Extending the novel |ρ|-based phasing algorithm to the solution of anomalous scattering substructures from SAD data of protein crystals.

Owing to the importance of the single-wavelength anomalous diffraction (SAD) technique, the recently developed |ρ|-based phasing algorithm (SM,|ρ|) incorporating the inner-pixel preservation (ipp) procedure [Rius & Torrelles (2021). Acta Cryst A77, 339-347] has been adapted to the determination of anomalous scattering substructures and its applicability tested on a series of 12 representative experimental data sets, mostly retrieved from the Protein Data Bank. To give an idea of the suitability of the data sets, the main indicators measuring their quality are also given. The dominant anomalous scatterers are either SeMet or S atoms, or metals/clusters incorporated by soaking. The resulting SAD-adapted algorithm solves the substructures of the test protein crystals quite efficiently.

A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures.

The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489-493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.

Water-Induced Reversal of the TiO2(011)-(2 × 1) Surface Reconstruction: Observed with in Situ Surface X-ray Diffraction.

The (011) termination of rutile TiO2 is reported to be particularly effective for photocatalysis. Here, the structure of the interface formed between this substrate and water is revealed using surface X-ray diffraction. While the TiO2(011) surface exhibits a (2 × 1) reconstruction in ultra-high vacuum (UHV), this is lifted in the presence of a multilayer of water at room temperature. This change is driven by the formation of Ti-OH at the interface, which has a bond distance of 1.93 ± 0.02 Å. The experimental solution is in good agreement with density functional theory and first-principles molecular dynamics calculations. These results point to the important differences that can arise between the structure of oxide surfaces in UHV and technical environments and will ultimately lead to an atomistic understanding of the photocatalytic process of water splitting on TiO2 surfaces.

Pristine and hydrated fluoroapatite (0001).

The surface structure of fluoroapatite (0001) (FAp0001) under quasi-dry and humid conditions has been probed with surface X-ray diffraction (SXRD). Lateral and perpendicular atomic relaxations corresponding to the FAp0001 termination before and after H2O exposure and the location of the adsorbed water molecules have been determined from experimental analysis of the crystal truncation rod (CTR) intensities. The surface under dry conditions exhibits a bulk termination with relaxations in the outermost atomic layers. The hydrated surface is formed by a disordered partially occupied H2O layer containing one water molecule (33% surface coverage) adsorbed at each of the three surface Ca atoms, and is coupled with one OH group randomly bonded to each of the three topmost P atoms with a 33% surface coverage.

Epitaxial growth and structure of cobalt ferrite thin films with large inversion parameter on Ag(001).

Cobalt ferrite ultrathin films with the inverse spinel structure are among the best candidates for spin filtering at room temperature. High-quality epitaxial CoFe2O4 films about 4 nm thick have been fabricated on Ag(001) following a three-step method: an ultrathin metallic CoFe2 alloy was first grown in coherent epitaxy on the substrate and then treated twice with O2, first at room temperature and then during annealing. The epitaxial orientation and the surface, interface and film structure were resolved using a combination of low-energy electron diffraction, scanning tunnelling microscopy, Auger electron spectroscopy and in situ grazing-incidence X-ray diffraction. A slight tetragonal distortion was observed, which should drive the easy magnetization axis in-plane due to the large magneto-elastic coupling of such a material. The so-called inversion parameter, i.e. the Co fraction occupying octahedral sites in the ferrite spinel structure, is a key element for its spin-dependent electronic gap. It was obtained through in situ resonant X-ray diffraction measurements collected at both the Co and Fe K edges. The data analysis was performed using FDMNES, an ab initio program already extensively used to simulate X-ray absorption spectroscopy, and shows that the Co ions are predominantly located on octahedral sites with an inversion parameter of 0.88 (5). Ex situ X-ray photoelectron spectroscopy gives an estimation in accordance with the values obtained through diffraction analysis.

Water Dissociates at the Aqueous Interface with Reduced Anatase TiO2 (101).

Elucidating the structure of the interface between natural (reduced) anatase TiO2 (101) and water is an essential step toward understanding the associated photoassisted water splitting mechanism. Here we present surface X-ray diffraction results for the room temperature interface with ultrathin and bulk water, which we explain by reference to density functional theory calculations. We find that both interfaces contain a 25:75 mixture of molecular H2O and terminal OH bound to titanium atoms along with bridging OH species in the contact layer. This is in complete contrast to the inert character of room temperature anatase TiO2 (101) in ultrahigh vacuum. A key difference between the ultrathin and bulk water interfaces is that in the latter water in the second layer is also ordered. These molecules are hydrogen bonded to the contact layer, modifying the bond angles.

Quantitative Structure of an Acetate Dye Molecule Analogue at the TiO2-Acetic Acid Interface.

The positions of atoms in and around acetate molecules at the rutile TiO2(110) interface with 0.1 M acetic acid have been determined with a precision of ±0.05 Å. Acetate is used as a surrogate for the carboxylate groups typically employed to anchor monocarboxylate dye molecules to TiO2 in dye-sensitized solar cells (DSSC). Structural analysis reveals small domains of ordered (2 × 1) acetate molecules, with substrate atoms closer to their bulk terminated positions compared to the clean UHV surface. Acetate is found in a bidentate bridge position, binding through both oxygen atoms to two 5-fold titanium atoms such that the molecular plane is along the [001] azimuth. Density functional theory calculations provide adsorption geometries in excellent agreement with experiment. The availability of these structural data will improve the accuracy of charge transport models for DSSC.

Structural phases of ordered FePc-nanochains self-assembled on Au(110).

Iron-phthalocyanine molecules deposited on the Au(110) reconstructed channels assemble into one-dimensional molecular chains, whose spatial distribution evolves into different structural phases at increasing molecular density. The plasticity of the Au channels first induces an ordered phase with a 5×5 symmetry, followed by a second long-range ordered structure composed by denser chains with a 5×7 periodicity with respect to the bare Au surface, as observed in the low-energy electron-diffraction (LEED) and grazing incidence X-ray diffraction (GIXRD) patterns. The geometry of the FePc molecular assemblies in the Au nanorails is determined by scanning tunneling microscopy (STM). For the 5×7 phases, the GIXRD analysis identifies a "4-3" rows profile along the [001] direction in the Au surface and an on-top FePc adsorption site, further confirmed by density functional theory (DFT) calculations. The latter also reveals the electronic mixing of the interface states. The chain assembly is driven by the molecule-molecule interaction and the chains interact with the Au nanorails via the central metal atom, while the chain-chain distance in the different structural phases is primarily driven by the plasticity of the Au surface.

An EPR analysis of ß-dimerization in α-blocked pyrroles in oxidant conditions.

Electron paramagnetic resonance (EPR) analysis of neutral and acidic solutions of 2,5-dimethyl-1-phenylpyrrol (1) and meta-, para-, and ortho-bis(2,5-dimethylpyrrol-1-yl)benzenes (4-6) in the presence of Tl(III) trifluoroacetate as oxidant reveals the poor stability of their generated monomeric radical cations which dimerize through C(ß)-C(ß) bond formation. EPR spectra of the monomeric radical cations 4(•+) , 5(•+) , and 6(•+) coincide with that of 1(•+) , suggesting that the unpaired electron in these charged species is confined in one of the pyrrolic rings. The very twisted angles between pyrrolic and phenyl planes due to steric hindrance in the X-ray analysis of the molecular structure of 4 confirm the absence of extended conjugation in the π-system.

Competitive adsorption of glycine and water on the fluorapatite (100) surface.

The atomic structure of the aqueous glycine-fluorapatite (100) interface was investigated using grazing incidence X-ray diffraction. Experimental data analysis of crystal truncation rod intensities revealed detailed information on lateral as well as perpendicular ordering of the adsorbate molecules and the nature of atomic relaxations in the fluorapatite (FAp) (100) surface. Glycine and water molecules are arranged in two periodically ordered layers at the aqueous glycine-mineral interface. The adsorption process on the mineral surface is site competitive as both the glycine and water molecules show equal affinity toward surface Ca2+ cations. The glycine molecules interact directly with the FAp (100) surface, where one of their carboxylate groups coordinates with the surface Ca2+ cations. From the surface structure refinement, atomic positions of one glycine and four water molecules per unit cell were determined, along with the atomic relaxations in the FAp (100) surface. Molecular dynamic simulations were used to determine the long-range order of the adsorbate layers by investigating the hydrogen bonds.

Structure of interfacial water on fluorapatite (100) surface.

The structure relaxation mechanism of the fluorapatite (100) surface under completely hydrated ambient conditions has been investigated with the grazing incidence X-ray diffraction (GIXRD) technique. Detailed information on lateral as well as perpendicular ordering corresponding to the water molecules and atomic relaxations of the (100) surface of fluorapatite (FAp) crystal was obtained from the experimental analysis of the CTR intensities. Two laterally ordered water layers are present at the water/mineral interface. The first layer consists of four water molecules located at 1.6(1) A above the relaxed fluorapatite (100) surface while the second shows the presence of only two water molecules at a distance of 3.18(10) A from the mineral surface. Thus, the first layer water molecules complete the truncated coordination sites of the topmost surface Ca atoms, while the second water layer molecules remain bonded by means of H-bonding to the first layer molecules and the surface phosphate groups. Molecular mechanics simulations using force field techniques are in good agreement with this general structural behavior determined from the experiment.

Reducing power of simple polyphenols by electron-transfer reactions using a new stable radical of the PTM series, tris(2,3,5,6-tetrachloro-4-nitrophenyl)methyl radical.

The synthesis and characterization of a new radical and its use for testing the antioxidant activity of polyphenols by electron transfer are reported. This new and stable species of magnetic nature, tris(2,3,5,6-tetrachloro-4-nitrophenyl)methyl (TNPTM) radical, has been characterized by electron paramagnetic resonance and its molecular structure determined by X-ray analysis. This new radical of the PTM (perchlorotriphenylmethyl) series, unlike 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical, is stable in conditions of hydrogen abstraction reactions. TNPTM radical is able to discriminate between the antioxidant activities of catechol and pyrogallol in hydroxylated solvent mixtures such as chloroform/methanol (2:1). These features determine the antioxidant/pro-oxidant character and the biological activities of natural and synthetic flavonoids.

Crystalline order of a water/glycine film coadsorbed on the (104) calcite surface.

For biomineralization processes, the interaction of the surface of calcite crystals with organic molecules is of particular importance. Especially, biologically controlled biomineralization as in exoskeletons of mollusks and echinoderms, e.g., sea urchin with single-crystal-like spines and shells,1-3 requires molecular control of seed formation and growth process. So far, experiments showing the obvious influence of organic molecules on the morphology and habit of calcite crystals have demonstrated the molecular dimension of the interaction.4-7 Details of the kinetics of growth and dissolution of mineral surfaces influenced by additives are available,8,9 but other experimental data about the structure of the organic/inorganic interface on the atomic scale are rare. On the other hand, complicated organic macromolecules which are involved in biomineralization are numerous, with only a small fraction solved in structure and function so far.10-13 Therefore, model systems have to be designed to provide a basic understanding for the interaction process.14 Using grazing incidence X-ray diffraction combined with molecular modeling techniques, we show that glycine molecules order periodically on the calcite (104) face in competition with the solvent water when exposed to an aqueous solution of the most simple amino acid. In contrast to the general concept of the charge-matching fit of organic molecules on mineral surfaces,4,14 glycine is not attached to the calcite surface directly but substitutes for water molecules in the second hydration layer.

A direct phasing method based on the origin-free modulus sum function and the FFT algorithm. XII.

An alternative way of refining phases with the origin-free modulus sum function S is shown that, instead of applying the tangent formula in sequential mode [Rius (1993). Acta Cryst. A49, 406-409], applies it in parallel mode with the help of the fast Fourier transform (FFT) algorithm. The test calculations performed on intensity data of small crystal structures at atomic resolution prove the convergence and hence the viability of the procedure. This new procedure called S-FFT is valid for all space groups and especially competitive for low-symmetry ones. It works well when the charge-density peaks in the crystal structure have the same sign, i.e. either positive or negative.

Two-site adsorption model for the (square root 3 x square root 3)-R30 degrees dodecanethiolate lattice on Au(111) surfaces.

The surface structure of dodecanethiolate self-assembled monolayers (SAMs) on Au(111) surfaces, formed from the liquid phase, have been studied by grazing incidence X-ray diffraction (GIXRD), scanning tunneling microscopy (STM), and electrochemical techniques. STM images show that the surface structure consists of (square root 3 x square root 3)-R30 degrees domains with only a few domains of the c(4 x 2) lattice. The best fitting of GIXRD data for the (square root 3 x square root 3)-R30 degrees lattice is obtained with alkanethiolate adsorption at the top sites, although good fittings are also obtained for the fcc and hcp hollow sites. On the basis of this observation, STM data, electrochemical measurements, and previously reported data, we propose a two-site model that implies the formation of incoherent domains of alkanethiolate molecules at top and fcc hollow sites. This model largely improves the fitting of the GIXRD data with respect to those observed for single adsorption sites and, also, for the other possible two-site combinations. The presence of alkanethiolate molecules adsorbed at the less favorable top sites could result from the adsorption pathway that involves an initial physisorption step which, for steric reasons, takes place at on top sites. Once the molecules are chemisorbed, the presence of energy barriers for alkanethiolate surface diffusion, arising mostly from chain-chain interactions, "freezes" some of them at the on top sites, hindering their movement toward fcc hollow sites. By considering the length of the hydrocarbon chain and the adsorption time, the two-site model could be a tool to explain most of the controversial results on this matter reported in the literature.

The role of intermolecular and molecule-substrate interactions in the stability of alkanethiol nonsaturated phases on Au(111).

The structure and stability of alkanethiols self-assembled on Au(111) have been studied as a function of the molecular chain length by means of atomic force microscopy (AFM) and grazing incidence X-ray diffraction (GIXD). Below saturation, phases consisting of molecules with different tilt angles and periodicities are formed. Differences in the mechanical stability of these phases are revealed by AFM experiments and discussed in terms of the competition between intermolecular and molecule-substrate interactions as a function of chain length. For long molecules, intermolecular interactions play a dominant role which stabilizes the formation of closed packed 30 degrees tilted ( radical 3x radical 3)R30 degrees structures. For short molecules, the van der Waals interaction with the gold substrate favors the formation of a 50 degrees tilted phase in which the molecules are arranged in a rectangular configuration.

A new interpretation and practical aspects of the direct-methods modulus sum function. VIII.

Since the first publication of the direct-methods modulus sum function [Rius (1993). Acta Cryst. A49, 406-409], the application of this function to a variety of situations has been shown in a series of seven subsequent papers. In this way, much experience about this function and its practical use has been gained. It is thought by the authors that it is now the right moment to publish a more complete study of this function which also considers most of this practical knowledge. The first part of the study relates, thanks to a new interpretation, this function to other existing phase-refinement functions, while the second shows, with the help of test calculations on a selection of crystal structures, the behaviour of the function for two different control parameters. In this study, the principal interest is focused on the function itself and not on the optimization procedure which is based on a conventional sequential tangent formula refinement. The results obtained are quite satisfactory and seem to indicate that, when combined with more sophisticated optimization algorithms, the application field of this function could be extended to larger structures than those used for the test calculations.