Determination of fluid--solid transitions in model protein solutions using the histogram reweighting method and expanded ensemble simulations

Protein crystallization conditions are usually identified by empirical screening methods because of the complexity of the process, such as the existence of nonequilibrium phases and the different crystal forms that may result from changes in solution conditions. Here the crystallization of a model protein is studied using computer simulation. The model consists of spheres that have both an isotropic interaction of short range and anisotropic interactions between patch-antipatch pairs. The free energy of a protein crystal is calculated using expanded ensemble simulations of the Einstein crystal, and NpT-Monte Carlo simulations with histogram reweighting are used to determine the fluid-solid coexistence. The histogram reweighting method is also used to trace out the complete coexistence curve, including multiple crystal phases, with varying reduced temperature, which corresponds to changing solution conditions. At a patch-antipatch interaction strength five times that of the isotropic interaction, the protein molecules form a stable simple cubic structure near room temperature, whereas an orientationally disordered face-centered-cubic structure is favored at higher temperatures. The anisotropic attractions also lead to a weak first-order transition between orientationally disordered and ordered face-centered-cubic structures at low temperature, although this transition is metastable. A complete phase diagram, including a fluid phase, three solid phases, and two triple points, is found for the six-patch protein model. A 12-patch protein model, consistent with the face-centered-cubic structure, leads to greater thermodynamic stability of the ordered phase. Metastable liquid-liquid phase equilibria for isotropic models with varying attraction tails are also predicted from Gibbs ensemble simulations.     

Structure Determination of a Complex Tubular Uranyl Phenylphosphonate, (UO(2))(3)(HO(3)PC(6)H(5))(2)(O(3)PC(6)H(5))(2).H(2)O, from Conventional X-ray Powder Diffraction Data

The three-dimensional structure of a complex tubular uranyl phosphonate, (UO(2))(3)(HO(3)PC(6)H(5))(2)(O(3)PC(6)H(5))(2).H(2)O, was determined ab initio from laboratory X-ray powder diffraction data and refined by the Rietveld method. The crystals belong to the space group P2(1)2(1)2(1), with a = 17.1966(2) ?, b = 7.2125(2) ?, c = 27.8282(4) ?, and Z = 4. The structure consists of three independent uranium atoms, among which two are seven-coordinated and the third is eight-coordinated. These metal atoms are connected by four different phosphonate groups to form a one-dimensional channel structure along the b axis. The phenyl groups are arranged on the outer periphery of the channels, and their stacking forces keep the channels intact in the lattice. The determination of this structure which contains 50 non-hydrogen atoms in the asymmetric unit, from conventional X-ray powder data, represents significant progress in the application of powder techniques to structure solution of complex inorganic compounds, including organometallic compounds.     

[H2en]2{La2M(SO4)6(H2O)2} (M=Co, Ni): First organically templated 3d-4f mixed metal sulfates

The first organically templated 3d-4f mixed metal sulfates, [H₂en]₂{La₂M(SO₄)₆(H₂O)₂} (M=Co 1, Ni 2) have been synthesized and structurally determined from non-merohedrally twinned crystals. The two compounds are isostructural and their structures feature a three-dimensional anionic network formed by the lanthanum(III) and nickel(II) ions bridged by sulfate anions. The La(III) ions in both compounds are 10-coordinated by four sulfate anions in bidentate chelating fashion, and two sulfate anions in a unidentate fashion. The transition metal(II) ion is octahedrally coordinated by six oxygens from four sulfate anions and two aqua ligands. The doubly protonated enthylenediamine cations are located at the tunnels formed by 8-membered rings (four La and four sulfate anions).     

Characterisation and cryomagnetic study of a hydrothermally synthesised hydrogen bonded L–M–L type co-ordination polymer

A ligand–metal–ligand type co-ordination polymer [Ni (C₆H₁₂N₄)(NCS)₂(H₂O)₂] _n has been synthesised under controlled hydrothermal conditions. Here 1,3,5,7-tetraazatricyclo[3.3.1]decane [or hexamethylenetetramine (hmt)] has been used as a μ-(N,N′) bidentate spacer molecule. The prepared polymeric complex has been characterised by elemental and spectral analyses. The structure has been confirmed by a single crystal X-ray diffraction study. Magneto-structural correlation has been drawn from cryomagnetic susceptibility measurements (2–300 K) which unequivocally reflects very weak magnetic spin interactions among the long distant octahedral Ni(II) metal centres mediated by hmt and weak hydrogen bonding interactions between the adjacent zigzag one-dimensional polymeric chains carrying into a two-dimensional infinite polymeric framework.     

Pretreatment studies of cellulose wastes for optimization of cellulase enzyme activity

The composition of cellulose, hemicellulose, starch, lignin, pectin, protein, and total lipid content in the selected cellulosic wastes-tapioca (Manihot esculenta) stem, leaf, petiole, and water hyacinth (Eichhornia crassipes) were determined. The effectiveness of various physical and chemical pretreatments on the enzymatic digestibility of these wastes were identified. In general, chemical pretreatments were more effective than physical pretreatments. The efficiency of the pretreatment was checked by subjecting these wastes to enzymatic saccharification after the pretreatments.     

Charge calculations in molecular mechanics. IX. A general parameterisation of the scheme for saturated halogen,oxygen and nitrogen compounds

Summary The CHARGE2 program for the calculation of partial atomic charges has been amended to include bond parameters for a number of organic functional groups, including halogens, nitrogen and oxygen. These minor amendments to the original scheme produce dipole moments for the fluoro and chloro compounds which are in complete agreement with the observed values.The less complete data sets for the bromo and iodo compounds are also well reproduced, and the dipole moments of a variety of mixed halo compounds are now in better agreement with experiment than previously.The calculated dipole moments of the saturated nitrogen and oxygen compounds are now in much better agreement than in the original scheme, thus the revised parameterisation may be employed with confidence to predict the electrostatic energies of these compounds.Furthermore, the revised scheme now gives a precise proportionality between the charge on the proton in a CH group and the ¹H chemical shift of the corresponding proton, allowing the general prediction, in principle, of ¹H chemical shifts. In addition, attempts to include variable electronegativity in the effect are described for fluoro compounds.For part VIII see Ref. 1.     

Hydrothermal syntheses, characterizations and crystal structures of three new cadmium (II) amino-diphosphonates: effects of substitute groups on the structures of metal phosphonates

Hydrothermal reactions of cadmium(II) chloride with three amino-diphosphonic acids, C₆H₅CH₂N(CH₂PO₃H₂)₂ (H₄L¹), C₆H₅CH₂CH₂N(CH₂PO₃H₂)₂ (H₄L²) and 4-CH₃-C₆H₄CH₂N (CH₂PO₃H₂)₂) (H₄L³) resulted in three new metal amino-diphosphonates, namely, Cd(H₃L¹)₂, 1 Cd(H₃L²)₂·2H₂O 2 and Cd(H₃L³)₂3. In all three complexes, the Cd(II) ion is octahedrally coordinated by six phosphonate oxygen atoms from six ligands. Complexes 1 and 3 have a similar structure in which the CdO₆ octahedra are cross-linked by bridging ligands into a double chain along the c-axis, such double chains are further interlinked via hydrogen bonds between non-coordinated phosphonate oxygen atoms to form 〈100〉 and 〈200〉 layers with the phenyl groups of the ligands orientated toward the interlayer space. The structure of complex 2 features a 〈100〉 cadmium(II) diphosphonate layer. The effects of the substitute groups attached to the amine groups on the structures of the metal phosphonates are also discussed.     

Synthesis and crystal structure of new uranyl tungstates M2(UO2)(W2O8) (M=Na, K), M2(UO2)2(WO5)O (M=K, Rb), and Na10(UO2)8(W5O20)O8

The solid-state reactions of UO₃ and WO₃ with M₂CO₃ (M=Na, K, Rb) at 650°C for 5 days result, accordingly the starting stoichiometry, in the formation of M₂(UO₂)(W₂O₈) (M=Na (1), K (2)), M₂(UO₂)₂(WO₅)O (M=K (3), Rb (4)), and Na₁₀(UO₂)₈(W₅O₂₀)O₈ (5). The crystal structures of compounds 2, 3, 4, and 5 have been determined by single-crystal X-ray diffraction using Mo(Kα) radiation and a charge-coupled device detector. The crystal structures were solved by direct methods and Fourier difference techniques, and refined by a least-squares method on the basis of F² for all unique reflections. For (1), unit-cell parameters were determined from powder X-ray diffraction data. Crystallographic data: 1, monoclinic, a=12.736(4) Å, b=7.531(3) Å, c=8.493(3) Å, β=93.96(2)°, ρ_cal=6.62(2) g/cm³, ρ_mes=6.64(1) g/cm³, Z=4; 2, orthorhombic, space group Pmcn, a=7.5884(16) Å, b=8.6157(18) Å, c=13.946(3) Å, ρ_cal=6.15(2) g/cm³, ρ_mes=6.22(1) g/cm³, Z=8, R1=0.029 for 80 parameters with 1069 independent reflections; 3, monoclinic, space group P2₁/n, a=8.083(4) Å, b=28.724(5) Å, c=9.012(4) Å, β=102.14(1)°, ρ_cal=5.83(2) g/cm³, ρ_mes=5.90(2) g/cm³, Z=8, R1=0.037 for 171 parameters with 1471 reflections; 4, monoclinic, space group P2₁/n, a=8.234(1) Å, b=28.740(3) Å, c=9.378(1) Å, β=104.59(1)°, ρ_cal=6.13(2) g/cm³,  g/cm³, Z=8, R1=0.037 for 171 parameters with 1452 reflections; 5, monoclinic, space group C2/c, a=24.359(5) Å, b=23.506(5) Å, c=6.8068(14) Å, β=94.85(3)°, ρ_cal=6.42(2) g/cm³,  g/cm³, Z=8, R1=0.036 for 306 parameters with 5190 independent reflections. The crystal structure of 2 contains linear one-dimensional chains formed from edge-sharing UO₇ pentagonal bipyramids connected by two octahedra wide (W₂O₈) ribbons formed from two edge-sharing WO₆ octahedra connected together by corners. This arrangement leads to [UW₂O₁₀]²⁻ corrugated layers parallel to (001). Owing to the unit-cell parameters, compound 1 probably contains similar sheets parallel to (100). Compounds 3 and 4 are isostructural and the structure consists of bi-dimensional networks built from the edge- and corner-sharing UO₇ pentagonal bipyramids. This arrangement creates square sites occupied by W atoms, a fifth oxygen atom completes the coordination of W atoms to form WO₅ distorted square pyramids. The interspaces between the resulting [U₂WO₁₀]²⁻ layers parallel to plane are occupied by K or Rb atoms. The crystal structure of compound 5 is particularly original. It is based upon layers formed from UO₇ pentagonal bipyramids and two edge-shared octahedra units, W₂O₁₀, by the sharing of edges and corners. Two successive layers stacked along the [100] direction are pillared by WO₄ tetrahedra resulting in sheets of double layers. The sheets are separated by Na⁺ ions. The other Na⁺ ions occupy the rectangular tunnels created within the sheets. In fact complex anions W₅O₂₀¹⁰⁻ are built by the sharing of the four corners of a WO₄ tetrahedron with two W₂O₁₀ dimmers, so, the formula of compound 5 can be written Na₁₀(UO₂)₈(W₅O₂₀)O₈.     

Reactions of [HOs3(CO)8{µ3-Ph2PCH(R)P(Ph)C6H4}] (R = H,Me) with Bu3SnH: synthesis and structure of bimetallic Os-Sn clusters

Reactions of unsaturated [HOs₃(CO)₈{µ₃-Ph₂PCH(R)P(Ph)C₆H₄}] (R?=?H, Me) with Bu₃SnH are examined. [HOs₃(CO)₈{µ₃-Ph₂PCH(R)P(Ph)C₆H₄}] reacts with Bu₃SnH at room temperature to afford [H₂Os₃(CO)₈(SnBu₃){µ₃-Ph₂PCH(R)P(Ph)C₆H₄}] (1) via oxidative addition of the Sn?H bond to the parent cluster. Heating 1 in refluxing toluene leads to the formation of [H₂Os₃(CO)₇(SnBu₃){µ₃-Ph₂PCH(R)P(Ph)C₆H₄}] (2) through decarbonylation. Cluster 2 exists in two isomeric forms in solution which has been probed by VT NMR spectroscopy. The new Os-Sn bimetallic clusters have been characterized by a combination of analytical and spectroscopic data together with single-crystal X-ray diffraction analysis.

Graphic abstract