Gas-phase Electron Diffraction Method Research Articles

Molecular structure of 1,1',6,6'-tetraaza-7,7'-bi(bicyclo[4.1.0]heptane) in gas, solid and solution phases: GED, XRD and NMR data combined with quantum chemical calculations

The equilibrium molecular structure of 1,1',6,6'-tetraaza-7,7'-bi(bicyclo[4.1.0]heptane) in the gas phase has been determined from the data of the gas phase electron diffraction method using quantum chemical calculations up to the RI-MP2/def2-QZVPP level of theory. Structure studies were also carried out in CDCl3 solution using 1D and 2D 1H and 13C NMR spectroscopy and in the solid state using X-ray diffraction analysis. In the gas phase, three conformers of the molecule have been identified, while only one conformer is present in the CDCl3 solution and in the solid state, in which the substance crystallizes in space group P1¯.

Direct Observation of Scattering Angle Dependence of the Inelasticity Effect on the Interference Term Obtained from Time-of-Flight Neutron Diffraction Experiments

Abstract Scattering angle dependence has been experimentally examined for inelasticity effect on the intramolecular interference term observed from the time-of-flight neutron diffraction method. Internuclear distance and its root-mean-square displacement for liquid pure D2O, C6D6 and CCl4, have been determined from the least squares fitting analysis of the observed total interference term in the high-Q region. Although “apparent shrinkage” in the intramolecular distance has been observed obviously for the light nuclei pair at large scattering angle data (2θ > ca. 70°), it has been revealed that the apparent shrinkage in the D⋯D distance for D2O and C6D6, in which the inelasticity effect is expected to be most significant, is found to be suppressed well within ca. 1% for the data observed for the scattering angle below ca. 2θ < ca. 50°. Structural parameters determined have been compared with those determined from the gas-phase electron diffraction method in order to obtain insight of the effect of intermolecular interaction to molecular geometry in the liquid phase.

MOLECULAR STRUCTURE OF TRYPTOPHAN: GAS PHASE ELECTRON DIFFRACTION AND QUANTUM-CHEMICAL STUDIES

The molecular structure and conformational properties of tryptophan have been investigated by gas-phase electron diffraction and theoretical methods. Quantum chemical calculations realized by program Gaussian 03 (B3LYP/cc-pVTZ) have been predicted the existence of six conformers at the temperature of experiment (T = 495 K). The ability of gas-phase electron diffraction method to distinguish the structure of conformers was estimated theoretically. Conformers have different orientations of carboxylic and amine group, backbone and indole fragment to each other. These conformers can be divided on two groups: distinguishable parameters (with different torsion angle C(OOH)-C(HNH2)-C(H2)-C(ind)) and weekly distinguishable ones (with different torsion angles H-N-C-C and H-O-C-C) by gas-phase electron diffraction. The molecular parameters of the conformers were determined. The conformers have intramolecular hydrogen bonding of the H2N···HO. The analysis of the gas-phase electron diffraction data have been carried out assuming the saturated vapor of tryptophan at T = 495 K consists of mixture at least of two conformers with lowest energy. It was shown that optimal ratio between conformers I : II was 50 : 50, respectively. The geometrical parameters of amino acids molecules (glycine, alanine, tryptophan) obtained by gas-phase electron diffraction were compared. The influence of the intramolecular hydrogen bond was established onto the structural parameters of the backbone of the above amino acids molecules.

DFT STUDY OF MOLECULAR STRUCTURE OF 5,10,15,20-TETRAKIS(4’-HALOGENOPHENYL)PORPHYRINS AND THEIR ISOMERS

Conformational manifold of 5,10,15,20-tetrakis(4¢-halogenophenyl)porphyrins (p-4C6H4X-H2P; X=F, Br) was studied by DFT calculations (functional B3LYP). The conformers are different by positions of -4C6H4X groups relative to the macrocyclic core. Relative energies of the conformers of 4C6H4F-H2P were calculated with use of different basis sets in order to find the optimal ratio «quality/ computational cost». According to the results of the calculations, conformers of C2V symmetry are the most energetically favorable. However, relative energies of other conformers are quite low, therefore they should be taken into account at the treatment of the gas-phase electron diffraction (GED) experimental data. The sensitivity of the GED method to structural changes induced by different relative positions of halogenophenyl substituents was examined. Model radial distribution curves f(r) for conformers of p-4C6H4X-H2P, as well as meta- and ortho- isomers (m-4C6H4X-H2P and o-4C6H4X-H2P) were compared. The results of the model studies demonstrate that the bond distances can be reliably determined from experimental data, while the refinement of the positions of halogenophenyl substituents relative to the macrocyclic core is at the limit of the possibilities of the GED method. Meta- and ortho- isomers of 4C6H4X-H2P can be distinguished based on the experimental data, especially in the case of bromine-substituted phenyl groups.

Conformation analysis of copper(II) etioporphyrin-II by combined gas electron diffraction/mass-spectrometry methods and DFT calculations

Molecular structure of copper(II) etioporphyrin-II (CuEP-II) has been studied by a combined gas-phase electron diffraction and mass spectrometry (GED/MS) method in synchronous mode. The experimental results were complemented by DFT calculations using the B3LYP and PBE functionals with pVTZ basis sets for describing H, C, N atoms and cc-pVTZ for describing Cu atom. The CuEP-II molecule was found to possess quasiplanar geometry of macroheterocycle. DFT calculations predict six conformers for the molecule, which differ by the orientation of the ethyl groups with respect to the macrocycle. Energy differences of five conformers are less, than 0.1kJ/mol (UPBE) or 0.3kJ/mol (UB3LYP). Rotation barriers of single ethyl-group are 14.6 and 19.8kJ/mol (UPBE), 15.7 and 21.6kJ/mol (UB3LYP). Sixth conformer has relatively high energy. Structural parameters of the CuEP-II molecule yielded by DFT calculations are, in general, in a good agreement with the GED data. Structural analysis indicated that the gas-phase electron diffraction method is robust for determination of the macroheterocyclic fragment, but is not enough sensitive to conformational composition of CuEP-II. Substitution effect in pyrrole fragments of CuP, CuOFP, CuOMP and CuEP-II complexes has been analyzed.

The molecular structure of N-methylsuccinimide studied by gas-phase electron diffraction (GED) and quantum-chemical methods

The molecular structure of N-methylsuccinimide was studied by the GED method at a nozzle temperature of 69–73°C. Anharmonic vibrational corrections to thermal-average r a bond lengths, Δ(r a − r e), were calculated using the quadratic and cubic force constants from B3LYP/6-31G(df, p) calculations. The molecular skeleton was found to be planar within measurement errors. Some structural effects were likely caused by the conjugation of the N atom with two C=O bonds. The equilibrium geometric parameters derived from the experimental data and those from MP2/cc-pVTZ(seg-opt) calculations were in close agreement.

Accurate Gas-Phase Experimental Structures of Octasilsesquioxanes (Si8O12X8; X = H, Me)

The accurate structures of silsesquioxanes Si8O12H8 and Si8O12Me8 have been determined by gas-phase electron diffraction methods in order to obtain experimental data on single molecules unconstrain...

Molecular structure of octachlorotrisilane Si3Cl8

The parameters of the geometrical configuration of octachlorotrisilane Si3Cl8 were determined by quantum-chemical and gas-phase electron diffraction methods at 303±2 K. The calculated barrier to the internal rotation of SiCl3 groups relative to the Si-Si bond was calculated.

Molecular Structure of 1,5-Diazabicyclo[3.1.0]hexane as Determined by Gas Electron Diffraction and Quantum-Chemical Calculations

The equilibrium molecular structure and conformation of 1,5-diazabicyclo[3.1.0]hexane (DABH) has been studied by the gas-phase electron-diffraction method at 20 degrees C and quantum-chemical calculations. Three possible conformations of DABH were considered: boat, chair, and twist. According to the experimental and theoretical results, DABH exists exclusively as a boat conformation of C s symmetry at the temperature of the experiment. The MP2 calculations predict the stable chair and twist conformations to be 3.8 and 49.5 kcal mol(-1) above the boat form, respectively. The most important semi-experimental geometrical parameters of DABH (r(e), A and angle)e), deg) are (N1-N5) = 1.506(13), (N1-C6) = 1.442(2), (N1-C2) = 1.469(4), (C2-C3) = 1.524(7), (C6-N1-C2) = 114.8(8), (N5-N1-C2) = 107.7(4), (N1-C2-C3) = 106.5(9), and (C2-C3-C4) = 104.0(10). The natural bond orbital (NBO) analysis has shown that the most important stabilization factor in the boat conformation is the n(N) --> sigma*(C-C) anomeric effect. The geometry calculations and NBO analysis have been performed also for the bicyclohexane molecule.

The initial processing of the gas electron diffraction data: New method for simultaneous determination of the sector function and electron wavelength from gas standard data

The accuracy of the routine investigations by the modern gas-phase electron diffraction method is no more than 0.1%. The full error of parameters determination consists of several contributions including the scale error and the errors in sector function. For correction of the scale error and estimation of the sector function, the gas standard method is used in gas electron diffraction. We have developed the new method for simultaneous determination of the electron wavelength and the sector function from the intensity curves of the gas standards. The new method allows to achieve the electron wavelength precision of about 0.02–0.05%. The distinguishing feature of the new method is the use of several intensity curves for determination of the sector function, resulting in an increase of the reliability of the sector function determination. The additional information from alternative determinations of sector function can be also used for regularization.

The initial processing of the gas electron diffraction data: An improved method for obtaining intensity curves from diffraction patterns

The present maximum precision of the geometric parameters of molecules obtained by gas-phase electron diffraction method (GED) is about 0.1%. The most important factors that control the accuracy of GED structural analysis are the accuracy of electron wave length estimation and measuring of the intensity curves. In this article an improved algorithm and a program for estimating the center of gas-phase electron diffraction patterns, sector center, intensity curve, and additive asymmetric background are presented. The application of proposed method of the initial processing of electron diffraction patterns to benzene molecule leads to least squares error of about 0.01% in ra(C–C) distance. The suggested algorithm can be used with primary data obtained both with scanner and the Image Plates technique. The dependence of estimated parameters on scanning conditions (resolution and bit depth) was also investigated.

Gas-phase electron diffraction study of cyclic dimer of dimethylphosphinic acid (Me 2P(O)OH) 2 using quantum chemical data and a priori force field

The molecular structure of the hydrogen bonded cyclic dimer of dimethylphosphinic acid (Me 2P(O)OH) 2 was determined by gas-phase electron diffraction (GED) at 433 K. The presence of monomer cannot be determined at this temperature within the error limits for the GED method. Structural analysis was performed with consideration of non-linear kinematic effects at the first-order level of perturbation theory ( h1). The vibrational characteristics of internuclear distances were calculated from a priori scaled quantum chemical (RHF/6-311G**) force field. The analysis aided by a constraint based on the RHF/6-311G** calculations yielded the following r h1 -parameters of the C 2-symmetry dimer configuration: PO 1.497(3); P–O 1.573(4); P–C 1.806(1) and 1.811(1) Å; (C–H) av. 1.109(3) Å; ∠O–PO 120(1)°. Unlike PO and P–O bonds, whose lengths in the gas phase and in the solid state differ insignificantly, the –O⋯O distance in the gas phase ( r h1 2.81(4) Å) is considerably longer than in the solid state ( r α 2.48(2) Å). The latter is in accordance with the conclusion based on the IR spectra that transition from gas to a solid sample leads to strengthening of the H-bonds. Due to its small contribution to the diffraction pattern, the donor O–H bond length ( r h1 0.99(1) Å) was forcedly bound up with the parameters of C–H bonds. With this assumption, the other geometrical parameters characterizing the H-bond fragment have the following r h1 values: O⋯H 1.84(4) Å, ∠–OHO164(6)°, and ∠P–O–H 117(4)°. Conformational flexibility of the non-planar eight-atom ring of the dimer is experimentally verified by absence of any apparent peaks of the f( r) curve at the r-region of more than 4.2 Å.

The molecular structure of gaseous 2-bromofuran as studied from electron diffraction and microwave data

The molecular structure of 2-bromofuran has been studied by the gas phase electron diffraction method. The results were used in conjunction with the rotational constants in combined structure analysis. Experimental vibrational frequencies were used to conduct a normal coordinate analysis. The obtained general valence force field was employed for calculating the mean amplitudes of vibrations, coefficients of perpendicular amplitudes and corrections for vibration—rotation interaction. The force constants reproduce well the experimental frequencies of the molecule under study and of the furan molecule and its deuterated analogs. The following values of geometrical parameters are obtained assuming C 2V molecular symmetry for the furan ring. The distances r ev are given in Å, angles in degrees. The parenthesized values are three times the standard deviations. CBr 1.848(4); CC 1.425(13); CC 1.379(10); CO 1.358(9); ∠COC 106.4(4); ∠OCC 111.0(5); ∠CCBr 132.4(5). The mean amplitudes were fixed on calculated values. A comparison has been made of the obtained geometrical parameters with molecules of related structure.

The molecular structure of cyan trichloride ClN=C ClCl

The geometric structure of cyan trichloride has been derived by gas phase Electron Diffraction methods. The r α o-parameters are (in Å and deg.): r NC: 1.266(5), r NCl: 1.683(10), r CCl: 1.718(6), φ CNCl: 117.11(40), φ NCCl,cis: 127.52(40) and φ NCCl,trans: 118.68(50).

An azidopiperideine ? dihydrodiazepine ring expansion of the fluorocarbon class: synthesis of perfluoro-(1,4-dimethyl-2,3-diazacyclo-hepta-1,3-diene)via thermolysis of perfluoro-(6-azido-2,6-dimethyl-1 azacyclohexene)

Flow pyrolysis of perfluoro-(6-azido- 2,6 dimethyl-1-azacyclohexene) at ca. 380 °C and 1 mmHg yields Perfluoro-(1,4-dimethyl-2,3-diazacyclohepta-1,3-diene)(mainly) plus its isomers perfluoro-(1,5-dimethyl-6,7-diazabicyclo[3.2.0]hept-6-ene) and perfluoro-(2,4-dimethyl- 1,3-diazacyclohepta- 1,3-diene); the molecular geometry of the first of these products has been determined by gas-phase electron diffraction methods.

An electron diffraction determination of the molecular structures of silyl- and germyl-manganese pentacarbonyl in the gas phase

The molecular structures of the title compounds have been determined by gas phase electron diffraction methods. The SiMn and GeMn bond lengths are 240.7 ∓ 0.5 and 248.7 ∓ 0.2 pm respectively and the CMnC angles in the silyl and germyl cases are 94.5 ± 2° and 97 ± 2° respectively. Comparisons are made with the reported structure of CH 3Mn(CO) 5 and He I photoelectron spectra of these compounds in an attempt to determine the extent of d → d π-bonding in the SiMn or GeMn bonds.

An electron-diffraction determination of the molecular structure of bis(difluorophosphino)ether, F 2POPF 2, in the gas phase

Gas-phase electron-diffraction methods have been used to determine the molecular structure of bis(difluorophosphino)ether, F 2POPF 2. Most of the geometrical parameters are strongly correlated due to overlapping peaks in the radial distribution curve. In the structure that fits the experimental data most closely, the P-F and P-O bond lengths are 159.7 ± 0.4 and 153.3 ± 0.6 pm respectively, and the POP angle is 2.53 ± 0.02 rad (145°). The conformation is such that the molecule has no symmetry elements other than I (point group C 1). In other refinements somewhat longer P-O and shorter P-F distances were obtained.