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PubMed2003

Determination of the B820 subunit size of a bacterial core light-harvesting complex by small-angle neutron scattering.

The B820 subunit is an integral pigment-membrane protein complex and can be obtained by both dissociation of the core light-harvesting complex (LH1) in photosynthetic bacteria and reconstitution from its component parts in the presence of n-octyl beta-D-glucopyranoside (OG). Intrinsic size of the B820 subunit from Rhodospirillum rubrum LH1 complex was measured by small-angle neutron scattering in perdeuterated OG solution and evaluated by Guinier analysis. Both the B820 subunits prepared by dissociation of LH1 and reconstitution from apopolypeptides and pigments were shown to have a molecular weight of 11,400 +/- 500 and radius of gyration of 11.0 +/- 1.0 A, corresponding to a heterodimer consisting of one pair of alphabeta-polypeptides and two bacteriochlorophyll a molecules. Molecular weights of micelles formed by OG alone in solutions were determined in a range from 30,000 to 50,000 over concentrations of 1-5% (w/v), and thus are much larger than that of the B820 subunit. Similar measurement on the pigment-depleted apopolypeptides revealed highly heterogeneous behavior in the OG solutions, indicating that aggregates with various sizes were formed. The result provides evidence that bacteriochlorophyll a molecules play a crucial role in stabilizing and maintaining the B820 subunits in the dimeric state in solution. Further measurements on individual alpha- and beta-polypeptides exhibited a marked difference in aggregation property between the two polypeptides. The alpha-polypeptides appear to be uniformly dissolved in OG solution in a monomeric form, whereas the beta-polypeptides favor a self-associated form and tend to form large aggregates even in the presence of detergent. The difference in aggregation tendency was discussed in relation to the different behavior between alpha- and beta-polypeptides in reconstitution with bacteriochlorophyll a molecules.

Apoproteins↗
PubMed1997

Amide-proton exchange of water-soluble proteins of different structural classes studied at the submolecular level by infrared spectroscopy.

For eleven films of various water-soluble alpha-, beta-, alpha-/beta-, and alpha-+beta-proteins, the amide-proton exchange, initiated by exposure of the protein film to 2H2O, has been monitored using infrared spectroscopy. The approach to obtain the kinetics of exchange for four different classes of amide protons, correlating to the different secondary structure types, has been described in detail in the preceding paper. In this work the more general applicability of the approach is illustrated by testing it for different types of proteins. The results obtained are shown not only to be comparable to reported time-resolved nuclear magnetic resonance data (as in the case of myoglobin, phospholipase A2, lysozyme, and cytochrome c), or to the more qualitative data obtained by neutron diffraction (trypsin, ribonuclease S, papain, and subtilisin BPN'), but the infrared approach us also provides with quantitative detailed insight on the distribution of exchange rate constants at the submolecular level of proteins, too complex to be studied by other techniques, as for tetrameric hemoglobin, and of proteins in which exchange is too fast to be detected by these other techniques, as is shown in this work for alpha-casein and apocytochrome c.

Amides↗
PubMed2000

Cation disorder in Ga1212.

Substitution of calcium for strontium in LnSr2-xCaxCu2GaO7 (Ln = La, Pr, Nd, Gd, Ho, Er, Tm, and Yb) materials at ambient pressure and 975 degrees C results in complete substitution of calcium for strontium in the lanthanum and praseodymium systems and partial substitution in the other lanthanide systems. The calcium saturation level depends on the size of the Ln cation, and in all cases, a decrease in the lattice parameters with calcium concentration was observed until a common, lower bound, average A-cation size is reached. Site occupancies from X-ray and neutron diffraction experiments for LnSr2-xCaxCu2GaO7 (x = 0 and x = 2) confirm that the A-cations distribute between the two blocking-layer sites and the active-layer site based on size. A quantitative link between cation distribution and relative site-specific cation enthalpy for calcium, strontium, and lanthanum within the gallate structure is derived. The cation distribution in other similar materials can potentially be modeled.

Journal Article↗
PubMed2003

The arrangement of first- and second-shell water molecules in trivalent aluminum complexes: results from density functional theory and structural crystallography.

The structural and energetic features of a variety of gas-phase aluminum ion hydrates containing up to 18 water molecules have been studied computationally using density functional theory. Comparisons are made with experimental data from neutron diffraction studies of aluminum-containing crystal structures listed in the Cambridge Structural Database. Computational studies indicate that the hexahydrated structure Al[H(2)O](6)(3+) (with symmetry T(h)()), in which all six water molecules are located in the innermost coordination shell, is lower in energy than that of Al[H(2)O](5)(3+).[H(2)O], where only five water molecules are in the inner shell and one water molecule is in the second shell. The analogous complex with four water molecules in the inner shell and two in the outer shell undergoes spontaneous proton transfer during the optimization to give [Al[H(2)O](2)[OH](2)](+).[H(3)O(+)](2), which is lower in energy than Al[H(2)O](6)(3+); this finding of H(3)O(+) is consistent with the acidity of concentrated Al(3+) solutions. Since, however, Al[H(2)O](6)(3+) is detected in solutions of Al(3+), additional water molecules are presumed to stabilize the hexa-aquo Al(3+) cation. Three models of a trivalent aluminum ion complex surrounded by a total of 18 water molecules arranged in a first shell containing 6 water molecules and a second shell of 12 water molecules are discussed. We find that a model with S(6) symmetry for which the Al[H(2)O](6)(3+) unit remains essentially octahedral and participates in an integrated hydrogen bonded network with the 12 outer-shell water molecules is lowest in energy. Interactions between the 12 second-shell water molecules and the trivalent aluminum ion in Al[H(2)O](6)(3+) do not appear to be sufficiently strong to orient the dipole moments of these second-shell water molecules toward the Al(3+) ion.

Aluminum Compounds↗
PubMed2003

Aqua Ions. 2. Structural manifestations of the Jahn-Teller effect in the beta-alums.

Variable-temperature single-crystal neutron diffraction structures of the alums CsM(III)(SO(4))(2).12D(2)O, where M(III) = Ti, V, Mn, and Ga, are reported. Structural differences are highlighted by the titanium and manganese alums, which undergo cubic (Pathremacr;) to orthorhombic (Pbca) phase transitions at approximately 13 and approximately 156 K, respectively. The structural instability exhibited by these salts is interpreted as arising from cooperative Jahn-Teller interactions, and these measurements characterize the structural changes that result from the coupling between the electronic and vibrational states. Although the symmetry changes associated with the phase transformations are analogous for the Ti and Mn alums, the low-temperature geometries of the tervalent hexaaqua cations are markedly different. Whereas the MnO(6) framework is subject to a pronounced tetragonal elongation, changes in the Ti-O bond lengths are very modest; but significant changes in the O-Ti-O bond angles and in the disposition of the coordinated water molecules are identified. The large differences in the transition temperatures and in the low-temperature stereochemistries of the [Ti(OD(2))(6)](3+) and [Mn(OD(2))(6)](3+) cations are related to the sensitivity of the energies of the t(2g) (O(h)) and e(g) (O(h)) orbitals to the various asymmetric vibrations of the hexaaqua complex.

Journal Article↗
PubMed2004

Structural study of the T#2-LixCoO2 (0.52 < x < or = 0.72) phase.

The metastable O2-LiCoO(2) phase undergoes several reversible phase transitions upon lithium deintercalation. The first transition leads to an unusual oxygen stacking in such layered compounds. This stacking is found to be stable for 0.52 < x < or = 0.72 in Li(x)()CoO(2) and is called T(#)2. We studied this phase from a structural viewpoint using X-ray and neutron diffraction (ab initio method). The new stacking derives from the O2 one by gliding every second CoO(2) slab by (1/3, 1/6, 0). The lithium ions are found to occupy very distorted tetrahedral sites in this structure. We also discuss the possibility of this T(#)2 phase to exhibit stacking faults, whose amount depends on the method used to prepare this deintercalated phase.

Journal Article↗
PubMed2004

Syntheses, structure, and selected physical properties of CsLnMnSe3 (Ln = Sm, Gd, Tb, Dy, Ho, Er, Tm, Yb, Y) and AYbZnQ3 (A = Rb, Cs; Q = S, Se, Te).

CsLnMnSe(3) (Ln = Sm, Gd, Tb, Dy, Ho, Er, Tm, Yb, Y) and AYbZnQ(3) (A = Rb, Cs; Q = S, Se, Te) have been synthesized from solid-state reactions at temperatures in excess 1173 K. These isostructural materials crystallize in the layered KZrCuS(3) structure type in the orthorhombic space group Cmcm. The structure is composed of LnQ(6) octahedra and MQ(4) tetrahedra that share edges to form [LnMQ(3)] layers. These layers stack perpendicular to [010] and are separated by layers of face- and edge-sharing AQ(8) bicapped trigonal prisms. There are no Q-Q bonds in the structure of the ALnMQ(3) compounds so the formal oxidation states of A/Ln/M/Q are 1+/3+/2+/2-. The CsLnMnSe(3) materials, with the exception of CsYbMnSe(3), are Curie-Weiss paramagnets between 5 and 300 K. The magnetic susceptibility data for CsYbZnS(3), RbYbZnSe(3), and CsYbMSe(3) (M = Mn, Zn) show a weak cusp at approximately 10 K and pronounced differences between field-cooled and zero-field-cooled data. However, CsYbZnSe(3) is not an antiferromagnet because a neutron diffraction study indicates that CsYbZnSe(3) shows neither long-range magnetic ordering nor a phase change between 4 and 295 K. Nor is the compound a spin glass because the transition at 10 K does not depend on ac frequency. The optical band gaps of the (010) and (001) crystal faces for CsYbMnSe(3) are 1.60 and 1.59 eV, respectively; the optical band of the (010) crystal faces for CsYbZnS(3) and RbYbZnSe(3) are 2.61 and 2.07 eV, respectively.

Journal Article↗
PubMed2004

Magnetic ordering in iron tricyanomethanide.

Magnetic susceptibility, heat capacity, and neutron diffraction studies of Fe[C(CN)(3)](2) reveal the existence of two magnetic phase transitions at T(N,I) = 2.45 K and T(N,II) = 1.85 K. Between 1.85 and 2.45 K, the magnetic ordering is incommensurate with a temperature-dependent propagation vector (k(I,x) 0 0), k(I,x) = 0.525-0.540. In zero magnetic field, below 1.85 K the ordered structure is described by the propagation vector k(II) = ((1/2) 0 (1/2)), i.e., a doubling of the unit cell along the a and c directions of the orthorhombic lattice. The ordered moments of 3.4(1) and 3.2(1) micro(B), respectively, are aligned approximately parallel to the principal axis of the elongated Fe coordination octahedron. At T < T(N,II), application of an external magnetic field of about 18 kOe destroys the commensurate phase and the incommensurate phase is established. The latter phase is stable in fields up to about 40 kOe. The magnetic ordering of Fe[C(CN)(3)](2) is discussed in terms of the 2D triangular topology of the lattice, producing partial frustration, and in comparison with the behavior of other compounds of the series M[C(CN)(3)](2), where M is a 3d transition metal.

Journal Article↗
PubMed2004

Local structure and charge distribution in the UO(2)-U(4)O(9) system.

Analysis of X-ray absorption fine structure spectra of UO(2+x) for x = 0-0.20 (UO(2)--U(4)O(9)) reveals that the adventitious O atoms are incorporated as oxo groups with U--O distances of 1.74 A, most likely associated with U(VI), that occur in clusters so that the UO(2) fraction of the material largely remains intact. In addition to the formation of some additional longer U--O bonds, the U sublattice consists of an ordered portion that displays the original U--U distance and a spectroscopically silent, glassy part. This is very different from previous models derived from neutron diffraction that maintained long U--O distances and high U--O coordination numbers. UO(2+x) also differs from PuO(2+x) in its substantially shorter An-oxo distances and no sign of stable coordination with H(2)O and its hydrolysis products.

Journal Article↗
PubMed2005

Structural and magnetic properties of hexagonal perovskites La1.2Sr2.7MO7.33 (M = Ru, Ir) containing peroxide ions.

The structures of the new compound La(1.2)Sr(2.7)IrO(7.33) and the recently discovered La(1.2)Sr(2.7)RuO(7.33) have been solved using a combination of X-ray and neutron diffraction. Both compounds crystallize in the trigonal space group Rm and consist of isolated MO6 (M = Ru, Ir) octahedra, which are arranged in well-defined hexagonal perovskite slabs. These slabs are separated by (Sr2O(1+delta)) layers containing both O2- and (O2)2- ions. The composition can therefore be written as La(1.2)Sr(2.7)MO(7-delta)(O2)delta with delta = 0.33. Results of the magnetic susceptibility and XANES measurements show that the transition metal cations are in a pentavalent state. While in La(1.2)Sr(2.7)RuO(7.33) an antiferromagnetic interaction between the Ru5+ ions is found, La(1.2)Sr(2.7)IrO(7.33) shows a very small temperature-independent paramagnetism down to 1.8 K due to the strong spin-orbit coupling characteristic for the 5d element iridium.

Journal Article↗
PubMed2005

Ln18Li8Rh5O39 (Ln = La, Pr): a mixed-metal oxide with a charge-ordered arrangement of Rh3+ and Rh4+.

Polycrystalline samples of Ln18Li8Rh5O39 (Ln = La, Pr) have been synthesized by the ceramic method and characterized by X-ray and neutron diffraction. The compounds crystallize in the cubic space group Pmn, with a0 approximately 12.1 Angstroms. The unit cell contains four intersecting 111 chains, each comprised of an alternating sequence of face-sharing RhO6 octahedra and LiO6 trigonal prisms. The octahedra located at the points of intersection contain Rh4+, whereas the remainder contain Rh3+; the compounds thus contain a charge-ordered arrangement of the two cations. The polyhedral chains are enclosed in tunnels formed by the Ln-O sublattice. The magnetic properties of the two new compounds are discussed briefly: both are paramagnetic over the temperature range 5 < TK < 300.

Journal Article↗
PubMed2005

Synthesis, structure, and magnetic properties of Sr2NiOsO6 and Ca2NiOsO6: two new osmium-containing double perovskites.

Two new double perovskite oxides, Ca(2)NiOsO(6) and Sr(2)NiOsO(6), have been prepared as polycrystalline powders by solid state synthesis. The two oxides were structurally characterized by variable-temperature powder neutron diffraction. Ca(2)NiOsO(6) was found to adopt a monoclinic structure (P2(1)/n), while Sr(2)NiOsO(6) was found to be tetragonal (I4/m). Magnetic susceptibility measurements indicate that Ca(2)NiOsO(6) orders in a canted antiferromagnetic state at about 175 K while Sr(2)NiOsO(6) orders antiferromagnetically at about 50 K.

Journal Article↗
PubMed2007

Syntheses and structures of asymmetric Bis(silyl) niobocene hydrides.

This paper deals with the preparation and structural investigation of asymmetric bis(silyl) niobocene hydrides, Cp2Nb(SiHMe2)(H)(SiXMe2) (2; X = F (a), Cl (b), Br (c), I (d)) and Cp2Nb(SiXMe2)(H)(SiYMe2) (X,Y= F-I; X not equal Y). Complexes 2a-d were prepared by selective electrophilic activation of the Si-H bond in Cp2Nb(SiHMe2)2(H). The Cp2Nb(SiXMe2)(H)(SiYMe2) complexes were prepared by electrophilic activation of the Si-H bond in 2a-d and, in some cases, by electrophilic exchange of the X halides in Cp2Nb(SiXMe2)2(H) (1) for other halides, Y. The structures of complexes 2b and 2c have been studied by X-ray and neutron diffraction (ND). The ND results unequivocally established that the hydride ligand in 2c is shifted toward the SiBrMe2 ligand and that in 2b is positioned symmetrically between two nonequivalent silyl groups, with the H...SiClMe2 distance being shorter because of the shorter Nb-SiClMe2 bond length. Analysis of the X-ray structures of complexes 2a-d and complexes Cp2Nb(SiXMe2)(H)(SiYMe2) shows that the largest structural distortions are observed for the silyl groups substituted by heavy halogen atoms. These trends are rationalized in terms of stronger interligand hypervalent interactions (IHI) Nb-H...Si-X for heavy atoms X from Group 7.

Journal Article↗
PubMed1997

The True Structure and Metal-Metal-Bonded Framework of LiMo(III)O(2) Determined from Total Neutron Scattering.

Total neutron diffraction studies show that the layered lithium molybdate, LiMo(III)O(2), contains zigzag molybdenum chains within the MoO(2) layers. The short distances along the zigzag, d(Mo)(-)(Mo) = 2.618 Å, are indicative of strong metal-metal bonds. The structure adopted is in agreement with theoretical predictions for a d(3) metal system and differs from that previously published. The average structure is best described in the space group = C2/m, with a = 10.543(6) Å, b = 2.8626(5) Å, c = 10.899(6) Å, and beta = 153.29(1) degrees. The utility of determining radial correlation functions from diffraction data as a check on the final structure obtained from Bragg scattering studies of polycrystalline materials is demonstrated.

Journal Article↗
PubMed1997

Structure and Stability of Carboxylate Complexes. 20. Diaqua Bis(methoxyacetato) Complexes of Nickel(II), Copper(II), and Zinc(II): A Structural Study of the Dynamic Pseudo-Jahn-Teller Effect.

The crystal structure of trans-diaquabis(methoxyacetato)copper(II), C(6)H(14)O(8)Cu, has been determined by neutron diffraction at 4.2 K (monoclinic, P2(1)/n, a = 6.88(1), b = 7.19(1), c = 9.77(2) Å, gamma = 95.7(1) degrees, (Z = 2)) and by X-ray diffraction at 125, 165, 205, 240, 265, 295, and 325 K. These measurements show that there is no phase change in the temperature range 4.2-325 K. The copper(II) coordination at 4.2 K is a tetragonally distorted elongated rhombic octahedron (Cu-OOC 1.955(1), Cu-OMe 2.209(1), and Cu-OH(2) 2.031(2) Å). As the temperature increases to 325 K, the Cu-OOC bonds shorten slightly to 1.934(5) Å, the Cu-OMe bonds shorten more markedly to 2.137(4) Å, and Cu-OH(2) lengthens to 2.155(6) Å to give a tetragonally distorted compressed rhombic octahedron. For comparison the structure of the isomorphous nickel(II) complex (monoclinic, P2(1)/n, a = 6.633(1), b = 7.192(1), c = 10.016(2) Å, gamma = 98.30(2) degrees, (Z = 2)) has been redetermined at 295 K and the structure of the analogous zinc(II) complex (orthorhombic, F2dd, a = 7.530(1), b = 13.212(1), c = 21.876(2) Å (Z = 8)) has also been determined. The nickel(II) complex has an almost regular trans (centrosymmetric) octahedral coordination (Ni-OOC 2.022(1), Ni-OMe 2.043(1), and Ni-OH(2) 2.077(2) Å). However, zinc(II) has a very distorted octahedral coordination with the zinc atom on a 2-fold axis with the water molecules and the methoxy ligators cis and the carboxylate ligators trans (Zn-OOC 1.985(1), Zn-OMe 2.304(2), and Zn-OH(2) 2.038(2) Å). The variation in the dimensions of the copper(II) coordination sphere is discussed in terms of static (low temperature) and planar dynamic (high temperature) pseudo-Jahn-Teller effects.

Journal Article↗
PubMed1998

Crystal Structures of AuCN and AgCN and Vibrational Spectroscopic Studies of AuCN, AgCN, and CuCN.

The crystal structures of AuCN and AgCN have been determined by powder neutron diffraction measurements. The structure of AuCN consists of rows of linear AuCN chains parallel to [001] with alternating long Au-C = 2.06(2) and short Au-N = 1.82(2) Å. The Au atoms form sheets and are bonded to 6 other Au atoms at a distance of 3.396(2) Å, so that the local environment of each Au atom can be described as a compressed scalehedron. The Au- - -Au distance is within the range expected for an "aurophilic attraction" between these atoms. The AgCN structure is very similar to that for AuCN, in that it consists of rows of AgCN chains with alternating long Ag-C = 2.15(6) and short Ag-N = 1.86(8) Å. The major difference is that the Ag- - -Ag separation within the Ag sheets is noticeably longer, 3.881(5) Å, so that there are no significant Ag- - -Ag interactions. The IR spectra of MCN show nu(CN) at 2170, 2164, 2236; nu(MC,MN) at 591, 480, 598; delta(MCN) at 326, 272, 358; and delta(NMC) = 168, 112, 224 cm(-)(1) for M = Cu, Ag, and Au, respectively. This pattern of band positions strongly suggests that CuCN has the same infinite linear chain structure as AgCN and AuCN. Anomalies in the previously reported IR spectrum of CuCN are shown to be due to the formation of an unusual CuCN/KBr/H(2)O product in KBr disks, which is possibly an intercalation compound involving incorporation of KBr and H(2)O between the chains in the CuCN structure.

Journal Article↗
PubMed1998

Structure of LaMo(2)O(5) Containing Both Isolated Mo(6)O(18) Clusters and Sheets of Fused Triangular Mo(3) Clusters.

The structure of the disordered lanthanum molybdate, LaMo(2)O(5), has been solved and refined using powder neutron diffraction data collected at 300 K. The average structure is described in P6(3)/mmc, a = 8.373(1) Å, c = 19.1510(1) Å, Z = 12. The compound contains two types of Mo-Mo bonded units: isolated octahedral Mo(6)O(18) clusters, and infinite molybdenum oxide sheets, formed from condensed triangular Mo(3)O(13) clusters joined together to give a total of four Mo-Mo bonds for each molybdenum. The Mo(6)O(18) clusters have 16 electrons available for metal-metal bonding and the Mo-Mo distances within the unit are 2.643(4) Å x 6 and 2.695(5) Å x 6. In the infinite sheets the molybdenum-molybdenum distances are 2.612(9) Å within one equilateral triangular cluster and 2.621(8) Å within another. Each of the molybdenum atoms in the two different Mo(3) clusters has two molybdenum neighbors from the other cluster at a distance of 2.882(6) Å. Disorder in this layered structure occurs because of interchange of layers of Mo sheets with layers of lanthanum ions. The Bragg scattering is accounted for by including layers occupied with a 50% probability by each of these structural elements and their associated oxygen atoms. A model showing how ordered subunits are stacked together to produce the average structure is presented. Extended X-ray absorption fine structure spectroscopy (EXAFS) at the Mo K-edge was used to give information on the local structure around molybdenum and to confirm that the final structural model gives a good description of Mo-O and Mo-Mo bonding.

Journal Article↗
PubMed1999

Synthesis and Structure of NaZnSiO(3)OH, a New Chiral Zincosilicate Framework Material.

The structure of NaZnSiO(3)OH, synthesized hydrothermally by reaction of Na(2)ZnSiO(4) and NaOH, has been determined from single-crystal X-ray and powder neutron diffraction data (orthorhombic, space group P2(1)2(1)2(1,) a = 7.6872(2) Å, b = 9.3899(2) Å, c = 5.155(1) Å, Z = 4). The structure has a framework constructed from ZnO(4) and SiO(3)OH tetrahedra with bridging and trigonal oxygen atoms. Channels formed from eight-membered rings of tetrahedra house the sodium ions and are also partially blocked by moderately strongly hydrogen bonded OH groups.

Journal Article↗