Molecular structure of N-chlorosuccinimide studied by gas-phase electron diffraction and quantum-chemical methods

The molecular structure of N-chlorosuccinimide has been studied by GED method at the nozzle temperature of 116 °C. Vibrational corrections to the r _a parameters, Δ(r _a − r _e), have been calculated using the scaled quadratic and cubic force constants from B3LYP/6-31G(df,p) calculations. The force field scaling has been carried out using the IR and Raman spectra of the solid N-chlorosuccinimide. The molecular skeleton and the bond conformation around nitrogen were found to be planar within large experimental errors. The equilibrium geometrical parameters derived from the experimental data assuming C _2v molecular symmetry and those from MP2(fc)/6-311G(3df,2pd) calculations are in a good agreement.     

Molecular Structure and Conformational Composition of 1-[(Methylthio)methyl]-2-nitrobenzene (MTMNB): A Theoretical and Experimental Study

The conformational composition of gaseous MTMNB and the molecular structures of the rotational forms have been studied by electron diffraction at 130^∘C aided by results from ab initio and density functional theory calculations. The conformational potential energy surface has been investigated by using the B3LYP/6-31G(d,p) method. As a result, six minimum-energy conformers have been identified. Geometries of all conformers were optimized using MP2/6-31G(d,p), B3LYP/6-31G(d,p), and B3LYP/cc-pVTZ methods. These calculations resulted in accurate geometries, relative energies, and harmonic vibrational frequencies for all conformers. The B3LYP/cc-pVTZ energies were then used to calculate the Boltzmann distribution of conformers. The best fit of the electron diffraction data to calculated values was obtained for the six conformer model, in agreement with the theoretical predictions. Average parameter values (r_a in angstroms, angle α in degrees, and estimated total errors given in parentheses) weighted for the mixture of six conformers are r(C–C) = 1.507(5), r(C–C)_{ring, av} = 1.397(3), r(C–S)_av = 1.814(4), r(C–N) = 1.495(4), r(N–O)_av = 1.223(3), ∠(C–C–C)_ring = 116.0–122.5, ∠ C6–C4–C7 = 118.2(4), ∠ C–C–S = 113.6(6), ∠ C–S–C = 98.5(12), ∠ N–C–C4 = 121.9(3), ∠(O–N–C)_av = 116.8(3), ∠ O–N–O = 127.0(4). Torsional angles could not be refined. Theoretical B3LYP/cc-pVTZ torsional angles for the rotation about C–N bond, φ_C−N, were found to be 30.5–36.5^∘ for different conformers. As to internal rotation about C–C and C–S bonds, values of φ_C−C = 68–118^∘ and φ_C−S = 66–71^∘ were obtained for the three most stable conformers with gauche orientation with respect to these bonds. Some conclusions of this work were presented in a short communication in Russ. J. Phys. Chem. 2005, 79, 1701.     

Molecular structure and conformation of triphenylsilane from gas-phase electron diffraction and theoretical calculations, and structural variations in H4?nSiPhn molecules (n?=?1–4)

The molecular structure of triphenylsilane has been investigated by gas-phase electron diffraction and theoretical calculations. The electron diffraction intensities from a previous study (Rozsondai B, Hargittai I, J Organomet Chem 334:269, 1987) have been reanalyzed using geometrical constraints and initial values of vibrational amplitudes from calculations. The free molecule has a chiral, propeller-like equilibrium conformation of C ₃ symmetry, with a twist angle of the phenyl groups τ = 39° ± 3°; the two enantiomeric conformers easily interconvert via three possible pathways. The low-frequency vibrational modes indicate that the three phenyl groups undergo large-amplitude torsional and out-of-plane bending vibrations about their respective Si–C bonds. Least-squares refinement of a model accounting for the bending vibrations gives the following bond distances and angles with estimated total errors: r _g(Si–C) = 1.874 ± 0.004 ?, 〈r _g(C–C)〉 = 1.402 ± 0.003 ?, 〈r _g(C–H)〉 = 1.102 ± 0.003 ?, and ∠_aC–Si–H = 108.6° ± 0.4°. Electron diffraction studies and MO calculations show that the lengths of the Si–C bonds in H_4−n SiPh _n molecules (n = 1–4) increase gradually with n, due to π → σ*(Si–C) delocalization. They also show that the mean lengths of the ring C–C bonds are about 0.003 ? larger than in unsubstituted benzene, due to a one hundredth angstrom lengthening of the C_ipso–C_ortho bonds caused by silicon substitution. A small increase of r(Si–H) and decrease of the ipso angle with increasing number of phenyl groups is also revealed by the calculations.     

Investigation of the structure and energetics ofΒ-diketonates. VI. Molecular structure of calcium dipivaloylmethanate Ca(DPM)2 according to gas phase electron diffraction data

Combined mass spectrometric and electron diffraction study of the overheated vapor over calcium dipivaloylmethanate was performed. It was established that one molecular form, Ca(DPM)₂, predominates in the vapor at 420–460‡C. The r_a, r_g and r_a parameters of the Ca(DPM)₂ molecule were determined, and the symmetry of the molecule was found to be D_2d.     

Kinetics of reductive stripping of Pu(IV) in the tributylphosphate-kerosene/nitric acid-water system using dihydroxyurea

The kinetics of the reductive stripping of plutonium(IV) by dihydroxyurea (DHU) in 30% TBP/kerosene-HNO₃ system was studied with a constant interfacial area cell. The stripping rate of plutonium(IV) increases with the increase of the stirring speed of two phases and the interfacial area. The activation energy of this process is 28.4 kJ/mol. Under the given experimental conditions, the mass transfer of Pu is not controlled by redox reaction, but controlled by molecular diffusion from the organic phase to organic film layer and from the aqueous film layer to aqueous phase. The rate equation of reductive stripping (process is controlled by diffusion) was obtained as: r ₀ = k′[Pu(IV)]₀[DHU]_a ^0.16[HNO₃]_a ^−0.34. The rate constant k′ is (5.0±0.4)·10⁻² (mol/L)^0.18·min⁻¹ at 18.0°C.     

Conformational properties of <Emphasis Type="Italic">ortho</Emphasis>-nitrobenzenesulfonamide in gas and crystalline phases. Intra- and intermolecular hydrogen bond

A combined gas-phase electron diffraction and quantum chemical (B3LYP/6-311+G**, B3LYP/cc-pvtz, MP2/cc-pvtz) study of molecular structure of 2-nitrobenzenesulfonamide (2-NBSA) was carried out. Quantum chemical calculations showed that 2-NBSA has four conformers, two of which are stabilized by intramolecular hydrogen bond. The latter (with the S–N bond in a close to orthogonal position around the phenyl ring and differing from each other by staggered or eclipsed positions of the N–H and S=O bonds in the SO₂NH₂ group) presented in a saturated vapor over 2-NBSA at T = 433 (3) K in commensurable amounts. Experimental internuclear distances (Ǻ) for the staggered conformer are (?): r _h1(C–H)_av. = 1.071(9), r _h1(C–C)_av. = 1.390(4), r _h1(C–S) = 1.789(8), r _h1(S=O)_av. = 1.427(6), r _h1(S–N) = 1.644(6), r _h1(N–O)_av. = 1.221(4), r _h1(C′–N) = 1.487(8), r _h1(N–H)_av. = 1.014. Calculations at B3LYP/cc-pvtz level were performed to determine the structure and the energies of the transition states between conformers. It was shown that the conformer structures of free molecule differ from those of a molecule stabilized by intermolecular hydrogen bonds in a crystal. Influence of a substituent X (X = –CH₃, –NO₂) on conformational features of the ortho-substituted benzenesulfonamide was established.     

Investigation of the structure and energy of β-diketonates. XIV. Composition of overheated vapors and the molecular structure of monomeric yttrium tris-hexafluoroacetylacetonate Y(C5O2HF6)3

Simultaneous electron diffraction and mass spectrometry along with a quantum chemical (DFT/B3LYP) calculation are applied to study the molecular structure of yttrium tris-hexafluoroacetylacetonate Y(hfa)₃. The superheating of the vapor in a double two-temperature effusion cell shows that up to a temperature of ∼200°C ions containing from one to three metal atoms are formed, and the most intensive ion has the stoichiometry of (Y₂L₅)⁺ at a temperature below ∼120°C. The monomer starts to noticeably decompose at temperatures above 330°C.The electron diffraction patterns of monomers are obtained at T _exp = 208(5)°C. According to the results of theoretical and experimental investigations, Y(hfa)₃ molecule has D ₃-symmetry. The rotation angle of triangular O-O-O faces with respect to their position in the regular prism is equal to 14.4(1)°C. The values of internuclear distances and valence angles (r _h1-geometry) are: r(Y-O) = 2.259(6) Å, r(C-O) = 1.263(6) Å, r(C-C_r) = 1.413(4) Å, r(C-C_F) = 1.531(4) Å, r(C-F) = 1.344(3) Å, O-Y-O = 75.2(2)°, O-C-C_F = 113.8(2)°, C-C_F-F = 112.4(2)°. The results of quantum chemical calculations are well consistent with the experimental data. Original Russian Text Copyright ? 2007 by G. V. Girichev, V. V. Rybkin, N. V. Tverdova, S. A. Shlykov, N. P. Kuz’mina, and I. G. Zaitseva __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 48, No. 5, pp. 871–879, September–October, 2007.     

The strength and length of donor-acceptor bonds in molecular complexes

Numerous published data on the structure and thermodynamics of formation of molecular complexes are analyzed. The enthalpies of complexation (−ΔH) are related to the characteristic parameter Δr = [r _DA−a ₁(r _D+r _A)], where r _DA is the donor-acceptor bond length determined by microwave spectroscopy and X-ray analysis, r _D and r _A are the tabulated values of the homopolar covalent radii of the heteroatoms that form the donor-acceptor bond, and a ₁ is an empirical coefficient equal to 0.901±0.007. The relation between −ΔH and Δr values has the form −ΔH = a ₂/Δr (a ₂ = 21.6±1.6 kJ Å mol⁻¹), with a mean relative error of approximation of about 15% and a correlation coefficient of 0.97. As the strength of the complex increases, the donor-acceptor bond length approaches the sum of the heteropolar covalent radii of the atoms involved in the bond (Δr tends to zero). At Δr ≫ 1, the strength of complexes is determined by weak van der Waals interactions between the complex components and the −ΔH values tend to zero. Dedicated to the memory of E. N. Guryanova (1911–2004), a prominent scientist who formulated the basic principles elaborated by her disciples in this review. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1869–1878, October, 2007.     

Structure and energy studies of Β-diketonates. 5. structure of the Y(DPM)2 radical from gas-phase electron diffraction data

The overheated vapor of yttrium tris-dipivaloyl methanate was studied by combined electron diffractometry and mass spectrometry. It was established that at 760 K the vapor of Y(DPM)₃ contains the Y(DPM)₂ molecular form. The r_a, r_g, and r_a parameters of Y(DPM)₂ were determined, and it was found that the chelate system of Y(DPM)₂ has a planar structure. Possible reasons for differences in the intemuclear distances of the Y(DPM)₂ and Y(DPM)₃ molecular forms are discussed. Translated fromZhurnal Strukturnoi Khimii, Vol. 38, No. 3, pp. 480–488, May–June, 1997.     

The influence of steric hindrance on conformation properties and molecular structure of 2,4,6-trinitrobenzenesulfonic acid: gas electron diffraction and quantum chemical calculations

A combined gas-phase electron diffraction and quantum chemical (B3LYP/cc-pVTZ, MP2/cc-pVDZ) study of molecular structure of 2,4,6-trinitrobenzenesulfonic acid (2,4,6-tri-NBSA) was carried out. Quantum chemical calculations showed that 2,4,6-tri-NBSA possesses six conformers, which form three pairs of enantiomers with the relative energy of 0, 4.4/3.9, and 2.5/2.5 kcal/mol. It was experimentally established that at T = 444(5) K a saturated vapor over 2,4,6-tri-NBSA is, predominantly (up to 93 mol.%), represented by a low-energy enantiomers II and II′ characterized by intramolecular hydrogen bond between an H atom of the hydroxyl group and one of the O atoms of the NO₂ group. Experimental internuclear distances for the low-energy enantiomers are (?): r _h1(C–C)_av. = 1.387(4), r _h1(C–S) = 1.811(6), r _h1(S=O)_av. = 1.424(4), r _h1(S–O) = 1.579(4), r _h1(N–O)_av. = 1.214(3), r _h1(C–N)_av. = 1.491(5). Geometry of the conformer II points on existance of strong steric interactions between SO₂OH group and two ortho-nitro groups. Analysis of the orbital interactions between the substituents and benzene ring was carried out. Geometric parameters and energies of transition states between conformers were calculated (B3LYP).     

Comparison of the molecular structures of five benzene derivatives as determined independently by gas-phase electron diffraction in two different laboratories: a perspective

The merits and limitations of gas-phase electron diffraction as a technique for determining accurately the structures of small organic molecules are demonstrated by comparing the molecular structures of five benzene derivatives studied in two different laboratories. The existence of many possible representations of the structure of a molecule (r _a, r _g, r _α, r _α⁰, r _e, …), implying differences in the physical meaning of geometrical parameters, is discussed in some detail as it may cause difficulties in a comparison. Also illustrated are different ways of estimating and expressing uncertainties in the geometrical parameters from a gas-phase electron diffraction study.     

Structure and energetics of β-diketonates. IX. Molecular structure of Sr(DPM)2 according to gas phase electron diffraction data

Simultaneous electron diffraction and mass spectrometric investigation of overheated vapor of strontium dipivaloyl methanate was carned out. It was found that at 437(5)°C one molecular form, Sr(DPM)₂, prevails in the vapor. The r_a, r_g, and r_α structural parameters of the Sr(DPM)₂ monomeric molecule were determined; the molecule was found to have D_2d symmetry. The structural characteristics are compared in the series Ca(DPM)₂—Sr(DPM)₂—Ba(DPM)₂.     

Molecular structure study of 1,2,3-trimethyldiaziridine by means of gas electron diffraction method

The molecular structure of 1,2,3-trimethyldiaziridine has been determined from the gas-phase electron diffraction data supplemented spectral and quantum chemical calculations. The configuration of studied compound incorporates trans-position of methyl groups attached to nitrogen atoms of diaziridine cycle. The following principal structural parameters were determined (r_h1 bond lengths in Å, bond angles in degrees with 3σ in parentheses): r(N–C), 1.489(9); r(N–N), 1.480(15); r(C–C), 1.503(15); ∠NCN, 61.5(9); ∠(H₃C)CN, 124.0(15). The obtained structural parameters of 1,2,3-trimethyldiaziridine were compared with those for structural analogues. The gaseous standard enthalpy of formation of 1,2,3-trimethyldiaziridine was estimated to be 176.2?±?5.0 kJ/mol.

     

Investigation of the structure and energetics of Β-diketonates. VIII. Molecular structure of the Ba(dpm)2 monomer according to gas phase electron diffraction data

A combined electron diffraction and mass spectrometric study of the overheated vapor over barium dipivaloylmethanate was performed. It was found that at 488°C the monomeric molecular form predominates in the vapor. The Ba(dpm)₂ molecule has D_2d symmetry. Its r_a, r_g, and r_α parameters were determined.     

Thermodynamic characteristics of alanine-18-crown-6 ether complexes in binary water-acetone solvents

The formation of 18-crown-6 ether (18C6) complexes with D,L-alanine (Ala) in mixed wateracetone solvents with 0.0, 0.08, 0.17, 0.22, and 0.30 mole fractions of acetone (T = 298.15 K) was investigated by means of calorimetry. Thermodynamic characteristics of the reaction of the molecular [Ala18C6] complex formation (Δ_r G°, Δ_r H°, and TΔ_r S°) were calculated on the basis of calorimetric data. Analysis of solvation contributions of reagents into the enthalpy of the [Ala18C6] formation reaction showed that the changes in the reaction energy when the solvent composition is varied are determined by the changes in the solvate state of 18C6.     

Effect of solvation on the thermodynamics of the formation of molecular complexes of 18-crown-6 ether with glycine in water-dimethylsulfoxide solutions

Complexation of the 18-crown-6 ether (18C6) with glycine (Gly) in mixed H₂O-DMSO solvents with the composition of 0.1, 0.2, and 0.25 mole fraction of DMSO (T = 298.15 K) was studied calorimetrically. Thermodynamic characteristics of the reaction of the formation of the molecular Gly18C6 complex (Δ_r G°, Δ_r H°, TΔ_r S°) were calculated from the calorimetric data. It was established that the change in the stability of the Gly18C6 complex is mainly determined by the predominance of the enthalpy component of the Gibbs energy over the entropy component. It was shown during the analysis of the enthalpy contributions of the reagents to the enthalpy of the reaction of the formation of Gly18C6 that the change in the enthalpy of the reaction upon a change the solvent composition was due to changes in the solvation state of 18C6.     

The Dissociation Constant of Antimonic Acid at 10–40 °C

The hydrolytic behavior of antimonic acid, Sb(OH)₅^o, was experimentally investigated, at fixed temperatures within the range 10–40 °C, by both titration of dilute Na-antimonate solutions with HClO₄ and single-point pH measurements of diluted Sb(OH)₅^o solutions. The thermodynamic constants, K _a, for the reaction:

A QM/MM study of the binding of RAPTA ligands to cathepsin B

We have carried out quantum mechanical (QM) and QM/MM (combined QM and molecular mechanics) calculations, as well as molecular dynamics (MD) simulations to study the binding of a series of six RAPTA (Ru(II)-arene-1,3,5-triaza-7-phosphatricyclo-[3.3.1.1] decane) complexes with different arene substituents to cathepsin B. The recently developed QM/MM-PBSA approach (QM/MM combined with Poisson–Boltzmann solvent-accessible surface area solvation) has been used to estimate binding affinities. The QM calculations reproduce the antitumour activities of the complexes with a correlation coefficient (r ²) of 0.35–0.86 after a conformational search. The QM/MM-PBSA method gave a better correlation (r ² = 0.59) when the protein was fixed to the crystal structure, but more reasonable ligand structures and absolute binding energies were obtained if the protein was allowed to relax, indicating that the ligands are strained when the protein is kept fixed. In addition, the best correlation (r ² = 0.80) was obtained when only the QM energies were used, which suggests that the MM and continuum solvation energies are not accurate enough to predict the binding of a charged metal complex to a charged protein. Taking into account the protein flexibility by means of MD simulations slightly improves the correlation (r ² = 0.91), but the absolute energies are still too large and the results are sensitive to the details in the calculations, illustrating that it is hard to obtain stable predictions when full flexible protein is included in the calculations.     

Validation experiment for large-sample prompt-gamma neutron activation analysis

A method is proposed for the implementation of large-sample prompt-gamma neutron activation analysis (LS-PGNAA). The method was tested with four different sample materials at the thermal PGNAA facility at JAERI, Japan. The macroscopic scattering cross section (Σ _s) and absorption cross section (Σ _a) of the samples were determined by monitoring the neutron flux in four positions just outside the sample container. With the Σ _s and Σ _a determined, the spatial neutron density distribution [n(r)] inside the sample material was derived. Taking n(r) and the gamma-ray self-absorption into account simultaneously, the effective geometric gamma-ray detection efficiency for large samples as a function of gamma-ray energy was calculated. Taking silicon as test element, the concentrations found agreed to within 7% with the known concentrations in the four sample materials examined, both when using relative standardization and with absolute standardization.     

DFT studies and AIM analysis of AlN-polycycles

The structure and properties of AlN-polycycles were studied by DFT (density functional theory) method. The results of calculations were obtained at B3LYP/6-311G(d, p) level on model species. Topological parameters such as electron density, its Laplacian, kinetic electron energy density, potential electron energy density, and total electron energy density at the ring critical points (RCP) from Bader’s ‘Atoms in molecules’ (AIM) theory were analyzed in detail. These results indicate a good correlation between ρ(3, +1), G(r), H(r), and V(r) averaged values and hardness of AlN-polycycles. The aromaticity of all molecules has been studied by nucleus-independent chemical shift. There is a linear correlation between ΣNICS(0.0)_molecule values and polarizability.