Molecular structure and conformation of nitrobenzene reinvestigated by combined analysis of gas-phase electron diffraction,rotational constants,and theoretical calculations

The molecular structure and conformation of nitrobenzene has been reinvestigated by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) spectroscopic data, and quantum chemical calculations. The equilibrium r _e structure of nitrobenzene was determined by a joint analysis of the GED data and rotational constants taken from the literature. The necessary anharmonic vibrational corrections to the internuclear distances (r _e ? r _a) and to rotational constants (B _e ⁽ⁱ⁾  ? B ₀ ⁽ⁱ⁾ ) were calculated from the B3LYP/cc-pVTZ quadratic and cubic force fields. A combined analysis of GED and MW data led to following structural parameters (r _e) of planar nitrobenzene (the total estimated uncertainties are in parentheses): r(C–C)_av = 1.391(3) Å, r(C–N) = 1.468(4) Å, r(N–O) = 1.223(2) Å, r(C–H)_av = 1.071(3) Å, \({\angle}\)C2–C1–C6 = 123.5(6)°, \({\angle}\)C1–C2–C3 = 117.8(3)°, \({\angle}\)C2–C3–C4 = 120.3(3)°, \({\angle}\)C3–C4–C5 = 120.5(6)°, \({\angle}\)C–C–N = 118.2(3)°, \({\angle}\)C–N–O = 117.9(2)°, \({\angle}\)O–N–O = 124.2(4)°, \({\angle}\)(C–C–H)_av = 120.6(20)°. These structural parameters reproduce the experimental B ₀ ⁽ⁱ⁾ values within 0.05 MHz. The experimental results are in good agreement with the theoretical calculations. The barrier height to internal rotation of nitro group, 4.1±1.0 kcal/mol, was estimated from the GED analysis using a dynamic model. The equilibrium structure was also calculated using the experimental rotational constants for nitrobenzene isotopomers and theoretical rotation–vibration interaction constants.     

Gas-phase structure and conformational properties of copper (I) pivalate dimer (CuC5H9O2)2

The molecular structure and conformational properties of gaseous dimer of copper (I) pivalate, Cu₂piv₂, have been studied by gas electron diffraction (GED) at 413(5) K and quantum chemical calculations (DFT and MP2). The molecule possesses a planar eight-membered skeleton. Two conformers, “staggered” of C _2h symmetry and “eclipsed” of C _2v symmetry, were found for Cu₂piv₂ in the gas phase. The following geometric parameters of the skeleton ring and the tert-butyl groups have been determined from the GED experiment for the “staggered” form: r_g(Cu···Cu) = 2.520(8) Å, r_g(Cu–O)_ave = 1.871(4) Å, r_g(C–O)_ave = 1.273(3) Å, r_g(C–C)_ring-tert = 1.531(4) Å, r_g(C–C)_{tert-out-of-plane-ring} = 1.536(4) Å, r_g(C–C)_{tert-in-the-plane-ring} = 1.527(4) Å, r_g(C–H)_ave = 1.087(5) Å, (O–Cu–O) = 172.12°(3). Computations predict the internal rotation of the tert-butyl groups to be independent. The value of calculated Wiberg bond index for Cu···Cu testifies the existence of weak bonding between two copper atoms.

     

The structure of μ-oxo dimer of aluminium(III) porphyrin: a theoretical study

The gas-phase molecular structure of μ-oxo dimer of aluminium(III) porphyrin, (AlP)₂O, has been studied for the first time by density functional theory calculations using the B3LYP and M06 functionals and triple-ζ valence basis sets. The molecule has two conformers with equilibrium structures of D _4d and D _4h symmetries with parallel macrocycles and aluminium-oxygen distances of 1.680–1.684 Å (M06/cc-pVTZ). The aluminium atom lies out of the plane of the four central nitrogen atoms and forms a square-based pyramid with them, with the following parameters (M06/cc-pVTZ): r(Al–N) = 2.030–2.031 Å, r(N···N) = 2.803–2.804 Å (the side of the pyramid base), z(Al)–z(N) = 0.434–0.446 Å (the height of the pyramid).     

The molecular structure of tris-2,2,6,6-tetramethyl-heptane-3,5-dione indium: gas-phase electron diffraction and quantum chemical calculations

The molecular structure of tris-2,2,6,6-tetramethyl-heptane-3,5-dione indium, or In(thd)₃, has been determined by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both the DFT calculations and the GED data collected at 387(8) K indicate that the molecules have D ₃ symmetry with a distorted anti-prismatic InO₆ coordination geometry. According to GED refinements, the twist angle θ, i.e. the angle of rotation of the upper and lower O₃ triangles in opposite directions relative to their positions in a regular prism is θ = ±24.9(1.2)° and the bond distances (r _h1) in the chelate ring are In–O = 2.127(4) Å, C–O = 1.268(3) Å and C–C = 1.411(3) Å, respectively. The DFT calculations yielded structure parameters in close agreement with those found experimentally.     

Molecular structure and barriers to internal rotation of α-naphthalenesulfonyl chloride: a study by gas-phase electron diffraction and quantum chemical calculations

α-Naphthalenesulfonyl chloride, α-NaphSC, was studied by gas-phase electron diffraction (GED) and quantum chemical calculations (HF/6-311 + G**, HF/aug-cc-pVDZ, B3LYP/cc-pVDZ, B3LYP/cc-pVTZ, B3LYP/aug-cc-pVDZ, B3LYP/aug-cc-pVTZ, MP2/cc-pVDZ, and MP2/cc-pVTZ). The calculations predict the existence of two conformers with C ₁ (I) and C _s (II) symmetries. The most stable conformer I has an enantiomer. The experimental data of α-NaphSC obtained at 370(5) K could be best fitted by a C ₁ symmetry model indicating that only this form exists in the gas-phase. In this model the C_α–S–Cl plane deviates from the perpendicular orientation relative to the plane of the naphthalene skeleton. Under the applied experimental conditions, the mole fraction of a second less stable conformer II of α-NaphSC predicted by calculations is no more than 1 %. The following geometrical parameters of conformer I were obtained from the experiment (Å and °; uncertainties are in parentheses): r _h1(C–H) = 1.082(6), r _h1(C–C)_cp = 1.407(3), r _h1(C–S) = 1.764(5), r _h1(S–O)_av = 1.425(3), r _h1(S–Cl) = 2.051(5), ∠C–C_α–C = 122.5(1), ∠C_α–S–Cl = 101.5(10); C9–C1–S–Cl = 71.4(21). The calculated barriers to internal rotation of the sulfonyl chloride group exceed considerably the thermal energy values corresponding to the temperatures of the GED experiments. Natural bond orbitals analysis of the electron density distribution was carried out to explain the peculiarities of the molecular structure of the studied compound and the deviation from the structures of β-NaphSHal molecules and their benzene analogs.     

Molecular structure of N,N′-o-phenylene-bis(salicylideneaminato)copper(II) studied by gas-phase electron diffraction and quantum-chemical calculations

The molecular structure of N,N′-o-phenylene-bis(salicylideneaminato)copper(II) (Cu(saloph)) was determined using the combination of gas-phase electron diffraction (GED), mass spectrometry, and quantum-chemical calculations. According to both experimental and theoretical approaches the molecule of Cu(saloph) is planar and possesses C _2v symmetry. Main structural parameters determined by GED experiment are the following (total error is given in a brackets): r _h1(Cu–N) = 1.960(20) Å, r _h1(Cu–O) = 1.913(17) Å, ∠NCuN = 82.7(18)°, ∠OCuO = 91.6(21)°, ∠NCuO = 92.9(9)°. The experimental structural parameters of Cu(saloph) molecules determined by X-ray single crystal analysis and GED experiments were discussed and compared to the theoretical ones.

     

Synthesis,characterization, and thermochemical property of a novel mixed alkali metal borate: NaCs[B10O14(OH)4]

A novel mixed alkali metal hydrated borate NaCs[B₁₀O₁₄(OH)₄] was synthesized under hydrothermal conditions. Its structure was determined by single-crystal X-ray diffraction and further characterized by FT-IR spectroscopy, TG-DTA, powder X-ray diffraction, and chemical analysis. NaCs[B₁₀O₁₄(OH)₄] crystallizes in monoclinic space group P2/c with a = 7.6588(3) Å, b = 9.0074(3) Å, c = 11.8708(6) Å, and β = 115.682(3)°. The crystal structure of NaCs[B₁₀O₁₄(OH)₄] consists of Na–O, Cs–O polyhedral, and [B₁₀O₁₄(OH)₄]^2? polyborate anions. [B₁₀O₁₄(OH)₄]^2? units are connected together through common oxygen atoms forming a 1D helical chain-like structure, which are further connected by O–H···O hydrogen bonds forming a 3D supramolecular structure. Through a designed thermochemical cycle, the standard molar enthalpy of formation of this borate was determined to be ?7888.6 ± 8.1 kJ mol^?1 by using a heat conduction microcalorimeter.     

The molecular structures of tris(dipivaloylmethanato)chromium and tris(dipivaloylmethanato)cobalt determined by gas electron diffraction and density functional theory calculations

The molecular structures of tris(dipivaloylmethanato)chromium and tris(dipivaloylmethanato)cobalt have been determined by quantum chemical calculations and gas electron diffraction. Both the experimental data and the theoretical results are consistent with molecular structures having D ₃ symmetry which is in agreement with the Kepert model. The experimental bond distances, r _h1(Å), and bond angles, ∠ _h1(°), are: Cr–O = 1.976(5), C–O = 1.287(3), C–C_r = 1.392(6), C–C_t = 1.547(3), OCrO = 90.1(0.9), CC_rC = 122.3(0.9), OCC_t = 114.7(0.9) and Co–O = 1.891(4), C–O = 1.269(3), C–C_r = 1.411(5), C–C_t = 1.546(3), OCoO = 95.2(0.5), CC_rC = 122.5(0.9), OCC_t = 115.1(0.8).     

Molecular and crystal structure of 15-acetylsongorine and songoramine isolated from <Emphasis Type="Italic">Aconitum szechenyianum</Emphasis> Gay

Two napelline skeletal diterpenoid alkaloids 15-acetylsongorine, C₂₄H₃₃NO₄ I, and songoramine, C₂₂H₂₉NO₃ II, were first isolated from the roots of Aconitum Szechenyianum Gay. The crystal structures were determined by X-ray single-crystal diffraction analysis. The crystal I is the triclinic system with space group P1 having unit cell parameters of a = 9.360(8) Å, b = 11.593(9) Å, c = 11.830(16) Å, α = 113.223(15)°, β = 105.950(16)°, γ = 101.296(12)°, and Z = 2. Hydrogen bonds O–H···O and O–H···N joint the molecules into dimer. The crystal II belongs to the orthorhombic system with space group P2₁2₁2₁ having unit cell parameters of a = 8.950(2) Å, b = 13.272(3) Å, c = 15.454(4) Å and Z = 4. The O–H···O hydrogen bonding interaction links the molecule into linear chains. The distortion of rings of compound I and II were evaluated by calculation of the Cremer and Pople puckering parameters. The presence of the C–O–C bond in the compound II results in the changes of ring conformations compared with that of the compound I.     

Hydrogen bonding and structural complexity in the Cu<Subscript>5</Subscript>(PO<Subscript>4</Subscript>)<Subscript>2</Subscript>(OH)<Subscript>4</Subscript> polymorphs (pseudomalachite,ludjibaite, reichenbachite): combined experimental and theoretical study

Hydrogen bonding in the Cu₅(PO₄)₂(OH)₄ polymorphs pseudomalachite, ludjibaite and reichenbachite has been studied by low-temperature single-crystal X-ray diffraction (XRD; pseudomalachite) and solid-state density functional theory (DFT; pseudomalachite, ludjibaite, reichenbachite) calculations. Pseudomalachite at 100 K is monoclinic, P2₁/c, a = 4.4436(4), b = 5.7320(5), c = 16.9300(15) Å, β = 91.008(8)°, V = 431.15(7) ų and Z = 2. The structure has been refined to R ₁ = 0.025 for 1383 unique observed reflections with |F _o| ≥ 4σ_F. DFT calculations were done with the CRYSTAL14 software package. For pseudomalachite, the difference between the calculated and experimental H sites does not exceed 0.152 Å. Structural configurations around hydroxyl groups in all three polymorphs show many similarities. Each OH5 group is involved in a three-center (bifurcated) hydrogen bond with the H···A distances in the range of 2.141–2.460 Å and the D–H···A angles in the range of 122.41°–139.30°, whereas each OH6 group forms a four-center (trifurcated) bond (H···A = 2.093–2.593 Å; D–H···A = 122.79°–137.71°). The crystal structures of the Cu₅(PO₄)₂(OH)₄ polymorphs are based on three-dimensional frameworks of Cu and P polyhedra. The copper-centered octahedra share edges to form two-dimensional layers parallel to (100) in all three structures. The layers have square voids above and beneath PO₄ tetrahedra that link adjacent layers by sharing O atoms with two CuO₆ octahedra each. From the topological point of view, none of the polymorphs can be obtained from another by a displacive transformation, and therefore pseudomalachite, ludjibaite and reichenbachite can be viewed as combinatorial polymorphs. According to information-based structural complexity considerations, the three phases are very similar in their configurational entropies and preferential crystallization of one phase over another cannot be entropy driven and is probably governed by other mechanisms that may involve such factors as structures of prenucleation clusters, chemical admixtures, etc.     

A New Organic-Paradodecatungstate Hybrid Compound: Synthesis, Characterization and Crystal Structure

An organic–inorganic hybrid compound Na₂(HAn)₈[H₂W₁₂O₄₂]·16H₂O (HAn: p-anisidinium, C₇H₁₀NO) has been synthesized under soft acidic conditions and characterized by infrared and UV–visible spectroscopies, thermogravimetric analysis, cyclic voltammetry and single crystal X-ray diffraction. The compound crystallizes in the monoclinic P2₁/n space group with a = 10.1920(4) Å, b = 34.2901(9) Å, c = 14.0745(5) Å, β = 95.830(3)°, V = 4,893.4(3) Å³ and Z = 4. The compound exhibits a 2D supramolecular structure formed by alternated [paradodecatungstate/Na] and p-anisidinium layers. The catalytic activity of the compound for oxidation of cyclooctene with H₂O₂ was proved and gives rise to good reaction yield.     

Neutron Diffraction Study on the Structure of Aqueous LiNO3 Solutions

Neutron diffraction measurements were carried out at 25 °C for aqueous LiNO₃ heavy water solutions, (*LiNO₃) _x (D₂O)_1?x where x = 0.1, 0.05 and 0.01, in which the ⁶Li/⁷Li isotopic ratios were varied. Structural information on intermolecular nearest neighbor Li⁺···D₂O interactions in the extensive concentration range was derived from the first-order difference function, ?_Li(Q), obtained from the difference in scattering cross sections between ⁶Li- and ⁷Li-enriched sample solutions. The nearest neighbor Li⁺···O distance and coordination number for sample solution with x = 0.1 were determined to be r _LiO = 1.969 (8) Å and n _LiO = 4.12 (6), respectively, corresponding to the four-coordinated Li⁺ ion in the solution. On the other hand, those obtained for the solution with x = 0.01 are r _LiO = 2.00 (2) Å and n _LiO = 6.0 (2), respectively, indicating that hexaaqua Li⁺ is dominant in the dilute solution. These results clearly indicate that a concentration dependence of the hydration number of Li⁺ occurs in the aqueous solutions.     

Synthesis,Structural Characterization and Properties of Two Strontium Borates Constructed from Oxo Boron Clusters

Two strontium borates Sr₂[B₆O₉(OH)₄] (1) and Sr₂B₅O₉(OH)·H₂O (2), with acentric structures have been synthesized under hydro/solvothermal conditions. Compound 1 is reported for the first time in the strontium borates system, and it crystallizes in the monoclinic space group P2₁ with unit cell parameters a = 6.8445(5) Å, b = 8.7033(6) Å, c = 8.4632(6) Å, β = 100.581(6)°, V = 495.58(6) ų and Z = 2. Its structure consists of unusual borate layers of 3, 11-membered rings, which are interconnected via Sr–O ionic bonds and hydrogen bonds to generate a 3D supramolecular network. Compound 2 is a known strontium borate, crystallizing in the monoclinic space group C ₂ with a = 10.161 (13) Å, b = 7.965(4) Å, c = 6.393(11) Å, β = 128.0(2)°, V = 407.7(14) ų and Z = 2. Second-harmonic generation measurements on the powder samples reveal that 1 and 2 exhibits good SHG efficiency about 1.5 and 2 times that of KDP (KH₂PO₄) powder respectively.     

Synthesis,characterization, crystal and molecular structure analysis of a novel 1-benzhydryl piperazine derivative: 1-benzhydryl-4-(2-nitro-benzenesulfonyl)-piperazine

A novel 1-benzhydryl piperazine derivative 1-benzhydryl-4-(2-nitro-benzenesulfonyl)-piperazine was synthesized by the nucleophilic substitution of 1-benzhydryl piperazine with 2-nitro-benzenesulfonyl chloride. The product obtained was characterized spectroscopically and finally confirmed by X-ray diffraction study. The title compound, C₂₃H₂₃N₃O₄S crystallizes in the monoclinic space group C2/c with cell parameters a = 13.1120(9) Å, b = 21.4990(9) Å, c = 16.655(1) Å, β = 111.352(2)°, Z = 8, and V = 4372.7(4) Å. The structure reveals that the piperazine ring is in a chair conformation. The geometry around the S atom is distorted tetrahedral. There is a large discrepancy in the bond angles around the piperazine N atoms. The structure is stablized by C–H···O type intermolecular hydrogen bonding interactions.     

Investigation into the crystal structure of bis(pyridine)-bis(trichloroacetato) copper(II) and its electrophotochemical properties

A novel chained Cu(II) complex was synthesized from trichloroacetato copper(II) and pyridine in ethanol solvent, and characterized by elemental analysis and infrared (IR) spectroscopy. The special crystal structure of the Cu(II) complex was determined by X-ray single-crystal diffraction. The results indicate that a chained structure of the Cu(II) complex formed through intermolecular hydrogen bonds. Cu(CCl₃COO)₂(C₅H₅N)₂(H₂O) was monoclinic, with unit cell P21/c and cell parameters as follows: a = 14.389(3) Å, b = 7.1911(14) Å, c = 23.107(8) Å, V = 2,257.5(10) Å³, Z = 4, M _r = 564.51, D _c = 1.661 mg/m³, T = 293(2) K, F(000) = 1,124, μ(Mo K_α) = 1.704 mm^?1, R = 0.0984, and ωR = 0.2791. The electrochemical behavior of the Cu(II) complex on a glassy carbon working electrode determined by cyclic voltammetry showed the electrochemical activity of the title compound at 0.2 to ?0.3 V (versus SCE) in NH₃–NH₄Cl buffer solution (pH 9.2), and the redox peak current of the complex had a good linear relationship with the square root of the scan rate in the range 0.02–0.2 V/s.     

Molecular structure of p-diisocyanobenzene from gas-phase electron diffraction and theoretical calculations and effects of intermolecular interactions in the crystal on the benzene ring geometry

In this study, the molecular structure of p-diisocyanobenzene has been determined by gas-phase electron diffraction and quantum chemical calculations. The electron diffraction intensities from a previous study by Colapietro et al. (J Mol Struct 125:19–32, 1984) have been reanalyzed using geometrical constraints and initial values of vibrational amplitudes from computations. The equilibrium structure of the molecule has D _2h symmetry, whereas the average geometry in the gaseous phase is best described by a non-planar model of C _2v symmetry. The lowering of symmetry is due to large-amplitude motion of the substituents out of the plane of the benzene ring. The non-planar model has an internal ring angle at the ipso position, ∠_aC2–C1–C6 = 120.6 ± 0.2°, about 1° smaller than that from the previous study, but consistent with the quantum chemical calculations. The mean length of the ring C–C bonds and the length of the triple bond are accurately determined as 〈r _g(C–C)〉 = 1.398 ± 0.003 Å and r _g(N≡C) = 1.177 ± 0.002 Å, respectively. Comparison with the gaseous isoelectronic molecules p-diethynylbenzene and p-dicyanobenzene shows that the differences in the mean lengths of the ring C–C bonds and in the lengths of the triple bonds determined by electron diffraction are equal or closely similar to the corresponding differences from quantum chemical calculations. The present experimental value of the ipso angle in free p-diisocyanobenzene is slightly, but significantly smaller than that obtained by X-ray crystallography. The difference is confirmed by computational modeling of the crystal structure and appears to be due to –N≡C···H–C intermolecular interactions in the crystal.     

Synthesis,characterization, crystal structure and cytotoxicity of 2,4-bis(selenomethyl)quinazoline

Organoselenium compounds have already been reported to be good anticarcinogenic candidates. A new selenoquinazoline derivative, 2,4-bis(selenomethyl)quinazoline (compound 1), has been synthesized, spectroscopically characterized and its crystal structure has been studied. An intermolecular coupling between C₂ and \( {\text{H}}_{5}^{\prime } \) in the Heteronuclear Multiple Bond Correlation (HMBC) experiment has been observed. Assuming that the head-to-tail overlap of parallel molecules (as identified by X-ray diffraction) remains in solution to give bimolecular entities, the π–π interaction enables heteronuclear coupling between the former atoms with a three-bond distance [C₂···(π–π)···\( {\text{C}}_{5}^{\prime } \)–\( {\text{H}}_{5}^{\prime } \)]. The crystal structure of compound 1 has been solved by X-ray diffraction. It crystallizes in triclinic system, space group P?1. Unit cell parameters are a = 7.4969(7) Å, b = 8.7008(8) Å, c = 10.1666(9) Å, α = 110.215(2)°, β = 90.354(2)°, γ = 115.017(1)°. Linear chains in crystals of compound 1 are generated by C–H···Se and Se···Se bonds between molecules. Furthermore, head-to-tail overlap of parallel molecules, in which π–π interactions can occur, is observed. Compound 1 exhibited a cytotoxic effect in all of the evaluated tumoral cell lines and showed a higher cytotoxic effect in colon and breast cancer cell lines than etoposide, which was used as a reference compound.     

Solvothermal Syntheses and Crystal Structures of Two Novel Borates: [(CH3)3NH][B5O6(OH)4] and Na2[H2TMED][B7O9(OH)5]2

Two novel borates [(CH₃)₃NH][B₅O₆(OH)₄] (I) and Na₂[H₂TMED][B₇O₉(OH)₅]₂ (II) have been synthesized under solvothermal conditions, and characterized by elemental analyses, FT-IR spectroscopy, and single crystal X-ray diffraction. Crystal data for I: monoclinic, P2₁/c, a = 9.3693(11) Å, b = 14.0375(17) Å, c = 10.0495(9) Å, β = 91.815(9)°, Z = 4. Crystal data for II: monoclinic, P2₁/c, a = 11.6329(2) Å, b = 11.9246(3) Å, c = 10.2528(2) Å, β = 100.178(2)°, Z = 4. Their crystal structures both have 3D supramolecular framework with large channels constructed by O–H···O hydrogen-bonding among the polyanions of [B₅O₆(OH)₄]^? or [B₇O₉(OH)₅]^2? clusters. The templating organic amines cations in I and II are both located in the channels of 3D supramolecular frameworks, respectively, and interact with the polyborate frameworks both electrostatically and via hydrogen bonds of N–H···O. Na₂[H₂TMED][B₇O₉(OH)₅]₂ is the first example of heptaborate co-templated by alkali metal and organic base, which is also rare in borates. The photoluminescence property of the synthetic sample of Na₂[H₂TMED][B₇O₉(OH)₅]₂ in the solid state at room temperature was also investigated by fluorescence spectrophotometer.     

Palladium complexes bearing the dipyridyl ligand: synthesis,structural studies,and use in the Heck reaction

Two new palladium complexes derived from the di(2-pyridinyl)methanone N-(2-pyridinyl)hydrazone (DPMNPH) ligand are reported. The compounds were characterized by elemental analysis, spectroscopic studies, and, for the DPMNPH ligand, single-crystal X-ray diffraction analysis. The DPMNPH ligand crystallized as orthorhombic with the space group P2₁2₁2₁. The H1 atom is intramolecularly bonded to the pyridinic N4 with N1–H1 = 0.92(3) Å, H1···N4 = 1.87(2) Å, N1···N4 = 2.615(2) Å, and N1–H1···N4 = 137(2)°. Both complexes were excellent catalysts in the Heck reaction in the presence of base.