Nonequivalent Atoms Research Articles

Crystal structure of catena-(2-thiobarbiturato) dithallium(I)

By powder X-ray diffraction the crystal structure of catena-(2-thiobarbiturato)dithallium(I) C4H2N2O2STl2 (C4H4N2O2S is 2-thiobarbituric acid, H2TBA), Tl2TBA, is determined. Crystallographic data for Tl2TBA are as follows: a = 15.1039(3) A, b = 12.0818(2) A, c = 3.86455(6) A, β = 97.203(1)°, V = 741.34(2) A3, space group P21/n, Z = 4. There are two non-equivalent thallium atoms in the structure. The Tl1 polyhedron is a distorted trigonal prism due to the shortened Tl-S contact (3.634 A), and the Tl2 polyhedron is a distorted square antiprism.

Single-crystal diffraction at megabar conditions by synchrotron radiation

Crystal structure determination at extreme pressures is currently possible at synchrotron beamlines optimized for such a purpose. We report the description of the experimental setup available at European Synchrotron Radiation Facility ID09 beamline (Grenoble, France) and, with two examples, we illustrate the state-of-the-art experiments currently performed at third-generation synchrotrons. The first example concerns the determination of the equation of state and the structural behavior of low-spin Fe-bearing siderite in the megabar pressure range. Siderite, in fact, undergoes a first-order isosymmetric transition at 45 GPa, and, above this pressure, it features Fe2+ in electronic low-spin configuration. The local configuration of Fe coordination polyhedra, determined by structural refinements, significantly deviates from a regular octahedron. Nevertheless, no further structural transition is detected up to the maximum pressure reached in our experiments, 135 GPa. The analysis of the Fe–O bond length extrapolated to ambient pressure, which indicates that the difference in ionic radii between the high- and the low-spin state of Fe2+ is 0.172 Å, in excellent agreement with the tabulated data by Shannon and Prewitt [Effective ionic radii in oxides and fluorides. Acta Crystallogr. 1969;B25:925–946]. The second example concerns the determination and refinement of the oP8 structure adopted by sodium in the pressure interval 118–125 GPa, using an experimental dataset collected at 118 GPa. The orthorhombic [a=4.7687(15) Å, b=3.0150(6) Å, c=5.2423(7) Å, V=75.4(3) Å3] oP8 structure is topologically related to the MnP structure, with two non-equivalent atoms in the unit cell. Despite the weak scattering factor of Na atoms, the quality of the data also allows meaningful displacement parameters refinements (R1=4.6%, 14 parameters, 190 diffractions, and 105 unique) demonstrating that the current accuracy of diffraction data at extreme pressures can be comparable with ambient condition measurements.

Correlation of electronic structure and magnetic moment in Fe16N2: First-principles calculations

The structural and magnetic properties of Fe 16 N 2 have been investigated with the help of the GGA+U method. Calculations of the magnetic properties of Fe 16 N 2 indicate that the average magnetic moment of Fe atoms increases in line with the electron correlation effects in Fe 16 N 2 . The differences of magnetic moments for non-equivalent Fe atoms in Fe 16 N 2 mainly result from interstitial N atoms, different degrees of hybridization between non-equivalent Fe atoms and N atoms, and interaction among different d electron orbits of non-equivalent Fe atoms.

Crystal structure and magnetic properties of a new heterometallic complex of Pd(II)-Cu(II) with 1-aminoethylidene-1,1-diphosphonic acid

A heterometallic complex of Pd(II)-Cu(II) with 1-aminoethylidene-1,1-diphosphonic (AEDP) acid (C4H22CuN2O16P4Pd) n (I) is synthesized. Single crystals of compound I are obtained; its crystal structure is determined by X-ray crystallography. The crystals are orthorhombic, space group Pbcn, a = 18.366(3) A, b = 9.7661(17) A, c = 20.198(4) A, V = 3622.8(11) A3, Z = 8, d x = 2.376 g/cm3. The compound crystallizes as a coordination polymer; the square environment of Pd(II) is formed by nitrogen atoms of amino groups and oxygen atoms of phosphonic groups, while at two non-equivalent copper atoms the octahedral environment is formed by oxygen atoms of phosphonic groups and water molecules. The crystal structure of compound I is characterized by the formation of a branched network of hydrogen bonds. Based on the analysis of the temperature dependence of the magnetic susceptibility it is found that for the heterometallic complex of Pd(II)-Cu(II) with AEDP antiferromagnetic interactions between the paramagnetic centers are dominant.

Bobmeyerite, a new mineral from Tiger, Arizona, USA, structurally related to cerchiaraite and ashburtonite

AbstractBobmeyerite, Pb4(Al3Cu)(Si4 O12)(S0.5Si0.5O4)(OH)7 Cl(H2O)3, is a new mineral from the Mammoth - Saint Anthony mine, Tiger, Pinal County, Arizona, USA. It occurs in an oxidation zone assemblage attributed to progressive alteration and crystallization in a closed system. Other minerals in this assemblage include atacamite, caledonite, cerussite, connellite, diaboleite, fluorite, georgerobinsonite, hematite, leadhillite, matlockite, murdochite, phosgenite, pinalite, quartz, wulfenite and yedlinite. Bobmeyerite occurs as colourless to white or cream-coloured needles, up to 300 m m in length, that taper to sharp points. The streak is white and the lustre is adamantine, dull or silky. Bobmeyerite is not fluorescent. The hardness could not be determined, the tenacity is brittle and no cleavage was observed. The calculated density is 4.381 g cm-3. Bobmeyerite is biaxial (-) with α ≈ β = 1.759(2), γ = 1.756(2) (white light), it is not pleochroic; the orientation is X = c; Y or Z = a or b. Electron-microprobe analyses provided the empirical formula Pb3.80Ca0.04Al3.04Cu2+0.96Cr3+0.13Si4.40S0.58O24.43Cl1.05F0.52H11.83. Bobmeyerite is orthorhombic (pseudotetragonal), Pnnm with unit-cell parameters a = 13.969(9), b = 14.243(10), c = 5.893(4) Å, V = 1172.5(1.4) Å3 and Z = 2. The nine strongest lines in the X-ray powder diffraction pattern, listed as [dobs (Å)(I)(hkl)], are as follows: 10.051(35)(110); 5.474(54)(011,101); 5.011(35)(220); 4.333(43)(121,211); 3.545(34)(040,400); 3.278(77)(330,231,321); 2.9656(88)(141,002,411); 2.5485(93)(051,222,501); 1.873(39)(multiple). Bobmeyerite has the same structural framework as cerchiaraite and ashburtonite. In the structure, which refined to R1 = 0.079 for 1057 reflections with F > 4σF, SiO4 tetrahedra share corners to form four-membered Si4O12 rings centred on the c axis. The rings are linked by chains of edge-sharing AlO6 octahedra running parallel to [001]. The framework thereby created contains large channels, running parallel to [001]. The Cl site is centred on the c axis alternating along [001] with the Si4O12 rings. Two non-equivalent Pb atoms are positioned around the periphery of the channels. Both are elevencoordinate, bonding to the Cl atom on the c axis, to eight O atoms in the framework and to two O (H2O) sites in the channel. The Pb atoms are off-centre in these coordinations, as is typical of Pb2+ with stereo-active lone-electron pairs. A (S, Si, Cr)O4 group is presumed to be disordered in the channel. The name honours Robert (Bob) Owen Meyer, one of the discoverers of the new mineral.

The effect of arsenic vacancies on the electronic and magnetic properties of LaFeAs1−xO

By means of the first principles calculations, the influence of arsenic deficiency on the electronic and magnetic properties of the layered phase LaFeAsO was examined. We found that As vacancies affect mainly the near-Fermi Fe-derived bands leading to their splitting and changing their dispersion and the level of filling. The Fermi surface for LaFeAs1−xO adopts a complicated multi-sheet morphology, with a number of linked 2D-like sheets and a set of new sheets (which are absent for ideal LaFeAsO) at the lateral sides of the Brillouin zone. Besides, for the most stable As-deficient phase an antiferromagnetic stripe-like spin configuration was found, for which an inhomogeneous distribution of magnetic moments of Fe atoms arises near and away from vacancy owing to differences in local magnetic moments of non-equivalent Fe atoms.

Spin Density and Cluster Dynamics in Sc3N@C80– upon [5,6] Exohedral Functionalization: An ESR and DFT Study

A radical-anion of [5,6]-pyrrolidine-Sc3N@C80 is generated both chemically and electrochemically and studied by ESR spectroscopy. The rotation of the Sc3N cluster is shown to be frozen on the ESR time scale resulting in nonequivalent Sc atoms with hyperfine coupling constants noticeably smaller than in the radical anion of the pristine Sc3N@C80 but larger than in any other derivatives of Sc3N@C80. Experimental ESR studies are supported by extended DFT calculations of the cluster rotational pathways, spin density distribution, and hyperfine coupling constants.

Single Crystal X-Ray Diffraction Studies on Magnetic Yb<sub>5</sub>Co<sub>4</sub>Ge<sub>10</sub>

The high quality single crystals of Yb5Co4Ge10 have been grown by the indium metal flux method and characterized by means of single crystal X-ray diffraction data. Yb5Co4Ge10 crystallizes in the Sc5Co4Si10 structure type, tetragonal space group P4/mbm and lattice constants are a = b = 12.6369(18) ? and c = 4.1378(8) ?. Crystal structure of Yb5Co4Ge10 composed of three-dimensional [Co4Ge12] network having five, six and eight membered rings. The three non-equivalent Yb atoms are sandwiched in three different channels created by the [Co4Ge12] network. Based on the bond length analysis from the crystallographic information, we confirmed that Yb1 and Yb2 atoms are in the trivalent magnetic state and Yb3 is in the divalent non-magnetic state.

Non-local Effects on Oxygen-Induced Surface Core Level Shifts of Re(0001)

The electronic structure of clean and oxygen-covered Re(0001) was investigated by combining high energy resolution core level photoelectron spectroscopy and density functional theory. For the clean surface, we detect two distinct Re 4f7/2 components shifted by 95 meV, which we ascribe to photoemission from the bulk and the top layer of the crystal. Oxygen adsorption at room temperature leads to the appearance of new core level components, which we associate to non-equivalent Re atoms from the topmost layer. In addition to the linear relationship between oxygen-induced core level shifts and number of O–Re bonds, we find that the binding energy shift also depends on the number of oxygen atoms at second and third nearest neighbor positions. This non-local effect is discussed in terms of 5d band center shift and of charge transfer between the metallic substrate and the O atoms.

Preparation, Structure, and Optical Properties of the 1D Chain Red Luminescent Europium Coordination Polymer: {[Eu2L6(DMF)­(H2O)]·2DMF·H2O}n(L = C9H6ClO2–)

AbstractThe 1D chain red luminescent europium coordination polymer: {[Eu2L6(DMF)(H2O)]·2DMF·H2O}n(I) (L = 4‐chloro‐cinnamic acid anion, C9H6ClO2–, DMF =N, N‐dimethylformamide) was synthesized by the reaction of Eu(OH)3and 4‐chloro‐cinnamic acid ligand. The structure of the coordination polymer was determined by single‐crystal X‐ray diffraction analysis. It reveals that there exists two crystallographically nonequivalent europium atoms in each unit of this coordination polymer and Eu3+ions are connected by two alternating bridging modes to form an endless polymer structure. The luminescent properties and energy transfer process in the complex are investigated at room temperature.

Supramolecular Hybrid Bidentate Ligands in Asymmetric Hydrogenation

AbstractIn this study we introduce a novel class of supramolecular bidentate hybrid ligands and their application in the rhodium‐catalysed asymmetric hydrogenation of prochiral olefins. A new supramolecular strategy is reported in which the two nonequivalent phosphorus atoms are linked covalently to a chiral scaffold, and the supramolecular interactions are used to control the second coordination sphere of the transition‐metal catalyst. The supramolecular assembly is formed in situ by selective interaction between the nitrogen‐donor atoms and the zinc(II) template, which is essential for obtaining high activity and selectivity. The investigations of the different zinc(II) and ruthenium(II) templates on the reaction parameters revealed a dependence of the activity and selectivity on the association constant between the supramolecular template and the pyridyl ligands. The scope of the supramolecular assemblies was explored in the Rh‐catalysed asymmetric hydrogenation of α‐dehydroamino acid esters and Roche ester derivatives. High activities and good to excellent enantioselectivities up to 99 % ee were obtained with the supramolecular ligands. Application of the supramolecular strategy on the basis of variations of the steric and electronic properties of zinc(II) templates demonstrate that these changes can influence key reaction parameters such as activity and selectivity.

Dynamic heterogeneity in the glass-like monoclinic phases of CBrnCl4−n, n = 0,1,2

Glassy dynamics of rigid molecules is still a matter of controversy: the physics behind the relaxation process at time scales faster than that ruled by the viscosity, the so called Johari-Goldstein process, is not known. In this work we unravel the mechanism of such a process by using a simple molecular model in which the centers of mass of the molecules are forming an ordered lattice, and molecular reorientation is performed by jumps between equilibrium orientations. We have studied the dynamics of simple quasi-tetrahedral molecules CBr(n)Cl(4-n), n = 0, 1, 2, in their monoclinic phases by means of dielectric spectroscopy and nuclear quadrupole resonance: the first technique allows to measure in a broad time scale but it is insensitive to molecular particularities, while the second has a restricted time window but senses the movement of each chlorine atom separately. The dynamic picture emerging from these techniques is that the secondary relaxation process is related to the different molecular surroundings around each nonequivalent atom of the molecule. Dynamical heterogeneities thus seem to be the cause of the secondary relaxation in this simple model of glass.

Solid-State Methylamine VUV Irradiation Study Using Carbon Monoxide as an H Radical Scavenger

Solid-phase methylamine (CH3NH2) was vacuum ultraviolet (VUV) photoprocessed at low temperature (20 K) using a hydrogen flow discharge lamp, which allows irradiation down to 120 nm. Methanimine (CH2=NH), the methylammonium cation (CH3NH3+) and the counterion CN–, as well as the amino radical (NH2), methane (CH4) and ammonia (NH3), were identified as the photoproducts by using FTIR spectroscopy. So far, the branching ratios of the photodissociation pathways of methylamine in the solid phase remain unknown. The methylamine molecule holds two non-equivalent hydrogen atoms on the methyl and the amino group, so we can expect the formation of two distinct radicals via a carbon–hydrogen or a nitrogen–hydrogen bond cleavage, namely CH2NH2 and CH3NH. These radicals are highly reactive and may reform methylamine with hydrogen atom recombination. Their direct infrared spectroscopic detection is therefore tricky. To solve that problem, we use carbon monoxide (CO) as an H radical scavenger, forming the intermediate species HCO. After the irradiation of a CH3NH2 : CO binary ice mixture, formamide (NH2CHO) and N-methylformamide (CH3NHCHO) were identified as the main photoproducts using both infrared and mass spectrometry. We give a rough approximation of the branching ratios, which are in agreement with previous studies in the gas phase.

Diorganotin(IV) complexes of N-mono-, di- and tri-chloroacetyl, N′, N″-bis(isopropyl) phosphoric triamide

Three new carbacylamidophosphates with formula CH n Cl 3− n C(O)NHP(O)(NHCH(CH 3) 2) 2 ( n = 2 ( 1); n = 1 ( 2); n = 0 ( 3)) and their organotin compounds with formula (1)SnCl 2Me 2(μ- 1)SnCl 2Me 2 ( 4), SnCl 2Me 2( 2) 2·C 6H 5CH 3 ( 5) and [SnCl 2Me 2( 3)] n ( 6) were synthesized and characterized by elemental, IR and NMR spectra analyses. The spectroscopic properties of complexes were compared with those corresponding ligands. The crystal structures of complexes were determined by X-ray crystallography, which reveals that complex 4 is binuclear structure with two non-equivalent Sn atoms. One adopts a distorted trans(C,C) cis(O P,O P) cis(Cl,Cl) octahedral configuration, while the other adopts a distorted trigonal bipyramidal geometry composed of two methyl groups, two chlorine atoms and carbonyl group. Molecule 5 is centrosymmetric with two O P, disordered chlorine and methyl groups in trans positions. Toluene molecules are located in the interlayer spaces of 5. In compound 6, bonding via both PO and CO functionalities forms 1D infinite chain structures along b axis. The Sn–O P bond length in 6 is significantly longer than the same distance in 4 and 5, while the O P and Sn–Cl bonds are shorter. The bond lengths in these complexes were compared with those of N-benzoyl carbacylamidophosphates.

Nuclear quadrupole resonance of norephedrine

Toward searching for illegal drugs, we investigated the pulsed nuclear quadrupole resonance (NQR) response of 14N in (1R,2S)-(-)-norephedrine, based on the predictions of quantum chemical calculations. Two pairs of spectral lines ( ν +=3.089, 3.093 MHz and ν −=2.594, 2.608 MHz) were observed despite its molecule structure having only a single nitrogen atom. This indicates that the molecular crystal has two nonequivalent nitrogen atoms in the unit cell. The temperature dependence of the NQR frequencies and relaxation properties were investigated for the purpose of accurate remote sensing of the drugs. The NQR frequency shift was approximately 0.23 kHz/K around room temperature. The spin-lattice relaxation and spin-phase memory times were 5.2–10.2 ms and 0.6–1.5 ms, respectively.

Zeeman shift – A tool for assignment of 14N NQR lines of nonequivalent 14N atoms in powder samples

The use of Zeeman perturbed 14N nuclear quadrupole resonance (NQR) to determine the ν + and ν − 14N lines in polycrystalline samples with several nonequivalent nitrogen atoms was investigated. The 14N NQR line shift due to a weak external Zeeman magnetic field was calculated, assuming isotropic distribution of EFG tensor directions. We calculated the broad line distribution of the ν + and ν − line shifts and experimentally confirmed the calculated Zeeman field dependence of singularities (NQR peaks) in cyclotrimethylenetrinitramine (RDX) and aminotetrazole monohydrate (ATMH). The calculated and measured frequency shifts agreed well. The proposed measurement method enabled determination of which 14N NQR lines in ATMH belong to ν + and which to ν − transitions.

Structural and vibrational properties of the van der Waals compound (N2)11He up to 135 GPa

The structural and vibrational properties of the van der Waals compound (N${}_{2}$)${}_{11}$He have been measured up to 175 GPa. The structure, as determined at 14.5 GPa using single-crystal x-ray diffraction, is hexagonal $(P{6}_{3}/m)$ with seven nonequivalent atoms: 6 N and 1 He. The ${\mathrm{N}}_{2}$ molecule centered at (0,0,0) is orientationally disordered. A close relationship with the $\ensuremath{\varepsilon}$ structure of pure solid ${\mathrm{N}}_{2}$ is observed. A phase transition to a hexagonal superstructure occurs at 28 GPa, which is attributed to the ordering of these disordered ${\mathrm{N}}_{2}$ molecules, driven by quadrupole-quadrupole interaction. A transition to an amorphous state then takes place at 135 GPa. Strong similarities in the structural evolution under pressure of the (N${}_{2}$)${}_{11}$He compound and of $\ensuremath{\varepsilon}$-N${}_{2}$ are discussed.

Sc2C2@C80 Rather than Sc2@C82: Templated Formation of Unexpected C2v(5)-C80 and Temperature-Dependent Dynamic Motion of Internal Sc2C2 Cluster

Unambiguous X-ray crystallographic results of the carbene adduct of Sc(2)C(82) reveal a new carbide cluster metallofullerene with the unexpected C(2v)(5)-C(80) cage, that is, Sc(2)C(2)@C(2v)(5)-C(80). More interestingly, DFT calculations and NMR results disclose that the dynamic motion of the internal Sc(2)C(2) cluster depends strongly on temperature. At 293 K, the cluster is fixed inside the cage with two nonequivalent Sc atoms on the mirror plane, thereby leading to C(s) symmetry of the whole molecule. However, when the temperature increases to 413 K, the (13)C and (45)Sc NMR spectra show that the cluster rotates rapidly inside the C(2v)(5)-C(80) cage, featuring two equivalent Sc atoms and weaker metal-cage interactions.

(Co-)solvent selection for single-wall carbon nanotubes: best solvents, acids, superacids and guest–host inclusion complexes

Analysis of 1-octanol-water, cyclohexane-water and chloroform (CHCl(3))-water partition coefficients P(o-ch-cf) allows calculation of molecular lipophilicity patterns, which show that for a given atom log P(o-ch-cf) is sensitive to the presence of functional groups. Program CDHI does not properly differentiate between non-equivalent atoms. The most abundant single-wall carbon nanotube (SWNT), (10,10), presents a relatively small aqueous solubility and large elementary polarizability, P(o-ch-cf) and kinetic stability. The SWNT solubility is studied in various solvents, finding a class of non-hydrogen-bonding Lewis bases with good solubility. Solvents group into three classes. The SWNTs in some organic solvents are cationic while in water/Triton X mixture are anionic. Categorized solubility is semiquantitatively correlated with solvent parameters. The coefficient of term β is positive while the ones of ε and V negative. The electron affinity of d-glucopyranoses (d-Glcp(n)) suggests the formation of colloids of anionic SWNTs in water. Dipole moment for d-Glcp(n)-linear increases with n until four in agreement with 18-fold helix. The I(n)(z-) and SWNT(-) are proposed to form inclusion complexes with cyclodextrin (CD) and amylose (Amy). Starch, d-Glcp, CD and Amy are proposed as SWNT co-solvents. Guests-hosts are unperturbed. A central channel expansion is suggested.

Synthetic, spectroscopic, and structural studies on organoimido molybdenum, tungsten, and rhenium phthalocyanines

Unprecedented imido phthalocyaninato complexes of pentavalent refractory metals [PcM(NR)Cl] (M = Mo, W, Re; R = tBu: 1, 3, 6, Mes: 2, 4, 7 or Ts: 5) have been synthesized by reductive cyclotetramerization of phthalonitrile in the presence of appropriate bis(imido) complexes of Mo, W and Re as templates. While d(1) Mo(V) and W(V) species 1-5 show distinctive EPR spectra corresponding to metal centered radicals with hyperfine coupling of two magnetically non-equivalent nitrogen atoms (4 equatorial and 1 axial N), corresponding d(2) Re(V) compounds 6 and 7 are diamagnetic. [PcMo(NtBu)Cl] 1 crystallizes from 1-chloronaphthalene in the tetragonal space group P4/n. The molecular structure reveals, that the metal center is located above the plane of the equatorial N4 and displaced towards the axial π-donor ligand. Due to the thermodynamic trans effect the Mo-Cl bond trans to the imido group is elongated to about 2.600(2) Å.