Bond Lenghts Research Articles

Bis[S-octyl 3-(2-methyl-propyl-idene)di-thio-carb-az-ato-κ2N3,S]nickel(II).

The central NiII atom in the title complex, [Ni(C13H25N2S2)2], is located on an inversion center and adopts a roughly square-planar coordination environment defined by two chelating N,S donor sets of two symmetry-related ligands in a trans configuration. The Ni-N and Ni-S bond lenghts are 1.9193 (14) and 2.1788 (5) Å, respectively, with a chelating N-Ni-S bond angle of 86.05 (4)°. These data are compared with those measured for similar di-thio-carbazato ligands that bear n-octyl or n-hexyl alkyl chains. Slight differences are observed with respect to the phenyl-ethyl-idene derivative where the ligands are bound cis relative to one another.

The crystal structure of tetrameric copper(II) complexes, Hirshfeld surface analysis, and vector analyses of Cu4OCl6L4 complexes with N-donor ligands

It is known, that in the Cu4OX6L4 (X = Cl, Br) complexes can be present many different ligands L, including bioligands. The synthesis and characterization of Cu4OBCl6(ron)4 (1) and Cu4OCl6(3-Mepy)4 (2) (where ron is ronicol or 3-methanolpyridine and 3-Mepy is 3-methylpyridine) are reported. The complexes under study were X-ray structure analysis and Hirshfeld surface analysis. Tetranuclear Cu4OX6L4 complexes with molecular structure (Fig. 1) can help to better understand the role of donor–acceptor and electron-transfer properties in copper proteins. The coordination sphere about each copper(II) atom is trigonal bipyramidal with three chlorine atoms in the equatorial plane. The apical positions are occupied by the central oxygen atom and the nitrogen atom of the respective ligand (CuCl3ON). Here are studied chloridocomplexes of some N-donor ligands, L = chloro-promazine, ronicol (3-pyridylmethanol), 2-ethylpyrazine, seven derivatives of pyrazol and for comparisons 3-methylpyridine. The Cu4OCl6L4 molecule is regarded as a supramolecular model of interactions between bioligand L and hypothetical “round-shaped” coordination tetra-receptor Cu4OCl6. Vector calculations applied usualy to mechanical and electrical macroconstructions are here applied to microconstructions represented by structures of Cu4OX6L4 molecules. For vector calculations each Cu4OX6L4 structure is placed (Fig. 1) into the three-dimensional Cartesian coordinate system with the central oxygen atom O1 placed in its origin 0. Studied bioligands are compared and described by molecular structural dynamics and corresponding shifts of electron densities by means of bond lenghts (O1–Cu, Cu–L, Cu–X) and structural distances (O1···X, O1···L).

EXPERIMENTAL AND THEORETICAL ANALYSIS OF N,N’-(ETHANE-1,2-DIYLBIS(4,1-PHENYLENE))BIS(1-(THIOPHEN-2-YL)METHANIMINE) AND N,N’-(ETHANE-1,2-DIYLBIS(4,1-PHENYLENE))BIS(1-(4-METHYLTHIOPHEN-2-YL)METHANIMINE) SCHIFF BASE LIGANDS

N,N’-(ethane-1,2-diylbis(4,1-phenylene))bis(1-(thiophen-2-yl)methanimine) and N,N’-(ethane-1,2-diylbis(4,1-phenylene))bis(1-(4-methylthiophen-2-yl) methanimine) ligands are formed by diamine and two aromatic aldehyde using Schiff base condensation method. Ligands are characterised by fourier transform infrared spectroscopy (FT-IR), 1H- and 13C- nuclear magnetic resonance spectroscopy (1H- and 13C- NMR) and mass spectroscopy (LC ESI/MS) methods. Furthermore, geometric properties such as bond lenghts, bond angles, dihedral angles, electronic properties, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies are calculated by using Gaussian 09w program. Experimental and theoretical spectrum datas are compared.

Structure of (2E)-Ethyl 2-((4-(cyanomethoxy)benzylidene)hydrazono)-3,4-dimethyl-2,3-dihydrothiazole-5-carboxylate Studied by X-ray and DFT Calculations

The molecular structure of (2E)-ethyl 2-((4-(cyanomethoxy)benzylidene)hydrazono)-3,4-dimethyl-2,3-dihydrothiazole-5-carboxylate was determined using X-ray diffraction. The crystals are triclinic: sp. gr. P1; Z = 2; the unit cell parameters a = 8.4747(7) A, b = 8.9382(8) A, c = 11.9913(10) A. The title compound has two C–H···O type intramolecular hydrogen bonds, one C–H···O and one C–H···N type intermolecular hydrogen bonds. For theoretical calculations, the molecular structure was investigated by DFT/B3LYP method with 6-311G(d) and 6-311G(d, p) basis sets. The calculated and experumental results (bond lenghts, bond angles, and dihedral angles) were compared with each other. Total energy, dipole moment, and mulliken atomic charges were calculated using two different basis sets.

X-ray and Theoretical Studies of 2-((5-Amino-1,3,4-thiadiazol-2-yl)thio)-1-phenylethanone

The crystal structure of 2-((5-amino-1,3,4-thiadiazol-2-yl)thio)-1-phenylethanone was determined by X-ray diffraction method. The compound crystallizes in orthorhombic crystal system, sp. gr. Pbca. The atoms that constitute thiadiazole and phenyl rings do not form any significant deviation from the ring planes. Compound has two intermolecular N–H···N hydrogen bonds and one C–H···π interaction. Using DFT/B3LYP method with 6-31G(d), 6-311G(d), 6-311G(d, p), and 6-311++G(d, p) basis sets, the molecular geometry of the compound was optimised. Bond lenghts, bond angles, torsion angles, dihedral angles, and HOMO–LUMO were calculated from the optimised geometry of the compound. The results obtained by X-ray diffraction method were compared with the results obtained through four different basis sets. Total energy of the molecule was calculated for four different basis sets.

Benchmark calculations of density functionals for organothiol adsorption on gold surfaces

A comparison of density functionals was carried out for systems consisting of a methanethiyl radical adsorbed on gold in different configurations. PW91, PBE, B3LYP and BLYP were tested in a periodic slab approach. Cluster calculations were carried out so as to compare the above mentioned functionals and many others with CR-CCSD (T) and MRMP2 as references. PW91 and PBE provide close results. Energy surfaces calculated by means of PW91, PBE, M06 and TPSSh are in good agreement with the references. M11 performs dissimilarly from M06, in particular it predicts slightly shorter bond lenghts. BLYP gives rather poor results. The semiempirical scheme of Grimme as parameterized in B97-d and the local response dispersion as parameterized in long range corrected BOP-LRD provide very different estimates of the dispersion energy. Unexpectedly rPBE, B3LYP and CAM-B3LYP perform alike and do not match well with the references, though application of a dispersion energy correction in the Grimme scheme, brings them in a much more favorable position.

A study on quantum chemical calculations of 3-, 4-nitrobenzaldehyde oximes

The molecular geometry, vibrational frequencies, 1H and 13C NMR chemical shifts, UV–vis spectra, HOMO–LUMO analyses, molecular elektrostatic potantials (MEPs), thermodinamic properties and atomic charges of 3- and 4-Nitrobenzaldehyde oxime (C 7H 6N 2O 3) molecules have been investigated by using Hartree–Fock (HF) and density functional theory (DFT/B3LYP) methods with the 6–311++G(d, p) basis set. The calculated optimized geometric parameters (bond lenghts and bond angles), the vibrational frequencies calculated and 13C and 1H NMR chemical shifts values for the mentioned compounds are in a very good agreement with the experimental data. Futheremore, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) have been simulated and the transition states, energy band gaps and molecular electrostatic potantial (MEP) maps for each oxime compound have been determined. Additionally, we also report the infrared intensities and Raman activities for the compounds under study.

Conformational properties of thiazyldifluoride imidosulfurdifluoride, N [tbnd]SF 2[sbnd]N [dbnd]SF 2, and thiazyldifluoride imidosulfuryldifluoride, N [tbnd]SF 2[sbnd]N [dbnd]S(O)F 2: Vibrational spectra and quantum chemical calculations

Thiazyldifluoride imidosulfurdifluoride, N SF 2 N SF 2, and thiazyldifluoride imidosulfuryldifluoride, N SF 2 N S(O)F 2 were studied by vibrational spectroscopy (FT IR (gas) and Raman (liquid)) and by quantum chemical calculations (B3LYP and MP2 with 6-31G(d) and 6-311+G(2df) basis sets). Depending on the computational method two, three or four stable conformers are predicted for N SF 2 N SF 2, whereas all methods predict the existence of four stable conformers for N SF 2 N S(O)F 2. The most stable conformer of both compounds possesses cis–syn structure ( cis configuration of the N S N S skeleton and syn orientation of the terminal SF 2 and S(O)F 2 groups relative to the N S single bond). The experimental vibrational spectra were assigned on the basis of reported data for analogous compounds and calculated wavenumbers for the most stable conformers. The NS triple, double and single bond lenghts are discussed and compared to such bonds in other compounds.

Crystal Structure of N-Benzoyl-N',N"-bis(2-ethylhexyl)phosphoric triamide

N-Benzoyl-N′,N″-bis(2-ethylhexyl)phosphoric triamide crystallizes in the triclinic space group P1 with a = 9.9333(16)A b = 10.5356(17)A c = 12.343(2)A α = 77.34(0)° β = 85.68(0)° γ = 85.09(0)° and Z = 2. The crystal structure indicates disorder in two amine groups that are connected to a phosphor atom. The molecule is obtained in the form of a one-dimensional polymer via intermolecular N-H…O hydrogen bonds. The environment of the three nitrogen atoms is planar, and the P-N bond lenghts are significantly shorter than the P-N single bond.

Crystal and molecular structures of some tri-aryltin isothiocyanates (Ar 3SnNCS; Ar = C 6H 5, p-CH 3C 6H 4, o-CH 3C 6H 4, o-CH 3OC 6H 4) and of the adduct hexamethylphosphoamide ( N-thiocyanato) tris ( o-tolyl) tin

Full crystal structures are reported for several tri-aryltin isothiocyanates. Ar 3SnNCS [Ar  Ph (A), p-Tol ( B), o-Tol (C), o-CH 3OC 6H 4 ( D)], as well for the adduct ( o-Tol) 3SnNCS·HMPA (E) (HMPA = hexamethylphosphoramide). Compound B like A has bridging thiocyanates with five-coordinate tin but C and D are the first accurately characterised monomeric Ar 3SnNCS, with four-coordinate tin. The adduct has unambiguously five-coordinate tin even with the ortho-methyls present. The small but significant changes in thiocynate bond lenghts correlate with changes in the geometry at tin, and these changes confirm that ν(CN) values do indeed accurately monitor trends in modes of thiocynate bonding when involving coordination to the same type of Lewis acid environment.

2-(Diphenylphosphino)pyridine (dppy) as monodentate or bridging ligand in homoleptic silver(I) complexes. Crystal structures of [Ag( η1-dppy) 4][ClO 4] and [Ag 2( η1-dppy)( μ-dppy) 2][ClO 4] 2

The silver( I) homoleptic complexes [Ag 2(dppy) n ](ClO 4) 2 n = 2 for 1 or 3 for 2) and [Ag(dppy) n ]ClO ( n = 3 for 3 or 4 for 4) [dppy = 2-(diphenylphosphino) pyridine] have been isolated in the solid state and characterised in solution by means of variable-temperature 31P NMR spectroscopy. Both dinuclear species 1 and 2 possess an 8-membered annular core structure with two ligands bridging head-to-tail the metal ions, while in the mononuclear derivatives all dppy ligands act as P-bound monodentate. Treatment of 1 with increasing amounts of dppy revealed (by 31P NMR spectroscopy) that complexes 2, 3 and 4 are formed in a stepwise manner. Surprisingly, no stable single complex is formed when the dppy/Ag(I) ratio is 2. A mixture of complexes 2, 3 and 4, along with unidentified products, is conversely present in solution. The solid state structures of complexes 2 and 4 have been determined by single-crystal X-ray diffraction. In 2 the Ag(I) centres posses different environments, one metal ion being two-coordinated (NP donor set) and the other being three-coordinated (NP 2 donor set). The cations of 4 present the metal bound to four dppy ligands in a slightly distorted tetrahedral environment. Of the two crystallographically independent cations, one showsthe axial Ag-P bond lenght shorter (2.566(8) Å) than the value for the off-axis Ag bonds (2.624(5) Å).

X-ray absorption study of potential barrier effect in group 14 tetrachlorides (GeCl 4, SnCl 4) and group 15 trichlorides (PCl 3, AsCl 3)

Inner-shell excitation spectra of GeCl 4, SnCl 4, PCl 3 and AsCl 3 were obtained in gas phase at room temperature with a total ion-yield technique at the LURE Super ACO and DCI storage rings in Orsay. The inner-shell excitation spectra include Ge 2p, Sn 2p, P 1s, As 2p, and Cl 1s in GeCl 4, SnCl 4, PCl 3 and AsCl 3, respectively, and are interpreted in the framework of the potential barrier concept, according to electric dipole selection rules. The well-resolved below-edge features in the metal 2p excitation spectra of GeCl 4 and SnCl 4 show a similar shape. Moreover, complementary experimental results of ETS with the support of MS-X α calculations are reported and correlated with the C 1s, Si 2p, Ge 2p and Sn 2p term values of the lowest vacant orbitals for CCl 4, SiCl 4, GeCl 4 and SnCl 4, respectively, in order to study the trend of the stabilization energy of the various empty orbitals in the neutral and in the core ionized molecules. The P 1s spectrum of PCl 3 has been assigned and the As 2p spectrum of AsCl 3 compared with the published P 2p spectrum of PCl 3. The 1s excitation spectra of the chlorine ligand in the tetrachloride (GeCl 4, SnCl 4 and trichloride (PCl 3, AsCl 3) series are very sensitive to the change of symmetry and bonding. A linear correlation between (MCl) bond lenght (with M  Ge, Sn, P, As) and the energy of the Cl 1 s → σ ∗ (MCl) shape resonance observed above the Cl is ionization threshold has been obtained.

Square planar nickel compounds with bulky thiols

Details of the syntheses and the results of X-ray structural analyses of square planar Ni compounds with aliphatic thiolato-sulfur ligands, [Ni(dpmep) 2] ( 1) and [Ni(tpttd)] ( 2), where Hdmep and H 2tpttd are the abbreviations for 2-(2,2-diphenyl-2-mercaptoethyl) pyridine and 2,2′,11,11′-tetraphenyl-1,5,8,12-tetrahiadodecane, respectively, are presented. Each of the thialato-sulfur atoms of these compounds is sterically protected by two benzene rings at the α carbon position to suppress dimerization upon synthesis. 1 · 1.5CH 2Cl 2 · MeCN crystallizes monoclinic P2 1/ n with a = 18.362(3), b = 16.894(4), c = 13.273(4) A ̊ , β = 104.59(2)°, V = 3984(3) A ̊ 3 and Z = 4.2 · 1.5 MeCn crystallizes triclinic P 1 with a = 15.091(6), b = 15.661(3), c = 14.085(7) A ̊ , α = 96.00(2), β = 90.89(4), γ = 99.70(2)°, V = 3261(4) A ̊ and Z = 4. The NiS and NiN bond lenghts of 1 were compared with those of the nickel center in the A-cluster of carbon monoxide dehydrogenase.

Synthesis and characterization of cobalt(III) azido complexes of some disubstituted pyridine ligands and X-ray crystal structure of mer-[Co(3,4-dimethylpridine) 3(N 3) 3] and mer-Co(3,5-dimethylpyridine) 3(N 3) 3

Cobalt(III) azido complexes of some disubstituted pyridine ligands of the type CoL 3(N 3) 3 have been prepared and characterized. The complexes gave non-conducting solutions and their solid state and solution electronic spectra are discussed. The IR spectra reveal the asymmetric nature of the azido ligands and the mer-formulation was confirmed by the number of Co—N(N 3 and Co—N(L) stretching bands observed in the far-IR region. X-ray crystal structure determinations were done for mer-[Co(3,4-dimethylpyridine) 3(N 3) 3] ( 1) and mer-[Co(3,5-dimethylpyridine) 3(N 3) 3] ( 2). Both compounds contain discrete molecules with approximately octahedral cobalt(III) ion. The Co—N(N 3) distances are variable from 1.931(4) to 1.959(4) Å and from 1.944(3) to 1.965(3) Å whereas Co—N(L) bond lenghts are from 1.955(3) to 1.994(3) and from 1.973(3) to 1.990(3) Å for 1 and 2, respectively. The thermal decomposition of complexes ( 1) and ( 2) were investigated drivatographically in nitrogen. Complex ( 1) explodes completely in one step at 175°, whereas complex ( 2) loses one 3,5-DMPy molecule and an azide ion in the first step around 139° and then explodes at 172°.

The prediction of the structure of technetium (V) complexes using density-functional techniques

Electronic structure calculations using the local-density functional method were shown to accurately reproduce the geometry of five oxo-Tc(V)-based radiopharmaceuticals containing a variety of donor ligands. Calculations were performed using the DGauss program on a Cray C90 supercomputer, requiring approximately 40 CPU h for each molecule. The predicted bond lenghts were within ±0.04 Å of the crystallograpic coordinates, and bond angles within ±4 degrees. Root mean square (RMS) deviations between the predicted and crystallographic coordinates were less than 0.06, and visual inspection demonstrated nearly perfectly superimposible structures.

Dynamics of Oxygen Binding in Hemocyanin and Tyrosinase by XANES and the Multiple Scattering Approach

The Cu K-edge X-ray Absorption Near Edge Structure (XANES) spectra of hemocyanin (Hc) in its deoxy- form has been simulated by the multiple scattering approach in the real space of coordinates. The features of the experimental spectra are related to structural parameters such as bond lenghts and the overall simmetry at the Cu site(s), whose changes are directly linked to the ligand binding dynamics. The experimental spectrum is compared with that of deoxy-tyrosinase, for which diffraction data are still unavailable, and the structure of its copper site(s) is inferred. These calculations, together to the previously reported ones on oxy-Hc [1], provide new theoretical support to any XANES investigation of the oxygen binding dynamics in Hc and its related proteins.

Ab-initio-Rechnungen, Schwingungsspektren und Normalkoordinatenanalyse von closo-[B6H5F]2– / ab initio Calculations, Vibrational Spectra, and Normal Coordinate Analysis of closo-[B6H5F]2–

Abstract The structural parameters of closo-[B6H5F]2- with C4v symmetry have been determined by MP2/6-31G* optimization. They reveal typical B-F and B-B bond lenghts of 143.4 and 172.5 -173.9 pm, respectively. A frequency analysis at the same theoretical level has been performed. The vibrational spectra of [B6H5F]2- labelled with 10B, 11B and D have been additionally assigned by normal coordinate analysis based on a modified valence force field using the ab initio structure parameters. With a set of 10 force constants (e.g. fd(BB)=1.92, fd(BF)=5.25 mdyn/Å) a good agreement between observed and calculated frequencies can be achieved. The results correspond with the scaled (Fscale=0.97) ab initio frequencies and assignments.

Crystal structures of trans-[Mo(CO) 4(PPh 3) 2] and 1,4-bis (diphenylphosphino)-2,5-difluorobenzene

Thermolysis of [(Mo(CO) 4(μ-DPFB) 2] (DPFB = 1,4-bis (diphyenylphosphino)-2,5-difluorobenzene) in acetonitrile followed by addition of triphenylphosphine yields trans-[Mo(CO) 4(PPH 3) 2] and free DPFB which co-crystallise. Crystal data: triclinic, space group P 1 , α = 9.4976(20), b = 10.0708(21), c = 16.1178(29) A ̊ , α = 100.333(16), β = 101.741(15), γ = 94.445(17)°, V = 1474.48 A ̊ 3, Z = 1 . Only half of each molecule is unique, being related to the second by the inversion centre. In trans-[Mo(CO) 4(PPh 3) 2], little deviation from ideal octahedral geometry is seen and the MoP bond lenght of 2.500(1) Å is significantly shorter than those found in the cis isomer.

Facile thermal desolvation of Ce 2(OPr i) 8(Pr iOH) 2: Characterization and molecular structure of Ce 4( μ4-O)( μ3-OPr i)( μ-OPr i) 4(OPr i) 8

Thermal treatment of Ce 2(OPr i) 8(Pr iOH) 2 yielded Ce 4( μ 4-O)(OPr i) 14 by desolvation under mild conditions. The tetranuclear oxoalkoxide has been characterized by elemental analysis, FT-IT, 1H NMR and X-ray diffraction. The structure is described as [Ce 4( μ 4-O)( μ 3-OPr i) 4( μ-OPr i) 4( OPr i ) 8]. The Ce 4(μ 4-O) core corresponds to a distorted flattened tetrahedron, with two hexa- and two hepta-coordinated metals. The CeO bond lenghts spread over the range 2.03(2) to 2.54(1) Å and follow the orcer CeOR < Ce μOR < Ceμ 3OR.

Synthesis, Structure and Vibrational Spectra of Ba14InP11

AbstractBa14InP11 was prepared from the elements in a sealed stainless steel ampoule at 1345 K. The compound is black, brittle and very sensitive to air and moisture. Ba14InP11 crystallises in the tetragonal Ca14AlSb11 type (space group I41/acd, No. 142; a = 17.097 (2) Å, c, = 8, Pearson code tI208). The structure contains isolated P3‐, linear [P3]7‐ and tetrahedral [InP4]9‐ anions. The X‐ray structure analysis and the vibrational spectra show that the [P3]7‐ polyanion is strongly asymmetric with d(P–P) = 2.28 Å and 4.10 Å, corresponding to a [P2]4‐ dumbbell weakly coupled to a single p3‐ anion. The tetraphosphidoindate(III) anion [InP4]9‐ is slightly compressed along the 4 axis, with bond lenght d(In–P) = 2.71 Å. It is shown that the structure is hierarchically related to that of Cu2O, with two interpenetrating frameworks, in which the O and Cu atoms are replaced by condensed [InP4/2] tetrahedron and [BaP4P2/2] octahedra, respectively. Both frameworks are meso configured, containing alternate R and S fragments. The other Ba cations envelop the P6 octahedra and P3 triads forming condensed cubes, tetragonal antiprisms and bicapped trigonal prisms. Therefore, the structure also forms a heterogeneous framework of centred PBa8/2tap tetragonal antiprisms and BaBa8/2cub cubes, consisting of two interpenetrating enantiomorphic nets (R and S) similar to those in the cubic phase RhBi4.