Inclusion of secondary extinction in least-squares calculations

A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model

This paper compares variations on a structure model derived from an X-ray diffraction data set from a solid solution of chalcogenide derivatives of cis-1,2-bis-(di-phenyl-phosphan-yl)ethyl-ene, namely, 1,2-(ethene-1,2-di-yl)bis-(di-phenyl-phoshpine sulfide/selenide), C26H22P2S1.13Se0.87. A sequence of processes are presented to ascertain the composition of the crystal, along with strategies for which aspects of the model to inspect to ensure a chemically and crystallographically realistic structure. Criteria include mis-matches between F obs 2 and F calc 2, plots of |F obs| vs |F calc|, residual electron density, checkCIF alerts, pitfalls of the OMIT command used to suppress ill-fitting data, comparative size of displacement ellipsoids, and critical inspection of inter-atomic distances. Since the structure is quite small, solves easily, and presents a number of readily expressible refinement concepts, we feel that it would make a straightforward and concise instructional piece for students learning how to determine if their model provides the best fit for the data and show students how to critically assess their structures.

A Multi-Methodological Investigation of Natural and Synthetic Red Beryl Gemstones

In this study, we report the experimental findings of a multi-methodological and comparative investigation of a natural (from the Wah Wah Mountains of Beaver County, Utah) and three synthetic (hydrothermally grown) gem-quality red beryls by means of: gemmological standard testing, laser ablation inductively coupled mass spectroscopy, infrared and Raman spectroscopy, ultraviolet–visible–near infrared absorption spectroscopy, and single-crystal X-ray diffraction. Gemmological, crystallo-chemical, and spectroscopic features of the natural and synthetic stones enabled us to unveil the causes of their color (from red, to purplish-red, or orange-red) and how different and complementary techniques can be efficiently used to discriminate between natural and synthetic materials, based on non-destructive, micro-destructive, and destructive techniques.

Quantitative analysis of hydrogen sites and occupancy in deep mantle hydrous wadsleyite using single crystal neutron diffraction

Evidence from seismological and mineralogical studies increasingly indicates that water from the oceans has been transported to the deep earth to form water-bearing dense mantle minerals. Wadsleyite [(Mg, Fe²⁺)₂SiO₄] has been identified as one of the most important host minerals incorporating this type of water, which is capable of storing the entire mass of the oceans as a hidden reservoir. To understand the effects of such water on the physical properties and chemical evolution of Earth's interior, it is essential to determine where in the crystal structure the hydration occurs and which chemical bonds are altered and weakened after hydration. Here, we conduct a neutron time-of-flight single-crystal Laue diffraction study on hydrous wadsleyite. Single crystals were grown under pressure to a size suitable for the experiment and with physical qualities representative of wet, deep mantle conditions. The results of this neutron single crystal diffraction study unambiguously demonstrate the method of hydrogen incorporation into the wadsleyite, which is qualitatively different from that of its denser polymorph, ringwoodite, in the wet mantle. The difference is a vital clue towards understanding why these dense mantle minerals show distinctly different softening behaviours after hydration.

Crystal structure refinements of magnesite, calcite, rhodochrosite, siderite, smithonite, and dolomite, with discussion of some aspects of the stereochemistry of calcite type carbonates

The crystal structures of magnesite, calcite, rhodochrosite, siderite, smithonite and dolomite were refined by standard single crystal X-ray methods using diffraction data up to sin[unk]/λ = 1.0 Å−1. The C – O bond lengths are essentially the same. Attention is drawn to short O – O contacts (2.85 Å in both magnesite and smithonite) outside the coordination figures. The MeO6 octahedra are always elongated parallel [00.1]; the distortion is not a monotone function of the Me – O distance. The approximation of four point charges for the [CO3]2− ion for calcite gives good agreement between observation and classical electrostatic calculation when charges of 1 + for carbon and 1 − for oxygen are used.

Röntgenstrukturanalysen an wasserhaltigen Thalliumpolyboraten I. Die Struktur von Tl2[B4O6(OH)2] · 2H2O

The crystal structure of synthetic Tl2[B4O6(OH)2] · 2H2O was determined from single-crystal X-ray diffractometer data. The compound crystallizes orthorhombic, space group P212121; the lattice constants are a = 10.909(2) Å, b = 9.762(3) Å and c = 9.450(3) Å; the unit cell contains four formula units. The crystal structure was solved from 1289 total (1089 observed) reflections by the Patterson method and refined by least-squares calculations to an index R of 3.7%. The structure contains infinite chains of polyanions [B4O6(OH)2]2−, similar to those found in the mineral kernite. The crystallographically different atoms Tl 1 and Tl 2 are coordinated by seven O atoms with distances between 2.75 and 3.46 Å and 2.59 and 3.35 Å, respectively. Connections between the B – O chains are provided by a hydrogen bonding system of the OH groups and the water molecules, thus forming a three-dimensional framework.

Röntgenstrukturanalysen an wasserhaltigen Thalliumpolyboraten II. Die Struktur von Tl[B5O6(OH)4] · 2H2O

The crystal structure of synthetic Tl[B5O6(OH)4] · 2H2O was determined from single-crystal X-ray diffractometer data. The compound is monoclinic, space groupP21/c; the lattice constants area= 11.275(4) Å,b= 7.155(3) Å andc= 13.928(4) Å,β= 94.16(4)°; the unit cell contains four formula units. The crystal structure was solved from 2440 total (1759 observed) reflections by the Patterson method and refined by least-squares calculations to an indexRof 4.9%. The structure contains isolated [B5O6(OH)4]−polyanions, similar to those found in the structures of other monoclinic pentaborates, e.g. in the mineral sborgite Na[B5O6(OH)4] · 3 H2O, in synthetic Na[B5O6(OH)4], in syntheticβ-NH4[B5O6(OH)4] · 2H2O or in synthetic Cs[B5O6(OH)4] · 2 DMSO. The Tl atom is coordinated in a distored octahedron by six O atoms with distances between 2.84 and 3.02 Å. Connections between the B – O rings are provided by the hydrogen bonding system from O atoms of the rings to OH groups and/or water molecules, thus forming a three-dimensional framework.

X-ray and neutron diffraction studies on the ferroelastic phase of Rb2Hg(CN)4

The ferroelastic low temperature phase of Rb2Hg(CN)4 is trigonal, R[unk] c , with a 1 = 907.6(2), a 3 = 4605.0(2)pm, Z = 12. The structure was solved by Patterson and Fourier methods on the basis of X-ray and neutron diffraction data (906 and 665 independent reflections, resp.) The least-squares refinement yielded Rw -values of 0.046 and 0.048, resp. The structure deviates only slightly from that of the cubic high temperature spinel phase. The Hg(CN)4 tetrahedra exhibit an alternating twist around the trigonal axis of about 10.6°. Both rubidium positions are nearly octahedrally surrounded by CN groups. The ferroelastic behaviour is connected with a high librational mobility of the Hg(CN)4 tetrahedra.

Structure of calcium dizinc hexabromide hexahydrate Ca(H2O)6Zn2Br6

[Ca(H2O)6] [Zn2Br6], Mr = 758.36, monoclinic, C2/m, a = 13.276(6), b = 10.665(3), c = 13.785(7) Å, β = 113.30(3)°, V = 1792.2(12) Å3, Z = 4, Dx = 2.81 Mg m−3, MoKα radiation, λ = 0.71069 Å, μ = 15.99 mm−1, F(000) = 1400, room temperature, R = 0.055 (wR = 0.053) for 640 unique observed [I > 3σ(I)] reflections. The structure consists of independent octahedral Ca(H2O)6 2+ complexes (〈Ca–O〉 = 2.32 Å) and dimeric tetrahedral Zn2Br6 2− complexes [〈Zn–Br〉 = 2.48 (bridging) and 2.35 Å (terminal)] linked together by O–H…Br hydrogen bonds. The structure is related to those of MgZn2Br6 · 6H2O and ZnBr2 · 2H2O but the packing of the complex ions (and, hence, the hydrogen bonding) is different.

Die Kristallstruktur von Zinkformiat-Dihydrat

Zinc formate cristallizes isomorphous to the formates of Mg, Sr, Cd, Mn and Ni in the monoclinic space group P21/c. The lattice constants are a = 8.685 Å, b = 7.160 Å, c = 9.323 Å and β = 97.58°.

The structure has been refined including an isotropic extinction correction to RF = 0.043.

The octahedra of the two nonequivalent zinc atoms are slightly distorted. Zn(l) in (000) is surrounded by six oxygen atoms of the formate groups [distances Zn(l)–O = 2.071 Å–2.145 Å]; the octahedron of Zn(2) in (½½0) consists of the oxygen atoms of the two formate groups and two water molecules [distances Zn(2)–O = 2.053 Å–2.165 Å].

The three-dimensional structure is stabilized by hydrogen bonding between formate groups and water molecules.

Na3/4(NH4)1/4ZnPO4, a new framework zincophosphate. Survey of MZnPO4 tetrahedral topologies

The synthesis and single crystal structure of Na3/4(NH4)1/4ZnPO4, a new sodium-ammonium zinc phosphate, are reported. This phase adopts a previously unseen tetrahedral topology and is built up from a three-dimensional network of ZnO4 [dav(Zn-O) = 1.952 (2) Å] and PO4 [dav(P-O) = 1.538 (2) Å] units, fused together via Zn-O-P links [θav = 125.1 (1)°]. Extra-framework Na+ and NH4 + cations complete the crystal structure. The tetrahedral topology of this phase may be described as being built up from 63 hexagonal sheets containing two types (SSCSSC and SSSCSC) of six-rings arrayed normal to [100]. The crystal structures of related MZnPO4 type phases (M = univalent cation) are reviewed. Crystal data: Na3/4(NH4)1/4ZnPO4, Mr = 364.23, orthorhombic, space group Pbcn (No. 60), a = 8.251 (2) Å, b = 10.371 (3) Å, c = 17.430 (4) Å, V = 1491.4 (6) Å3, Z = 16, R = 2.71%, Rw = 2.56% [133 parameters, 1585 observed reflections with I > 3σ(I)].

New and versatile routes to zirconium imido dichloride compounds

Reactions of zirconium dialkyl- or bis(amido)-dichloride complexes "[Zr(CH2SiMe3)2Cl2(Et2O)2]" or [Zr(NMe2)2Cl2(THF)2] with primary alkyl and aryl amines are described. Reaction of "[Zr(CH2SiMe3)2Cl2(Et2O)2]" with RNH2 in THF afforded dimeric [Zr2(mu-NR)2Cl4(THF)4](R=2,6-C6H3iPr2 (1), 2,6-C6H3Me2 (2) or Ph (3)), [Zr2(mu-NR)2Cl4(THF)3](R=tBu (5), iPr (6), CH2Ph (7)), or the "ate" complex [Zr2(mu-NC6F5)2Cl6(THF)2{Li(THF)3}2](4, the LiCl coming from the in situ prepared "[Zr(CH2SiMe3)2Cl2(Et2O)2]"). With [Zr(NMe2)2Cl2(THF)2] the compounds [Zr2(mu-NR)2Cl4(L)x(L')y](R=2,6-C6H3iPr2 (8), 2,6-C6H3Me2 (9), Ph (10) or C6F5 (11); (L)x(L')y=(NHMe2)3(THF), (NHMe2)2(THF)2 or undefined), [Zr2(mu-NtBu)2Cl4(NHMe2)3] (12) and insoluble [Zr(NR)Cl2(NHMe2)]x(R=iPr (13) or CH2Ph (14)) were obtained. Attempts to form monomeric terminal imido compounds by reaction of or with an excess of pyridine led, respectively, to the corresponding dimeric adducts [Zr2(mu-2,6-C6H3Me2)2Cl4(py)4] (15) and [Zr2(mu-NtBu)2Cl4(py)3] (16). The X-ray structures of 1, 2, 4, 8, 12 and 15 have been determined.

Group 6 imido complexes supported by diamido-donor ligands

Reactions of the lithiated diamido-pyridine or diamido-amine ligands Li(2)N(2)N(py) or Li(2)N(2)N(am) with [W(NAr)Cl(4)(THF)] (Ar = Ph or 2,6-C(6)H(3)Me(2); THF = tetrahydrofuran) afforded the corresponding imido-dichloride complexes [W(NAr)(N(2)N(py))Cl(2)] (R = Ph, 1, or 2,6-C(6)H(3)Me(2), 2) or [W(NAr)(N(2)N(am))Cl(2)] (R = Ph, 3, or 2,6-C(6)H(3)Me(2), 4), respectively, where N(2)N(py) = MeC(2-C(5)H(4)N)(CH(2)NSiMe(3))(2) and N(2)N(am) = Me(3)SiN(CH(2)CH(2)NSiMe(3))(2). Subsequent reactions of 1 with MeMgBr or PhMgCl afforded the dimethyl or diphenyl complexes [W(NPh)(N(2)N(py))R(2)] (R = Me, 5, or Ph, 6), respectively, which have both been characterized by single crystal X-ray diffraction. Reactions of Li(2)N(2)N(py) or Li(2)N(2)N(am) with [Mo(NR)(2)Cl(2)(DME)] (R = (t)Bu or Ph; DME = 1,2-dimethoxyethane) afforded the corresponding bis(imido) complexes [Mo(NR)(2)(N(2)N(py))] (R = (t)Bu, 7, or Ph, 8) and [Mo(N(t)Bu)(2)(N(2)N(am))] (9).

New diamide-diamine ligands and their zirconium and hafnium dichloride and bis(dimethylamide) complexes

The multigram syntheses of the protio ligands (2-NC(5)H(4))CH(2)N(CH(2)CH(2)NHSiMe(2)R)(2) (R = Me, H(2)N(2)NN' 3; R = (t)Bu, H(2)N(2)NN() 4) are described via reactions of the previously reported (2-NC(5)H(4))CH(2)N(CH(2)CH(2)NH(2))(2) (1). A new synthesis of 1 is reported starting from 2-aminomethylpyridine and N-tosylaziridine, proceeding via (2-NC(5)H(4))CH(2)N(CH(2)CH(2)NHTs)(2) (2). Reaction of H(2)N(2)NN' or H(2)N(2)NN* with (n)BuLi gives good yields of the dilithiated derivatives Li(2)N(2)NN' and Li(2)N(2)NN*. Reaction of H(2)N(2)NN' or H(2)N(2)NN* with [MCl(2)(CH(2)SiMe(3))(2)(Et(2)O)(2)] gives the cis-dichloride complexes [MCl(2)(L)] (L = N(2)NN', M = Zr 7 or Hf 8; L = N(2)NN(), M = Zr 9). The corresponding reactions of H(2)N(2)NN' or H(2)N(2)NN* with [Zr(NMe(2))(4)] afford the bis(dimethylamide) derivatives [Zr(NMe(2))(2)(L)] (L = N(2)NN' 10 or N(2)NN* 11). All of these protonolysis reactions proceed smoothly and in good yields. Attempts to prepare the titanium complexes [Ti(X)(2)(N(2)NN')] (X = Cl or NMe(2)) were unsuccessful. The X-ray crystal structures of (2-NC(5)H(4))CH(2)N(CH(2)CH(2)NHTs)(2).EtOH, [ZrCl(2)(N(2)NN')].0.5C(6)H(6), [Zr(NMe(2))(2)(N(2)NN')], and [Zr(NMe(2))(2)(N(2)NN*)] are reported.

Eight-membered-ring solid-state conformational interconversion via the atom-flip mechanism, a CPMAS 13C NMR and crystallographic stereochemical study

Nefopam methohalide (chloride, bromide, and iodide) medium-ring quaternary ammonium salts of the non-narcotic analgesic tertiary amine drug give crystals belonging to the identical monoclinic P2(1)/c space group, and all of these pseudopolymorphs exhibit the same packing motif. A singular boat-boat (BB) more compact conformation is observed in the nefopam methochloride crystal. Larger halide anions (bromide and iodide) increase the void distance between the 2(1)-screw axis related adjacent ammonium cations to accommodate void-size dependent equilibrium quantities of the twist-chair-chair (TCC) more extended conformation. The BB:TCC occupancy factors are 0.961(5):0.039(5) [193 K], 0.780(5):0.220(5) [293 K], and 0.755(6):0.245(6) [343 K] for the methobromide crystal, while values of 0.657(5):0.343(5) [193 K] and 0.592(7):0.408(7) [293 K] were measured for the methiodide. Above a minimum of ca. 2.53 A, the occupancy factors were found to be linearly correlated to the intermolecular (TCC)Me(eq)-H...H-Me(ax)(TCC) distance between abutting methyl group protons in 2(1)-screw axis related neighbors. Temperature-dependent occupancy factors for the two conformers are interpreted in terms of a medium ring atom-flip facile interconversion between the two low energy conformations in crystals containing the appropriate size intercation void. A BB/TCC atom-flip interconversion in the methochloride unit cell would result in van der Waals interactions due to an estimated 2.31 A close intermolecular (TCC)Me(eq)-H...H-Me(ax)(TCC) distance between adjacent 2(1)-screw symmetry ammonium cations. The 203 K low-temperature CPMAS 13C NMR spectrum of the methiodide salt showed two slow exchange limit (SEL) delta 57.91 [BB] and delta 63.10 [TCC] OCH2CH2N peaks. A variable low-temperature CPMAS NMR investigation of the solid methiodide showed complex dynamic behavior that cannot be interpreted solely on the basis of an atom-flip conformational interconversion. Local magnetic fields from the gem-dimethyl rapidly rotating proton magnetic dipoles provide a distance-dependent T1 relaxation mechanism for neighboring carbons in the solid-state.

Structure-activity relationships of acyloxyamidine cytomegalovirus DNA polymerase inhibitors

This paper describes the structure activity relationships of a new class of cytomegalovirus DNA polymerase inhibitors having two aryl groups joined by an acyloxyamidine linker. Examination of a series of analogues in which the terminal groups are varied revealed a very narrow SAR around the 2,4-dichlorophenyl group of the lead compound, but a variety of replacements for the benzothiazole ring are compatible with activity. The most notable of these is the isoxazole ring of compound 78, which provides a 30-fold enhancement in potency compared to the lead compound. We also describe the design, synthesis and evaluation of 10 analogues in which the acyloxyamidine linker is modified or replaced by an isosteric group. Structure-activity relationship studies identified the linker -NH2 group as a critical pharmacophoric element. Ab initio molecular orbital calculations combined with qualitative estimates of steric interaction energies suggest that the lowest energy conformations of the acyloxyamidine linker are characterized by an extended planar CAr-C=N-O-C arrangement and either a syn-periplanar or anti-periplanar N-O-C-C(Ar') arrangement. Only the anti-periplanar conformation was observed in the crystal structures of three acyloxyamidines. The most active of the linker-modified compounds designed on the basis of these studies is the amidine carbamate 20, which is approximately one-third as potent in the cytomegalovirus DNA polymerase inhibition assay as the comparator acyloxyamidine 53. The activity of 20 suggests that acyloxyamidines may bind to the cytomegalovirus DNA polymerase via an anti-periplanar conformation similar to that observed in the crystal structure of acyloxyamidine 36.

Titanium Imido Complexes with Tetradentate Schiff Base Ligands

New mono- and binuclear titanium imido complexes supported by tetradentate, dianionic N(2)O(2)-donor Schiff base ligands were prepared in good yield from the readily available [Ti(NBu(t))Cl(2)(py)(3)] (1a). Thus treatment of 1a with Na(2)[substituted-salen] gave monomeric [Ti(NBu(t))(substituted-salen)] where substituted-salen = Et(2)salen (2) or Bu(t)(4)salen (4). In contrast, the binuclear complex [Ti(NBu(t)){&mgr;-(MeO)(2)salen}](2) (5) was obtained from 1a and Na(2)[(MeO)(2)salen]. The less sterically crowded compounds 2 and 5 undergo tert-butyl imide/arylamine exchange reactions to form [Ti(N-2,6-C(6)H(3)Me(2))(Et(2)salen)] (3) and [Ti(N-2,6-C(6)H(3)Me(2)){&mgr;-(MeO)(2)salen}](2) (6), respectively, whereas 4 does not exhibit this kind of reactivity. The compound 3 can also be obtained directly from Na(2)[Et(2)salen] and [Ti(N-2,6-C(6)H(3)Me(2))Cl(2)(py)(3)] (1b). Crystal data for 3: triclinic, P&onemacr;, a = 12.216(4) Å, b = 12.312(11) Å, c = 17.246(2) Å, alpha = 90.352(12) degrees, beta = 102.59(2) degrees, gamma = 104.96(2) degrees, V = 2440.3(8) Å(3), Z = 4, R = 0.051, R(w) = 0.066 for 7011 data with I > 2sigma(I). Crystal data for 5.CH(2)()Cl(2)(): orthorhombic, Pbca, a = 14.747(4) Å, b = 17.042(4) Å, c = 20.545(3) Å, V = 5163.5(13) Å(3), Z = 4, R(1) = 0.096, wR(2) = 0.086 for 3765 data with I > 2sigma(I). Crystal data for 6: monoclinic, C2/c, a = 17.902(5) Å, b = 12.411(4) Å, c = 21.068(5) Å, beta = 90.27(2) degrees, V = 4681(2) Å(3), Z = 4, R = 0.034, R(w)() = 0.039 for 3633 data with I > 2sigma(I).