Home – Home – Jornals – Journal of Structural Chemistry 2017 number 3

By the DFT/B3LYP method the equilibrium structures of oxygen complexes with water are calculated in various geometric conformations with symmetries C_2v and C_s. By the MRCI/CASSCF method potential energy surface cross-sections of the ^1.3[O₂-H₂O] complexation reaction are constructed. With taking into account the spin-orbit coupling, the forbidden transition moments a¹Δ_g-X³, b¹-a¹Δ_g, c¹-a¹Δ_g, A³-X³ of the complexes are calculated and changes in their intensities at different geometric configurations of the complex are revealed.

The spatial and electronic structures of three-coordinate aluminum molecules with Al-C bonds are calculated using the GAMESS-Firefly program package at DFT and HF levels of theory. By NBO and AIM methods the main characteristics of Al-C bonds in these molecules are determined. It is shown that by their topological characteristics the Al-C bonds can be characterized as weakened intermediate bonds close to the bonds between closed shell atoms.

By the DFT (U)PBE0 method the structural parameters of molecules, cations, dications, and anions of gallium(III) (μ-oxo)bis[phthalocyaninate], gallium(III) (μ-oxo)bis[perfluorophthalocyaninate], and heteroleptic bis-phthalocyaninate ^FPcGaOGaPc are determined. The ∠GaOGa bond angle and the Ga⋯Ga internuclear distance depend non-monotonically on the charge. The ionization potential of the (PcGa)₂O molecule of 5.71 eV, the second electron detachment energy of 7.94 eV, and the electron affinity of 2.14 eV increase to 6.14 eV, 8.37 eV, and 2.72 eV after the perfluorination of one Pc moiety and to 6.60 eV, 8.70 eV, and 3.13 eV respectively after complete fluorination.

At the DFT (U)PBE0/cc-pVDZ level the structural parameters of a hypothetical Fe@ C ₆₀ endocomplex are determined. The ( A ₁// C _{3 v} )-Fe@ C ₆₀ state characterized by the electron spin square of 3.07 au, the free valence of 4.15, the dipole moment of 1.15 D, and the 172 pm Fe nuclear shift relative to the center of inertia of С₆₀ corresponds to the energy minimum. The Stone-Wales rearrangement in the quasi-triplet state increases the endocomplex energy by 1.56 eV and by 0.79 eV in the quasi-quintet state.

Sixth order connectivity indices are calculated for 29 benzotriazole derivatives. Correlations between the connectivity indices, physicochemical characteristics, and retention factors of the mentioned compounds are obtained for reversed-phase high-performance liquid chromatography conditions. Based on the correlations obtained, a predictive calculation of the retention factors of some benzotriazole derivatives is performed.

In this work, using quantum mechanics, the noncovalent interactions and two mechanisms of covalent functionalization of drug gentamicin with (5, 5) COOH and COCl functionalized carbon nanotubes are studied. All of the calculations are performed using a hybrid density functional method (UB3LYP) in the solution phase. Quantum molecular descriptors for four possible modes of the noncovalent interaction are investigated. It is found that the binding of gentamicin with COOH (NCOOH) and COCl (NCOCl) functionalized carbon nanotubes is thermodynamically favorable. Among NCOOH and NCOCl, the first one has higher binding energy and can act as a suitable system for the drug gentamicin delivery within biological systems (noncovalent). COOH and COCl functionalized carbon nanotubes can bond to gentamicin via OH (COOH mechanism) and Cl (COCl mechanism) groups, respectively. The activation energies of four pathways in two mechanisms are calculated and compared with each other. It is specified that the COOH mechanism has an energy barrier higher than that of the COCl mechanism, being the reason for the suitability of the COCl mechanism for covalent functionalization.

Topological analyses of the electron density on N-benzoyl-L-pheylalanine and its palladium(II) complexes are carried out using the quantum theory of atoms in molecules (QTAIM) at the M06/6-31G( d ) theoretical level. The topological parameters derived from the Bader theory are also analyzed; these are characteristics of Pd bond critical points and ring critical points. The calculated structural parameters are the highest occupied molecular orbital energy ( E _HOMO), the lowest unoccupied molecular orbital energy ( E _LUMO), the hardness (h), the softness ( S ), the absolute electronegativity (c), the electrophilicity index (w), and the fractions of electrons transferred (D N ) from ethylenediamine, 2,2¢-bipyridine and 1,10-phenanthroline complexes to N-benzoyl-L-pheylalanine. The numerous correlations and dependences between the energy terms of the symmetry adapted perturbation theory approach, geometrical, topological, and energy parameters are detected and described.

The effects of doping heteroatoms on the structure, electronic and adsorption properties of graphene are investigated using density functional theory calculations. Six different doped graphenes (with Al, B, Si, N, P, and S) are considered, and to obtain the interaction and adsorption properties, three sulfur-containing molecules (H₂S, SO₂, and thiophene) were interacted with selected graphenes. The adsorption energies (E_ad) in the gas phase and solvents show the exothermic interaction for all complexes. The maximum E_ad values are observed for aluminum doped graphene (AG) and silicon doped graphene (SiG), and adsorption energies in the solvent are not so different from those in the gas phase. NBO calculations show that the AG and SiG complexes have the highest E⁽²⁾ interaction energies and simple graphene (G) and nitrogen doped graphene (NG) have the least E⁽²⁾ energies. Population analyses show that doping heteroatoms change the energy gap. This gap changes more during the interaction and these changes make these structures useful in sensor devices. All calculated data confirm better adsorption of SO₂ by graphenes versus H₂S and thiophene. Among all graphenes, AG and then SiG are the best adsorbents for these structures.

Molecular structural descriptors (MVEIs) are developed from the molecular vertex electronegativity interaction, and the molecular structures of 43 organic acids are characterized. Two quantitative structure-retention relationship models are built up by the multiple linear regression and the partial least squares regression. The correlation coefficients (R) of the two models are 0.990 and 0.988, and the standard deviations of them are 2.935 and 3.024, respectively. Then the two models are evaluated by the leave-one-out cross-validation and the correlation coefficients (R_CV) are 0.985 and 0.976, the standard deviations are 3.527 and 3.628, respectively. It is confirmed that MVEIs are largely dependent on the properties of the organic molecules.

The structure and internal rotation of the 2-methyl-2-nitropropane molecule is studied by electron diffraction and quantum chemical calculations with the use of microwave and vibrational spectroscopy data. The electron diffraction data are analyzed within the general intramolecular anharmonic force field model and the quantum chemical pseudoconformer model, considering the adiabatic separation of the degree of freedom of large amplitude motion, i.e., the internal rotation of the NO₂ group. The equilibrium eclipsed configuration of the C_s symmetry molecule has the following experimental bond lengths and valence angles: r_e(N=O) = 1.226//1.226(8) Å, r_e(C-N)// r_e(C-C) = 1.520//1.515/1,521(4) Å, ∠_еC-C-N = 109.1/106,1(8)°, ∠_еO=N=O = 124.2(6)°, ∠_eC-C-H_avg = 110(3)°. The equilibrium geometry parameters are well consistent with MP2/cc-pVTZ quantum chemical calculations and microwave spectroscopy data. The thermally average parameters previously obtained within the small vibration model show a satisfactory agreement with the new results. The electron diffraction data used in this work do not allow a reliable determination of the barrier to internal rotation. However, at a barrier of 203(2) cal/mol, which is derived from the microwave study, it follows from the electron diffraction data that the equilibrium configuration must correspond to an eclipsed arrangement of C-C and N=O bonds, which is also consistent with the results of quantum chemical calculations of various levels.

Quantum chemical calculations are performed for the spatial and electron structure of complex compounds of L-histidine and its ionized forms with copper(II) for a variety of compositions within the density functional theory (DFT) using the B3LYP functional and 6-311G(d) basis. The solvent (water) is considered within the PCM approximation. EPR spectroscopy is used to study the equilibrium in the copper(II)-L-histidine system in an aqueous solution at рН 2-11. A comparison between the theoretical calculations and the EPR spectra suggests the following geometry for the coordination environment of the copper(II) ion in the complex compounds: CuHLL - square-planar coordination; CuL₂, CuHLL', and CuLL' - distorted square pyramid; and - octahedral environment.

The results of the investigation of the phase and quantitative composition of reinforcing phases of the Nb-Nb₅Si₃ in situ eutectic composite during high-gradient directional crystallization are reported. The crystal structures of the hexagonal γ and tetragonal α modifications of Nb₅Si₃ silicide are comparatively characterized. Possible structural positions for the stabilizing atoms in the structure of hexagonal silicide are proposed. The dependence of the creep deformation resistance on the silicide structure is discussed.

Two new dimethylglyoximate complexes [Co(DmgH)₂(Im)Cl] (I) and (ImH)[Co(DmgH₂)₂Cl₂] (II), where DmgH‾ is the dimethylglyoxime residue and Im is the imidazole molecule, are synthesized. The composition and structure of the crystals are determined from the elemental analysis, IR spectra, and single crystal X-ray diffraction. Complex I is molecular, containing the Im molecule as a coordinated ligand; complex II is of the ionic type with (ImH)⁺ involved as an outer-sphere organic cation. The mode of component packing in the crystals mainly depends on the imidazole position in the compounds.

The procedures are developed and the complexation products are preparatively isolated from GeO₂-H₄Cit-phen-CH₃CN-H₂O (I) and GeO₂-H₄Cit-CuCl₂-phen-C₂H₅OH-H₂O (II) systems (phen is 1,10-phenanthroline, H₄Cit is citric acid). The (Hphen)₂[Ge(HCit)₂]x3H₂O (I) and [Cu(phen)₂Cl]₂[Ge(HCit)₂]x6H₂O (II) complexes are characterized by elemental analysis, IR spectroscopy, and single crystal X-ray diffraction. The compounds are formed from centrosymmetric octahedral [Ge(HCit)₂]^2- anions, Hphen⁺ (I) and [Cu(phen)₂Cl]⁺ (II) cations, and crystallization water molecules. The structural units in the crystals are linked via a system of hydrogen bonds.

The structure (CIF file CCDC No. 1401886) of the hexaaqua-hexakis(2-thiobarbiturato)-disamarium [Sm₂(H₂O)₆(HTBA)₆] _n polymeric complex (I), where H₂ТВА is 2-thiobarbituric acid, is determined; its thermal decomposition and IR spectrum are studied. The crystals of I are monoclinic: a = 14.072(1) Å, b = 10.0842(6) Å, c = 15.323(1) Å, β = 110.408(2)°, V = 2037.9(2) ų, space group P2/n, Z = 2. All three independent thiobarbiturate anions HTBA^- coordinate to Sm³⁺ through oxygen atoms. To one of independent Sm³⁺ ions six (two terminal and four bridging) HTBA^- ions and two water molecules are coordinated; the second is bonded with four bridging HTBA^- and four water molecules, forming square antiprisms. The bridging HТВА^- anions arrange antiprisms in layers. The structure is stabilized by hydrogen bonds and a π-π interaction between the HТВА^- ions. The topology of the polymer network of I is analyzed.

The crystal and molecular structures of β-(N-benzoxazoline-2-thione)propionic acid, its monoethanolammonium (NН₂(CH₂)₂OH) and ethylenediammonium (NН₂(CH₂)₂NH₂) salts are studied. In the salts the monoethyleneamine amine group participates in the deprotonation of one ethylenediamine - two β-(N-benzthiazolin-2-one)propionic acid molecules. The geometry of the molecules and intermolecular hydrogen and donor-acceptor bonds in crystals are analyzed. In the crystal structures weak interactions form a two-dimensional layer whose thickness corresponds to unit cell sizes.

The new coumarine derivate with methyl ester of 2-(( Z )-1(2,4-dioxochroman-3-ylidene)ethylamino)-3-methylbutanoic acid and the corresponding palladium(II) complex are synthesized and characterized by microanalysis, infrared, ¹H and ¹³C NMR spectroscopy. The proposed structure of the ligand was confirmed based on the X-ray structural study.

On the example of aromatic alcohols, amines and thiols, weak hydrogen bonds ОН⋯π, NH⋯π, SН⋯π, CН⋯O, CН⋯N in the adsorption of nonrigid molecules on graphitized thermal carbon black (GTCB) are discussed in the review. The main theoretical approaches used for the description of the nature and the determination of the hydrogen bond energy are analyzed and formation criteria are defined. By B3LYP/aug-cc-pVDZ, B3LYP/aug-cc-pVTZ methods and the molecular statistical theory of adsorption the structural-energy parameters of conformers stable in the gas phase and the adsorbed state are determined. It is shown that for the correspondence of the experimental and calculated thermodynamic characteristics of adsorption of nonrigid molecules it is principally important to determine the exact structure of stable conformers is of The contribution of weak hydrogen bonds to the stabilization of conformer is confirmed by the non-covalent interaction method.

A new indium(III) fluoride complex with the ammonium cation (NH₄)₂[InF₅] is synthesized and its crystal structure is studied. The structure of (NH₄)₂[InF₅] is formed of cations and complex [InF₅]^2- anions. The In atom in the complex anion surrounded by four terminal and two bridging F atoms forms an almost regular octahedral coordination polyhedron (CN 6) with two terminal F atoms in the axial positions and two terminal and two bridging F atoms in the equatorial plane. Through bridging F atoms, the InF₆ polyhedra are arranged in polymer trans- vertex-connected corrugated anion chains (InF₅) directed along the c axis. The N-H⋯F hydrogen bonds organize the chains in a three-dimensional framework.

Single crystals of a mixed-ligand cadmium complex of the composition Cd(PHBA)₂(MEA) ₂ are grown from the solution of Cd(CH₃OO)₂, p-hydroxybenzoic acid (PHBA) and monoethanolamine (MEA) in aqueous ethanol. The crystallographic data are as follows: a = 11.6400(2) Å, b = 10.1363(1) Å, c = 16.6296(2) Å, β = 93.937(1)°, space group I2/a, V = 1957.44(5) ų, Z = 4. In the complex molecule located on the twofold axis, ligands of both types are bidentately bound to the cadmium ion having the coordination number 8. In the crystal structure, two H bonds of the O-H⋯O type combine complex molecules into layers parallel to the ab plane.

Binuclear bismuth complexes [H₂dabco]₂[Bi₂Cl₁₀]x2H₂O and (H₃O)₂[H₂dabco]₄[Bi₂Br₁₀] x [BiBr₆]₂x4.5H₂O are obtained by heating (100 °C) acidic solutions of a mixture of bismuth chloride and bromide with dabco. The structure of the complexes is determined by single crystal X-ray diffraction.

The X-ray crystal structure of (CH₃NH₃)₄[(Mg(H₂O)₅)₂(H₆W₁₂O₄₂)]Br₂×8H₂O (1) obtained by a reaction of Li₂WO₄×H₂O and Mg(NO₃)₂×6H₂O in the presence of MeNH₃Br is reported. Crystallographic parameters are: triclinic, space group P-1, a = 10.8280(4) Å, b = 12.4866(5) Å, c = 12.6201(5) Å, α = 108.501(1)°, β = 111.542(1)°, γ = 91.139(1)°, V = 1486.98(10) ų, Z = 1, C₄H₆₆Br₂Mg₂N₄O₆₀W₁₂, d_x = 3.959 g/cm³, T = 150 K, R₁ = 0.030 for 9914 F_o > 4δ(F) until 2θ_max = 66.6° The structure contains tetraprotonated [H₂W₁₂O₄₂]^10- anions coordinated with {Mg(H₂O)₅}²⁺ cations as ditopic ligands via terminal oxygen atoms. The crystal structure also incorporates outer-sphere CH₃NH₃⁺ and Br^- ions. The Mg²⁺ cations are in the octahedral environment, Mg-O(H₂O) and Mg-O(W) bond lengths being 2.102(5)÷2.044(5) Å and 2.071(5) Å, respectively.

The single crystal X-ray diffraction study of the heterometallic cluster CpMnFePt(m₃-C=CHPh)(PPh₃)(CO)₆ is performed. The crystallographic characteristics are as follows: a = 32.356(15) Å, b = 11.754(5) Å, c = 20.114(9) Å, β = 115.707(6)°, V = 6893(5) ų, space group C2/c, Z = 8, d_calc = 1.741 g/cm³. The cluster molecule contains a bridging phenylvinylidene ligand coordinated to a metallic core in the form of a Mn-Fe-Pt chain (the Mn-Fe and Fe-Pt bond lengths are 2.6768(14) Å and 2.6280(11) Å respectively and the Mn⋯Pt distance is 3.6425(19) Å).

A one-dimensional Cu(II) complex [Cu(BTE)₂(ClO₄)₂] _n (1) (BTE = 2,2'-bis(1H-1,2,4-triazolyl)ether) is synthesized and characterized using single crystal X-ray diffraction, IR, and elemental analysis. Single crystal X-ray diffraction analysis reveals that complex 1 is a one-dimensional chain based on the rhomboid subunit [Cu₂(BTE)₂] with a Cu…Cu separation of 9.0912(2) Å. There is no magnetic coupling between the Cu^II ions. Complex 1 displays a high photocatalytic degradation activity for methylene blue.

The title compound, 1,4,13,22,27-pentaaza-6,9:17,20:29,32-tribenzo-10,16,33-trioxabicyclo [11,11,11] pentatriacontane (C₃₃H₄₅N₅O₃), is synthesized by [1+1] tripodal condensation of trialdehyde (4,4',4"-triformyl-triphenoxytriethylamine) with tris(2-aminoethyl)amine (tren) in the presence of La(NO₃)₃x6H₂O as a template, followed by reduction with KBH₄. There are six unique molecules in the unit. The molecule has a threefold symmetry axis passing through the bridgehead nitrogen atoms in the structure. As a result, only one strand of the cryptand molecule is present in the asymmetric unit. The structure presents an endo-endo conformation, with the distance between the two bridgehead nitrogen atoms of 10.030(8) Å.

The XRD method is used to determine the molecular and crystal structure of 2,8,9-trioxa-5-aza-1-silabicyclo[3.3.3]undec-1-ylmethyl-2-methylacrylate (H₂C=C(Me)C(O)OCH₂Si(OCH₂CH₂)₃N). The crystallographic data are as follows: space group Р2₁2₁2₁, а = 9.7659(1) Å, b = 10.017(1) Å, с = 17.915(2) Å, V = 1753.3(3) ų, Z = 4. The coordination polyhedron of the silicon atom is a distorted trigonal bipyramid. The length of the N→Si coordination bond is 2.099 Å.

The synthesis of an analog of memantine-containing sulfanilamide gives single crystals of a by-product in the form of a salt. The results of the XRD structure determination of the obtained product are presented.

Single-crystal X-ray diffraction combined with quantum-chemical calculations and ¹⁵N NMR spectroscopy is used to investigate the molecular and crystal structures of the high-energy 2,4,6-triazidopyrimidine and 2,4,6-triazido-5-chloropyrimidine and analyze the dependence of the structural parameters of their azido groups on the position in the pyrimidine ring.

A new dinuclear nitrido-bridged ruthenium complex with pyridine ligands ([PyH][Ru₂N(Py)₄Cl₆] (1) is synthesized by reacting K₃[Ru₂NCl₈(H₂O)₂] (2) and excessive pyridine, then crystallized from dilute hydrochloric acid. Its crystal structure is determined by single crystal X-ray diffraction. The complex crystallizes in the form of red block crystals of the monoclinic symmetry and the space group C2. The nitrido-bridged ruthenium complex has very short Ru-N distances.

While growing 2-ethylbenzimidazole crystals from methanol, polymorph 1с is obtained. In polymorphs 1а-с, 2-ethylbenzimidazole molecules have a different arrangement in the packing and the position of the ethyl group relative to the benzimidazole plane. At the same time, the character (sequence) of intermolecular N-H…N bonds is maintained. In polymorph 1b with four independent molecules, there is an intermolecular Н bond between homonymous molecules. The study of the crystal structure of another benzimidazole derivative (2-(1-hydroxyethyl)benzimidazole (2)) reveals a new polymorph. The results of the comparative analysis of the crystal structures of two polymorphs 2а, 2b are presented.

Tetrakis(hydroxyacetato)bis(dimethyl sulfoxide)dirhodium(II) (1) is synthesized by the reaction of dimethyl sulfoxide (DMSO) with Rh₂(OOCCH₂OH)₄. The complex is characterized by elemental analysis, FT-IR, ESI⁺-MS, ¹H and ¹³C NMR, along with single crystal X-ray diffraction. The ambidentate DMSO ligands are bound to the rhodium center of 1 through their sulfur atoms, which is firstly predicated by its orange color, then confirmed by the observation of an increase in the S-O stretching frequencies, and finally, unambiguously determined by single crystal X-ray diffraction. The structure of 1 contains two similar but crystallographically independent molecules. Both molecules contain lantern dirhodium units, joined equatorially by four bidentate hydroxyacetate ligands and two monodentate DMSO axial ligands. Four hydrogen bonds link the molecules together with d(O⋯O) of 2.767(4)-2.824(4) Å to form a three dimensional network.

A Schiff base, 4-hydroxy-6-methyl-3-[(1E)-1-(2-phenylhydrazinylidene)ethyl]-2H-pyran-2-one, is synthesized and characterized by ¹H and ¹³C NMR, IR spectroscopy, ESI-mass spectrometry and single crystal X-ray diffraction analysis. There are three crystallographically independent molecules in the asymmetric unit, space group C2/c, a = 30.011(2) Å, b = 17.601(2) Å, c = 13.6878(13) Å, β = 92.532(4)°, and Z = 24. The final reliable index is 0.0406 for 5997 reflections. The molecules are linked through intermolecular N-H…O hydrogen bonds into three-linked molecules forming a supramolecular ring.