Split-site Model Research Articles

H/D isotope effects in brucite at low temperatures

Joint refinement of powder neutron diffraction data of hydrogenated and deuterated brucite over the temperature range of 10-295 K clearly shows significant isotope effects in the structural parameters. Mg(OH)2 has a 0.31% larger volume than that of Mg(OD)2 at room temperature, which is mostly due to the c-axis expansion of Mg(OH)2 as compared to Mg(OD)2. The isotope effect in the a-axis has the opposite, but smaller, behavior as compared to the c-axis. These differences are slightly enhanced with reduction of the cell volume upon cooling. The temperature dependence of the isotropic atomic displacement parameters (ADPs) with the single site model show that the ADP of the H atom is approximately larger than that of the D atom by the amount expected from the reduced-mass difference, but this difference is not evident with the split site model. Despite the shorter c-axis of the deuterated form, nearest-neighbor D···D distances are longer than the H···H distances, because the O-H distances are longer than the O-D distances, which necessarily places the H atoms closer together by 0.03 Å or more within the interlayer space. This study showcases an example of when a joint Rietveld refinement is ideally suited, by combining data for the deuterated and hydrogenated forms of brucite. The approach reduces the number of least-squares variables, and reduces the systematic errors. It can be a general method to analyze isotope effects in materials studied by neutron diffraction.

Reverse Monte Carlo study of Cu—O bond distortions in YBa2Cu3O6.9

A combination of neutron total scattering measäurement and reverse Monte Carlo (RMC) refinement is applied to the study of apical Cu—O bond distortions in the high-Tc superconductor YBa2Cu3O6.93. We show that the average structure is not consistent with a split-site model for the corresponding Cu and O positions, but that the local structure nevertheless reveals the existence of two separate apical Cu—O bond lengths. Using G(r) data obtained from a variety of Qmax values we show that this result is independent of the data treatment methodology. We also find that the resulting ‘short’ and ‘long’ Cu—O bond lengths agree well with the results of previous äEXAFS studies. The existence of bimodal apical Cu—O bond distributions in the context of a single-site average structure model is interpreted in terms of correlated displacements of the Cu and O atoms. We investigate the possibility of clustering of short apical Cu—O bonds within our RMC configurations.

Anion disorder in LnF3 (Ln = La, Ce, Pr) crystals

The mechanism of lattice “melting” in tysonite-structure superionic trifluorides is analyzed in relation to the structure of LaF3 crystals. The ion displacements within the unit cell are shown to correlate with the dynamics of the Raman scattering parameters of the crystals. The frequency and intensity of the lines at 370, 392 (LaF3), 376, and 404 cm−1 (PrF3) show anomalous behavior in three temperature ranges: 160–180, 240–280, and 420–460 K. The anomalies in the two higher temperature ranges are due to lattice disordering in the superionic transition region. The scattering in the range 160–180 K is tentatively attributed to fluoride ion displacements in split sites with a few potential wells. It is shown based on a split-site model that the thermally activated formation of interstices comparable in size to the mobile fluoride ion is an inherent feature of the LnF3 structure.

Antigen-specific Proteolysis by Hybrid Antibodies Containing Promiscuous Proteolytic Light Chains Paired with an Antigen-binding Heavy Chain

The antigen recognition site of antibodies consists of the heavy and light chain variable domains (V(L) and V(H) domains). V(L) domains catalyze peptide bond hydrolysis independent of V(H) domains (Mei, S., Mody, B., Eklund, S. H., and Paul, S. (1991) J. Biol. Chem. 266, 15571-15574). V(H) domains bind antigens noncovalently independent of V(L) domains (Ward, E. S., Güssow, D., Griffiths, A. D., Jones, P. T., and Winter, G. (1989) Nature 341, 544-546). We describe specific hydrolysis of fusion proteins of the hepatitis C virus E2 protein with glutathione S-transferase (GST-E2) or FLAG peptide (FLAG-E2) by antibodies containing the V(H) domain of an anti-E2 IgG paired with promiscuously catalytic V(L) domains. The hybrid IgG hydrolyzed the E2 fusion proteins more rapidly than the unpaired light chain. An active site-directed inhibitor of serine proteases inhibited the proteolytic activity of the hybrid IgG, indicating a serine protease mechanism. The hybrid IgG displayed noncovalent E2 binding in enzyme-linked immunosorbent assay tests. Immunoblotting studies suggested hydrolysis of FLAG-E2 at a bond within E2 located approximately 11 kDa from the N terminus. GST-E2 was hydrolyzed by the hybrid IgG at bonds in the GST tag. The differing cleavage pattern of FLAG-E2 and GST-E2 can be explained by the split-site model of catalysis, in which conformational differences in the E2 fusion protein substrates position alternate peptide bonds in register with the antibody catalytic subsite despite a common noncovalent binding mechanism. These studies provide proof-of-principle that the catalytic activity of a light chain can be rendered antigen-specific by pairing with a noncovalently binding heavy chain subunit.

Effects of stacking fault on the diffraction intensities of β-FeSi 2

β-FeSi 2 was synthesized by heating mixtures of Si and Fe powder sealed with Na metal and Ar gas in a stainless tube. Diffuse streaks elongated along the a axis were observed in the electron diffraction (ED) patterns of β-FeSi 2 prepared at 873 K in the Na melt. No streaks appeared on the spots indexed by k + l = 2 n ( n: integer), which indicated existence of stacking faults caused by a slip system of (1 0 0)[0 1 1]/2. The powder X-ray diffraction (XRD) patterns of the samples prepared at 873 K for 48 h in the Na melt and at 1173 K for 24 h under reduced Na vapor pressure were analyzed by the Rietveld method with a statistical split-site model based on the stacking fault structure. The powder X-ray diffraction patterns of the samples prepared at 873 K for 48 h in the Na melt and at 1173 K for 24 h in Na vapor which evaporated from a mixture of Na and Si were analyzed by the Rietveld method with a statistical split-site model based on the stacking fault structure. The ratios of the normal stacking layer and stacking fault layer of the samples prepared at 873 and 1173 K were estimated to be 0.95:0.05 and 0.84:0.16, respectively. Main features of the observed powder X-ray diffraction patterns were well reproduced by the calculation based on a general recursion method for calculating diffracted intensities from crystals containing stacking fault.

Structural features of zinc hydroxyfluoride

Zinc hydroxyfluoride (ZnOHF), obtained by coprecipitation of a zinc salt in aqueous HF, exhibits a variable stoichiometry Zn(OH) 2− x F x , where x is tuneable from 0.63 to 0.87 by controlling the pH of the solution. The structure was determined from Rietveld refinements using X-ray powder diffraction data. Crystallizing with the orthorhombic symmetry (SG : Pna2 1), the ZnOHF-type structure exhibits two different anionic sites. A bond valence analysis shows that fluorine exclusively occupies the anionic site that has shorter contacts to zinc. This site is split into two partially occupied sites, one corresponding to the position of a fluoride ion and the other to the position of a hydroxide ion. Bond valence calculations show that the split site model gives a more accurate picture of the local coordination of the anions on this site.

Splitting of guest atom sites and lattice thermal conductivity of type-I and type-III clathrate compounds in the Ba–Ga–Ge system

The crystal structures of type-I and type-III clathrate compounds in the Ba–Ga–Ge system have been investigated by synchrotron X-ray powder diffraction at room temperature with single- and split-site models to describe thermal vibration of the Ba atoms that are believed to ‘rattle’ in the encapsulating cages. The split-site model is verified to be more plausible when judged from the changes of the extent of thermal vibration of the Ba atoms and the shape changes of the encapsulating cages with the Ga content for both types of compound. When described with the split-site model, the value of lattice thermal conductivity at room temperature decreases with increasing split distance of the Ba atom site for both types of compound, indicating that the split distance can be used as a parameter to describe the extent of thermal vibration (rattling motion) of the Ba guest atoms in the encapsulating cages.

Splitting of Guest Atom Sites and Lattice Thermal Conductivity in Ba-Ga-Ge Clathrate Compounds

ABSTRACTThe crystal structures of some type-I and -III clathrate compounds in the Ba-Ga-Ge system have been investigated by synchrotron X-ray powder diffraction at room temperature, paying special attention to the changes of the cage structure and the splitting behavior at the guest atom site upon alloying with Ga. For both types of the clathrate compounds, the split distance of the Ba(2) sites increases with the increase in the Ga content, corresponding to the change in the size and shape of the encapsulating polyhedral cage. Lattice thermal conductivity at room temperature has a positive correlation with the atomic displacement parameter (ADPsplit) based on the split-site model but has an inverse correlation with the split distance of the Ba(2) sites, indicating that a dominant factor of reducing the lattice thermal conductivity is not thermal vibration at the split sites but thermal jump among the split sites.

Reconciliation of Split-Site Model with Fundamentalist Formulation Enabled by Equilibrium Assumption

By the use of multi-loop thermodynamic boxes developed here by us, we show that models of enzyme catalysis (e.g., split-site model) developed in an attempt to emphasize the importance of the reactant-state destabilization and, thus, demonstrate misleading nature of the fundamentalist position which defines Pauling's transition-state stabilization as the entire and sole source of enzyme catalytic power, should be reduced to the fundamentalist formulation which completely neglects dynamical aspects of mechanism between the reactant and the transition states and dwells only on events restricted to the reactant and transition states alone, because the splitsite (and other canonical) formulations as well as fundamentalist formulations are based, in common, on equilibrium assumptions stipulated by the thermodynamic box logics. We propose to define the equilibrium assumptions as the requisite and sufficient conditions for the fundamentalist position to enjoy its primacy as central dogma, but not as sufficient conditions for its validity, because it is subjected to contradictions presented by existing data.

Synthesis and Structure of Ba8Cu3In4N5 with Nitridocuprate Groups and One-Dimensional Infinite Indium Clusters

Single crystals of the quaternary compound Ba8Cu3In4N5 were prepared by heating Ba, Cu, and In in a Na flux at 1023 K under 7 MPa of N2, and by slow cooling from this temperature. The crystal structure was analyzed by single-crystal X-ray diffraction. It crystallizes in an orthorhombic cell (space group Immm (No. 71), Z=2) with a=4.0781(6), b=12.588(2), and c=19.804(3) Å at 298 K. The structural formula is expressed as Ba8[CuN2]2 [CuN]In4. Nitridocuprates of one-dimensional chains 1∞[CuN2/2] and isolated units 0[CuN2], and one-dimensional indium clusters 1∞[In2In4/2] are contained in the structure. A split-site model applied for the arrangement of 1∞[CuN2/2] chains suggested that there is a short-bond, long-bond alternation of the Cu–N bondings. The electrical resistivity of Ba8Cu3In4N5 was 3.44 mΩ·cm at 298 K. A metallic temperature dependence of the resistivity was observed down to 10 K.

Pressure dependence of hydrogen bonding in metal deuteroxides: a neutron powder diffraction study of Mn(OD) 2 and β-Co(OD) 2 .

The structures of deuterated pyrochroite, Mn(OD)2 and β−Cο(OD)2 have been refined using the Rietveld method and neutron powder diffraction data collected in an opposed-anvil high pressure (Paris-Edinburgh) cell from room pressure to 9 GPa. The equation of state for Mn(OD)2 was determined (K=41(3) GPa for fixed K′=4.7) and found to be consistent with previous studies of the isostructural brucite, Mg(OD)2. The compressibility of β−Cο(OD)2 on the other hand is apparently anomalous. The c-axis initially decreases at 3 times the rate of decrease of the a-axis; the ratio decreases to about 1.5 at an estimated 6 GPa before increasing again beyond this pressure. There is no obvious corresponding anomaly in the details of the atomic structure. In both materials there is an increase in the D-site disorder with pressure. A split-site model for the D-positions best fits the data at pressures above 8 GPa. There is no statistically significant increase in the O-D interatomic distance at increased pressure while the hydrogen bonding interaction D...O appears to increase as this distance decreases and the O-D...O angle increases. The intramolecular O-D bond valences, determined indirectly from the intermolecular D...O distances, decrease steadily for both materials as pressure is increased.

Revisiting ground-state and transition-state effects, the split-site model, and the "fundamentalist position" of enzyme catalysis

In 1978 Schowen laid out the "fundamentalist position" of enzyme catalysis: "...the entire and sole source of catalytic power is the stabilization of the transition state; reactant-state interactions are by nature inhibitory and only waste catalytic power." In 1992 Menger developed the "split-site model" in order to demonstrate contradictions of the fundamentalist position. One of Menger's examples is recounted in which the energy of the enzyme-substrate complex (delta GES) is lowered, yet the catalytic rate increases, incompatible with the claim that reactant- (i.e., ground-) state interactions are inhibitory. A rigorous definition of ground-state effect is proposed which resolves the apparent contradictions. A ground-state effect (delta delta GES) is defined as one in which the energy of the ground state has changed, but the energy of the catalyzed transition state is unchanged when one enzyme is compared to another. This is a result of the constraint that the free energy of binding of the enzyme to the uncatalyzed reaction transition state, delta Gb*, is constant. That ground-state interactions are inhibitory when a single enzyme-catalyzed reaction is considered has been proven by Schowen: this definition of ground-state effect achieves the result of making additional ground-state interactions inhibitory also. This definition is rather restrictive, however, and does not describe many of the possible changes in enzyme energy levels. A proposal is therefore put forth to simply explain the changes in terms of alterations in intrinsic and utilized binding energy.

Neutron-diffraction study of ErBa2Cu3Ox in the composition range 6.1

Structural properties of homogeneous orthorhombic and tetragonal ErBa{sub 2}Cu{sub 3}O{sub {ital x}} powder samples (6.1{le}{ital x}{le}7.0), prepared by a careful absorption-desorption procedure, were investigated by elastic neutron scattering. With decreasing oxygen content the distance between Cu(2)-O(2,3) planes and Cu(1)-O(4)-Cu(1) chains increases and the oxygen 2{ital q}(0,0,{ital z}) apex atoms O(1) move closer to the Cu-O-Cu chains. The copper-oxygen (1) distances do not vary continuously in the {ital z} direction but seem to change more rapidly when {ital x}{lt}6.5. The change of these distances can be correlated to the suppression of superconductivity in orthorhombic ErBa{sub 2}Cu{sub 3}O{sub {ital x}}. A distinction between the large anisotropic vibrational amplitudes of the Cu(1)-O(4)-Cu(1) broken-chain oxygen atoms and a split-site model for O(4) is not possible on the basis of the present data.

Neutron diffraction study of highly oxygen deficient superconducting YBa 2Cu 3O 6.39

Structural and magnetic properties of highly oxygen deficient orthorhombic YBa 2Cu 3O 6.39 prepared by a desorption-absorption procedure were investigated by elastic neutron scattering and SQUID measurements. Unusually large anisotropic vibrational amplitudes of the Cu-O-Cu broken chain oxygen atoms are discussed in terms of an anisotropic thermal vibration model and compared with a split site model. The Cu-O planes remain unaffected, their distance to the Cu-O-Cu chains increases. In contrast to quenched material no indications for any oxygen occupation at ( 1 2 , 0, 0) were found. The diamagnetic shielding (ZFC) signal is reduced compared to oxygen rich material, the Meissner signal remains 65% of the shielding value.