Gas-phase Electron Diffraction Research Articles

Conformation and Structure of Dichlorophosphoryl Isocyanate in the Gaseous and Solid Phases

The conformational properties and the molecular structure of dichlorophosphoryl isocyanate, Cl2P(O)NCO, were studied by combining vibrational spectroscopy (IR and Raman), gas‐phase electron diffraction (GED), X‐ray crystallography (XRD), and quantum‐chemical calculations. Computationally, two conformers of Cs symmetry with the P=O bond being in syn or anti configuration relative to the NCO group are predicted to be close in energy (ca. 2 kJ mol–1). Experimentally, both gas‐phase and matrix‐isolation IR spectra of Cl2P(O)NCO suggest the presence of a single conformer, which was determined to be the energetically more favorable syn‐conformer. This was also found to exist in the solid state by low‐temperature XRD. However, the molecule in the solid state is significantly distorted from ideal Cs symmetry with an O–P–N–C dihedral angle of 38.1(1)° due to intermolecular C···O contacts [2.881(4) Å]. In the gas phase, the GED analysis suggests that the molecule exists predominantly as syn‐conformer but with dynamic behavior about the two minimum structures (syn and anti).

Disulfuryl Dichloride ClSO2OSO2Cl: A Conformation and Polymorphism Chameleon

Disulfuryl dichloride ClSO2 OSO2 Cl was characterized by vibrational spectroscopy in the gaseous and liquid phase as well as in the Ar-matrix. By varying the temperature, certain bands could be assigned to several conformers. Gas-phase electron diffraction revealed a dominance of the anti-conformer at ambient temperature. The same conformation was found in the solid state. Via the in situ technique for crystallization, not less than four different modifications were identified. Among these different modifications, the structural parameters of the molecules remain relatively constant, but the aggregation pattern changes. Although the molecules aggregate by chlorine⋅⋅⋅oxygen contacts in each modification, the geometrical parameters of these interaction show significant differences and were evaluated and are in part inconsistent with the halogen bonding concept.

Synthesis, conformational preferences in gas and solution, and molecular gear rotation in 1-(dimethylamino)-1-phenyl-1-silacyclohexane by gas phase electron diffraction (GED), LT NMR and theoretical calculations

1-(Dimethylamino)-1-phenyl-1-silacyclohexane 1, was synthesized, and its molecular structure and conformational properties studied by gas-phase electron diffraction (GED), low temperature 13C NMR spectroscopy and quantum-chemical calculations. The predominance of the 1-Phax conformer (1-Pheq:1-Phax ratio of 20:80%, ΔG°(317 K) = −0.87 kcal/mol) in the gas phase is close to the theoretically estimated conformational equilibrium. In solution, low temperature NMR spectroscopy showed analyzable decoalescence of Cipso and C(1,5) carbon signals in 13C NMR spectra at 103 K. Opposite to the gas state in the freon solution employed (CD2Cl2/CHFCl2/CHFCl2 = 1:1:3), which is still liquid at 100 K, the 1-Pheq conformer was found to be the preferred one [(1-Pheq: 1-Phax = 77%: 23%, K = 77/23 = 2.8; −ΔG° = −RT ln K (at 103 K) = 0.44 ± 0.1 kcal/mol]. When comparing 1 with 1-phenyl-1-(X)silacylohexanes (X = H, Me, OMe, F, Cl), studied so far, the trend of predominance of the Phax conformer in the gas phase and of the Pheq conformer in solution is confirmed.

Molecular Structure of 5-Methyl-2-(trifluoromethyl)furan-3-carbonitrile According to Gas-Phase Electron Diffraction and Quantum Chemistry

The mutual influence of atoms and atomic groups is one of the most important problems of structural chemistry. Gas-phase electron diffraction allows us to obtain the geometrical parameters of molecules that describe them most accurately in the free state. Such parameters constitute the basis of modern chemistry because they contain none of the contributions from intermolecular interactions that are typical of X-ray diffraction data.

Cyanocyclohexane: Axial-to-equatorial “seesaw” parity in gas and condensed phases

Conformational properties and molecular structure of cyanocyclohexane 1 were studied by gas-phase electron diffraction (GED) and dynamic NMR as well as by detailed quantum chemical (QC) computations. This compound violates the so called ‘equatorial rule’ according to which the substituents attached to one of the carbon atom of the ring prefers to occupy an equatorial position relative to the frame of cyclohexane. In case of 1, both conformers contribute nearly equally in gas and liquid phases, with slight domination of the equatorial form as found from the experimental data, Eq:Ax of ca. 3:2. The QC calculations predict contradictive conformer preference depending on method/basis set combination applied. Enthalpy and entropy contributions to Eq↔Ax equilibrium are analyzed.

The equilibrium molecular structure of 3-cyanopyridine according to gas-phase electron diffraction and microwave data and the results of quantum-chemical calculations

The equilibrium structure of the 3-cyanopyridine molecule was experimentally obtained for the first time. The calculations performed by the CCSD(T) method show a good agreement with the results of the electron diffraction and microwave data analysis.

Structural analysis and probing the conformational space of dansylamide by means of gas-phase electron diffraction and quantum chemistry

Dansylamide is perhaps the most ubiquitous fluorophore due to its donor-acceptor bifunctionality and its ability to form intra- and intermolecular hydrogen bonding. Among the diversity of its applications is the development of new generation of biosensors for the in vivo monitoring of traces of metals. The structure and conformational stability of dansylamide in the gas phase were investigated for the first time by a combined gas-phase electron diffraction-mass spectrometry (GED/MS), complemented by quantum chemical calculations. GED data indicate that different skewed conformers exist at T = 464 K, which are characterized by the deviation of two S–N bonds from the perpendicular orientation relative to the naphthalene plane. Maybe the most indicative structural parameters for electronic interactions between the donor-acceptor substituents and the aromatic naphthalene and the subsequent stabilization of the favorable skewed eclipsed-syn conformer are the dihedral angles C9–C1–S–N and C10–C5–N–C with the experimentally determined values of 66.8° (32) and 68.1° (72), respectively. The role of –SO2NH2 by forming intramolecular hydrogen bonds was scrutinized by employing the natural bond orbital approach (NBO), quantum theory atoms in molecules (QTAIM), and molecular electrostatic potential (MESP). The non-planarity of the naphthalene skeleton due to the electronic interactions with the substituents and its consequence for the fluorescence activity of dansylamide have been discussed.

3-Cyclopropyl-1,2-dimethyldiaziridine: synthesis and study of molecular structure by gas electron diffraction method

The molecular structure and conformational behavior of 3-cyclopropyl-1,2-dimethyldiaziridine have been for the first time experimentally studied by gas-phase electron diffraction and quantum chemical calculations. The two most stable conformers at 298 K possess anti and gauche mutual ring orientation (with prevalence of the anti conformer) whereas only one anti conformer is observed in solution. The determined structural parameters of gaseous 3-cyclopropyl-1,2-dimethyldiaziridine have been compared with those for 3,3-bidiaziridine structural analogues in the crystal phase. The simple and convenient procedure for the synthesis of 3-cyclopropyl-1,2-dimethyldiaziridine comprising cyclopropane and diaziridine rings in one molecule was developed. The standard enthalpy of formation of 3-cyclopropyl-1,2-dimethyldiaziridine in the gas phase was calculated using Gaussian-4 theory, yielding value of 281.9 ± 5.0 kJ/mol.

Synthesis of 3-fluoro-3-methyl-3-silatetrahydropyran and its conformational preferences in gas and solution by GED, NMR and theoretical calculations

The 3,3-disubstitued 3-silaheterocyclohexane with an electronegative substituent at silicon, 3-fluoro-3-methyl-3-silatetrahydropyran 1, was synthesized, and its molecular structure and conformational properties studied by gas-phase electron diffraction (GED) and low temperature 13C and 19F NMR spectroscopy. Quantum-chemical calculations were carried out both for the isolated species and H-complexes in gas and in polar medium. The predominance of the 1-FeqMeax conformer (1-Feq:1-Fax ratio of 65:35, ΔG° = 0.37 kcal/mol) determined from GED is close to the theoretically estimated conformational equilibrium, especially at the DFT level. In solution, low temperature NMR spectroscopy showed no decoalescence of the signals in 13C (down to 95 K) and 19F NMR spectra (down to 123 K). However, the calculated 19F chemical shift of −173.6 ppm for the 1-FeqMeax conformer practically coincides with the experimentally observed value (−173 to −175 ppm) as distinct from that for the 1-FaxMeeq conformer (−188.8 ppm), suggesting compound 1 to be anancomeric in solution, in compliance with its theoretical and experimental preference in the gas phase.

Syntheses, Geometrical and Electronic Structure of Alkyladamantanes and Their Thermodynamic Characteristic According to the Density Functional Theory

Propyladamantanes synthesized by of alkylation adamantane with isopropyl alcohol temperature range from 5 to 40°C in the presence of 96% sulfuric acid. Tetramethyl- and Dimethylethyladamantanes synthesized by of isomerization of Perhydroanthracene in the presence of aluminium oxide catalyst on the setting of the flow type. Isomers Butyladamantanes was obtained by the reaction of alkylation of the adamantane with n-butane and isobutane. Adamantane and its derivatives have been the subject of many experimental and theoretical studies. The molecular structure of adamantane was studied by gasphase electron diffraction, Penning ionization electron spectroscopy, photoelectron spectroscopy, electron spin resonance, and quantum calculations of ionization potentials (IP) and electron affinity (SE). The structure 1-n-propyladamantane (1), 1-isopropyladamantane (2), 2-n-propyladamantane (3), 1,2-di-n-propyladamantane (4), 1,3-dimethyl-5-ethyladamantane (5), 1,3,5,6-tetramethyladamantane (6), 1,3,5,7-tetramethyladamantane (7), perhydroanthracene (8), 1-n-butyladamantane (9), 1-isobutyladamantane (10), 1-sec-butyladamantane (11) has been studied using the Becke–Lee–Yang–Parr (B3LYP) hybrid energy functional of electron density with the 6-31G* basis set. The geometric and electronic characteristics of the compounds and their total energy, normal vibration frequencies have been calculated. It has been shown that the calculated Gibb free energies of formation for the perhydroanthracene isomerization products are in qualitative agreement with the experimental product composition of the isomerate and alkylation of adamantane with isopropyl alcohol are in qualitative agreement with the experimental composition of the products. Obtained good agreement of calculated and experimental data on the composition of equilibrium mixtures.

Experiment and theory at the convergence limit: accurate equilibrium structure of picolinic acid by gas-phase electron diffraction and coupled-cluster computations.

The accurate molecular structure of picolinic acid has been determined from experimental data and computed at the coupled cluster level of theory. Only one conformer with the O[double bond, length as m-dash]C-C-N and H-O-C[double bond, length as m-dash]O fragments in antiperiplanar (ap) positions, ap-ap, has been detected under conditions of the gas-phase electron diffraction (GED) experiment (Tnozzle = 375(3) K). The semiexperimental equilibrium structure, rsee, of this conformer has been derived from the GED data taking into account the anharmonic vibrational effects estimated from the ab initio force field. The equilibrium structures of the two lowest-energy conformers, ap-ap and ap-sp (with the synperiplanar H-O-C[double bond, length as m-dash]O fragment), have been fully optimized at the CCSD(T)_ae level of theory in conjunction with the triple-ζ basis set (cc-pwCVTZ). The quality of the optimized structures has been improved due to extrapolation to the quadruple-ζ basis set. The high accuracy of both GED determination and CCSD(T) computations has been disclosed by a correct comparison of structures having the same physical meaning. The ap-ap conformer has been found to be stabilized by the relatively strong NH-O hydrogen bond of 1.973(27) Å (GED) and predicted to be lower in energy by 16 kJ mol-1 with respect to the ap-sp conformer without a hydrogen bond. The influence of this bond on the structure of picolinic acid has been analyzed within the Natural Bond Orbital model. The possibility of the decarboxylation of picolinic acid has been considered in the GED analysis, but no significant amounts of pyridine and carbon dioxide could be detected. To reveal the structural changes reflecting the mesomeric and inductive effects due to the carboxylic substituent, the accurate structure of pyridine has been also computed at the CCSD(T)_ae level with basis sets from triple- to 5-ζ quality. The comprehensive structure computations for pyridine as well as for carbon dioxide have been used to examine the convergence with respect to the basis set size.

The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations

The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both, quantum chemistry and GED analyses resulted in CS molecular symmetry with the planar pyridine ring. Obtained molecular parameters confirm the hyperconjugation in the pyridine ring and the sp2 hybridization concept of the nitrogen and carbon atoms in the ring. The experimental geometric parameters are in a good agreement with the parameters for non-substituted N-oxide and reproduced very closely by DFT calculations. The presence of the electron-donating CH3 substituent in 4-MePyO leads to a decrease of the ipso-angle and to an increase of r(N→O) in comparison with the non-substituted PyO. Electron density distribution analysis has been performed in terms of natural bond orbitals (NBO) scheme. The nature of the semipolar N→O bond is discussed.

Intramolecular London Dispersion Interaction Effects on Gas-Phase and Solid-State Structures of Diamondoid Dimers.

The covalent diamantyl (C28H38) and oxadiamantyl (C26H34O2) dimers are stabilized by London dispersion attractions between the dimer moieties. Their solid-state and gas-phase structures were studied using a multitechnique approach, including single-crystal X-ray diffraction (XRD), gas-phase electron diffraction (GED), a combined GED/microwave (MW) spectroscopy study, and quantum chemical calculations. The inclusion of medium-range electron correlation as well as the London dispersion energy in density functional theory is essential to reproduce the experimental geometries. The conformational dynamics computed for C26H34O2 agree well with solution NMR data and help in the assignment of the gas-phase MW data to individual diastereomers. Both in the solid state and the gas phase the central C-C bond is of similar length for the diamantyl [XRD, 1.642(2) Å; GED, 1.630(5) Å] and the oxadiamantyl dimers [XRD, 1.643(1) Å; GED, 1.632(9) Å; GED+MW, 1.632(5) Å], despite the presence of two oxygen atoms. Out of a larger series of quantum chemical computations, the best match with the experimental reference data is achieved with the PBEh-3c, PBE0-D3, PBE0, B3PW91-D3, and M06-2X approaches. This is the first gas-phase confirmation that the markedly elongated C-C bond is an intrinsic feature of the molecule and that crystal packing effects have only a minor influence.

The Structure of Mn(acac)3 -Experimental Evidence of a Static Jahn-Teller Effect in the Gas Phase.

The structure of free manganese(III) tris(acetylacetonate) [Mn(acac)3 ] was determined by mass-spectrometrically controlled gas-phase electron diffraction. The vapor of Mn(acac)3 at 125(5) °C is composed of a single conformer of Mn(acac)3 in C2 symmetry with the central structural motif of a tetragonal elongated MnO6 octahedron and 47(2) mol % of acetylacetone (Hacac) formed by partial thermal decomposition of Mn(acac)3 . Three types of Mn-O separations have been refined (rh1 =2.157(16), 1.946(5), and 1.932(5) Å. We have found no indication for a significant deviation of the -C-C-C-O-Mn-O- six-membered rings from planarity, which is observed in the solid state.

The molecular structure of 5-X-isatines where (X = F, Cl, and Br) determined by gas-phase electron diffraction with theoretical calculations

The molecular structures of 5-X-isatines where X = F (1), Cl (2), and Br (3) were studied by gas-phase electron diffraction (GED) and theoretical calculations at M062X/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels. The best fit of the experimental scattering intensities was obtained for a molecular model of Cs symmetry. The small differences between similar geometric parameters were constrained at the values calculated at the M062X level. The bond distances in the benzene ring are in agreement with their standard values. The (O)CC(O) carbon-carbon bonds of the pyrrole moiety in title compounds (1.581(11), 1.578(8), 1.574(12) Å, respectively) are remarkably lengthened in comparison with standard C(sp2)–C(sp2) value, 1.425(11) Å for N-methylpyrrole. According to NBO analysis this lengthening cannot be attributed to the electrostatic repulsion of oxygen lone pairs alone and is, mainly, due to the hyperconjugation, that is delocalization of oxygen lone pairs of π-type into the corresponding carbon-carbon antibonding orbital, nπ(O)→σ*(CC). Deletion of σ*(CC) orbital followed by subsequent geometry optimization led to shortening of the corresponding CC bond by 0.05–0.06 Å. Electronegative halogen atoms led to increase of CCXC endocyclic bond angles at ipso carbon atom as compared with the value of 120° in regular hexagon. According to different aromaticity descriptors, aromaticity of benzene moiety of title compounds is smaller in comparison with benzene molecule. External magnetic field induces diatropic ring current in benzene moiety. Local reactivity descriptors that indicate sites in a molecule that are susceptible to nucleophilic, electrophilic and radical attack are calculated.

Structure Determination Techniques Flex Their Muscles.

A historical challenge: Gas-phase electron diffraction and single-crystal X-ray diffraction are both established techniques, but they were both pushed to their limits by the challenge posed by the highly flexible tetranitromethane molecule. New approaches had to be developed for the structure of the molecule to be elucidated.

Molecular structure of tryptamine in gas phase according to gas electron diffraction method and quantum chemistry calculations

The molecular structure of tryptamine was studied by gas-phase electron diffraction (GED) and quantum chemical calculations (DFT/B3LYP and MP2 methods with cc-pVTZ basis set). The best fit of the experimental scattering intensities (R-factor = 3.8%) was obtained for the four-conformer model. The experimental structural parameters are found to be in good agreement with the results of theoretical calculations. The geometric parameters of gaseous tryptamine are compared with those in the crystal phase. The standard enthalpy of formation of tryptamine in the gas phase was calculated using Gaussian-4 theory, yielding value of 133.6 ± 3.3 kJ/mol.

Improved methods and calibration technique in gas-phase electron-diffraction experiments: Use of nitrogen as a wavelength standard

Improved methods are described for extracting electron-scattering data from films used in gas-phase electron-diffraction (GED) experiments. These involve use of a precision transmission scanner in conjunction with powerful, public-domain image-processing software (ImageJ). Procedures for finding an accurate center of the diffraction ring pattern are given and the software permits flexible determination of the intensity average of each radial circle or any arc thereof. In addition, nitrogen gas is proposed as the ideal calibration molecule because virtually all molecules are in the ground vibrational state at all temperatures normally encountered in GED experiments. For this state the rotational constant is very accurately known, as are several small corrections needed to obtain an appropriate calibration value for the GED experiment. The result from theory is ra(N≡N) = 1.10087 Å with a standard deviation (σ) of 0.00035 Å from fitting experiments.

Combined Electron-Diffraction and Spectroscopic Determination of the Structure of Spiropentane, C5H8.

Gas-phase electron-diffraction (GED) data have been combined with recent spectroscopic rotational constants to determine the rα0 structural parameters for spiropentane, C5H8. The structure has D2d symmetry, and the results yield values of 1.105(2) Å for the CH bond length, 1.557(3) Å for the distal CC bond length, and a smaller value of 1.482(1) Å for the four lateral CC bonds that connect to the central carbon atom. The HCH angle is 113.7(13)°, and the HCH flap angle, defined as the angle of the HCH bisector and the distal CC bond, is 150.2(16)°. Corresponding rg values are 1.122(2) Å, 1.560(3) Å, 1.485(1) Å, 115.1(13)°, and 148.9 (16)°. The results are in good accord with values from density functional calculations (B3LYP/cc-pVTZ) and resolve some questions about the structure reported in an earlier GED study, in particular about the HCH angle and anomalous rotational constants calculated for the structure.

Tris(perfluorotolyl)borane-A Boron Lewis Superacid.

Tris[tetrafluoro-4-(trifluoromethyl)phenyl]borane (BTolF) was prepared by treating boron tribromide with tetrameric F3 CC6 F4 -CuI . The F3 CC6 F4 -CuI was generated from F3 CC6 F4 MgBr and copper(I) bromide. Lewis acidities of BTolF evaluated by the Gutmann-Beckett method and calculated fluoride-ion affinities are 9 and 10 %, respectively, higher than that of tris(pentafluorophenyl)borane (BCF) and even higher than that of SbF5 . The molecular structures of BTolF and BCF were determined by gas-phase electron diffraction, that of BTolF also by single-crystal X-ray diffraction.