Molecular structure of 1,2,3-triethyldiaziridine: Gas-phase electron diffraction and theoretical calculations

For the first time, the equilibrium molecular structure and conformational composition (6 to 8 conformers) of 1,2,3-triethyl-diaziridine in the gas phase were determined by gas-phase electron diffraction. Using 1D and 2D ¹H and ¹³C NMR spectro-scopy, it was shown that in a CDCl₃ solution under normal conditions on the NMR time scale, the molecule exists only as one conformer. The enthalpy of formation Δ_fH ⁰₂₉₈ of the studied molecule in the gas phase was calculated by the method of atomization reactions and is equal to 92.2 ± 1.7 kJ mol⁻¹.     

Determining molecular structures and conformations directly from electron diffraction using a genetic algorithm.

A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.     

Ultrafast electron diffraction: oriented molecular structures in space and time.

The technique of ultrafast electron diffraction allows direct measurement of changes which occur in the molecular structures of isolated molecules upon excitation by femtosecond laser pulses. The vectorial nature of the molecule-radiation interaction also ensures that the orientation of the transient populations created by the laser excitation is not isotropic. Here, we examine the influence on electron diffraction measurements--on the femtosecond and picosecond timescales--of this induced initial anisotropy and subsequent inertial (collision-free) molecular reorientation, accounting for the geometry and dynamics of a laser-induced reaction (dissociation). The orientations of both the residual ground-state population and the excited- or product-state populations evolve in time, with different characteristic rotational dephasing and recurrence times due to differing moments of inertia. This purely orientational evolution imposes a corresponding evolution on the electron scattering pattern, which we show may be similar to evolution due to intrinsic structural changes in the molecule, and thus potentially subject to misinterpretation. The contribution of each internuclear separation is shown to depend on its orientation in the molecular frame relative to the transition dipole for the photoexcitation; thus not only bond lengths, but also bond angles leave a characteristic imprint on the diffraction. Of particular note is the fact that the influence of anisotropy persists at all times, producing distinct differences between the asymptotic "static" diffraction image and the predictions of isotropic diffraction theory.     

Gas Phase Structures of Peroxides: Experiments and Computational Problems

Gas‐phase structures of several organic and inorganic peroxides X‐O‐O‐X and X‐O‐O‐X′, which have been determined experimentally by gas electron diffraction and/or microwave spectroscopy, are discussed. The O?O bond length in these peroxides varies from 1.481(8) Å in Me₃SiOOSiMe₃ to 1.214(2) Å in FOOF and the dihedral angle ?(XO‐OX) between 0° in HC(O)O‐OH and near 180° in Bu^tO‐OBu^t. Some of the peroxides cause problems for quantum chemistry, since several computational methods fail to reproduce the experimental structures. Extreme examples are MeO‐OMe and FO‐OF. In the case of MeO‐OMe only about half of the more than 100 computational methods reported in the literature reproduce the experimentally determined double‐minimum shape of the torsional potential around the O?O bond correctly. For FO‐OF only a small number of close to 200 computational methods reproduce the O?O and O?F bond lengths better than ±0.02 Å.     

Chlorobis(pentafluoroethyl)phosphane: improved synthesis and molecular structure in the gas phase

(C₂F₅)₂PCl is now accessible through a significantly improved synthesis protocol starting from the technical product (C₂F₅)₃PF₂. (C₂F₅)₃PF₂ was reduced in the first step with NaBH₄ in a solvent‐free reaction at 120 °C. The product, P(C₂F₅)₃, was treated with an excess of an aqueous sodium hydroxide solution to afford the corresponding phosphinite salt Na⁺(C₂F₅)₂PO^? selectively under liberation of pentafluoroethane. Subsequent chlorination with PhPCl₄ resulted in the selective formation of (C₂F₅)₂PCl, which was isolated by fractional condensation in an overall yield of 66 %. The gas electron diffraction (GED) pattern for (C₂F₅)₂PCl was recorded and found to be described by a two‐conformer model. A quantum chemical investigation of the potential‐energy surface revealed the possible existence of many low‐energy conformers, each with a number of low‐frequency vibrational modes and therefore large‐amplitude motions. The conformer calculated to be most stable was also found to be most abundant by GED and comprised 61(5) % of the total. The molecular structure parameters determined by GED were in good agreement with those calculated at the MP2/TZVPP level of theory; the only significant difference was a discrepancy of about 3° in the C‐P‐C angle, which, for the lowest‐energy conformer, was refined to 98.2(4)° and was calculated to be 94.9°.     

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, spectroscopy and matrix photochemistry of fluorocarbonyl iodide, FC(O)I

The molecular structure of FC(O)I has been determined by gas electron diffraction. High-level ab initio methods, including coupled-cluster and the new correlation-consistent basis sets for fourth row elements, have been used to calculate the structure of FC(O)I. A comprehensive vibrational spectroscopic study (both IR and Raman) complemented by high-level calculations has also been performed. Furthermore, UV, mass, and NMR spectra have been recorded for FC(O)I. The matrix photochemistry of FC(O)I has been studied with a low-pressure mercury lamp and with a high-pressure xenon lamp in combination with interference and cut-off filters. UV photolysis revealed the formation of the OC. IF and OC.FI complexes and further photolysis of these complexes at lambda>320 nm resulted in a re-formation of FC(O)I. The structural conformation of the complexes has been characterized by comparing shifts in their CO and IF vibrational modes with respect to those of the free species. The structures, vibrational properties, and stability of the complexes were analyzed with the aid of coupled-cluster ab initio calculations.     

Structure and conformational properties of carbonylbisimidosulfuryl fluoride, O=C(N=S(O)F2)2

The molecular structure and conformational properties of O=C(N=S(O)F₂)₂ (carbonylbisimidosulfuryl fluoride) were determined by gas electron diffraction (GED) and quantumchemical calculations (HF/3-21G* and B3LYP/6-31G*). The analysis of the GED intensities resulted in a mixture of 76(12)% syn–syn and 24(12)% syn–anti conformer (ΔH⁰=H⁰(syn–anti)−H⁰(syn–syn)=1.11(32) kcal mol⁻¹) which is in agreement with the interpretation of the IR spectra (68(5)% syn–syn and 32(5)% syn–anti, ΔH⁰=0.87(11) kcal mol⁻¹). syn and anti describe the orientation of the S=N bonds relative to the C=O bond. In both conformers the S=O bonds of the two N=S(O)F₂ groups are trans to the C–N bonds. According to the theoretical calculations, structures with cis orientation of an S=O bond with respect to a C–N bond do not correspond to minima on the energy hyperface. The HF/3-21G* approximation predicts preference of the syn–anti structure (ΔE=−0.11 kcal mol⁻¹) and the B3LYP/6-31G* method results in an energy difference (ΔE=1.85 kcal mol⁻¹) which is slightly larger than the experimental values. The following geometric parameters for the O=C(N=S)₂ skeleton were derived (r_a values with 3σ uncertainties): C=O 1.193 (9) Å, C–N 1.365 (9) Å, S=N 1.466 (5) Å, O=C–N 125.1 (6)° and C–N=S 125.3 (10)°. The geometric parameters are reproduced satisfactorily by the HF/3-21G* approximation, except for the C–N=S angle which is too large by ca. 6°. The B3LYP method predicts all bonds to be too long by 0.02–0.05 Å and the C–N=S angle to be too small by ca. 4°.     

Acetylene decomposition on Rh(100): theory and experiment.

The decomposition of acetylene on a Rh(100) single crystal was studied by a combination of experimental techniques [static secondary ion mass spectrometry (SSIMS), temperature-programmed desorption (TPD), and low-energy electron diffraction (LEED)] to gain insight into the reaction pathway and the nature of the reaction intermediates. The experimental techniques were combined with a computational approach using density functional theory (DFT). Acetylene adsorbs irreversibly on the Rh(100) surface and eventually decomposes to atomic carbon and gas-phase hydrogen. The combination of experimental and computational results enabled us to determine the most likely reaction pathway for the decomposition process.     

一氯氧化物及其负离子的分子结构和热力学性质

利用两种杂化DFT方法(BHLYP和B3LYP，两种纯DFT方法(BP86和BLYP)，以DZP 为基函数对ClOO，ClOOO和ClO3及其负离子的平衡构型进行了量子化学计算，研究了它们的几何构型、相对能量、三种电子亲和势(绝热电子亲和势Ead＝E(optimized neutral)-E(optimized anion),垂直电子亲和势Evert=E(optimized neutral)-E(anion at neutral equilibrium geometry)和垂直电子解离能Evd=E(neutral at anion equilibrium)-E(optiminzed anion))和红外振动频率。     

Molecular Structure of Silatrane Determined by Gas Electron Diffraction and Quantum-Mechanical Calculations

The geometry of silatrane HSi(OCH₂CH₂)₃N has been determined by gas electron diffraction, ab initio calculations, and vibrational spectroscopy of crystal. Using the scaled force field from DFT calculations the amplitudes and perpendicular corrections were calculated. It was assumed that the silatrane molecule has C ₃ symmetry. The following values (r _g bond lengths in Å and _a bond angles in deg. with three standard deviations from the least-squared refinements using a diagonal weight matrix) are: SiN 2.406(27); NC 1.443(7); OC 1.399(11); SiO 1.648(3); CC 1.504(15); NSiO 78.8(21); SiOC 128.1(11); SiNC 105.4(14); CCO 117.0(26); CCN 108.2(30); CNC 113.2(17); OSiO 116.3(13). The 5-membered rings are flattened. The sum of its bond angles is equal to 537.5(42). It is shown that a very large difference is found for Si—N distance from ab initio and DFT calculating.     

Valence shell charge concentrations at pentacoordinate d0 transition-metal centers: non-VSEPR structures of Me2NbCl3 and Me3NbCl2

The molecular structures of the monomeric, pentacoordinated methylchloroniobium(IV) compounds Me3NbCl2 and Me2NbCl3 have been determined by gas electron diffraction (GED) and density functional theory (DFT) calculations, and, for Me3NbCl2, by single crystal X-ray diffraction. Each of the molecules is found to have a heavy-atom skeleton in the form of a trigonal bipyramid (TBP) with Cl atoms in the axial positions, in accord with their vibrational spectra. The TBP is somewhat distorted in the case of Me2NbCl3 with the two axial Nb--Cl bonds bent away from the equatorial, slightly shorter Nb--Cl bond. In the case of Me3NbCl2, moreover, the X-ray model suggests structural distortions away from the idealized C3h geometry, in line with the results of quantum chemical calculations. Structure optimizations by DFT calculations and least-squares refinement to the GED data yield the following structural parameters (calcd/exptl; eq=equatorial; ax=axial; distances in A, angles in degrees; average values in brackets): Me3NbCl2, in C(3v) symmetry, Nb--Cl 2.370/2.319(3), Nb--C 2.173/2.152(4), C--H 1.096/1.124(5), angle-spherical NbCH 109.3/105.2(8), angle-spherical ClNbC 92.2/93.3(2), angle-spherical CNbC 119.9/119.7(1); Me2NbCl3, in C(2v) symmetry, Nb--Cl(ax) 2.361/2.304(5), Nb--Cl(eq) 2.321/2.288(9), Nb--C 2.180/2.135(9), C--H 1.094/1.12(1), angle-spherical Cl(ax)NbCl(eq) 98.5/96.5(6), angle-spherical CNbC 121.0/114(2), angle-spherical NbCH 108.9/109(2). The electronic structures of Me2NbCl3 and Me3NbC(2 have been explored by rigorous analysis of both the wavefunction and the topology of the electron density, employing DFT calculations. Hence the structures of these compounds are shown to reflect repulsion between the Nb--C and Nb--Cl bonding electron density and charge concentrations induced by the methyl ligands in the valence shell of the Nb atom and arising mainly from use of Nb(4d) functions in the Nb--C bonds.     

Oriented ensembles in ultrafast electron diffraction.

Electron scattering expressions are presented which are applicable to very general conditions of implementation of anisotropic ultrafast electron diffraction (UED) experiments on the femto- and picosecond time scale. "Magic angle" methods for extracting from the experimental diffraction patterns both the isotropic scalar contribution (population dynamics) and the angular (orientation-dependent) contribution are described. To achieve this result, the molecular scattering intensity is given as an expansion in terms of the moments of the transition-dipole distribution created by the linearly polarized excitation laser pulse. The isotropic component (n=0 moment) depends only on population and scalar internuclear separations, and the higher moments reflect bond angles and evolve in time due to rotational motion of the molecules. This clear analytical separation facilitates assessment of the role of experimental variables in determining the influence of anisotropic orientational distributions of the molecular ensembles on the measured diffraction patterns. Practical procedures to separate the isotropic and anisotropic components of experimental data are evaluated and demonstrated with application to reactions. The influence of vectorial properties (bond angles and rotational dynamics) on the anisotropic component adds a new dimension to UED, arising through the imposition of spatial order on otherwise randomly oriented ensembles.     

Gas‐phase reactivity of 2‐hydroxy‐1,4‐naphthoquinones: a computational and mass spectrometry study of lapachol congeners

In order to understand the influence of alkyl side chains on the gas‐phase reactivity of 1,4‐naphthoquinone derivatives, some 2‐hydroxy‐1,4‐naphthoquinone derivatives have been prepared and studied by electrospray ionization tandem mass spectrometry in combination with computational quantum chemistry calculations. Protonation and deprotonation sites were suggested on the basis of gas‐phase basicity, proton affinity, gas‐phase acidity (ΔG_acid), atomic charges and frontier orbital analyses. The nature of the intramolecular interaction as well as of the hydrogen bond in the systems was investigated by the atoms‐in‐molecules theory and the natural bond orbital analysis. The results were compared with data published for lapachol (2‐hydroxy‐3‐(3‐methyl‐2‐butenyl)‐1,4‐naphthoquinone). For the protonated molecules, water elimination was verified to occur at lower proportion when compared with side chain elimination, as evidenced in earlier studies on lapachol. The side chain at position C(3) was found to play important roles in the fragmentation mechanisms of these compounds. Copyright © 2012 John Wiley & Sons, Ltd.     

Density functional theory on phase space

Forty‐five years after the point de départ [Hohenberg and Kohn, Phys Rev, 1964, 136, B864] of density functional theory, its applications in chemistry and the study of electronic structures keep steadily growing. However, the precise form of the energy functional in terms of the electron density still eludes us—and possibly will do so forever [Schuch and Verstraete, Nat Phys, 2009, 5, 732]. In what follows we examine a formulation in the same spirit with phase space variables. The validity of Hohenberg–Kohn–Levy‐type theorems on phase space is recalled. We study the representability problem for reduced Wigner functions, and proceed to analyze properties of the new functional. Along the way, new results on states in the phase space formalism of quantum mechanics are established. Natural Wigner orbital theory is developed in depth, with the final aim of constructing accurate correlation‐exchange functionals on phase space. A new proof of the overbinding property of the Müller functional is given. This exact theory supplies its home at long last to that illustrious ancestor, the Thomas–Fermi model. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Molecular structure of phenylsilane: a study by gas-phase electron diffraction and ab initio molecular orbital calculations

The molecular structure of phenylsilane has been determined accurately by gas-phase electron diffraction and ab initio MO calculations at the MP2(f.c.)/6-31G* level. The calculations indicate that the perpendicular conformation of the molecule, with a Si–H bond in a plane orthogonal to the plane of the benzene ring, is the potential energy minimum. The coplanar conformation, with a Si–H bond in the plane of the ring, corresponds to a rotational transition state. However, the difference in energy is very small, 0.13 kJ mol⁻¹, implying free rotation of the substituent at the temperature of the electron diffraction experiment (301 K). Important bond lengths from electron diffraction are: <r_g(C–C)>=1.403±0.003 Å, r_g(Si–C)=1.870±0.004 Å, and r_g(Si–H)=1.497±0.007 Å. The calculations indicate that the C_ipso–C_ortho bonds are 0.010 Å longer than the other C–C bonds. The internal ring angle at the ipso position is 118.1±0.2° from electron diffraction and 118.0° from calculations. This confirms the more than 40-year old suggestion of a possible angular deformation of the ring in phenylsilane, in an early electron diffraction study by F.A. Keidel, S.H. Bauer, J. Chem. Phys. 25 (1956) 1218.     

Gas‐phase dissociation of 1,4‐naphthoquinone derivative anions by electrospray ionization tandem mass spectrometry

Gas‐phase dissociation pathways of deprotonated 1,4‐naphthoquinone (NQ) derivatives have been investigated by electrospray ionization tandem mass spectrometry (ESI‐MS/MS). The major decomposition routes have been elucidated on the basis of quantum chemical calculations at the B3LYP/6‐31 + G(d,p) level. Deprotonation sites have been indicated by analysis of natural charges and gas‐phase acidity. NQ anions underwent an interesting reaction under collision‐induced dissociation conditions, which resulted in the radical elimination of the lateral chain, in contrast with the even‐electron rule. Possible pathways have been suggested, and their mechanisms have been elucidated on the basis of Gibbs energy and enthalpy values for the anions previously described at each pathway. Copyright © 2009 John Wiley & Sons, Ltd.