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The sugar-phosphate backbone of RNA can exist in diverse rotameric substates, giving RNA molecules enormous conformational variability. The most frequent noncanonical backbone conformation in RNA is α/γ = t/t, which is derived from the canonical backbone by a crankshaft motion and largely preserves the standard geometry of the RNA duplex. A similar conformation also exists in DNA, where it has been extensively studied and shown to be involved in DNA-protein interactions. However, the function of the α/γ = t/t conformation in RNA is poorly understood. Here, we present molecular dynamics simulations of several prototypical RNA structures obtained from X-ray and NMR experiments, including canonical and mismatched RNA duplexes, UUCG and GAGA tetraloops, Loop E, the sarcin-ricin loop, a parallel guanine quadruplex, and a viral pseudoknot. The stability of various noncanonical α/γ backbone conformations was analyzed with two AMBER force fields, ff99bsc0χOL3 and ff99bsc0χOL3 with the recent εζOL1 and βOL1 corrections for DNA. Although some α/γ substates were stable with seemingly well-described equilibria, many were unstable in our simulations. Notably, the most frequent noncanonical conformer α/γ = t/t was unstable in both tested force fields. Possible reasons for this instability are discussed. Our work reveals a potentially important artifact in RNA force fields and highlights a need for further force field refinement. [ABSTRACT FROM AUTHOR]

Despite its importance, the structure and dynamics of liquid water are still poorly understood in many apsects. Here, we report on the observation of optical fluorescence upon soft X-ray irradiation of liquid water. Detection of spectrally resolved fluorescence was achieved by a combination of the liquid microjet technique and fluorescence spectroscopy. We observe a genuine liquid-phase fluorescence manifested by a broad emission band in the 170-340 nm (4-7 eV) photon wavelength range. In addition, another narrower emission near 300 nm can be assigned to the fluorescence of OH (A state) in the gas phase, the emitting species being formed by Auger electrons escaping from liquid water. We argue that the newly observed broad-band emission of liquid water is relevant in search of extraterrestrial life, and we also envision the observed electron-ejection mechanism to find application for exploring solutes at liquid-vapor interfaces. [ABSTRACT FROM AUTHOR]

An ensemble-modeling scheme incorporating coarse-grained simulations with experimental small-angle X-ray scattering (SAXS) data is applied to dengue virus 2 (DENV2) nonstructural protein 5 (NS5). NS5 serves a key role in viral replication through its two domains that are connected by a 10-residue polypeptide segment. A set of representative structures is generated from a simulated structure pool using SAXS data fitting by the non-negativity least squares (NNLS) or standard ensemble optimization method (EOM) based on a genetic algorithm (GA). It is found that a proper low-energy threshold of the structure pool is necessary to produce a conformational ensemble of two representative structures by both NNLS and GA that agrees well with the experimental SAXS profile. The stability of the constructed ensemble is validated also by molecular dynamics simulations with an all-atom force field. The constructed ensemble successfully revealed the domain-domain orientation and domain-contacting interface of DENV2 NS5. Using experimental data fitting and additional investigations with synthesized data, it is found that energy restraint on the conformational pool is necessary to avoid overinterpretation of experimental data by spurious conformational representations. [ABSTRACT FROM AUTHOR]

Nanocellulose extracted from wood pulps using TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl radical)-mediated oxidation and sulfuric acid hydrolysis methods was characterized by small-angle neutron scattering (SANS), small-angle X-ray scattering (SAXS), and dynamic light scattering (DLS) techniques. The dimensions of this nanocellulose (TEMPO-oxidized cellulose nanofiber (TOCN) and sulfuric acid hydrolyzed cellulose nanocrystal (SACN)) revealed by the different scattering methods were compared with those characterized by transmission electron microscopy (TEM). The SANS and SAXS data were analyzed using a parallelepiped-based form factor. The width and thickness of the nanocellulose cross section were ∼8 and ∼2 nm for TOCN and ∼20 and ∼3 nm for SACN, respectively, where the fitting results from SANS and SAXS profiles were consistent with each other. DLS was carried out under both the VV mode with the polarizer and analyzer parallel to each other and the HV mode having them perpendicular to each other. Using rotational and translational diffusion coefficients obtained under the HV mode yielded a nanocellulose length qualitatively consistent with that observed by TEM, whereas the length derived by the translational diffusion coefficient under the VV mode appeared to be overestimated. [ABSTRACT FROM AUTHOR]

Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress-relaxation in hydrated lysozyme proteins stimulated and probed by X-ray Photon Correlation Spectroscopy (XPCS). This approach allows us to access the nanoscale dynamics in the deeply supercooled regime ( T = 180 K), which is typically not accessible through equilibrium methods. The observed stimulated dynamic response is attributed to collective stress-relaxation as the system transitions from a jammed granular state to an elastically driven regime. The relaxation time constants exhibit Arrhenius temperature dependence upon cooling with a minimum in the Kohlrausch-Williams-Watts exponent at T = 227 K. The observed minimum is attributed to an increase in dynamical heterogeneity, which coincides with enhanced fluctuations observed in the two-time correlation functions and a maximum in the dynamic susceptibility quantified by the normalized variance χ T . The amplification of fluctuations is consistent with previous studies of hydrated proteins, which indicate the key role of density and enthalpy fluctuations in hydration water. Our study provides new insights into X-ray stimulated stress-relaxation and the underlying mechanisms behind spatiotemporal fluctuations in biological granular materials.

We demonstrate a combined experimental and computational approach to probe the electronic structure and atomic environment of an ionic liquid, based on core level binding energies. The 1-butyl-3-methylimidazolium thiocyanate [C 4 C 1 Im][SCN] ionic liquid was studied using ab initio molecular dynamics, and results were compared against previously published and new experimental X-ray photoelectron spectroscopy (XPS) data. The long-held assumption that initial-state effects in XPS dominate the measured binding energies is proven correct, which validates the established premise that the ground state electronic structure of the ionic liquid can be inferred directly from XPS measurements. A regression model based upon site electrostatic potentials and intramolecular bond lengths is shown to account accurately for variations in core-level binding energies within the ionic liquid, demonstrating the important effect of long-range interactions on the core levels and throwing into question the validity of traditional single ion pair ionic liquid calculations for interpreting XPS data.

The amino group of proline is part of a pyrrolidine ring, which makes it unique among the proteinogenic amino acids. To unravel its full electronic structure, proline in solid state and aqueous solution is investigated using X-ray emission spectroscopy and resonant inelastic soft X-ray scattering. By controlling the pH value of the solution, proline is studied in its cationic, zwitterionic, and anionic configurations. The spectra are analyzed within a "building-block principle" by comparing with suitable reference molecules, i.e., acetic acid, cysteine, and pyrrolidine, as well as with spectral calculations based on density functional theory. We find that the electronic structure of the carboxyl group of proline is very similar to that of other amino acids as well as acetic acid. In contrast, the electronic structure of the amino group is significantly different and strongly influenced by the ring structure of proline.

Theinfluence of the monomer diallyldimethylammonium chloride (D) on thelamellar liquid crystal formed by the anionic surfactant aerosol OT(AOT) and water is investigated, determining the lamellar spacingsby SAXS and the quadrupolar splittings by deuterium NMR, as a functionof the D or AOT concentrations. The cationic monomer D induces a destabilizationof the AOT lamellar structure such that, at a critical concentrationhigher than 5 wt %, macroscopic phase separation takes place. Whenthe monomer, which is dissolved in the AOT lamellae, is polymerizedin situ by X-ray initiation, a new collapsed lamellar phase appears,corresponding to the complexation of the surfactant with the resultingpolymer. A theoretical model is employed to analyze the variationof the interactions between the AOT bilayers and the stability ofthe lamellar structure. [ABSTRACT FROM AUTHOR]

Theoreticaland experimental studies of the AgxGaxGe1–xSe2(x= 0.333, 0.250, 0.200, 0.167)single crystals are performed. These crystals possess a lot of intrinsicdefects which are responsible for their optoelectronic features. Thetheoretical investigations were performed by means of DFT calculationsusing different exchange-correlation potentials. The experimentalstudies were carried out using the modulated VUV ellipsometry fordielectric constants and birefringence studies. The comparison ofthe structure obtained from X-ray with the theoretically optimizedstructure is presented. The crucial role of the intrinsic defect statesis manifested in the choice of the exchange correlation potentialused. The data may be applicable for a large number of the ternarychalcogenides which are sensitive to the presence of the local disorderedstates near the band edges. [ABSTRACT FROM AUTHOR]

Usingthe X-ray structure of a recently discovered bacterial protein,the N-acetylneuraminic acid-inducible channel (NanC),we investigate computationally K+and Cl–ions’ permeation. We identify ion permeation pathways thatare likely to be populated using coarse-grain Monte Carlo simulations.Next, we use these pathways as reaction coordinates for umbrella sampling-basedfree energy simulations. We find distinct tubelike pathways connectingspecific binding sites for K+and, more pronounced, forCl–ions. Both ions permeate the porin preservingalmost all of their first hydration shell. The calculated free energybarriers are G#≈ 4 kJ/mol and G#≈ 8 kJ/mol for Cl–and K+, respectively. Within the approximations associatedwith these values, discussed in detail in this work, we suggest thatthe porin is slightly selective for Cl–versus K+. Our suggestion is consistent with the experimentally observedweak Cl–over K+selectivity. A rationalefor the latter is suggested by a comparison with previous calculationson strongly anion selective porins. [ABSTRACT FROM AUTHOR]

The structure of aqueous KNO 3 solutions was studied by wide-angle X-ray scattering (WAXS) and density functional theory (DFT). The interference functions were subjected to empirical potential structure refinement (EPSR) modeling to extract the detailed hydration structure information. In aqueous KNO 3 solutions with a concentration from 0.50 to 2.72 mol·dm -3 , water molecules coordinate K + with a mean coordination number (CN) from 6.6 ± 0.9 to 5.8 ± 1.2, respectively, and a K-O W (H 2 O) distance of 2.82 Å. To further describe the hydration properties of K + , a hydration factor ( f h ) was defined based on the orientational angle between the water O-H vector and the ion-oxygen vector. The f h value obtained for K + is 0.792, 0.787, 0.766, and 0.765, and the corresponding average hydration numbers (HN) are 5.2, 5.1, 4.8, and 4.5. The reduced HN is compensated by the direct binding of oxygen atoms of NO 3 - with the average CN from 0.3 ± 0.7 to 2.6 ± 1.7, respectively, and the K-O N (NO 3 - ) distance of 2.82 Å. The average number of water molecules around NO 3 - slightly reduces from 10.5 ± 1.5 to 9.6 ± 1.7 with r N-O W = 3.63 Å. K + -NO 3 - ion association is characterized by K-O N and K-N pair correlation functions (PCFs). A K-N peak is observed at 3.81 Å as the main peak with a shoulder at 3.42 Å in g K-N ( r ). This finding indicates that two occupancy sites are available for K + , i.e. , the edge-shared bidentate (BCIP) and the corner-shared monodentate (MCIP) contact ion pairs. The structure and stability of the KNO 3 (H 2 O) 10 cluster were investigated by a DFT method and cross-checked with the results from WAXS.

In the present work, characteristicproperties of tetrabutylammoniumbromide (TBAB) ionic clathrate hydrates structures were studied bysingle-crystal X-ray structure analysis. The structures of three differenttetragonal TBAB ionic clathrate hydrates that were formed in our experimentswere based on the same water lattice of tetragonal structure I (TS-I)differing in the ways of including bromide anions and arranging tetrabutylammoniumcations. We demonstrated that (1) Br–can be includedinto the water lattice, replacing two water molecules, (2) the butylgroup of the cation can be inserted not only in large T and P cavitiesbut also in small D cavities of the water lattice TS-I, and (3) oneof the reasons for polytypism of ionic clathrate hydrates on the basisof TS-I is the occurrence of alternative modes of arrangements offour-compartment cavities in adjacent layers of the water framework.The compositions of three TBAB ionic clathrate hydrates TBAB·38.1H2O, TBAB·32.5H2O, and TBAB·26.4H2O were determined by chemical analysis, and their enthalpies of fusionwere measured by differential scanning calorimetry (DSC). From theobtained results, the enthalpies of the TBAB hydrate formation fromTBAB and water were calculated thermodynamically. [ABSTRACT FROM AUTHOR]

Moleculardynamics simulations have been performed to prepare thestructural model of BaTi2O5glass. The totalcorrelation function obtained from the structural model agreed ratherwell with both the X-ray and neutron diffraction data. We found distorted4-, 5-, and 6-coordinated Ti atoms whose distortion increases withcoordination number. Furthermore, the distorted polyhedra were connectedto each other by corner-, edge-, or face-sharing. Using the optimalstructural model, the vibrational density of state was calculated,and the origin of the bands of Raman scattering spectrum was investigated.It was revealed that not only symmetric and antisymmetric vibrationin one TiOnpolyhedron but also stretching,bending, and rocking motions in Ti–O–Ti linkage contributedto the Raman bands above 600 cm–1, which governthe principal vibration in the glass. These results conclude thata Ti–O–Ti network consisting of various types of TiOnpolyhedra certainly exists in BaTi2O5glass, although the local structure around Ti deviatesfrom the Zachariasen’s rule of glass formation. [ABSTRACT FROM AUTHOR]

Protoglobin is the first globin found in Archaea.Its biological role is still unknown, although this protein can bind O2, CO, and NO reversibly in vitro. The X-ray structure of Methanosarcina acetivoransprotoglobin (MaPgb) has shown that access of ligands to the heme, which is completely buried within the protein matrix, can be granted by two apolar tunnels, which are mainly defined by helices G and B (tunnel 1), and helices B and E (tunnel 2). Here we analyze the structural and dynamical behavior of MaPgb through molecular dynamics and computational techniques aimed at shedding light on distinctive features of ligand migration through the tunnels that may be linked to functionality. While tunnel 2 is found to be accessible to diatomic ligands in both deoxygenated and oxygenated forms of the protein, the accessibility of tunnel 1 is controlled through the synergistic effect of both the protein dimeric state and the presence of the heme-bound ligand. Thus, dimerization mainly affects the spatial arrangement of helix G, which influences the shape of tunnel 1. Ligand accessibility through this tunnel is regulated by Phe(145)G8, which can adopt openand closedconformations. Noteworthy, the ratio between open and closed states is modulated by protein dimerization and more strikingly by ligand binding. In particular, sensing of the ligand is mediated by Phe(93)E11, and the steric hindrance between Phe(93)E11 and the heme-bound ligand alters the structural and dynamical behavior of helices B and E, which facilitates opening of tunnel 1. This functional mechanism provides a basis to understand the finding that ligation favors fast rebinding from ligand binding kinetic to MaPgb. Finally, it also suggests that MaPgb might be physiologically involved in a ligand-controlled bimolecular chemical process. [ABSTRACT FROM AUTHOR]

The ammonia plasma process was used for generating reactive groups, particularly primary amine functions on the surface of polyethylene (PE) films, to immobilize the enzyme trypsin. The attachment of the enzyme was achieved by directly applying an aqueous solution of trypsin to the plasma-activated surface or by using glutaraldehyde as a chemical linker. In both cases, the utilization of sodium cyanoborohydride efficiently stabilized the immobilization. The surfaces were analyzed by X-ray photoelectron spectroscopy (XPS) and enzymatic activity measurements. Active trypsin was successfully immobilized on the surface with a mean activity of 0.09 ± 0.02 U/cm². The study of the stability of the immobilized enzyme during repetitive assays showed that some activity could be maintained during several months. An original quantitative correlation between the immobilized enzyme activity and the XPS signal intensity of the S 2p electrons present in the sulfur-containing amino acid residues was evidenced. [ABSTRACT FROM AUTHOR]

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus(RmLamR) determined at 1.95 Å resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting β-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge–charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases. [ABSTRACT FROM AUTHOR]

To verify the possibility of “selective damage induction” in DNA, the yields of base lesions as well as strand breaks have been measured in dry plasmid DNA films irradiated with highly monochromatized soft X-rays in the energy region of 270−760 eV, which includes the carbon, nitrogen, and oxygen K-edges. The yields of both pyrimidine and purine base lesions, observed as Nth-sensitive and Fpg-sensitive sites, respectively, are strikingly high at the oxygen K-edge (560 eV) but extremely low at an energy just below the nitrogen K-edge (380 eV) as compared with the yields observed at other photon energies. The yields at 560 eV are enhanced 9.6-fold and 27-fold for Nth-sensitive and Fpg-sensitive sites, respectively, compared with those at 380 eV. The yield of prompt single strand breaks is also enhanced at the oxygen K-ionization energy, but only 2-fold, as compared with that at 380 eV. Our results strongly suggest that (1) the K-shell ionization of oxygen in both the nucleobases as well as in other parts of DNA and in the hydrating water molecules bound to DNA, but not the K-shell ionization of nitrogen in the nucleobases, most likely contributes to the induction of nucleobase lesions and that (2) migration of electrons and holes is involved differentially in the production of each type of DNA lesion. These results could potentially lead to new methods for “partially selective induction” of specific types of DNA damage through tuning the energy of soft X-rays. [ABSTRACT FROM AUTHOR]

We have investigated the experimental X-ray and far-infrared responses of three polythiophenes synthesized from a thiophene, α-bithiophene, and α-quaterthiophene monomer. The X-ray data show that the crystallinity of the different polythiophene samples depends on the synthesis conditions. An excellent correlation between the crystallinity of polythiophenes and their far-infrared signatures is demonstrated. In addition, the assignment of the far-infrared phonon modes in polythiophenes is given by using both an experimental filiation procedure and first-principles calculations. In particular, the ring libration inside the polymeric chain, directly involved in the electron−phonon coupling, is assigned. [ABSTRACT FROM AUTHOR]

The balance of weak CH···N bonds involving the H 3C− and −CN groups has been related to the structural rearrangement between centrosymmetric and polar acetonitrile structures. The linear highly polar molecules arrange antiparallel in phase α below a freezing temperature of 225 K/0.1 MPa and above a freezing pressure of 0.38(5) GPa/296 K and in a polar mode in phase β below 206 K/0.1 MPa and at pressures higher than 0.63(5) GPa/296 K. The α ↔ β phase transition has been considered as a supramolecular reaction between 2-dimensional and 3-dimensional hydrogen-bonding networks, the latter favoring the polar association. Acetonitrile has been in situ pressure-frozen, and its structure has been determined at room temperature by single-crystal X-ray diffraction at 0.57(5), 0.63(5), and 1.50(5)GPa. The crystallization pressure at 296 K has been determined as 0.38(5) GPa both by ruby fluorescence in a diamond anvil-cell and by the compressibility measurement in a cylinder-and-piston device. Acetonitrile mixed with methanol trimerized at 1.60 GPa and 473 K yielding 4-amino-2,6-dimethylpyrimidine: it was in situ crystallized, and the structure of a single crystal, recovered at ambient conditions, was determined. [ABSTRACT FROM AUTHOR]

Quantum calculations are applied to the active site of serine proteases, including four specific residues and a water molecule, as well as a substrate and proton donors in the oxyanion hole. Residues are tethered to the protein backbone of an X-ray structure but otherwise allowed to move freely to their lowest energy positions. The viability of the ring-flip hypothesis, which proposes that a 180° rotation of the His-57 imidazole ring facilitates the catalysis, is assessed by comparison of energies of configurations both before and after such a flip. Specifically considered is the contribution to catalysis of the Ser-214 residue and a water molecule that is observed in the active site. The calculations provide detailed information concerning the nature, geometry, and strength of hydrogen bonds that are formed within the active site at each stage of the enzymatic mechanism. [ABSTRACT FROM AUTHOR]

Here we wish to demonstrate a unique property of nanomaterials:  energy deposition with nanometer precision from low-energy electrons released from these nanostructures interacting with hard X-ray radiation in aqueous solution. Three effects combine to cause this phenomenon:  (1) localized absorption of X-rays by nanostructures, (2) effective release of low-energy electrons from small nanostructures, and (3) efficient deposition of energy in water in the form of radicals and electrons. This combination creates localized X-ray absorption and localized energy deposition of nanometer precision. We confirmed the theoretically predicted nanoscale energy deposition distribution by measuring hydroxyl radical-induced DNA strand breaks, and observed enhanced damage to a 5600-bp DNA molecule from approximately 10 chemically conjugated small gold nanoparticles under X-ray radiation. These results provide a general guidance to applications of this new concept in many fields including radiation chemistry, radiology, radiation oncology, biochemistry, biology, and nanotechnology. [ABSTRACT FROM AUTHOR]

We report rheological, X-ray, and dielectric investigations on a chromonic liquid-crystalline system formed by aqueous solutions of a food coloring agent, Sunset Yellow, in the absence and upon addition of salt. The salt-concentration dependence of the steady-state viscosity at low shear rates has a non-monotonic variation and is qualitatively similar to the behavior seen in wormlike micellar systems, a surprising result since chromonic systems are expected to be non-micellar in character. More interestingly, for a particular low concentration of the salt (20 mM), the viscosity increases by 3 orders of magnitude in comparison with that of the pure chromonic material. The dynamic (oscillatory) rheological data bring out features which can be described in terms of a microstructure formation. X-ray and dielectric studies show that certain characters of the aggregates formed by the Sunset Yellow molecules are not altered by the addition of salt. [ABSTRACT FROM AUTHOR]

We report on the neutral-to-ionic (N−I) phase transition in the one-dimensional organic complex (BEDT-TTF)-(ClMeTCNQ). The X-ray studies at room temperature show that the neutral phase of (BEDT-TTF)-(ClMeTCNQ) is already characterized by a polar long-range ordering, at variance with other charge-transfer compounds comprising noncentrosymmetric molecules. From a detailed neutron diffraction study of this complex under high pressure, we present the phase diagram of the N−I transition down to the quantum limit. We discuss the symmetry breaking associated with the transition and the evolution of its first-order character under pressure. [ABSTRACT FROM AUTHOR]

We show that the combination of X-ray reflectivity, tryptophan fluorescence spectrum, and fluorescence quenching by bromine provides a useful tool to probe the location of lysozyme in lipid bilayers. To this end, we prepare lamellar complexes composed of phospholipids and lysozyme on solid surfaces using a solution-casting method. The proteins lie spontaneously between adjacent bilayers in the complexes. The results indicate that lysozyme may penetrate into the lipid bilayers. But the penetration depth is very shallow, and the tryptophan residues do not penetrate beyond the interface between the hydrocardon core and the headgroup region of the lipid bilayer.The penetration becomes saturated when more proteins are incorporated into the lamellar complex. The excess proteins stay in the interlamellar aqueous layers. [ABSTRACT FROM AUTHOR]

A large domain motion in adenylate kinase from E. coli(AKE) is studied with molecular dynamics. AKE undergoes a large-scale rearrangement of its lid and AMP-binding domains when the open form closes over its substrates, AMP, and Mg2-ATP, whereby the AMP-binding and lid domains come closer to the core. The third domain, the core, is relatively stable during this motion. A reaction coordinate that monitors the distance between the AMP-binding and core domains is selected to be able to compare with the results of energy transfer experiments. Sampling along this reaction coordinate is carried out by using a distance replica exchange method (DREM), where systems that differ by a restraint potential enforcing different reaction coordinate values are independently simulated with periodic attempts at exchange of these systems. Several methods are used to study the efficiency and convergence properties of the DREM simulation and compared with an analogous non-DREM simulation. The DREM greatly accelerates the rate and extent of configurational sampling and leads to equilibrium sampling as measured by monitoring collective modes obtained from a principal coordinate analysis. The potential of mean force along the reaction coordinate reveals a rather flat region for distances from the open to a relatively closed AKE conformation. The potential of mean force for smaller distances has a distinct minimum that is quite close to that found in the closed form X-ray structure. In concert with a decrease in the reaction coordinate distance (AMP-binding-to-core distance) the lid-to-core distance of AKE also decreases. Therefore, apo AKE can fluctuate from its open form to conformations that are quite similar to its closed form X-ray structure, even in the absence of its substrates. [ABSTRACT FROM AUTHOR]

Structure analysis of unilamellar manganese oxide nanosheets obtained via exfoliation of layered manganese oxides was carried out utilizing synchrotron radiation (SR) X-ray in-plane diffraction and polarization-dependent total reflection fluorescence X-ray absorption fine structure (PTRF-XAFS) analyses. A combination of SR excitation and the total reflection of incoming X-rays provides signals strong enough for both analyses even from a monolayer of the MnO2nanosheets having a concentration of 0.7 g cm-2. In addition, the mean oxidation state of constituent manganese ions in the MnO2sheets was estimated on the basis of XANES spectra, and bond valence sum calculations with the bond length obtained from the present EXAFS analyses. The obtained structural data revealed that the two-dimensional lattice of the MnO2sheets underwent a slight elongation upon delamination. These changes correspond to approximately 1% expansion of sheet area and 1−2% expansion of thickness, which can be understood by reduction of the mean oxidation number of manganese ions in the sheet through the exfoliation process. [ABSTRACT FROM AUTHOR]

Ba deposition on a -Al2O3/NiAl(100) substrate and its oxidation with gas-phase O2at various surface temperatures are investigated using X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), and temperature programmed desorption (TPD) techniques. Oxidation of metallic Ba by gas-phase O2at 800 K results in the growth of 2D and 3D BaO surface domains. Saturation of a metallic Ba layer deposited on -Al2O3/NiAl(100) with O2(g) at 300 K reveals the formation of BaO2-like surface states. These metastable peroxide (O22-) states are converted to regular oxide (O2-) states at higher temperatures (800 K). In terms of thermal stability, BaO surface layers (Ba< 5 ML) that are formed by O2(g) assisted oxidation on the -Al2O3/NiAl(100) substrate are significantly more stable (with a desorption/decomposition temperature of c.a. 1050 K) than the thick (2 < Ba< 10 ML) metallic/partially oxidized Ba layers prepared in the absence of gas-phase O2, whose multilayer desorption features appear as low as 700 K. [ABSTRACT FROM AUTHOR]

In this work, two selectively deuterium-labeled isotopomers of the (S)-2-methylbutyl- 4‘-(4‘ ‘-heptyloxyphenyl)-benzoyl-4-oxy-(S)-2-((S)-2‘)-benzoyl)-propionyl)-propionate (ZLL 7/), one labeled on the phenyl ring (ZLL 7/-phe-D2) and the other one on the biphenyl fragment (ZLL 7/-biphe-D2), have been investigated by deuterium NMR (DNMR) spectroscopy and other experimental techniques. These compounds possess the paraelectric SmA, the ferroelectric SmC, the antiferroelectric SmCA, the re-entrant ferroelectric SmCre, and the ferroelectric hexaticphases down to room temperature. The orientational ordering properties of the two labeled fragments have been determined by means of DNMR, and the mesophase behavior at two magnetic fields is discussed. In particular, the effect of the magnetic field on the supramolecular structure of the SmC and SmCrephases is commented. This study revealed to be useful to understand the structural and conformational properties of the ferroelectric/antiferroelectric/re-entrant/hexatic smectic phases. Mesomorphic properties, spontaneous tilt angle, polarization, and layer spacing have been studied for the labeled materials and compared with those obtained for the nonlabeled compound. The two self-consistent set of data, from optical and DNMR measurements and X-ray results, allow us to associate at the transition from the SmC to the SmCAphase a change of the molecular conformation. [ABSTRACT FROM AUTHOR]

The knowledge of the structure of a molecular crystal is frequently a prerequisite for the understanding of its solid state properties. Even though single-crystal diffractometry is the method of choice when it comes to crystal structure determination, methods using powder diffraction data become more and more competitive. There has been much recent interest in the development of a new generation of “direct-space” approaches that are particularly suited for molecular crystals. The crystallographic structure of a steroid derivative molecule (17,17-di-n-propyl-17a-aza-D-homo-5-androstan-3-ol) was obtained in two independent ways:  from a single crystal by laboratory X-rays and from a polycrystalline powder by high-resolution synchrotron powder diffraction. The molecule crystallizes in the orthorhombic space group P212121(a 6.5346, b 17.6006 and c 19.6978 Å). Hydrogen bonds form infinite chains of molecules parallel to the caxis. [ABSTRACT FROM AUTHOR]

Bent-shaped molecules based on the oxadiazole central core with various side wings and terminal chain groups have been synthesized, and their liquid-crystalline behavior was investigated by optical microscopic, X-ray, and electrooptic measurements. These molecules exhibit liquid-crystal polymorphism including both the calamitic and banana phases. Such a characteristic polymorphism is attributable to the larger bend angle of the oxadiazole core compared to that of the resorcinol core used in conventional banana molecules. Only one type of banana phase, designated as the Bx phase, is formed. It appears upon cooling from the nematic and smectic liquid crystals and exhibits chiral domains with a very weak birefringence (apparently optically isotropic). By applying an electric field, the Bx phase is altered to a high-birefringence B2 phase with a homochiral SmCAPA structure that exhibits an antiferroelectric response. From detailed analyses of the optical texture and X-ray patterns through the transformation from well-oriented calamitic phases, the Bx phase was found to exhibit a helical structure, which arises as a frustration from the ground-state B2 phase in such a manner that the blocks of B2 layers are twisted with respect to each other in a direction parallel to the layer plane similarly to the twisted grain boundary (TGB) phase. [ABSTRACT FROM AUTHOR]

The structure of the Ag(111)(√7×√7)R19°-CH3S surface phase, formed by interaction of Ag(111) with gas-phase dimethyl disulfide, (CH3S)2, has been investigated by normal-incidence X-ray standing wave (NIXSW) analysis, using (111), (1̄11), and (200) Bragg reflections. The resulting NIXSW structural parameter values clearly exclude any simple overlayer adsorption model on an Ag unreconstructed surface. A reconstructed surface model is proposed that is consistent with the NIXSW measurements and with previous scanning tunneling microscopy results. This comprises a near-hexagonal Ag surface layer with an Ag density of only 3/7 that of the underlying substrate layers; the methanethiolate molecules are adsorbed into 3-fold coordinated hollow sites on this open layer. The results are discussed in the context of the very limited published studies of longer alkyl chain thiolates on Ag(111). [ABSTRACT FROM AUTHOR]

The adsorption of methanethiol and n-propanethiol on the Au(111) surface has been studied by temperature-programmed desorption (TPD), Auger electron spectroscopy (AES), and low-temperature scanning tunneling microscopy (LT-STM). Methanethiol desorbs molecularly from the chemisorbed monolayer at temperatures below 220 K in three overlapping desorption processes. No evidence for S−H or C−S bond cleavage has been found on the basis of three types of observations:  (1) A mixture of chemisorbed CH3SD and CD3SH does not yield CD3SD, (2) no sulfur remains after desorption, and (3) no residual surface species remain when the adsorbed layer is heated to 300 K as measured by STM. On the other hand, when defects are introduced on the surface by ion bombardment, the desorption temperature of CH3SH is extended to 300 K and a small amount of dimethyl disulfide is observed to desorb at 410 K, indicating that S−H bond scission occurs on defect sites on Au(111) followed by dimerization of CH3S(a) species. Propanethiol also adsorbs nondissociatively on the Au(111) surface and desorbs from the surface below 250 K. [ABSTRACT FROM AUTHOR]

Temperature behaviors of X-ray luminescence (XL), photoluminescence (PL), photostimulated luminescence, and thermoluminescence (TL) were studied in BaFCl:Eu2+ single crystals from room temperature to liquid nitrogen temperature. Six emissions at 275, 315, 365, 385, 435, and 500 nm were observed in the XL spectra and are attributed to Cl excitons, Vk(C[inline equation] ), the 4f65d1 (2eg) → 4f7 (8S7/2) transition of Eu2+, and oxygen vacancies, respectively. Three emission peaks at 315, 365, and 390 nm were observed in the PL and TL measurements. These three emissions are from the transitions of 4f7(6I7/2) → 4f7(8S7/2), 4f7(6P7/2) → 4f7(8S7/2), and 4f65d1 (2eg) → 4f7(8S7/2) of Eu2+, respectively. In our measurements, we observed that the emission of Eu2+ increases in intensity upon β-irradiation and did not see any signals related to Eu3+ ions, which indicates that Eu2+ ions might not be oxidized to Eu3+ upon X-ray or β-irradiation. Instead, the color centers, Cl excitons, and oxygen defects are created and are stable at room temperature, and they might play a key role in the storage luminescence. [ABSTRACT FROM AUTHOR]

The voltammetric characteristics of polycrystalline Au and W electrodes cleaned (thermal annealing at 1100 K) and characterized (Auger electron spectroscopy) in ultrahigh vacuum (UHV) have been examined in ultrapure AlCl3/1-ethyl-3-methylimidazolium chloride (EtMeImCl) melts in UHV. These experiments were performed using a custom-designed transfer system that allows for the all-Al electrochemical cell to be filled with EtMeImCl in an auxiliary UHV chamber and later transferred under UHV to the main UHV chamber that houses the Auger electron spectrometer. The results obtained for the underpotential (UPD) and bulk deposition of Al on Au were found to be very similar to those reported in the literature for measurements carried out under 1 atm of an inert gas in a glovebox. For the far more reactive W surfaces, voltammetric features ascribed to the stripping of underpotential-deposited Al could be observed following a single scan from 1.0 V vs Al3+/Al to a potential negative enough for bulk deposition of Al to ensue. This behavior is unlike that reported in the literature for experiments performed in a glovebox, which required either extensive potential cycling in the Al bulk deposition and stripping region or excursions to potentials positive enough for chlorine evolution to ensue for Al UPD features to be clearly discerned. These observations open new prospects for fundamental electrochemical studies of well-characterized, highly reactive metals, including single crystals, in a variety of low vapor pressure ionic liquids. [ABSTRACT FROM AUTHOR]

The interaction of oxygen with a carburized Mo(100) surface was investigated at different temperatures (300-1000 K). The different information depths of low-energy ion-scattering (LEIS) spectroscopy, with topmost layer sensitivity, Auger electron spectroscopy (AES), and angle-resolved X-ray photoelectron spectroscopy (ARXPS) allowed us to discriminate between reactions on the topmost layer and subsurface transformations. According to ARXPS measurements, a carbide overlayer was prepared by the high-temperature decomposition of C2H4 on Mo(100), and the carbon distribution proved to be homogeneous with a Mo2C stoichiometry down to the information depth of XPS. O2 adsorbs dissociatively on the carbide layer at room temperature. One part of the chemisorbed oxygen is bound to both C and Mo sites, indicated by LEIS. Another fraction of oxygen atoms probably resides in the hollow sites not occupied by C. The removal of C from the outermost layer by O2, in the form of CO, detected by mass spectroscopy (MS), was observed at 500-600 K. The carbon-depleted first layer is able to adsorb more oxygen compared to the Mo2C/Mo(100) surface. Applying higher doses of O2 at 800 K results in the inward diffusion of O and the partial oxidation of Mo atoms. This process, however, is not accompanied by the removal of C from subsurface sites. The depletion of C from the bulk starts only at 900 K (as shown by MS, AES, and XPS), very probably by the diffusion of C to the surface followed by its reaction with oxygen. At Tads = 1000 K, the carbon content of the sample, down to the information depth of XPS, decreased further, accompanied by the attenuation of the C concentration gradient and a substantially decreased amount of oxygen. [ABSTRACT FROM AUTHOR]

Temperature programmed desorption (TPD), Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), and scanning tunneling microscopy (STM) have been used to characterize molybdenum carbide nanoparticles prepared on a Au(111) substrate. The MoCx nanoparticles were formed by Mo metal deposition onto a reactive multilayer of ethylene, which was physisorbed on a Au(111) substrate at low temperatures (<100 K). The resulting clusters have an average diameter of ~1.5 nm and aggregate in the fcc troughs located on either side of the elbows of the reconstructed Au(111) surface. Core level XPS shows that the electronic environment of the Mo and C atoms in the nanoparticles is similar to that found in Mo2C(0001) single crystals and carburized Mo metal surfaces. Peak intensities in XPS and AES spectra were used to estimate an average Mo/C atomic ratio of 1.2 ± 0.3 for nanoparticles annealed above 600 K. [ABSTRACT FROM AUTHOR]

The effect of tin on the thermal chemistry of CH3 on Si/Cu(100) was investigated using temperature programmed desorption (TPD), X-ray photoelectron spectroscopy (XPS), ion scattering spectroscopy (ISS), low energy electron diffraction (LEED), Auger electron spectroscopy (AES), and high-resolution helium atom scattering (HAS). The Si/Cu(100) substrate was prepared by exposure to silane at 420 K. The TPD results showed that (CH3)3SiH was the dominant product desorbing from Si/Cu(100) after exposure to CH3 radical, and that its desorption was sensitive to the concentration of Si in the outermost surface. For the silane-saturated surface, Sisat/Cu(100), (CH3)3SiH desorbed near 500 K, while for subsaturated surfaces, Siunsat/Cu(100), (CH3)3SiH desorbed at both 270 and 500 K. The addition of Sn to the Sisat/Cu(100) surface, prior to CH3 exposure, led to a shift in the (CH3)3SiH desorption feature to higher temperatures. Tin addition to Siunsat/Cu(100) surface changed the product distribution. Specifically, with Sn coadsorption levels in excess of 0.7 ML, the dominant product is the fully methylated species, (CH3)4Si, at 430 K. [ABSTRACT FROM AUTHOR]

The effect of synthesis and reaction conditions on the structure and activity of Au clusters supported on nanocrystalline and mesoporous TiO2 was investigated. X-ray absorption spectroscopy was applied to correlate the particle size and the oxidation state with several parameters, such as pH of the precursor solution, Au loading, pretreatment, and support structure. The study using mesoporous TiO2 as the support shows that lower Au loadings resulted in bigger Au aggregates with lower reducibility. The high activity state for Au supported in different allotropic forms of TiO2 corresponds to Au in a fully reduced state. Furthermore, once reduced, no reoxidation occurs under reaction conditions, even after flowing air at higher temperatures (150 and 300 °C). Therefore, our results indicate that oxidized Au is not necessary for high activity. The activity decreased with particle growth, and, compared to the other allotropic TiO2, Au on brookite exhibited no significant particle agglomeration and was the most active catalyst after treatment at 300 °C. [ABSTRACT FROM AUTHOR]

In this study, the erosion of poly(tetrafluoroethylene) TFE Teflon by hyperthermal atomic oxygen (AO) has been examined using X-ray photoelectron spectroscopy (XPS). The initial F/C atom ratio of 1.66 decreases to 1.15 after a 2 h exposure to a flux of 2 × 1015 atoms/cm2 s AO with an average kinetic energy ~5 eV. The F/C atom ratio is further reduced to a value of 0.90 after a 25 h exposure. The high-resolution XPS C 1s data indicate that new chemical states of carbon form as the F is removed, and that the relative amounts of these states depend on the F content of the near-surface region. The states are most likely due to C bonded only to one F atom and C bonded only to other C atoms. Exposures of the AO-damaged surface to research-grade O2 results in chemisorption of a very small amount of O (~0.8 at. %); this indicates that large quantities of reactive sites are not formed during the chemical erosion by AO. Further exposure to AO removes this chemisorbed oxygen. After exposing the AO-exposed surface to air for 90 min, O2 is chemisorbed and the F/C atom ratio is reduced to 0.68. Another 46 h of AO exposure results in removal of this O and a further decrease in the F/C atom ratio to 0.58. [ABSTRACT FROM AUTHOR]

Highly crystallized TiO2 nanocrystallites (10-50 nm in size) with controlled phase structures (anatase and rutile) were synthesized using a one-step process. Flying TiC micrometer-size powder was oxidized in Ar-O2 and Ar-H2-CO2 plasmas with various configurations used for injecting oxygen into the reaction system. The oxide nanocrystallites formed were characterized by X-ray diffractometry, Raman spectroscopy, and high-resolution transmission electron microscopy. The TiO2 nanocrystallites formed in the Ar-O2 plasma consisted of isolated single-crystal particles of anatase with spherical shapes and rutile grains crystallized in a hexagonal morphology. The fraction of anatase increased greatly with the oxygen flow rate in the Ar-O2 plasma. On the other hand, oxidation of the carbide in the Ar-H2-CO2 plasma gave exclusively pure rutile nanocrystallites, regardless of the CO2 concentration. Injecting oxygen at the plasma tail greatly reduced the size of the nanocrystallites. These results suggest that both the size and the phase compositions of nanocrystalline TiO2 can be controlled using this thermal plasma oxidation process. [ABSTRACT FROM AUTHOR]

FAU-type zeolite was synthesized at room temperature to study the mechanism of its formation. The sluggish crystal growth kinetics at ambient conditions permitted us to track down the entire sequence of crystallization events from the formation of the initial gel to the complete transformation into a zeolite-type material. The processes taking place at the nanometer scale were studied by transmission electron microscopy (TEM). The crystalline character of the particles observed during the induction period was determined by in situ synchrotron XRD analysis. The study was completed by ex situ X-ray diffraction (XRD), infrared (IR), dynamic light scattering (DLS), N2 adsorption measurements and chemical analyses. The combined TEM/synchrotron XRD analysis of the initial crystallization stage revealed that zeolite nuclei were formed during the homogenization (1.5 h) of the initial reactants. Nevertheless, a relatively long induction period (10 days) was observed. During this period, extensive exchange between the solid and liquid parts of the system took place. However, the changes in the chemical composition of the gel and mother liquor were not coupled with a detectible increase of the number of nuclei. It seems that the critical factor that triggers the growth process and mass transformation of amorphous into crystalline zeolite material is the attainment of a specific level of chemical evolution of the system, expressed in homogenization of the starting gel approaching stoichiometric FAU compositon. The process of zeolite formation can be divided into four general stages: (i) 0-1.5 h, formation of an amorphous gel with highly variable composition, local formation of stable zeolite nuclei, and nanometer sized metastable hydrated silica phase; (ii) 1.5 h to 10 days, chemical evolution of the gel composition that is coupled with structural rearrangements of the amorphous gel and further development of zeolite nuclei; (iii) 10-14 days, spontaneous mass transformation of the amorphous gel into spherical aggregates of small (10-20 nm) crystals around individual crystallization centers of viable nuclei and collapse of the metastable phases; (iv) 17-38 days, crystal growth involving agglomeration, dissolution, and regrowth of individual nanoparticles around spherical aggregates. [ABSTRACT FROM AUTHOR]

The melting behavior of nanostructured organic materials (drugs) embedded into a cross-linked polymeric matrix was studied for the first time. The complex microstructure of these nanocomposites, yielded by the polymer matrix in which molecular clusters and nanocrystals of drug plus a cospiquous fraction of water are confined, demanded synergic application of thermal analysis and temperature resolved X-ray diffraction. A relevant depression of the melting point of the embedded drug with respect to the bulk drug was experimentally demonstrated. The coherent domain size of the embedded drug nanocrystals was independently evaluated by thermal and diffraction data and results were in agreement. This indicates that the adopted thermodynamic melting model, based on Laplace and Gibbs-Duhem equations and developed for simpler systems, can be successfully assessed for describing drug/polymer nanocomposites, and, potentially, other classes of organic nanocomposites. [ABSTRACT FROM AUTHOR]

Self-assembled monolayers (SAMs) formed from 4,4‘-terphenyl-substituted alkanethiols C6H5(C6H4)2(CH2)nSH (TPn, n = 1-6) on polycrystalline (111) gold and silver substrates have been characterized by X-ray photoelectron spectroscopy (XPS), high-resolution XPS, near-edge X-ray absorption fine structure spectroscopy, ellipsometry, and water contact angle measurements. The packing density of the SAM constituents and the orientation of the terphenyl moieties exhibited a pronounced odd-even variation with the number (n) of methylene groups in the aliphatic (CH2)n linker, which was opposite on silver as compared to gold. A higher packing density and a corresponding smaller inclination of the terphenyl moieties was observed for odd numbers of the methylene units in TPn on Au, and for even numbers of these units in TPn on Ag. The observed odd-even effects are explained by the strong dependence of the bending potentials in the metal-S-C bond on the deviation of the metal-S-C bond angle from an optimal value of ≉104° (Au) and ≉180° (Ag), respectively. The optimal metal-S-C angles are determined by the hybridization of the sulfur in the metal-thiolate bond, which is proposed to have sp3 hybridization on Au and an sp hybridization on Ag, respectively. [ABSTRACT FROM AUTHOR]

Ca films deposited on the surface of Pd(111) were studied by temperature-programmed desorption, X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy, and low-energy electron diffraction (LEED). Multilayer Ca films desorb at 1180 K, which is much higher than that value for any of the alkali metals. Ca adatoms alloy with Pd at temperatures as low as 700 K. Annealing sub-monolayer Ca films at 1100 K reproducibly formed two well-ordered surface structures with (2 × 2) and (√3×√3)R30° Ca/Pd(111) unit cells depending on the amount of Ca deposited on the Pd(111) substrate. Chemical shifts of Ca XPS peaks indicate that these ordered structures are correlated to the formation of Ca-Pd alloys. The presence of Ca at the Pd(111) surface increases the CO adsorption energy and causes a 110-K shift of the CO thermal desorption peak to a higher temperature than from a clean Pd(111) surface. This Ca-Pd-CO interaction is so strong that it drives Ca out of a Ca-Pd alloyed layer to the overlayer upon CO adsorption, which is evident from the disappearance of the characteristic LEED pattern of the alloy. This migration of Ca atoms occurs without oxidation of Ca. These observations are discussed with reference to possible active phases in Ca-modified, supported Pd catalysts for methanol synthesis and the special nature of Ca over alkali metal promoters for this catalysis. [ABSTRACT FROM AUTHOR]

Three Schiff-base-containing triazole derivatives have been synthesized and investigated by X-ray crystallography. Structural motifs (zigzag or linear chains) formed in the solid state are stabilized by C-Br···N halogen bond interactions, while hydrogen bonds do not seem to play a significant role in the molecular self-organization of studied compounds. Quantum-chemical studies confirm that these interactions are sufficient to account for both the arrangement of structural motifs and very short Br···N distances observed experimentally. It is also shown that Br···N interactions can lead to generally shorter donor-acceptor distances than Cl···N contacts. [ABSTRACT FROM AUTHOR]

The peroxyl radical location in horse heart myoglobin (Mb) oxidized with H2O2 was examined by 9-287 GHz electron paramagnetic resonance (EPR) spectroscopy along with the radicals formed upon oxidation of tyrosine (Tyr), tryptophan (Trp), and histidine (His) individual amino acids. X-ray crystallography of the horse heart Mb has revealed that Tyr103, Tyr146, Trp14, and His64 residues are in the vicinity of the Mb heme group and thus could be implicated in Mb oxidation. The 9 GHz axial EPR signal of the Mb peroxyl radical (g|| = 2.040 ± 0.003 and g⊥ = 2.001 ± 0.001) is nearly identical with those of the radicals produced by irradiation of the individual amino acids in the presence of H2O2 (77 K). The 95-287 GHz measurements were sufficient to resolve the individual g tensor components of the Mb, Tyr, Trp, and His peroxyl radicals which cannot be distinguished at 9-35 GHz. The high-field EPR spectra of the Mb peroxyl radical were simulated using a Hamiltonian that describes the exchange and dipolar interaction between an oxoferryl iron and a protein radical. The exchange-coupled oxoferryl-protein radical pair could be best fitted with g values of gX = 2.0356, gY = 2.0083, and gZ = 2.0024 for the radical, a dipolar coupling corresponding to a distance of 8.3 Å between the radical and the oxoferryl iron, and an exchange coupling (J) of 0.476 GHz. The determined g tensor and the distance related to the Tyr residue at position 146. Tyr146 is assumed to be the most likely candidate for the peroxyl radical location in oxidized Mb. [ABSTRACT FROM AUTHOR]

Nanometer thick layers of Mg metal vapor deposited onto a polycrystalline gold substrate at 22 K with and without O2 multilayers were examined after annealing. Auger electron spectroscopy and temperature-programmed desorption of N2 were used to determine the Mg oxidation state and the surface area of the deposits immediately after deposition at 22 K, and following annealing. Deposited on 20 layers of O2, Mg oxidizes and forms an MgO film having a high surface area (~700 m2/g). The surface area decreases upon annealing, approaching that of a well-ordered MgO(100) surface by 500 K. On thinner O2 multilayers, both oxidized and metallic Mg are observed at 22 K. Mild thermal annealing (200-400 K) results in transport of the excess metallic Mg to, and alloy formation with, the underlying Au substrate. MgO films annealed to 1000 K display a narrow distribution of N2 binding sites, similar to well-ordered MgO(100). The film sublimes above 1000 K when heated. [ABSTRACT FROM AUTHOR]

The phase diagram of the two-component system between two halomethanes, carbon tetrachloride (CCl4) and bromotrichloromethane (CBrCl3) has been determined by means of X-ray powder diffraction and thermal analysis techniques from 200 K to the liquid state. From the continuous series of mixed crystals, three relations of isomorphism have been evidenced: (i) between the stable low-temperature monoclinic (M) phases, (ii) between the stable orientationally disordered (OD) rhombohedral (R) phases, and (iii) between the stable OD face-centered cubic (FCC) of CBrCl3 and the metastable FCC phase of CCl4. The existence of such a metastable phase gives rise to the appearance, for a large range of composition, of metastable FCC mixed crystals that behave monotropically with respect to the R mixed crystals accordingly with the well-known monotropic character of the R to FCC phase transition of the CCl4. The isomorphism relationships i and ii enable us to validate the previously proposed structure of the monoclinic phase of CBrCl3 (C2/c, Z = 32) and to determine the lattice symmetry of the OD rhombohedral phase (relation ii) of CBrCl3, the symmetry of which is the same as that of the R phase of CCl4, respectively. The thermodynamic assessment reproduces coherently the phase diagram (stable two-phase equilibria, M + R, R + L, and a part of the FCC + L) as well as the partially metastable [FCC + L] two-phase equilibrium and provides a coherent set of data for the thermodynamic properties of nonexperimentally available phase transitions of pure components. [ABSTRACT FROM AUTHOR]

Langmuir-Blodgett deposition of a nonmagnetic-magnetic metal-organic bilayer film is reported here. The bilayers consist of a Au nanocluster upper layer over a monolayer of gadolinium stearate (GdSt) deposited on a hydrophilic Si(001) substrate. The morphology of the deposited GdSt layer and upper Au nanocluster layer were systematically analyzed using atomic force microscopy (AFM) and X-ray reflectivity techniques. The morphology of the Au nanoparticle layer changes remarkably depending on the surface pressure of the Langmuir monolayer employed for its transfer on to the gadolinium stearate layer. Three Langmuir phases at different degrees of compression formed the basis for the chosen surface pressure values for the transfer. The bilayer films are an essentially nanostructured network of islands and interconnects that exhibit nonohmic I-V characteristics when measured laterally across the film using a conducting AFM tip. [ABSTRACT FROM AUTHOR]

Despite the availability of an X-ray structure and many spectroscopic studies, important issues related to structural heterogeneity, excitonic structure, primary charge separation (CS), and excitation energy transfer dynamics of the isolated reaction center (RC) of photosystem II (PS II) remain unresolved. The issues addressed here include (1) whether the primary CS kinetics at low temperatures are highly dispersive (due to structural heterogeneity), as proposed by Prokhorenko and Holzwarth (J. Phys. Chem. B 2000, 104, 11563), and (2) the nature of the weak lowest-energy Qy absorption band at ~684 nm that appears as a shoulder on the intense primary electron donor band (P680). Results of low-temperature nonphotochemical hole burning (NPHB) and triplet bottleneck hole burning (TBHB) spectroscopic experiments (including effects of pressure and external electric (Stark) fields) are presented for the RC from spinach with one of the two peripheral chlorophylls removed. Both NPHB and TBHB are observed with excitations within the P680 and 684 nm bands. Both types of hole spectra exhibit a weak dependence on the burn wavelength (λB) between 680 and 686 nm. Furthermore, the permanent dipole moment change (f Δμ), as determined by Stark-NPHB spectroscopy, is identical (0.9 ± 0.1 D) for the two bands, as are the linear electron-phonon coupling parameters (Huang-Rhys factors S17 = 0.7 and S80 = 0.2 for 17 and 80 cm-1 phonons). These similarities, together with published fluorescence line narrowed spectra lead us to favor the gross heterogeneity model in which the 684 nm band is the primary electron donor band (P684) of a subset of RCs that may be more intact than P680-type RCs. It is concluded, based also on the linear pressure shift rates for the P680 and 684 nm bands, that population of either P680* (* ≡ Qy state) or P684* results in both TBHB (due to charge recombination of the primary radical ion pair) and NPHB. It was found that the values of parameters (e.g., electron-phonon coupling, site distribution function) used to simulate the NPHB spectra also provided reasonable fits to the TBHB spectra. Acceptable theoretical simulations of the line-narrowed TBHB spectra were not possible using a single primary CS time. However, satisfactory fits (including λB and burn intensity dependences) were achieved using a distribution of CS times. The observed TBHB is due to P680- and P684-type RCs with the faster CS kinetics since the persistent nonphotochemical holes were saturated prior to measuring the TBHB spectra. (RCs exhibiting the most efficient NPHB have slower CS kinetics as well as higher fluorescence quantum yields.) For the TBHB spectra, the same distribution (Weibull) was used for the P680- and P684-type RCs. The distribution describes quite well the distribution of Prokhorenko and Holzwarth for CS times shorter than 25 ps. Finally, the data indicate that electron exchange contributes only weakly (relative to electrostatics) to the inter-pigment excitonic interactions. [ABSTRACT FROM AUTHOR]