Home – Home – Jornals – Journal of Structural Chemistry 2012 number 6

The disc-like cluster C₇₂H₁₀₂N₁₂Ni₁₃O₄₀ is first time synthesized based on N-(2-pyridyl)methylimino-dipropionic acid. Single crystal X-ray diffraction is used to determine its atomic structure. The cluster consists of seven-nuclear core: nickel(II) hydrocomplex (Ni…Ni distance 3.012-3.032 Å) and six nickel chelates of the corresponding acid arranged around its perimeter (Ni…Ni distance 2.981-3.164 Å). In the chelate part of the complex, the ligand is pentadentate owing to the formation of a bridging bond, thus organizing a coordination geometry of the metal center as a distorted square bipyramid (4+2). Liquid chromatography-mass spectrometry is employed to study the structure of the obtained nickel(II) complexes.

Based on the similarity of subgraphs in the molecular graphs of a homological series of SiH₄–SiC₈H₂₀ alkylsilanes a 22-constant additive scheme is obtained for the calculation of their physicochemical properties. By the example of SiH₄–SiC₈H₂₀ alkylsilanes it is shown that for each alkylsilane molecule the sum of numbers of simple and complex heterochains equals a triangular number. A least squares method is applied to determine the numerical values of the parameters of the scheme for the calculation of Δ_fH_{газ,298 K}⁰ for alkylsilanes (SiC_nH_2n+4).

The structure and stability of endohedral TM@(AlN)₁₂ (TM = Ti, Mn, Fe, Co, Ni ) complexes are studied at the level of density functional theory. It is found that complexes with TM = Mn, Fe, and Ni are energy minimum structures with TM at the cage center in T_h symmetry, while those with TM = Ti and Co have more negative inclusion energies and the off-centered structures with TM placed towards one hexagon face in C₁ symmetry. The calculations predict that the HOMO and LUMO energy gap of TM@(AlN)₁₂ differs from those of the (AlN)₁₂ cage and a free TM atom. The amount of charge that is transferred from the encapsulated guests to the cage increases with the atomic radius. The electronic and magnetic properties of TM@(AlN)₁₂ are discussed.

5,6-Dihydrothymine (DHT) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this work, we present the hydrogen bonding base pairs involving 5,6-dihydrothymine bound to four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations are performed for the studied complexes by the B3LYP method. Interaction energies are corrected for the basis set superposition error, using the full Boys-Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs are characterized using NBO and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: DHT:G ~ DHT:A > DHT:C > DHT:T.

A complex experimental study of Cu(2p_3/2), Cu(2p_1/2) photoelectron and Kα_1,2 and Lα_1,2 X-ray emission spectra of copper in copper phthalocyanine CuPcH₁₆ and its fluoro-substituted analog CuPcF₁₆ is carried out. A charge transfer model is used to interpret the spectra. It is shown that Kα₁ and Kα₂ lines of the spin-doublet of copper have a complex structure due to the processes of metal-to-ligand charge transfer. The role of a satellite in the formation of emission lines is revealed.

The microwave spectrum of 2,5-dimethyl-1,3-dioxane is studied. The spectrum is identified to have the а and с type rotational transitions of the trans- and cis-isomers of the molecule. The experimental frequencies of the transitions are used to calculate the rotational constants and the quartic centrifugal distortion constants of the isomers. The dipole moments are determined. Quantum chemical calculations are performed by the B3PW91/aug-cc-pVDZ density functional method. The calculated results are compared with the experimental data. The equilibrium geometries of 1,3-dioxane and 2-methyl-, 5-methyl-, and 2,5-dimethyl-1,3-dioxanes are compared. It is found that the alkyl substitution leads to a change in the ring geometry.

An iron(III)-containing complex with the asymmetric tridentate azomethine ligand 4,4'-dodecyloxy-benzoyloxybenzoyl-4-salicylidene-N'-ethyl-N-ethylenediamine with a PF₆^- counterion is obtained. The presence of the complexing ion is confirmed by far IR Fourier spectra. The structure of the compounds is determined by matrix-assisted laser desorption/ionization with a time-of-flight mass analyzer (MALDI-ToF). The results of mass spectrometric studies are consistent with the elemental analysis data. It is found that the complexation of iron salt with an asymmetric tridentate ligand results in the formation of compounds of the composition 1:1 with octahedral packing of a metal ion in the complex. The electrochemical behavior of the compound in organic solvents is examined. The EPR study shows that iron(III) ions are in both low spin (LS) and high spin (HS) states in the complex. The LS and HS iron(III) centers are coupled into dimers in which a water molecule and the PF₆^- counterion act as bridges. It is also found that for LS complexes in the low-temperature phase (4.2-300 K), the (d_xz, d_yz)⁴(d_xy)¹ electronic state is the ground state. It is revealed that the conversion of the sample into a high-temperature liquid crystalline (387-405 K) phase is accompanied by the conversion of the LS states of the Fe(III) ion: (d_xz, d_yz)⁴(d_xy)¹ ↔ (d_xy)²(d_xz, d_yz)³. The conversion of LS states is temperature reversible and is driven by the temperature. X-ray crystallographic data confirm that the compound obtained consists of dimer formed by a hydrogen (O–H⋯F) bond.

Quantitative structure-spectrum relationship calculations of ¹³C NMR chemical shifts of both 302 carbon atoms in 56 alcohols and 62 carbon atoms in 15 thiols are described using several parameters: the atomic ionicity index (INI), the polarizability effect index (PEI), and stereoscopic effect parameters (ε) of the compounds. The ¹³C NMR chemical shifts for these compounds of both alcohols and thiols can be estimated through the multiple linear regression (MLR). A MLR model was built with variable screening by the stepwise multiple regression and examined by validation on its stability. The correlation coefficient of the established model as well as the leave-one-out cross-validation was 0.9724 and 0.9716 respectively. The results obviously indicate that INI and e are linearly related with ¹³C NMR chemical shifts, which provides a new method for calculating ¹³C NMR chemical shifts in the compounds of both alcohols and thiols.

UV spectroscopy is used to determine the molar absorption coefficients of C₆₀ fullerene and monosubstituted 1,2-dihydro-C₆₀-fullerenes in different solvents. It is found that the extinction coefficient of C₆₀ at 330 nm (the main absorption band most frequently used for qualitative and quantitative determination of the C₆₀ content) is independent of the nature of the solvent and is ~54400 M^–1×cm^–1. The molar absorption coefficients of a series of monosubstituted 1,2-dihydro-C₆₀-fullerenes are practically independent of the chemical structure and the length of the substituent and are 35700 M^–1×cm^–1 (λ ~ 328 nm) and 115250 M^–1×cm^–1 (λ ~ 257 nm). It is shown that the substitution in fullerene proceeds via the double 6,6 bond, as evidenced by the absorption band at 424 nm in the spectra of these compounds, which is characteristic of monosubstituted methanofullerenes.

The problem of the introduction of the term "internal pressure" from the standpoint of intermolecular forces is solved. It is shown that internal pressure is created by the macrosystem average force field of the structural units of a liquid. Internal pressure is shown to be not an energy characteristic, but a macrosystem average force parameter of the interaction between the structural units of a liquid phase system, although it has the energy density dimension, [J/m³].

The hydration numbers are investigated of the glycine amino acid in solutions of substances with different effects on the structure of water: urea, monomethylurea, and 1,3-dimethylurea. Glycine loses a half of its hydration water in a 20m urea solution and only a quarter of it in a 20m dimethylurea solution. The constancy of the hydration number of glycine in concentrated dimethylurea solutions is due to the compensatory effect of the interactions in the ternary and binary systems.

Specific features of the structure and phase composition of coatings obtained by the action of shaped charge jets are studied. Different molybdenum-containing compounds are used as precursors.

The molecular and crystal structure of halogen-substituted acetylacetonates of boron difluoride 2,2-difluoro-5-chloro-4,6-dimethyl-1,3,2-dioxaborin (1) and 2,2-difluoro-5-bromo-4,6-dimethyl-1,3,2-dioxaborin (2) is determined. In both compounds, a noticeable intermolecular interaction between the fluorine and carbon atoms of the chelate ring and between the fluorine atoms and substituents exists. In order to explain the revealed patterns of molecular packing, the charge distribution in the studied chelates is calculated.

The crystal structure of a solvate [Zn(НL)Cl]×EtOH is determined by single crystal X-ray crystallography (150 K, Bruker X8 Apex CCD autodiffractometer, МоK_a radiation). The crystals are triclinic, unit cell parameters are: a = 7.4755(4) Å, b = 13.9701(11) Å, c = 14.4593(19) Å, α = 82.277(2)°, β = 75.410(2)°, γ = 75.356(1)°, space group Р1. The structure of the solvate contains two crystallographically independent complex [Zn(НL)Cl] molecules and two non-coordinated ethanol molecules. In each of the molecules, Zn²⁺ ions coordinate N atoms of tetradentate chelating ligands НL^– and a Cl atom. ClN₄ polyhedra have a distorted tetragonal pyramidal geometry. EtOH molecules make H-bonds with the complex molecules, thus facilitating the formation of chains along the х axis.

Two new malonato-bridged copper(II) complexes of the composition [Cu ₂(mal) ₂(datz) ₂(H ₂O)]×5H ₂O (1) and [Cu ₂(mal) ₂(atz) ₂(H ₂O)]×3H ₂O (2) (mal = malonate, atz = 4-amino-1,2,4-triazole, datz = 3,5-diamino-1,2,4-triazole) are prepared and characterized by X-ray crystal structure determination and magnetic studies. The environment of each copper atom in 1 and 2 has distorted square pyramidal and octahedral geometries. The intrachain copper-copper separation is 6.305 Å and 3.640 Å across the carboxylates and trizolates bridges respectively for complexes 1 and 2. The magnetic properties of 1 and 2 are investigated in the temperature range 2—300 K. The overall antiferromagnetic behavior is observed in both cases.

A single crystal X-ray study of a novel volatile trans -isomeric complex of palladium Pd(L) ₂, obtained based on sterically hindered methoxy-β-iminoketone (HL = C(CH₃)₂(OCH₃)–C(NH)–CH₂–C(O)–CH(CH₃)₂), is performed. The crystallographic data for C₂₀H₃₆N₂O₄Pd are: a = 10.0408(2) Å, b = 9.9473(2) Å, c = 11.6413(2) Å, β = 96.789(1)°, space group P2₁/c, Z = 2. The structure is monomeric molecular; the palladium atom has a square coordination with two oxygen and two nitrogen atoms of two bidentately bound ketoiminate ligands in the trans-position. Geometric characteristics of the coordination sites: the bond length of Pd–O, Pd–N and the chelate N–Pd–O bond angle are 1.986 Å, 1.974 Å and 93.1° respectively. It is found that Pd, Ni, and Cu complexes with this ligand are isostructural.

Potassium salts of chalcohydroxo rhenium cluster complexes [Re₆Q₈(OH)₆]^4– (Q = S or Se) with the composition K₄[Re₆S₈(OH)₆]×4H₂O (1) and K₄[Re₆Se₈(OH)₆]×5H₂O (2) are produced by evaporation of the corresponding strongly alkaline aqueous solutions. The composition of the compounds is determined by the single crystal X‑ray diffraction study. The compounds crystallize in the triclinic space group P1^– with the following unit cell parameters: a = 8.408(2) Å, b = 9.096(2) Å, c = 9.222(2) Å, α = 95.110(4)°, β =107.085(4)°, γ = 113.026(4)°, V = 603.5(3) Å ³, Z = 1, d_x = 4.689 g/cm ³ (for 1) and a = 8.782(3) Å, b = 9.155(4) Å, c = 9.325(4) Å, α = 105.481(7)°, β = 109.266(6)°, γ = 99.104(6)°, V = 656.6(4) Å ³, Z = 1, d_x = 5.305 g/cm ³ (for 2).

The crystal structure of double complex salt [Pt(NH₃)₅Cl][ReCl₆]Cl×H₂O is determined. Crystallographic characteristics are: a = 23.9502(4) Å, b = 7.5963(1) Å, c = 8.9016(2) Å, V = 1619.49(5) ų, space group Pnma, Z = 4, d_x = 3.150 g/cm³. The packing of structural fragments is studied. It is shown that on heating the salt in a helium atmosphere up to 840 °С a mixture of two solid solutions of fcc Pt_0.90Re_0.10 and hcp Pt_0.25Re_0.75 forms.

The (EnH₂)[AuCl₄]₂×2H₂O (I) and (EnH₂)₂[AuCl₄]Cl₃ (II) (EnH₂²⁺ is diprotonated ethylenediamine) complexes are produced and characterized by elemental and thermogravimetric analysis, X‑ray diffraction, IR and Raman spectroscopy. For I, the crystals are monoclinic, crystallize in the space group P2₁/c: a = 7.5870(2) Å, b = 9.5665(2) Å, c = 11.4706(3) Å, β = 107.0480(10)°, V = 795.97(3) ų, Z = 4. For II, the crystals are orthorhombic, crystallize in the space group Pnma : a = 12.7088(3) Å, b = 17.7435(5) Å, c = 7.4992(2) Å, V = 1691.06(8) ų, Z = 8.

The X‑ray diffraction study of cis-2,3-dichlorobuth-2-ene-1,4-diol (3) obtained by the reduction of 3,4-dichloro-5-ethoxy- and 5-isopropoxi-2(5H)-furanones with lithium aluminum hydride is performed. The crystals of compound 3 are trigonal: a = b = 15.746(9) Å, c = 6.848(4) Å; V = 1470.5(15) ų, space group P3₁, Z = 9 (three independent molecules). Independent molecules have identical planar conformation, and hydroxyl groups are located on different sides of the multiple bond plane. The supramolecular motif of the crystal is spirals about the threefold screw axes; the neighboring spirals are linked by OH…O hydrogen bonds.

The title compound (2,6-di- tert -butyl-4-(3-(4-chlorophenyl)-4-methyl-4,5-dihydroisoxazol-5-yl)phenol is synthesized and studied by the single crystal X-ray diffraction method. The structure of the product was confirmed by IR, ¹H and ¹³C NMR spectroscopy. The crystal structure of 1,4-dioxane hemisolvate of the product is solved in the monoclinic space group P2₁/c with a = 17.713(6), b = 9.529(3), c = 13.972(4) Å, β = 94.09(4)°, V = 2352.3(13) ų, Z = 4, T = 120(2) K.

Magnetic resonance imaging (MRI) has become a prominent imaging technique in medicine. Gadolinium-based contrast agents are extensively used to enhance the contrast between normal and diseased tissues through MRI scans. The article illustrates the paramount significance of such contrast agents in MRI applications. Clinically approved contrast agents as well as those in trial period are discussed. Important parameters, i.e. hydration number, rotational correlation time, and mean residence lifetime, influencing the relaxivity (sensitivity) of such agents are described in detail. Various approaches towards relaxivity enhancement are discussed with appropriate examples from the recent literature. A decrease in the Gd-water proton distance results in significant relaxivity enhancement. A comprehensive classification and explanation of Gd³⁺-based contrast agents are presented. Each class is explained with suitable examples. The stability of contrast agents is dependent on their chemical structure. Future contrast agents need to be tissue specific of high relaxivity, low toxicity, and lower administered dose for in vivo use.

The density functional theory method with B3LYP/6-311++G(df,pd), B3LYP/6-311++G(df,2pd), and B3LYP/6-311++G(3df,3pd) basis sets is used to compute the geometrics and single point energy of aluminum carbide (AlC) and aluminium nitride (AlN) in their ground state. The Level 8.0 program is used to calculate spectroscopic constants and fit the energy potential curves. The effect of a basis set on the spectroscopic constants is discussed. The results show that the calculated potential curve matches well with the Level 8.0 fitting curve, and the calculated values of spectroscopic constants become more reliable with the improvement of the quality of basis sets. The spectroscopic constants are in good agreement with the existing experimental and theoretical values. For the first time, the reliable anharmonicity constant data of AlC are reported, which agrees so well with the experimental value.

2p_3/2,1/2 Photoelectron spectra of single crystalline specimens of chromium-copper disulfides CuCrS₂ and CuCr_0.85V_0.15S₂ are studied. It is shown that the spectra of single crystalline specimens substantially differ from the corresponding spectra of chromium-copper disulfides in the powder state.

The ¹H, ¹³C, and ¹⁵N NMR chemical shifts of ten 4-nitropyridine N-oxide derivatives are assigned. The shielding of the pyridine ring nitrogen is sensitive to ring substitution through inductive effects, steric effects by ortho-substituents, and the possibility for electron delocalisation (resonance energy). In solution, 3-ethylnitrosoamino-4-nitropyridine N-oxide has two tautomers. The proposed reason is the steric crowding between vicinal 4-nitro and 3-ethylnitrosoamino groups, causing a disturbance to amino nitrogen that can delocalize its lone pair to the oxygen atom of the nitroso group.

The molecule (h⁵-pentamethylcyclopentadienyl)(methyldiphenylphosphinite-P)dichlororhodium(III), [(h⁵-C₅Me₅)RhCl₂(PPh ₂OMe)], crystallizes in the monoclinic crystal system in space group P2₁/c with unit cell parameters a = 16.056(3) Å, b = 9.4331(18) Å, c = 15.745(3) Å, β = 108.330(4)°, V = 2263.8(7) ų and Z = 4. There is three-legged piano stool geometry about Rh. The Rh—P distance of 2.278(2) Å is shorter than those of [(h⁵-C₅Me₅)RhCl₂(PPh₂OR)] where R is an aryl group, and longer than those found in [(h⁵-C₅Me₅)RhCl₂{PPh(OR)₂}]. The structure reveals significant distortion of the pentamethylcyclopentadienyl towards 'h³,h²-enyl-ene' coordination.

The Schiff base thiophenyl-2-methylidene-2-aminophenol (ImineOH) is obtained from a stoichiometric mixture of 2-thiophenecarboxaldehyde and 2-aminophenol in ethanol under reflux at 90 °C. Its crystal structure is determined by single crystal X-ray diffraction. ImineOH packs in an orthorhombic unit cell in the Pbca space group with the unit cell parameters a = 16.942(4) Å, b = 13.4395(11) Å and c = 17.5857(12) Å, V = 4004.1(10) ų, Z = 16. Strong hydrogen bonds are present in the ImineOH structure. Apart from the X-ray study, ImineOH was characterized by elemental analysis (CHN-S) and FT—IR (4000 cm^–1 to 400 cm^–1), UV-Vis and ¹³C, ¹H, and ¹⁵N NMR spectroscopic measurements.

The crystal and molecular structure of 4-chloro(benzoyloxymethyl)trifluorosilane 4-ClC₆H₄COOCH₂SiF₃ was redetermined using X‑ray diffraction. The coordination polyhedron of the silicon atom in this structure is a trigonal bipyramid. The length of the axial O → Si coordination bond is 2.074(1) Å.