Vibrational spectra and reinvestigation of the crystal structure of a polymeric copper(II)-orotate complex, [Cu(μ-HOr)(H2O)2]n: The performance of new DFT methods, M06 and M05-2X, in theoretical studies

The crystal and molecular structure of a polymeric Cu(II)-orotate complex, [Cu(μ-HOr)(H₂O)₂]_n, has been reinvestigated by single crystal X-ray diffraction. It is shown that several synergistic interactions: two axial Cu-O interactions; intramolecular and intermolecular hydrogen bonds; and π-π stacking between the uracil rings contribute to the stability of the crystal structure. The Raman and FT-IR spectra of the title complex are reported for the first time. Comprehensive theoretical studies have been performed by using three unrestricted DFT methods: B3LYP; and the recently developed M06, and M05-2X density functionals. Clear-cut assignments of all the bands in the vibrational spectra have been made on the basis of the calculated potential energy distribution, PED. The very strong Raman band at 1219 cm⁻¹ is diagnostic for the N1-deprotonation of the uracil ring and formation of the copper-nitrogen bond, in this complex. The Cu-O (carboxylate) stretching vibration is observed at 287 cm⁻¹ in the IR spectrum, while the Cu-N (U ring) stretching vibration is assigned to the strong Raman band at 263 cm⁻¹. The molecular structure and vibrational spectra (frequencies and intensities) calculated by the M06 functional method are very similar to the results obtained by the B3LYP method, but M06 performs better than B3LYP in calculations of the geometrical parameters and vibrational frequencies of the interligand O-H?O hydrogen bonding. Unfortunately, the M05-2X method seriously overestimates the strength of interligand hydrogen bond.     

Synthesis,NMR‐Spectroscopy,and Molecular Structure of a Phosphonyl Ene Diamine

First examples of ene diamines with a phosphonate function at the C=C double bond were obtained by the reaction of dialkyl H‐phosphonates with bis(N‐tert‐butyl)‐diimine derived from glyoxal, [1,4‐bis(tert‐butyl)‐1,4‐diaza‐1,3‐butadiene], and isolated as hydrochlorides. Preferentially the cis‐diamine is formed. The new phosphonates are characterized by multinuclear NMR spectroscopy(¹H, ¹³C, ³¹P). In addition the methyl ester 8a was characterized by ^14,15N NMR spectroscopy as well as by several 2D NMR techniques and single‐crystal X‐ray diffraction, unequivocally establishing the ene diamine structure. In the crystal dimers of the cations are formed by P–O ··· H–N hydrogen bonding.     

Synthesis and Crystal Structure of [Cr(thd)2(OEt)]2

The mixed‐ligand complex [Cr(thd)₂(OEt)]₂ [(thd)^– = anion of H(thd) = C₁₁H₂₀O₂ = 2,2,6,6‐tetramethylheptane‐3,5‐dione] appears as by‐product when EtOH/H₂O is used as solvent during preparation of Cr(thd)₃. [Cr(thd)₂(OEt)]₂ can be difficult to separate from Cr(thd)₃ by sublimation, but separation is easily accomplished by extracting Cr(thd)₃ with acetone. A detailed account for the sublimation behavior of [Cr(thd)₂(OEt)]₂/Cr(thd)₃ mixtures is advanced. Good yields of [Cr(thd)₂(OEt)]₂ are obtained when CrCl₃, H(thd), and Na(EtO) react in absolute EtOH. [Cr(thd)₂(OEt)]₂ is obtained in the form of green needle‐shaped crystals by recrystallization from toluene. The crystal structure is triclinic [a = 10.2919(15), b = 10.6686(16), c = 14.194(3) Å, α = 106.559(2), β = 107.869(2), and γ = 98.326(2)° at 295 K; space group P . The complex contains two crystallographic equivalent chromium atoms, which are bridged by two cis‐configured ethoxy groups, the four remaining sites in the octahedral coordination around each chromium atom being occupied by oxygen atoms from two thd ligands. The bond lengths and angles concur with the findings for related molecular complexes. The temperature dependence of the magnetic susceptibility of [Cr(thd)₂(OEt)]₂ follows Curie–Weiss law with Weiss constant θ ≈? –65 K and μ_p = 3.87 μ_B.     

Structural investigation of high‐transmittance aluminum oxynitride films deposited by ion beam sputtering

Aluminum oxynitride films were deposited by ion beam sputtering technique at room temperature. The optical properties and morphologies of the aluminum oxynitride films were studied and reported previously. It was found that the optical properties are closely related to the O contents in the films. In this study, the structures of the films were investigated by X‐ray diffractometer and XPS. Three oxidation states of N_1s in oxynitride films, N⁺, N²⁺ and N³⁺, were clearly deduced from N_1s spectra in the amorphous films fabricated under various oxygen partial pressures (P_O2). To our knowledge, three oxidation states of N_1s have not been simultaneously observed and reported in the aluminum oxynitride films previously. Corresponding bonding variations in Al_2p and O_1s spectra indicated more oxygen in oxynitride in the film as P_O2 increases. Three aluminum oxynitride networks, AlO₂N, AlO_2.5N and AlO₃N were deduced. Optical properties of aluminum oxynitride films resemble those of AlN and Al₂O₃ films when P_O2 is low and high during the deposition. The refractive indices and extinction coefficients of the aluminum oxynitride films can be adjusted by using proper P_O2 during the film depositions. Copyright © 2010 John Wiley & Sons, Ltd.     

Crystal structures of Ziegler-Natta catalyst supports

The crystal structures of three MgCl(2)·nEtOH complexes with n=1.5, 2.8, and 3.3 have been fully determined. Such complexes are the fundamental precursors for Ziegler-Natta polymerization catalysts used to produce polyolefins on a multimillion-ton scale worldwide. The ab initio structure solution showed that the structure of MgCl(2)·nEtOH complexes with n=1.5 and 2.8 are based on ribbons of metal-centered octahedra, whereas for n=3.3 this chainlike arrangement breaks into a threadlike structure of isolated octahedra linked by hydrogen bonds. A clear correlation between catalyst performance and the crystal structure of precursors has been found, and reveals the fundamental role of the latter in determining catalyst properties. The direct knowledge of building blocks in the precursor structures will help to develop more accurate models for activated catalysts. These models will not require the arbitrary and oversimplified assumption of locating the catalyst active sites on selected cut surfaces of the α-MgCl(2) crystal lattice.     

Supramolecular engineering through temperature-induced chemical modification of 2H-tetraphenylporphyrin on Ag(111): flat phenyl conformation and possible dehydrogenation reactions

Scratching the surface: Formation of a monolayer of 2H-tetraphenylporphyrins (2H-TPP) on Ag(111), either by sublimation of a multilayer in the range 525-600?K or by annealing (at the same temperature) a monolayer deposited at room temperature, induces a chemical modification of the molecules. Rotation of the phenyl rings into a flat conformation is observed and tentatively explained, by using DFT calculations, as a peculiar reaction due to molecular dehydrogenation.     

Crystallographic analysis of metal-ion binding to human ubiquitin

The metal-binding ability of human ubiquitin (hUb) towards a selection of biologically relevant metal ions and complexes has been probed. Different techniques have been used to obtain crystals suitable for crystallographic analysis. In the first type of experiments, crystals of hUb have been soaked in solutions containing copper(II) acetate and two metallodrugs, Zeise salt (K[PtCl(3)(η(2)-C(2)H(4))]·H(2)O) and cisplatin (cis-[PtCl(2)(NH(3))(2)]). The Zeise salt is used in a test for hepatitis, whereas cisplatin is one of the most powerful anticancer drugs in clinical use. The Zeise salt readily reacts with hUb crystals to afford an adduct with three platinum residues per protein molecule, Pt(3)-hUb. In contrast, copper(II) acetate and cisplatin were found to be unreactive for contact times up to one hour and to cause degradation of the hUb crystals for longer times. In the second type of experiments, hUb was cocrystallized with a solution of copper(II) or zinc(II) acetate or cisplatin. Zinc(II) acetate gives, at low metal-to-protein molar ratios (8:1), crystals containing one metal ion per three molecules of protein, Zn-hUb(3) (already reported in previous work), whereas at high metal-to-protein ratios (70:1) gives crystals containing three Zn(II) ions per protein molecule, Zn(3)-hUb. In contrast, once again, copper(II) acetate and cisplatin, even at low metal-to-protein ratios, do not give crystalline material. In the soaking experiment, the Zeise anion leads to simultaneous platination of His68, Met1, and Lys6. Present and previous results of cocrystallization experiments performed with Zn(II) and other Group 12 metal ions allow a comprehensive understanding of the metal-ion binding properties of hUb with His68 as the main anchoring site, followed by Met1 and carboxylic groups of Glu16, Glu18, Glu64, Asp21, and Asp32, to be reached. In the case of platinum, Lys6 can also be a binding site. The amount of bound metal ion, with respect to that of the protein, appears to be a relevant parameter influencing crystal packing.     

Pd(II) and Pt(II) complexes of 2-(2'-pyridyl)-4,6-diphenylphosphinine: synthesis, structure, and reactivity

The coordination chemistry of the bidentate P,N hybrid ligand 2-(2'-pyridyl)-4,6-diphenylphosphinine (1) towards Pd(II) and Pt(II) has been investigated. The molecular structures of the complexes [PdCl(2)(1)] and [PtCl(2)(1)] were determined by X-ray diffraction, representing the first crystallographically characterized λ(3)-phosphinine-Pd(II) and -Pt(II) complexes. Both complexes reacted with methanol at the P=C double bond at an elevated temperature, leading to the corresponding products [MCl(2)(1H·OCH(3))]. The molecular structure of [PdCl(2)(1H·OCH(3))] was determined crystallographically and revealed that the reaction with methanol proceeds selectively by syn addition and exclusively to one of the P=C double bonds. Strikingly, the reaction of [PdCl(2)(1H·OCH(3))] with the chelating diphosphine DPEphos at room temperature in CH(2)Cl(2) led quantitatively to [PdCl(2)(DPEphos)] and phosphinine 1 by elimination of CH(3)OH and rearomatization of the phosphorus heterocycle.