Synthesis and reactions of [Et3NH]4[Mo8O6]: X-ray crystal structure of [Et3NH]3[NaMo8O26]

[Et3NH]4[Mo8O26] (1) was prepared by reacting triethylamine with either molybdenum trioxide dihydrate or with a solution of ammonium molybdate in aqueous HCl. An aqueous solution of complex 1 reacted with an excess of sodium chloride to give a mixture of [Et3NH]3[NaMo8O26] (2) and [Et3NH]2[Mo6O19] (3). Complex 2 was also formed on reacting sodium molybdate with triethylamine in aqueous HCl. In the reaction of 1 with potassium chloride the nature of the product obtained was critically dependent upon reaction time. After a 5.5 h reflux period a mixture of [Et3NH]3[KMo8O26] (4) and 3 was obtained, whereas upon prolonged reflux (24 h) only K4Mo8O26 · H2O (5) was precipitated. The X-ray crystal structure of 2 shows it to be polymeric, with each Na+ ion sandwiched between two β[Mo8O26]4− ions. Four oxygen atoms on one face of each β[Mo8O26]4− ion are coordinated to a Na+ ion, and four oxygens from the opposite face are bonded to the next Na+ ion in the polymer chain. This produces a zig-zag arrangement of Na+ ions throughout the molecular structure. Spectral, conductivity and voltammetry data are given.

Copper(II) complexes of benzene-1,2-dioxyacetic acid (bdoaH2): X-ray crystal structure of [Cu2(bdoa)(phen)4]bdoa·13H2O (phen = 1,10-phenanthroline)

Copper(II) acetate reacts with benzene-1,2-dioxyacetic acid (bdoaH2) in aqueous media to give [Cu(bdoa)(H2O)2] (1). Complex 1 reacts with the N-donor ligands pyridine (py), ammonia and 1,10-phenanthroline (phen) to give [Cu(bdoa)(NH3)2]·H2O (2), [Cu(bdoa)(py)2]·H2O (3) and [Cu2(bdoa)(phen)4]bdoa·13H2O (4), respectively. The X-ray crystal structure of the dicopper(II,II) complex 4 shows each copper atom at the centre of a distorted trigonal bipyramid comprising four nitrogen atoms from two chelating phen ligands and a single oxygen atom from one of the carboxylate moieties of the bridging bdoa2− ligand. The cyclic voltammogram of 4 shows a single reversible wave for the Cu2+/Cu+ couple at E = + 115 mV (vs Ag/AgCl). Spectroscopic and magnetic data for the complexes are given.

Synthesis and properties of tetra-μ-acetatodiruthenium(II,III) phenylphosphinate and phenylphosphonate complexes: X-ray crystal structures of [Ru2(μ-O2CCH3)4(HPhPO2)2]H and [Ru2(μ-O2CCH3)4(PhPO3H)2]H·H2O

Phenylphosphinic acid (HPhPO2H) and phenylphosphonic acid (PhPO3H2) react with a methanolic solution of [Ru2(μ-O2CCH3)4(O2CCH3)2]H·0.7H2O at room temperature to give [Ru2(μ-O2CCH3)4(HPhPO2)2H (1) and [Ru2(μ-O2CCH3)4 (PhPO3H)2]H·H2O (2), respectively. The X-ray crystal structures of 1 and 2 each show the RuRu core to be ligated by four bridging bidentate acetate ligands [RuRu distances: 1 = 2.272(1) Å; 2 = 2.267(2) Å] and two axial phenylphosphinate and phenylphosphonate ligands, respectively. In each complex the individual bimetallic molecules are linked together by a hydrogen ion which bridges the oxygen atoms of neighbouring axial ligands. In 2 the water molecule is also hydrogen-bonded to one of the axial phenylphosphonate groups. Spectroscopic, magnetic and cyclic voltammetric data for the complexes are given.

The synthesis and properties of [Fe3(CO)11(RCN)] derivatives, and a high-yield general route to mono- and di-substituted derivatives of [Fe3(CO)12]; the crystal and molecular structure of [Fe3(CO)11(NCC6H4-2-Me)]

The clusters [Fe3(CO)11(RCN)] (1: R = Me, C3H5, C6H5, or C6H4-2-Me) have been prepared at low temperature from [Fe3(CO)12] and RCN in the presence of Me3NO. Compounds 1 react essentially quantitatively with a wide range of two-electron donors, L, (viz.: CO, PPh3, P(OMe)3, PPh2H, PPh2Me, PF3, CyNC (Cy = cyclohexyl), P(OEt)3, SbPh3, PBu3, AsPh3, or SnR2 (R = CH(SiMe3)2)) to give [Fe3(CO)11L] (2). In some cases (2), on treatment with Me3NO and then L′ (L′ = a second two-electron donor) yields [Fe3(CO)10LL′] in high yield. The crystal and molecular structures of 1 (L = NCC6H4Me-2) have been determined by a full single crystal structure analysis, and shown to have an axial nitrile coordinated at the unique iron atom, with two CO groups bridging the other two metal atoms.

Metal cluster expansion by addition of low valent group 14 reagents: III. Reaction of bis[bis(trimethylsilyl)methyl]tin with M3(CO)12 or its derivatives (M = Fe, Ru, or Os): the crystal and molecular structures of M3(μ-SnR2)2(CO)10(R = CH(SiMe3)2; M = Ru or Os)

The stannylene [SnR2] (R = CH(SiMe3)2) reacts in different ways with the three dodecacarbonyls of the iron triad: [Fe3(CO)12] gives [Fe2(CO)8(μ-SnR2)], [Ru3(CO)12] gives the planar pentametallic cluster [Ru3(CO)10(μ-SnR2)2], for which a full structural analysis is reported, while [Os3(CO)12] fails to react. Different products are also obtained from three nitrile derivatives: [Fe3-(CO)11(MeCN)] gives [Fe2(CO)6(μ-SnR2)2], which has a structure significantly different from that of known Fe2Sn2 clusters, [Ru3(CO)10(MeCN)2] gives the pentametallic cluster described above, while [Os3(CO)10(MeCN)2] gives the isostructural osmium analogue, which shows the unusual feature of a CO group bridging two osmium atoms.

Metal cluster expansion by addition of low-valent group 4B reagents: crystal and molecular structure of [Os3SnH2(CO)10{CH(SiMe3)2}2]; a compound with hydrogen bridging osmium and tin

Cluster expansion of [Os3H2(CO)10] with [SnR2][R = CH(SiMe3)2] take place in high yield to give [Os3SnH2(CO)10R2], the first closed triosmium–main-group metal cluster to be structurally characterized; a novel feature is the presence of a hydrogen atom bridging the tin atom and one of the osmium atoms.

Unsaturated σ-hydrocarbyl transition-metal complexes. Part 3. Crystal and molecular structure of trans-chlorobis(diethylphenylphosphine)(vinyl)platinum(II)

The molecular structure of trans-[PtCl(CHCH2)(PEt2Ph)2] has been determined by X-ray diffraction methods. The crystals are orthorhombic, space group Pbcn, with a= 10.686(2), b= 13.832(4), c= 16.129(4)Å, and Z= 4. The structure has been solved by the heavy-atom method and refined by full-matrix least squares to R 0.044 for 1 420 diffractometric intensity data. The crystals contain discrete molecules in which the platinum co-ordination is square planar. The Pt–Cl bond vector coincides with a crystallographic diad axis about which the atoms of the vinyl group are disordered. Selected bond lengths (Å) are Pt–Cl 2.398(4), Pt–P 2.295(3), and Pt–C 2.03(2). The Pt–CC angle is 127(2)°. From a survey of the available structural data it is concluded that there is little, if any, back donation from platinum to carbon in platinum–alkenyl linkages.

Stepwise construction of [Os6(CO)18(μ6-P)]-, a hexanuclear osmium cluster monoanion with trigonal-prismatic co-ordination for phosphorus: X-ray crystal structures of [Os6(μ-H)2(CO)20(MeCN)(μ3-PH)] and [PPh3Me][Os6(CO)18(μ6-P)]

Treatment of the labile cluster [Os3(CO)11(MeCN)] with PH3 affords the substituted product [Os3(CO)11(PH3)](1) in high yield. Subsequent reaction of (1) with Na2CO3 in MeOH, followed by acidification, gives the hydrido phosphido cluster [Os3(µ-H)(CO)10(µ-PH2)](2). When (2) is heated to 45–60 °C in the presence of [Os3(CO)11(MeCN)] a hexanuclear complex with the formulation [Os6(µ-H)2(CO)21(µ3-PH)](3) is obtained. If this reaction is repeated using [Os3(CO)10(MeCN)2] instead of [Os3(CO)11(MeCN)], an acetonitrile-containing product, [Os6(µ-H)2(CO)20(MeCN)(µ3-PH)](4), is obtained. An X-ray analysis of (4) shows that two Os3 triangular units are linked by a µ3-phosphinidene ligand, which symmetrically bridges an Os–Os edge of one triangle and is terminally co-ordinated to one Os atom of the second triangle. When (3) is treated with a weak base, such as [N(PPh3)2]Cl or [PPh3Me] Br, deprotonation to the corresponding cluster monoanion [Os6(µ-H)(CO)21(µ3-PH)]–(5) occurs. Treatment of (5) with a weak acid regenerates (3) in quantitative yield. Thermolysis of (3) leads to a closing up of the metal framework, affording the cluster [Os6(µ-H)(CO)18(µ6-P)], which readily deprotonates to give the anion [Os6(CO)18(µ6-P)]–(7) in the presence of [N(PPh3)2] Cl or [PPh3Me]Br. The same anion (7) may also be obtained by direct thermolysis of (5). An X-ray analysis of the [PPh3Me]+ salt of (7) confirms that the phosphorus occupies an interstitial site in a trigonal-prismatic hexaosmium framework, and co-ordinates to all six metal atoms with an average Os–P distance of 2.31 (1)Å. Proton and 31P n.m.r. data on all the new clusters are presented, and the position of the phosphorus resonance in the 31P n.m.r. spectrum is related to the changes in the environment of the phosphorus atom.

On the relationship between the Indian summer monsoon and river flow in the Aral Sea basin

We study the contemporaneous relationship between the intensity of the Indian Summer Monsoon (ISM) and runoff in the major rivers of the Aral Sea basin (Amudarya, Syrdarya) and some of their subcatchments. To this end, we use All-India rainfall (AIR) data, CRU surface observations of precipitation and temperature, ERA40 atmospheric data, and natural discharge data corrected for human interference. We show that there is a highly significant positive correlation between ISM intensity and Amudarya runoff. This finding cannot be explained by the spill-over of ISM precipitation over the Hindu Kush into the Amudarya basin. Instead, we suggest that the observed co-variability is mediated by tropospheric temperature variations due to fluctuations in the ISM intensity. These variations are known to be due to Rossby-wave propagation in response to condensational heating during monsoon precipitation. We hypothesise that the corresponding anomalies in surface temperatures imply anomalies in meltwater formation.

Coverage-dependent molecular tilt of carbon monoxide chemisorbed on Pt{110}: A combined LEED and DFT structural analysis

The adsorption of carbon monoxide on the Pt{110} surface at coverages of 0.5 ML and 1.0 ML was investigated using quantitative low-energy electron diffraction (LEED IV) and density-functional theory (DFT). At 0.5 ML CO lifts the reconstruction of the clean surface but does not form an ordered overlayer. At the saturation coverage, 1.0 ML, a well-ordered p(2×1) superstructure with glide line symmetry is formed. It was confirmed that the CO molecules adsorb on top of the Pt atoms in the top-most substrate layer with the molecular axes tilted by ±22° with respect to the surface normal in alternating directions away from the close packed rows of Pt atoms. This is accompanied by significant lateral shifts of 0.55 Å away from the atop sites in the same direction as the tilt. The top-most substrate layer relaxes inwards by −4% with respect to the bulk-terminated atom positions, while the consecutive layers only show minor relaxations. Despite the lack of long-range order in the 0.5 ML CO layer it was possible to determine key structural parameters by LEED IV using only the intensities of the integer-order spots. At this coverage CO also adsorbs on atop sites with the molecular axis closer to the surface normal (b10°). The average substrate relaxations in each layer are similar for both coverages and consistent with DFT calculations performed for a variety of ordered structures with coverages of 1.0 ML and 0.5 ML.

The study of chiral adsorption systems using synchrotron- based structural and spectroscopic techniques: stereospecific adsorption of serine on Au-modified chiral Cu{531} surfaces

We apply modern synchrotron-based structural techniques to the study of serine adsorbed on the pure andAumodified intrinsically chiral Cu{531} surface. XPS and NEXAFS data in combination with DFT show that on the pure surface both enantiomers adsorb in l4 geometries (with de-protonated b-OH groups) at low coverage and in l3 geometries at saturation coverage. Significantly larger enantiomeric differences are seen for the l4 geometries, which involve substrate bonds of three side groups of the chiral center, i.e. a three-point interaction. The l3 adsorption geometry, where only the carboxylate and amino groups form substrate bonds, leads to smaller but still significant enantiomeric differences, both in geometry and the decomposition behavior. When Cu{531} is modified by the deposition of 1 and 2ML Au the orientations of serine at saturation coverage are significantly different from those on the clean surface. In all cases, however, a l3 bond coordination is found at saturation involving different numbers of Au atoms, which leads to relatively small enantiomeric differences.

Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

Complete Experimental Structure Determination of the p(3x2)pg Phase of Glycine on Cu{110}

We present a quantitative low energy electron diffraction (LEED) surface-crystallograpic study of the complete adsorption geometry of glycine adsorbed on Cu{110} in the ordered p(3×2) phase. The glycine molecules form bonds to the surface through the N atoms of the amino group and the two O atoms of the de-protonated carboxylate group, each with separate Cu atoms such that every Cu atom in the first layer is involved in a bond. Laterally, N atoms are nearest to the atop site (displacement 0.41 Å). The O atoms are asymmetrically displaced from the atop site by 0.54 Å and 1.18 Å with two very different O-Cu bond lengths of 1.93 Å and 2.18 Å. The atom positions of the upper-most Cu layers show small relaxations within 0.07 Å of the bulk-truncated surface geometry. The unit cell of the adsorbate layer consists of two glycine molecules, which are related by a glide-line symmetry operation. This study clearly shows that a significant coverage of adsorbate structures without this glide-line symmetry must be rejected, both on the grounds of the energy dependence of the spot intensities (LEED-IV curves) and of systematic absences in the LEED pattern.

Automatic prediction of functional site regions in low-resolution protein structures

World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of generating at least low resolution structural models of target proteins. Accurate detection and classification of functional sites within both solved and modelled protein structures therefore represents an important challenge. We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. The method is designed primarily to require only backbone residue positions without the need for specific side-chain atoms to be present. In order to highlight effective site detection in low resolution structural models FuncSite was used to screen model proteins generated using mGenTHREADER on a set of newly released structures. We found effective metal site detection even for moderate quality protein models illustrating the robustness of the method.

The importance of attractive three-point interaction in enantioselective surface chemistry: stereospecific adsorption of serine on the intrinsically chiral Cu{531} surface

Both enantiomers of serine adsorb on the intrinsically chiral Cu{531} surface in two different adsorption geometries, depending on the coverage. At saturation, substrate bonds are formed through the two oxygen atoms of the carboxylate group and the amino group (μ3 coordination), whereas at lower coverage, an additional bond is formed through the deprotonated β−OH group (μ4 coordination). The latter adsorption geometry involves substrate bonds through three side groups of the chiral center, respectively, which leads to significantly larger enantiomeric differences in adsorption geometries and energies compared to the μ3 coordination, which involves only two side groups. This relatively simple model system demonstrates, in direct comparison, that attractive interactions of three side groups with the substrate are much more effective in inducing strong enantiomeric differences in heterogeneous chiral catalyst systems than hydrogen bonds or repulsive interactions.