mammalian teeth, in which tooth crown features called cusps are frequently lost in mutant and transgenic mice. Here we report that mouse tooth complexity can be increased substantially by adjusting multiple signalling pathways simultaneously. We cultured teeth in vitro and adjusted ectodysplasin (EDA), activin A and sonic hedgehog (SHH) pathways, all of which are individually required for normal tooth development. We quantified tooth complexity using the number of cusps and a topographic measure of surface complexity. The results show that whereas activation of EDA and activin A signalling, and inhibition of SHH signalling, individually cause subtle to moderate increases in complexity, cusp number is doubled when all three pathways are adjusted in unison. Furthermore, the increase in cusp number does not result from an increase in tooth size, but from an altered primary patterning phase of development. The combination of a lack of complex mutants, the paucity of natural variants with complex phenotypes, and our results of greatly increased dental complexity using multiple pathways, suggests that an increase may be inherently different from a decrease in phenotypic complexity.

X-ray-Raman-scattering-based EXAFS beyond the dipole limit.

X-ray Raman scattering (XRS) provides a bulk-sensitive method of measuring the extended X-ray absorption fine structure (EXAFS) of soft X-ray absorption edges. Accurate measurements and data analysis procedures for the determination of XRS-EXAFS of polycrystalline diamond are described. The contributions of various angular-momentum components beyond the dipole limit to the atomic background and the EXAFS oscillations are incorporated using self-consistent real-space multiple-scattering calculations. The properly extracted XRS-EXAFS oscillations are in good agreement with calculations and earlier soft X-ray EXAFS results. It is shown, however, that under certain conditions multiple-scattering contributions to XRS-EXAFS deviate from those in standard EXAFS, leading to noticeable changes in the real-space signal at higher momentum transfers owing to non-dipole contributions. These results pave the way for the accurate application of XRS-EXAFS to previously inaccessible light-element systems.

Tablet preformulations of indomethacin-loaded mesoporous silicon microparticles.

In this study, indomethacin-loaded thermally oxidized mesoporous silicon microparticles (TOPSi-IMC) were formulated into tablets with excipients in order to improve the dissolution and permeability properties of the poorly soluble drug. Formulations of TOPSi-IMC particles and excipients were prepared at different TOPSi-IMC particle ratios (25, 30 and 35%). The formulations were compressed by direct compression technique with a single punch tablet machine. For comparison, a formulation containing the bulk IMC (indomethacin) and the same excipients without thermally oxidized mesoporous silicon microparticles particles (TOPSi) was prepared and compressed into tablets. The TOPSi-IMC tablets were characterised according to weight, thickness, crushing strength, disintegration time and dissolution rate. The results of this study show that TOPSi-IMC particles can be compressed to a conventional tablet. The release rate of the drug and its permeation across intestinal cells model (Caco-2) from TOPSi-IMC tablets was improved compared to the bulk IMC tablets. The dissolution rate and permeability of IMC from the tablets decreased with increasing ratio of the TOPSi-IMC particles in the formulation. The phenomenon is, presumably, a result of the loss of unique pore structure of the particles due to deformation of the particles under the compression load.

Temperature dependence of the near-edge spectrum of water.

The interpretation of the oxygen near-edge spectrum of water has been debated intensively. We present new measurements of the temperature dependence of the spectrum and perform a van't Hoff analysis for the pre-edge intensity. Many microscopical and thermodynamic properties of liquid water have been described in the literature in terms of mixture models, which presume the existence of two distinct species with different local structures. Assuming such a two-component model here leads to a van't Hoff enthalpy change ΔH = 0.9 ± 0.2 kcal/mol for the conversion between the two presumed components contributing to the pre-edge intensity. The small value of ΔH compared to the average bond energy implies that the components are nearly equally bonded, suggesting that the pre-edge is sensitive to structural changes that leave hydrogen bonds intact. We further show that the pre-edge intensity in the vapor, liquid, and ice Ih spectra can be correlated with enthalpy changes. While the pre-edge intensity in water has often been interpreted to imply a large fraction of broken hydrogen bonds in the liquid, we propose that the current results indicate that those bonds would not be considered broken by energetical criteria.

Direct tomography with chemical-bond contrast.

Three-dimensional (3D) X-ray imaging methods have advanced tremendously during recent years. Traditional tomography uses absorption as the contrast mechanism, but for many purposes its sensitivity is limited. The introduction of diffraction, small-angle scattering, refraction, and phase contrasts has increased the sensitivity, especially in materials composed of light elements (for example, carbon and oxygen). X-ray spectroscopy, in principle, offers information on element composition and chemical environment. However, its application in 3D imaging over macroscopic length scales has not been possible for light elements. Here we introduce a new hard-X-ray spectroscopic tomography with a unique sensitivity to light elements. In this method, dark-field section images are obtained directly without any reconstruction algorithms. We apply the method to acquire the 3D structure and map the chemical bonding in selected samples relevant to materials science. The novel aspects make this technique a powerful new imaging tool, with an inherent access to the molecular-level chemical environment.

Calculation of isotropic Compton profiles with Gaussian basis sets.

In this paper we present an adaptive algorithm for calculating the isotropic Compton profile (ICP) for any type of Gaussian basis set. The ICP is a measure of the momentum density of electrons and it can be obtained from inelastic X-ray scattering experiments employing synchrotron radiation. We have performed calculations of the ICP for water and helium monomers and dimers using density-functional theory, Hartree-Fock and post-Hartree-Fock methods, with Dunning-type ((d-)aug-)cc-p(C)VXZ basis sets. We have examined the convergence of the Compton profile as a function of the basis set and the level of theory used for the formation of the density matrix. We demonstrate that diffuse basis functions are of utmost importance to the calculation of Compton profiles. Basis sets of at least triple-ζ quality appended by diffuse functions should be used in Compton profile calculations in order to obtain sufficient convergence with regard to the current, experimentally feasible accuracy for systems consisting of light elements.

Experimental and computational study of crystalline formic acid composed of the higher-energy conformer.

Crystalline formic acid (FA) is studied experimentally and by first-principles simulations in order to identify a bulk solid structure composed of the higher-energy (cis) conformer. In the experiments, deuterated FA (HCOOD) was deposited in a Ne matrix and transformed to the cis conformer by vibrational excitation of the ground state (trans) form. Evaporation of the Ne host above 13 K prepared FA in a bulk solid state mainly composed of cis-FA. Infrared absorption spectroscopy at 4.3 K shows that the obtained solid differs from that composed of trans-FA molecules and that the state persists up to the annealing temperature of at least 110 K. The first-principles simulations reveal various energetically stable periodic chain structures containing cis-FA conformers. These chain structures contain either purely cis or both cis and trans forms. The vibrational frequencies of the calculated structures were compared to the experiment and a tentative assignment is given for a novel solid composed of cis-FA.

Time-dependent density functional approach for the calculation of inelastic x-ray scattering spectra of molecules.

We apply time-dependent density functional theory to study the valence electron excitations of molecules and generalize the typically used time-propagation scheme and Casida's method to calculate the full wavevector dependent response function. This allows the computational study of dipole-forbidden valence electron transitions and the dispersion of spectral weight as a function of the wavevector. The method provides a novel analysis tool for spectroscopic methods such as inelastic x-ray scattering and electron energy loss spectroscopy. We present results for benzene and CF(3)Cl and make a comparison with experimental results.

Momentum distribution and renormalization factor in sodium and the electron gas.

We present experimental and theoretical results on the momentum distribution and the quasiparticle renormalization factor in sodium. From an x-ray Compton-profile measurement of the valence-electron-momentum density, we derive its discontinuity at the Fermi wave vector. This yields an accurate measure of the renormalization factor that we compare with quantum Monte Carlo and G0W0 calculations performed both on crystalline sodium and on the homogeneous electron gas.