Gas Electron Diffraction Method Research Articles

Comprehensive Study of Equilibrium Structure of Trans-Azobenzene: Gas Electron Diffraction and Quantum Chemical Calculations

The geometrical re parameters of trans-azobenzene (E-AB) free molecule were refined by gas electron diffraction (GED) method using available experimental data obtained previously by S. Konaka and coworkers. Structural analysis was carried out by various techniques. First of all, these included the widely used molecular orbital constrained gas electron diffraction method and regularization method. The results of the refinements using different models were also compared—a semirigid model, three variants of one-dimensional dynamic models, and a two-dimensional pseudoconformer model. Several descriptions have been used due to the fact that E-AB has a shallow potential energy surface along the rotation coordinates of phenyl groups. Despite this, it turned out that the semirigid model is suitable for use for E-AB and allows good agreement with experimental data to be achieved. According to the results of GED structural analysis, coupled with the results of DLPNO-CCSD(T0) calculations, E-AB has a planar structure. Based only on GED data, it is impossible to unambiguously determine the rotational angle of the phenyl group due to the facts that (i) with rotation over a wide range of angles, the bonded distances in the molecule change insignificantly and (ii) potential function in a structural analysis within a dynamic model is not determined with the necessary accuracy. This work also examines the sensitivity of the GED method to structural changes caused by trans-cis isomerization. The paper also analyzes the applicability of different variants of density functional theory (DFT) calculations in GED structural analysis using E-AB as an example. There are not enough similar methodological works in the literature. This experimental and methodological information is especially important and relevant for planning and implementing GED experiments and corresponding processing of the results for azobenzene derivatives, in which the conformer and isomeric diversity are even more complicated due to the presence of different substituents.

Cyclic Dimers of 4-n-Propyloxybenzoic Acid with Hydrogen Bonds in the Gaseous State.

A comprehensive study of saturated vapors of 4-n-propyloxybenzoic acid (POBA) by gas electron diffraction (GED) and mass spectrometric (MS) methods supplemented by quantum chemical (QC) calculations was carried out for the first time. An attempt was made to detect dimeric forms of the acid in the gaseous state. It has been established that at the temperature of GED experiment, vapor over a solid sample contains up to 20 mol.% of cyclic dimers with two O-H...O hydrogen bonds. The main geometrical parameters of gaseous monomers and dimers of POBA are obtained. The distance r(O…O) = 2.574(12) Å in the cyclic fragment of the gaseous dimer is close to that in the crystal structure (2.611 Å). In the mass spectrum of the POBA recorded the ions of low intensity with a mass exceeding the molecular mass of the monomer were detected. The presence of ions, whose elemental composition corresponds to the dissociative ionization of the dimer, confirms the results of the GED experiment on the presence of POBA dimers in the gas state. The results of GED studies of acetic acid, benzoic acid, and POBA were compared. It is shown that the COOH fragment saves its geometric structure in monomers, as well as the COOH...HOOC fragment with two hydrogen bonds in dimers of different acids. The intermolecular interaction energy in considered acid dimers was estimated using QC calculations (B97D/6-311++G **). The significant value of last (>84 kJ/mol) is the reason for the noticeable presence of dimers in the gas phase.

ANALYSIS OF THE SENSITIVITY OF THE GAS ELECTRON DIFFRACTION METHOD TO THE DETERMINATION OF THE CONFORMATIONAL COMPOSITION OF PHENYL AND THIOPHENYL SUBSTITUTED AZA-BODIPY: THEORETICAL STUDY

Conformational manifold of 1,3,5,7-tetraphenyl-aza-BODIPY and 1,3,5,7-tetra(2-thiophenyl)-aza-BODIPY was studied by B3LYP calculations. The addition of four cyclic groups to the aza-BODIPY core defines the non-planarity of the molecule and movement of the substituents from the heterocycle plane. The rotation angles of the phenyl and thiophenyl groups in the molecules are about 30° and 17°, respectively. For phenyl-substituted aza-BODIPY four conformers were found using quantum chemical calculations (B3LYP/6-31G* and B3LYP/cc-pVTZ), for thiophenyl-substituted aza-BODIPY – 30 conformers. Relative energies of some conformers are quite low, therefore they should be taken into account in the treatment of the gas electron diffraction (GED) experimental data. In current work the sensitivity of the GED method to the structural changes induced by different positions of phenyl and thiophenyl substituents relative to the aza-BODIPY core and each other was examined. Model radial distribution curves f(r) for all conformers were compared. It demonstrates that the bond distances can be reliably determined from experimental data, while the refinement of mutual orientations of neighboring groups relating to each other is at the limit of the possibilities of the GED method. Based on experimental data, it is possible to distinguish 1,3,5,7-tetra(2-thiophenyl)-aza-BODIPY conformers, which differ in the mutual arrangement of sulfur atoms. The use of the results of various quantum chemical calculations leads to the same conclusions about the possibility of the gas electron diffraction method to determine the conformational composition.

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 (rh1 bond lengths in A, 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.

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.

An alternative approach to structural analysis for gas electron diffraction method

An alternative approach to structural analysis for gas electron diffraction method

1-Methoxy-1-silacyclohexane: Synthesis, molecular structure and conformational behavior by gas electron diffraction, Raman spectroscopy and quantum chemical calculations

The synthesis and results of gas electron diffraction (GED), temperature-dependent Raman spectroscopy, along with detailed quantum chemical (QC) study of 1-methoxy-1-silacyclohexane 1 are reported. Within the series of the QC results, DFT(B3LYP, PBE0, M06, M062X), and MP2, the conformational preference predictions are rather contradictive. From the both GED and Raman experimental methods applied, the vapour and liquid phases of 1 were found to exist as a mixture of two conformers, gauche-axial and gauche-equatorial, with almost equal contributions, while the trans-forms are much less stable. In addition, theoretical calculations on the cyclohexane analog, methoxycyclohexane 2, are performed in order to compare with the conformational properties of 1. The latter is predicted not to diminish the axial/equatorial ratio, as contrasted to the expectations at switching the point of the substituent attachment from Si to C.

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.

Accurate Determination of Equilibrium Structure of 3-Aminophthalonitrile by Gas Electron Diffraction and Coupled-Cluster Computations: Structural Effects Due to Intramolecular Charge Transfer.

For the first time, the molecular structure of 3-aminophthalonitrile with unique electronic properties has been determined by the gas electron diffraction (GED) method supported by a mass spectrometric analysis of the gas phase. Moreover, it has been optimized at the high-level quantum-chemical coupled-cluster theory, CCSD(T), in conjunction with the triple-ζ basis set. The equilibrium structure has been determined from the GED data taking into account harmonic and anharmonic vibrational corrections estimated from the quantum-chemical force field (up to cubic terms). The computed CCSD(T) structure has been corrected for the core-core and core-valence electron-correlation effects estimated at the MP2 level and extrapolated to the basis set of quadruple-ζ quality. A remarkable agreement between the experimental and theoretical equilibrium structural parameters (bond lengths and angles) points to a high accuracy of both the molecular structure and applied theories. The high accuracy of structure computations and experimental determination allows the observation of structural changes due to the intramolecular charge transfer predicted by natural bond orbital (NBO) calculations. According to the NBO analysis, the amino group is the electron-donating substituent, whereas the nitrile groups are able to withdraw the π electrons from the benzene ring. Noticeable variations in the structural parameters are also explained by the interaction of σ → π* orbitals of the nearest C≡N and N-H bonds.

Molecular structures and intramolecular dynamics of pentahalides

This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface – barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

Semi-experimental equilibrium structure of pyrazinamide from gas-phase electron diffraction. How much experimental is it?

A semi-experimental equilibrium structure of free molecules of pyrazinamide has been determined for the first time using gas electron diffraction method. The refinement was carried using regularization of geometry by calculated quantum chemical parameters. It is discussed to which extent is the final structure experimental. A numerical approach for estimation of the amount of experimental information in the refined parameters is suggested.The following values of selected internuclear distances were determined (values are in Å with 1σ in the parentheses): re(Cpyrazine—Cpyrazine)av = 1.397(2), re(Npyrazine—Cpyrazine)av = 1.332(3), re(Cpyrazine—Camide) = 1.493(1), re(Namide—Camide) = 1.335(2), re(Oamide—Camide) = 1.219(1). The given standard deviations represent pure experimental uncertainties without the influence of regularization.

Quantum corrections to parameters of interatomic distance distributions in molecular dynamics simulations

The problem of computation of interatomic distance distributions is considered in the context of gas electron diffraction method. A new theoretical approach has been developed for calculation of mean square amplitudes, corrections for interatomic distances and asymmetry parameters on the basis of ab initio molecular dynamics simulations with a posteriori quantum corrections. Several approximations have been evolved, and corresponding algorithms have been coded. Their testing has been performed by calculation of parameters for a set of diatomic molecules, ethane and 9,12-I2-1,2-dicarba-closo-dodecaborane. Comparison of the obtained amplitudes and distance corrections with those calculated by conventional methods demonstrates the superiority of the new approach. By contrast, asymmetry parameters remain numerically unstable after introduction quantum corrections. The best of the assessed approximations, termed MDC(5), is recommended for routine application to large molecules with small-amplitude vibrations.

Conformational and Bonding Properties of 3,3-Dimethyl- and 6,6-Dimethyl-1,5-diazabicyclo[3.1.0]hexane: A Case Study Employing the Monte Carlo Method in Gas Electron Diffraction.

Gas-phase structures of two isomers of dimethyl-substituted 1,5-diazabicyclo[3.1.0]hexanes, namely, 3,3-dimethyl- and 6,6-dimethyl-1,5-diazabicyclo[3.1.0]hexane molecules, have been determined by gas electron diffraction method. A new approach based on the Monte Carlo method has been developed and used for the analysis of precision and accuracy of the refined structures. It was found that at 57 °C 3,3-dimethyl derivative exists as a mixture of chair and boat conformers with abundances 68(8)% and 32(8)%, respectively. 6,6-Dimethyl-1,5-diazabicyclo[3.1.0]hexane at 50 °C has only one stable conformation with planar 5-ring within error limits. Theoretical calculations predict that the 6,6-dimethyl isomer is more stable in comparison to the 3,3-dimethyl isomer with energy difference 3-5 kcal mol(-1). In order to explain the relative stability and bonding properties of different structures the natural bond orbitals (NBO), atoms in molecules (AIM), and interacting quantum atoms (IQA) analyses were performed.

Effect of vibronic interactions on molecular structures determined by gas electron diffraction

This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum-chemical calculations in studies of the impact of vibronic interactions in free molecules on their structures and nuclear dynamics. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface (APES) parameters to the diffraction intensity, are described. It is suggested that by using the proposed approaches, it is possible to develop a common “language” with spectroscopy and computation methods. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the APES–vibronic interaction constants from electron diffraction intensities in solving the inverse GED problem is demonstrated on several examples. This approach makes it possible to get the proper symmetry of the molecule and the Euclidian relations between internuclear distances in the framework of the APES. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in vibronic systems by the GED method. Magdolna Hargittai and her associates have demonstrated the presence and importance of the Jahn–Teller, Renner–Teller, and pseudo-Jahn–Teller effects in gaseous metal halide molecules, and they are quoted in this paper. Results of other research groups are also included in the discussion.

From the determination of the accurate equilibrium structure of 1-methylthymine by gas electron diffraction and coupled cluster computations to the observation of methylation and flexibility effects in pyrimidine nucleobases.

1-Methylthymine is of particular interest because it can be considered as a simple model of thymidine, in which deoxyribose attaches to thymine precisely at the N1 atom. The structure of this molecule is still unknown and so far has been experimentally studied for the first time in this work. The semiexperimental equilibrium structural parameters (r(e)(se)/∠(e)(se)) of 1-methylthymine have been determined by the gas electron diffraction (GED) method, taking into account vibrational corrections calculated with the use of the anharmonic (cubic) MP2/cc-pVTZ force constants. The methyl torsion around the C–N bond has been treated as a large-amplitude motion. For the first time, the structure of this molecule has been optimized by the very time-consuming coupled-cluster method (CCSD(T)(ae)) with the triple-ζ (cc-pwCVTZ) basis set. The obtained results have been extrapolated to the quadruple-ζ basis set at the MP2 level. It has been revealed that the methylation of uracil, especially at the nitrogen atom, leads to an increase in the flexibility of the nucleobase as well as a noticeable deformation of the pyrimidine ring.

Interplay of Experiment and Theory: Determination of an Accurate Equilibrium Structure of 1-Methyluracil by the Gas Electron Diffraction Method and Coupled-Cluster Computations

As far as fundamental knowledge is concerned, the methyl derivatives of uracil can be considered as the simplest objects for studying the structural effects due to the substitution in the pyrimidyne nucleobases. From this point of view, 1-methyluracil is of special importance in biochemistry because uracil attaches ribose in ribonucleic acid (RNA) just precisely at the N1 atom. The semi-experimental equilibrium structure (r(e)(se)) of 1-methyluracil has been determined for the first time by the gas electron diffraction (GED) method taking into account rovibrational corrections to the thermal-average internuclear distances calculated with harmonic and anharmonic (cubic) MP2/cc-pVTZ force constants with consideration of the methyl torsion as a large-amplitude motion. For the first time, the structure of the molecule has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-ζ basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ) and extrapolated to the complete basis set (CBS) with the help of the MP2 calculations. Small differences between similar bond lengths of equilibrium configurations were assumed in the GED analysis at the CCSD(T)(all)/CBS values. A remarkable agreement between the semi-experimental and computed equilibrium structures points out the high accuracy of both the GED determination and the coupled-cluster computations. The effect of methylation on the structure of uracil has been analyzed.

Microwave Spectra and Structures of 1,2-(ortho)- and 1,7-(meta)-Carborane, C2B10H12

The microwave spectra of 1,2- and 1,7-dicarba-closo-dodecaborane(12), C(2)B(10)H(12) (ortho- and meta-carborane), have been recorded for the first time at room temperature in the 32-88 and 24-80 GHz spectral ranges, respectively. The spectra of the parent species (1,2-C(2)(11)B(10)H(12) and 1,7-C(2)(11)B(10)H(12)) have been assigned, together with those of four monosubstituted ((10)B) 1,2-C(2)(10)B(11)B(9)H(12) and 1,7-C(2)(10)B(11)B(9)H(12) isotopologues. The microwave spectra confirm that the structures of each of these two molecules are slightly distorted icosahedrons of C(2v) symmetry. A previous determination of the gaseous structures of these two carboranes by the gas electron-diffraction method was based on several assumptions about the B-B bond length differences. All B-B bond lengths have now been redetermined using the substitution (r(s)) method, which is independent of such restraints. Although several of the r(s) and electron-diffraction bond lengths are in good agreement, there are also differences of up to 0.026 Å. Quantum chemical calculations at the B3LYP/6-311++G(3df,3pd) level of theory have also been performed.

Why is the antipodal effect in closo-1-SB9H9 so large? A possible explanation based on the geometry from the concerted use of gas electron diffraction and computational methods

The molecular structure of 1-thia-closo-decaborane(9), 1-SB(9)H(9), has been determined by the concerted use of gas electron diffraction and quantum-chemical calculations. Assuming C(4v) symmetry, the cage structure was distorted from a symmetrically bicapped square antiprism (D(4d) symmetry) mainly through substantial expansion of the tetragonal belt of boron atoms adjacent to sulfur. The S-B and (B-B)(mean) distances are well determined with r(h1) = 193.86(14) and 182.14(8) pm, respectively. Geometrical parameters calculated using the MP2(full)/6-311++G** method and at levels reported earlier [MP2(full)/6-311G**, B3LYP/6-311G** and B3LYP/cc-pVQZ], as well as calculated vibrational amplitudes and (11)B NMR chemical shifts, are in good agreement with the experimental findings. In particular, the so-called antipodal chemical shift of apical B(10) (71.8 ppm) is reproduced well by the GIAO-MP2 calculations and its large magnitude is schematically accounted for, as is the analogous antipodal chemical shift of B(12) in the twelve-vertex closo-1-SB(11)H(11).

Unusual asymmetry in halobenzenes, a solid-state, gas-phase and theoretical investigation

The molecular structures of 1-Br-4-F-C6H4 and 1-Cl-4-F-C6H4 have been studied in the gas phase using gas electron diffraction (GED) and ab initio methods. The structure of 1-Cl,4-F-C6H4 in the crystalline phase has also been studied, but whilst the gaseous structures were found to possess C2v symmetry, the solid-state structure was found to be quite distorted, with three molecules in the asymmetric unit. These fragments only possess Cs symmetry in the plane of the molecules, as opposed to the C2v symmetry observed in the gas phase. The bonding motifs within the solid-state structure are very unusual and unexpected, with quite different C–F bond lengths for the three moieties, and are a result of weak hydrogen-halogen interactions within the structure.

Molecular structure and conformational preferences of gaseous methylthiodichlorophosphite, Br2PSCH3, studied by gas electron diffraction and quantum-chemical calculations

Molecule Br2PSCH3 has been studied by gas electron diffraction method with the use of additional data of quantum-chemical data at the MP2/SDB-AUG-cc-PVTZ and B3PW91/6-311+G* (DFT) levels of theory. The structure optimization of Br2PSMe molecule by both theoretical methods (DFT/MP2) indicate that the most stable conformer is an anti conformer of Cs symmetry, while the energy of the second gauche conformer is by about 1.47/1.05 kcal mol−1 higher. Each conformer is characterized by dihedral angle τ(CSPlp) where lp denotes the direction of the lone electron pair on the P atom. The calculated standard free energies at 298.15 K indicate that the mole fractions in the gas phase at this temperature are: μ(anti) = 75/62%, μ(gauche) = 25/38%. Experimental ED data agree well with joint presence of both conformers in the ratio μ(anti) = 65(6)% and μ(gauche) = 35(6)%. Natural bond orbital analysis (NBO) testifies that anti-conformer is an example of stabilization of the form that is extremely unfavorable from the point of view of steric and electrostatic interactions. It is shown that relative stabilities of two conformers, differences in geometrical parameters, and several NBO descriptors are defined by effects of hyperconjugation, the most important of which is the πlpS→σ*(P-Br) interaction, namely, the delocalization of lone electron pair of π-type of the S atom into the antibonding orbital of P-Br bond.