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Powder neutron diffraction studies show that boron and carbon atoms alternate in the planar pi-conjugated layers in CeB(2)C(2) and its lanthanide analogues, rather than being paired as was previously reported. Long and short B-C bonds correspond to the idealized arrangement of single and double bonds shown in the picture.
Lithium cations sit in the center of the oxygen "windows" defined by the vertex-sharing TiO(6) octahedra of the title compound (see picture), as shown from neutron diffraction data. The octahedra are tilted to optimize the bond distances between the atoms. The unusual coordination and the partially unoccupied sublattice (occupancy factors 1/6 and (1/2) for Li and La, respectively) account for the high mobility of the Li(+) cations.
In this paper we present the results of density functional theory (DFT) calculations on the ethyl ligand and some related organic moieties; we then proceed to consider a range of alkyllithium complexes studied by DFT calculations and high-resolution X-ray and neutron diffraction. Topological analysis of the charge density is used to follow changes in the electronic structure of the organic fragment. The charge concentrations (CCs) in the valence shell at the alpha and beta atoms reveal faithfully the delocalization of the lone pair at the Calpha atom or of the Li-C bonding electrons. Negative hyperconjugation is thus shown to arise from delocalization of the lone pair or the Li-C bonding electrons over the alkyl fragment, with depletion of the metal-directed charge concentration at Calpha, and characteristic ellipticity profiles for the bonds involved in hyperconjugative delocalization. In the case of so-called lithium agostic complexes, we show that close Li.H contacts are a consequence of this delocalization and further secondary interactions, with Li.H-C agostic interactions, playing only a minor role. The ellipticity profiles and the magnitude of the CCs at Calpha provide a quantitative measure of the extent of delocalization, and show excellent agreement between experiment and theory.
Algorithms and protocols are described for the optimization for H-bonding of isolated singular H2O molecules and entire networks of H2O molecules. Unlike other approaches that are prone to being trapped in local energy minima, these methods rely on exhaustive searches of orientation space for the H2O molecules. The results are scored with the HINT hydropathic interaction model, but the algorithms should be general for any energy-scoring computation. Two examples are provided: 1) the tightly-bound H2O molecule 301 of HIV-1 protease is shown to be more reasonably oriented in terms of forming H-bonds with this method than with a molecular mechanics energy minimization method; and 2) the H2O network surrounding carbonmonoxymyoglobin is constructed and analyzed for a 1.80-A neutron-diffraction structure. The H-atom positions calculated with this method show a somewhat better agreement with the experimental results than do the H-atom positions calculated with molecular mechanics, and both are considerably better than random.
In this paper, equations are proposed which relate various NMR parameters of OHN hydrogen-bonded pyridine-acid complexes to their bond valences which are in turn correlated with their hydrogen-bond geometries. As the valence bond model is strictly valid only for weak hydrogen bonds appropriate empirical correction factors are proposed which take into account anharmonic zero-point energy vibrations. The correction factors are different for OHN and ODN hydrogen bonds and depend on whether a double or a single well potential is realized in the strong hydrogen-bond regime. One correction factor was determined from the known experimental structure of a very strong OHN hydrogen bond between pentachlorophenol and 4-methylpyridine, determined by the neutron diffraction method. The remaining correction factors which allow one also to describe H/D isotope effects on the NMR parameters and geometries of OHN hydrogen bond were determined by analysing the NMR parameters of the series of protonated and deuterated pyridine- and collidine-acid complexes. The method may be used in the future to establish hydrogen-bond geometries in biologically relevant functional OHN hydrogen bonds.
The mechanism of magnetic interactions in the bulk ferromagnet para-(methylthio)phenyl nitronyl nitroxide crystal (YUJNEW) has been theoretically reinvestigated, using only data from ab initio calculations and avoiding any a priori assumptions. We first calculate the microscopic magnetic interactions (JAB exchange couplings) between all unique radical pairs in the crystal, and then generate the macroscopic magnetic properties from the energy levels of the corresponding Heisenberg Hamiltonian. We thus propose a first principles, bottom-up (i.e. micro-to-macro) approach that brings theory and experiment together. We have applied this strategy to study the magnetism of YUJNEW using data from the previously reported 298 and 114 K crystal structures, and also data from a 10 K neutron diffraction structure fully reported in this work. The magnetic topology at 298 K is two-dimensional: noninteracting planes, with three different in-plane JAB pair interactions (+0.24, +0.09, and -0.11 cm(-1)) and one numerically negligible (+0.02 cm(-1)) inter-plane JAB interaction. In contrast, the magnetic topology at 114 and 10 K is three-dimensional, with two non-negligible in-plane JAB constants (+0.11 and +0.07 cm(-1) at 114 K; +0.22 and +0.07 cm(-1) at 10 K) and one inter-plane pair interaction (+0.07 cm(-1) at 114 K; +0.08 cm(-1) at 10 K). Although this three-dimensional magnetic topology is consistent with YUJNEW being a bulk ferromagnet, there is only a qualitative agreement between computed and experimental magnetic susceptibility chiT(T) data at 114 K. However, the experimental chiT(T) curve is quantitatively reproduced at 10 K. The heat capacity curve presents a peak at around 0.12 K, close to the estimated experimental peak (0.20 K).
The crystal structure of Aurivillius phase ferroelectric Bi2WO6 has been studied in detail as a function of temperature by using high-resolution powder neutron diffraction. In agreement with an earlier study, a transition from space group P2(1)ab to B2cb occurs at about 660 degrees C. This transition corresponds to the loss of one octahedral tilt mode within the perovskite-like WO4 layer of the structure. A second, reconstructive, phase transition occurs around 960 degrees C, corresponding to the ferroelectric Curie point; in contrast to previous suggestions, the structure of this high-temperature phase contains layers of stoichiometry WO4, with WO6 octahedra sharing edges and corners, and with the fluorite-like Bi2O2 layers remaining essentially unchanged. This structure is closely related to that of the ambient temperature phase of lanthanide-doped derivatives, for example, Bi0.7Yb1.3WO6 recently reported. This phase-transition behaviour is in stark contrast to that of other members of the Aurivillius family, such as SrBi2Ta2O9 and Bi4Ti3O12, which retain the archetypal Aurivillius connectivity at all temperatures.
Sustainable energy storage in the form of Li-ion batteries requires new and advanced materials in particular with a higher power density. Nanostructuring appears to be a promising strategy, in which the higher power density in nanosized materials is related to the dramatically shortened Li-ion diffusion paths. However, nanosizing materials also changes intrinsic material properties, which influence both ionic and electronic conductivity. In this work neutron diffraction is used to show that in addition to these two aspects, nanostructuring changes the phase behavior and morphology. Lithiated 40-nm TiO(2) anatase crystallites become single phase, either having the Li-poor original anatase phase, or the Li-rich Li-titanate phase, in contrast to microsized crystallites where these two phases coexist in equilibrium within one crystal particle. In addition, Li(x)TiO(2) compositions occur with stoichiometries that are not stable in micron-sized crystallites, indicating enhanced solid solution behavior. Reduced conduction electron densities at the sites of the Li ions are observed by NMR spectroscopy. This is accompanied by reduced spontaneous Li-ion mobility, suggesting a correlation between the electron density at the Li-ion site and the Li-ion mobility. The present results show that in the case of lithiated anatase TiO(2), significant effects on phase composition, morphology, and electronic configurations are induced, as well as slower intracrystallite Li diffusion.
Many transition metal oxide materials of high chemical purity are not necessarily monophasic. Thus, single crystals of chemically pure rare earth manganites and cobaltates of the general formula Ln(1-x)A(x)MO(3) (Ln=rare earth metal, A=alkaline earth metal, M=Mn, Co) exhibit the phenomenon of electronic phase separation wherein "phases" of different electronic and magnetic properties coexist. Such phase separation, the length scale of which can vary anywhere between a few nanometers to microns, gives distinct signatures in X-ray and neutron diffraction patterns, electrical and magnetic properties, as well as in NMR and other spectroscopies. While the probe one employs to investigate electronic phase separation depends on the length scale, it is noteworthy that direct imaging of the inhomogeneities has been accomplished. Some understanding of this phenomenon has been possible on the basis of some of the theoretical models, but we are far from unraveling the varied aspects of this new phenomenon. Herein, we present the highlights of experimental techniques and theoretical approaches, and comment on the future outlook for this fascinating phenomenon.
Understanding the conformational flexibility of amino acid zwitterions (ZWs) and their associated conformational energies is crucial for predicting their interactions in biological systems. Gas-phase ab initio calculations of ZWs are intractable. Molecular mechanics (MM), on the other hand, is able to handle large systems but lacks the necessary force field parameters to model ZWs. To develop force field parameters that are able to correctly model ZW geometries and energetics we used a novel combinatorial approach: amino acid ZWs were broken down structurally into key functional components, which were parameterized separately. Møller-Plesset second-order perturbation calculations on small carboxylates, on the glycine cation, and on novel hydrogen bonded systems, coupled with available experimental data, were used to generate MM3(2000) ZW parameters (Allinger N. L.; Yuh, Y. H.; Lii, J.-H. J Am Chem Soc 1989, 111, 8551). The MM3 results from this combinatorial approach gave geometries that are in good agreement with neutron diffraction experiments, plus their frequencies and energies appear to be reasonably modeled. Current limitations and future development of MM force fields are discussed briefly.
The high Tc superconducting material YBa2Cu3O7 shows a complex relationship between microstructure and oxygen content, which are controlled by length of heat treatment, atmosphere, and quench rate. An AEM investigation studying changes in the oxygen near edge features was undertaken. Electron energy loss spectroscopy (EELS) measurements have the important advantage that they can be made on single crystal grains, allowing orientation-dependent studies. Both ion-milled and crushed samples with varying O2 content were analyzed. The structure of YBaCu3O7 was determined by neutron diffraction to be orthorhombic with distinct Cu-O chains along the b-axis as well as Cu-O planes in the a-b plane. Therefore, by looking for a crystallographic dependence of the oxygen K-edge one might be able to distinguish inequivalent oxygen atoms by their core level binding energy and correlate site occupancy with varying O2 content. The EELS results on the oxygen K-edge are strongly dependent on oxygen content, most noticeably when the c-axis is parallel to the electron beam.
Direct structure images of the YBa2Cu3O7-x high Tc superconducting ceramic (also called the 1-2-3 compound) at 1.7 A resolution have been obtained for the [100] and [001] orientations. It was found that for the purposes of studying oxygen ordering in this compound it is better to use lattice images of lower resolution. The oxygen ordering was studied via the measurement of the bending of (100) and (110) lattice planes on crossing the (110) twin boundaries in crystals oriented in the [001] zone. Significant variations were found in the b/a ratios, owning to a variation in oxygen ordering, between different crystal grains, and between different regions in the same grain. For the three different 1-2-3 samples studied, the average b/a ratio was 1.016, the same value as was found in neutron diffraction studies. The twin boundaries in the orthorhombic 1-2-3 phase are sharp and planar. It seems likely that the transformation from the high-temperature tetragonal phase to the lower-temperature orthorhombic phase is martensitic in nature. A new phase has been discovered on some of the twin boundaries. The new phase can be indexed as tetragonal with a = 7.5 +/- 0.2 A, and c = 6.8 +/- 0.2 A. It is possible that the new phase is stabilized by the stress which occurs at the twin boundaries.
Recombinant gelatins are currently evaluated as new excipients for pharmaceutical formulations. They can differ from nonrecombinant gelatins because of intentional alteration of the amino acid sequence and specific properties of the expression systems used. This may affect their solution behavior. In the present work, aqueous solutions of a histidine-containing recombinant gelatin (RG-15-His) were analyzed. Dynamic light scattering (DLS) and loss of absorbance at 200 nm upon centrifugation indicated the formation of aggregates within 1 day upon sample preparation. Static light scattering (SLS) and small-angle neutron scattering (SANS) experiments showed that the aggregate's size was > or =300 nm, and that aggregates are composed of thin, rigid rods of 37 +/- 5 nm in length. The observed aggregation was not detectable by circular dichroism (CD), Fourier transform infrared spectroscopy (FTIR), and cryo transmission electron microscopy (cryo-TEM). SANS experiments, which are not frequently used in the pharmaceutical field, provided additional morphological information about the recombinant gelatin in solution. The results show that combining SLS and SANS is a broadly applicable, complementary approach for detecting aggregation of proteins and other biomolecules and for obtaining structural information about the aggregates.
We applied the POST-C7 DQ-dipolar recoupling pulse sequence to the measurement of (1)H-(1)H distances with high precision. The spectral resolution is enhanced by detecting the (1)H magnetization via (13)C signals. A least-squares fitting of the build-up curve of the transferred magnetization to the exact numerical simulations yielded a (1)H(alpha)-(1)H(beta) distance of 248 +/- 4 pm for fully (13)C-labeled L-valine. This distance agrees with the neutron diffraction study. The negative transferred magnetization clearly indicates that the direct DQ (1)H-(1)H dipolar couplings have the largest effect. The signal for the magnetization transfer builds up rapidly by the direct (1)H-(1)H dipolar coupling, and decreases to zero at longer mixing time when the relayed magnetization transfer becomes significant. This large intensity change of the signal leads to the high precision in the distance measurement. We inspected factors that limit the effective bandwidth of the POST-C7 recoupling for the (1)H and (13)C homonuclear spin systems. The spin interactions at times shorter than the cycle time of the C7 sequence were also evaluated to measure the distances. The carbon-detected 2D (1)H DQ mixing experiment was demonstrated for the measurement of multiple (1)H-(1)H distances.
This paper presents a comparison of the embedded ion method (EIM) and the surface charge representation of the electrostatic embedding potential (SCREEP) method, two methods which can be used to calculate solid-state effects on NMR chemical shifts. The results in a selected group of compounds with known single-crystal solid-state NMR data and neutron diffraction structures, confirm that these effects are important in both (13)C and (15)N chemical shifts. The solid-state effects calculated by both methods are similar and of equal statistical quality when compared with the experimental data.
An automated method for the optimal placement of polar hydrogens in a protein structure is described. This method treats the polar, side chain hydrogens of lysine, serine, threonine, and tyrosine and the amino terminus of a protein. The program, called NETWORK, divides the potential hydrogen-bonding pairs of a protein into groups of interacting donors and acceptors. A search is conducted on each of the local groups to find an arrangement which forms the most hydrogen bonds. If two or more arrangements have the same number of hydrogen bonds, the arrangement with the shortest set of hydrogen bonds is selected. The polar hydrogens of the histidyl side chain are specifically treated, and the ionization state of this residue is allowed to change, if this change results in additional hydrogen bonds for the local group. The program will accept Protein Data Bank as well as Biosym-format coordinate files. Input and output routines can be easily modified to accept other coordinate file formats. The predictions from this method are compared to known hydrogen positions for bovine pancreatic trypsin inhibitor, insulin, RNase-A, and trypsin for which the neutron diffraction structures have been determined. The usefulness of this program is further demonstrated by a comparison of molecular dynamics simulations for the enzyme cytochrome P-450cam with and without using NETWORK.
Various studies have implicated a crucial role for the non-helical ends (telopeptides) of the collagen molecule during fibrillogenesis. In this paper, the first extensive conformational analysis of the type I collagen N-terminal telopeptide is reported. The commonly used "build-up" procedure for peptides and proteins has been used, with relevant modifications to take account of all the stereochemical constraints affecting the telopeptide. In particular, consideration was given not only to the interactions among the three chains that constitute the telopeptide, but also to the interactions between the telopeptide and the covalently linked triple helix. The computations led to a limited number of different structures within an energy range of 25 kcal/mol. Comparison of these models clearly shows that the portion of the telopeptide linked to the triple helix is rather rigid whereas its N terminus is more flexible. Furthermore, the lowest-energy structure has an energy that is markedly lower (by 7.75 kcal/mol) than that of other conformations with different structural features. The lowest-energy model of the N-terminal telopeptide, which differs from previous proposed models, has a contracted conformation compared to the triple helix region, in agreement with X-ray and neutron diffraction data on collagen fibers. Finally, the side-chains of the lysine residues of the telopeptide, involved in intermolecular cross-links in mature collagen fibers, are oriented to protrude to the exterior, in positions to interact with adjacent collagen molecules.
Hydrogen bonds are a major feature of protein structure. By a generally accepted definition, they occur whenever a proton is shared by two electronegative atoms. Hence, only hydrogens bonded to nitrogen and oxygen atoms are usually considered in analyses of protein hydrogen bond networks. However, X-ray and neutron diffraction studies have shown that crystals of various organic compounds exhibit close C-H...X contacts (where X is an electronegative atom, in most cases oxygen) which show all the stereochemical hallmarks of hydrogen bonds. In this work, we describe an analysis of short C-H...O interactions in a sample of known protein structures representing different categories of tertiary folds and refined at a resolution of at least 2 A. Although our analysis is based on the calculated coordinates of hydrogen atoms, its results are statistically significant: we find strong evidence that a large percentage of short C...O contacts constitute cohesive interactions. Moreover, the stereochemical study of C-H...O = C contacts, in which the orientation of free electron orbitals on the acceptor oxygen atom can be predicted, reveals that these interactions exhibit stereochemical features typical of hydrogen bonds. Among the hydrogen atoms involved in these contacts, the most common are those bonded to alpha carbon. This is consistent with the fact that these hydrogens are more acidic than others. We describe four different categories of C-H...O = C bonds. Those found between C alpha-H groups and main chain oxygens in adjacent strands of beta sheets are the most ubiquitous. Our results call for a revision of crystallographic restrained refinement programs which treat close carbon-oxygen contacts as purely repulsive; they may also have implications for the understanding of some enzymatic reaction mechanisms.