The molecular structure of tris-2,2,6,6-tetramethyl-heptane-3,5-dione indium: gas-phase electron diffraction and quantum chemical calculations

The molecular structure of tris-2,2,6,6-tetramethyl-heptane-3,5-dione indium, or In(thd)₃, has been determined by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both the DFT calculations and the GED data collected at 387(8) K indicate that the molecules have D ₃ symmetry with a distorted anti-prismatic InO₆ coordination geometry. According to GED refinements, the twist angle θ, i.e. the angle of rotation of the upper and lower O₃ triangles in opposite directions relative to their positions in a regular prism is θ = ±24.9(1.2)° and the bond distances (r _h1) in the chelate ring are In–O = 2.127(4) Å, C–O = 1.268(3) Å and C–C = 1.411(3) Å, respectively. The DFT calculations yielded structure parameters in close agreement with those found experimentally.     

The molecular structure of different species of cuprous chloride from gas-phase electron diffraction and quantum chemical calculations

The molecular geometry of gaseous cuprous chloride oligomers was determined by gas-phase electron diffraction at two different temperatures. Quantum chemical calculations were also performed for Cu(n)Cl(n) (n=1-4) molecules. A complex vapor composition was found in both experiments. Molecules of Cu(3)Cl(3) and Cu(4)Cl(4) were present at the lower temperature (689 K), while dimeric molecules (Cu(2)Cl(2)) were found in addition to the trimers and tetramers at the higher temperature (1333 K). All Cu(n)Cl(n) species were found to have planar rings by both experiment and computation. The bond lengths from electron diffraction (r(g)) at 689 K are 2.166+/-0.008 A and 2.141+/-0.008 A and the Cu-Cl-Cu bond angles are 73.9+/-0.6 degrees and 88.0+/-0.6 degrees for the trimer and the tetramer, respectively. At 1333 K the bond lengths are 2.254+/-0.011 A, 2.180+/-0.011 A, and 2.155+/-0.011 A, and the Cu-Cl-Cu bond angles 67.3+/-1.1 degrees, 74.4+/-1.1 degrees, and 83.6+/-1.1 degrees for the dimer, trimer, and tetramer, respectively.     

Molecular structure of noradrenaline according to gas-phase electron diffraction data and quantum chemical calculations

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Molecular structure, conformation, and potential to internal rotation of 2,6- and 3,5-difluoronitrobenzene studied by gas-phase electron diffraction and quantum chemical calculations

3,5-Difluoronitrobenzene (3,5-DFNB) and 2,6-difluoronitrobenzene (2,6-DFNB) have been studied by gas-phase electron diffraction (GED), MP2 ab initio, and by B3LYP density functional calculations. Refinements of r h1 and r e static and r h1 dynamic GED models were carried out for both molecules. Equilibrium r e structures were determined using anharmonic vibrational corrections to the internuclear distances ( r e - r a) calculated from B3LYP/cc-pVTZ cubic force fields. 3,5-DFNB possesses a planar structure of C 2 v symmetry with the following r e values for bond lengths and bond angles: r(C-C) av = 1.378(4) A, r(C-N) = 1.489(6) A, r(N-O) = 1.217(2) A, r(C-F) = 1.347(5) A, angleC6-C1-C2 = 122.6(6) degrees , angleC1-C2-C3 = 117.3(3) degrees , angleC2-C3-C4 = 123.0(3) degrees , angleC3-C4-C5 = 116.9(6) degrees , angleC-C-N = 118.7(3) degrees , angleC-N-O = 117.3(4) degrees , angleO-N-O = 125.5(7) degrees , angleC-C-F = 118.6(7) degrees . The uncertainties in parentheses are three times the standard deviations. As in the case of nitrobenzene, the barrier to internal rotation of the nitro group in 3,5-DFNB, V 90 = 10 +/- 4 kJ/mol, is substantially lower than that predicted by quantum chemical calculations. The presence of substituents in the ortho positions force the nitro group to rotate about the C-N bond, out of the plane of the benzene ring. For 2,6-DFNB, a nonplanar structure of C 2 symmetry with a torsional angle of phi(C-N) = 53.8(14) degrees and the following r e values for structural parameters was determined by the GED analysis: r(C-C) av = 1.383(5) A, r(C-N) = 1.469(7) A, r(N-O) = 1.212(2) A, r(C-F) = 1.344(4) A, angleC6-C1-C2 = 118.7(5) degrees , angleC1-C2-C3 = 121.2(2) degrees , angleC2-C3-C4 = 119.0(2) degrees , angleC3-C4-C5 = 121.1(4) degrees , angleC-C-N = 120.6(2) degrees , angleC-N-O = 115.7(4) degrees , angleO-N-O = 128.6(7) degrees , angleC-C-F = 118.7(5) degrees . The refinement of a dynamic model led to barriers V 0 = 16.5 +/- 1.5 kJ/mol and V 90 = 2.2 +/- 0.5 kJ/mol, which are in good agreement with values predicted by B3LYP/6-311++G(d,p) and MP2/ cc-pVTZ calculations. The values of C-F bond lengths are similar in both molecules. This is in contrast to the drastic shortening of the C-F bond in the ortho position in 2-fluoronitrobenzene compared to the C-F bond length in the meta and para position in 3- and 4-fluoronitrobenzene observed in an earlier GED study.     

Molecular structure of chloro-dodecafluorosubphthalocyanato boron(III) by gas-phase electron diffraction and quantum chemical calculations

The molecular structure of the chloro-dodecafluorosubphthalocyaninato boron(III) (F-SubPc) was determined with use of Gas Electron Diffraction (GED) and high-level quantum chemical calculations. The present results show that the F-SubPc molecule has a cone-shaped configuration, isoindole units are not planar, and the pyrrole ring has an envelope conformation. The structure parameters in the gas phase are determined. Some structural details can be observed such as the dihedral angle about the bond connecting the pyrrole ring and the benzene ring being ca. 174 degrees . High-level theoretical calculations with several extended basis sets for this molecule have been carried out. The calculations are in very good agreement with experimental methods: X-ray and GED. Nevertheless, some disagreements particularly related to the B-Cl bond distance found in GED are discussed. Vibrational frequencies were computed obtaining eight values below 100 cm-1 and three bending potentials were examined. They suggest that this molecule is very flexible.     

Molecular structure and benzene ring deformation of three ethynylbenzenes from gas-phase electron diffraction and quantum chemical calculations

The molecular structures of ethynylbenzene and s-triethynylbenzene have been accurately determined by gas-phase electron diffraction and ab initio/DFT MO calculations and are compared to that of p-diethynylbenzene from a previous study [Domenicano, A.; Arcadi, A.; Ramondo, F.; Campanelli, A. R.; Portalone, G.; Schultz, G.; Hargittai, I. J. Phys. Chem. 1996, 100, 14625]. Although the equilibrium structures of the three molecules have C2v, D3h, and D2h symmetry, respectively, the corresponding average structures in the gaseous phase are best described by nonplanar models of Cs, C3v, and C2v symmetry, respectively. The lowering of symmetry is due to the large-amplitude motions of the substituents out of the plane of the benzene ring. The use of nonplanar models in the electron diffraction analysis yields ring angles consistent with those from MO calculations. The molecular structure of ethynylbenzene reported from microwave spectroscopy studies is shown to be inaccurate in the ipso region of the benzene ring. The variations of the ring C-C bonds and C-C-C angles in p-diethynylbenzene and s-triethynylbenzene are well interpreted as arising from the superposition of independent effects from each substituent. In particular, experiments and calculations consistently show that the mean length of the ring C-C bonds increases by about 0.002 A per ethynyl group. MO calculations at different levels of theory indicate that though the length of the C[triple bond]C bond of the ethynyl group is unaffected by the pattern of substitution, the C(ipso)-C(ethynyl) bonds in p-diethynylbenzene are 0.001-0.002 A shorter than the corresponding bonds in ethynylbenzene and s-triethynylbenzene. This small effect is attributed to conjugation of the two substituents through the benzene ring. Comparison of experimental and MO results shows that the differences between the lengths of the C(ipso)-C(ethynyl) and C(ipso)-C(ortho) bonds in the three molecules, 0.023-0.027 A, are correctly computed at the MP2 and B3LYP levels of theory but are overestimated by a factor of 2 when calculated at the HF level.     

Molecular structure and benzene ring deformation of three cyanobenzenes from gas-phase electron diffraction and quantum chemical calculations

The molecular structures of cyanobenzene, p-dicyanobenzene, and 1,2,4,5-tetracyanobenzene have been accurately determined by gas-phase electron diffraction and ab initio/DFT MO calculations. The equilibrium structures of these molecules are planar, but their average geometries in the gaseous phase are nonplanar because of large-amplitude vibrational motions of the substituents out of the plane of the benzene ring. The use of nonplanar models in electron diffraction analysis is necessary to yield ring angles consistent with the results of MO calculations. The angular deformation of the benzene ring in the three molecules is found to be much smaller than obtained from previous electron diffraction studies, as well as from microwave spectroscopy studies of cyanobenzene. While the deformation of the ring CC bonds and CCC angles in p-dicyanobenzene is well interpreted as arising from the superposition of independent effects from each substituent, considerable deviation from additivity occurs in 1,2,4,5-tetracyanobenzene. The changes in the ring geometry and C ipso-C cyano bond lengths in this molecule indicate an enhanced ability of the cyano group to withdraw pi-electrons from the benzene ring, compared with cyanobenzene and p-dicyanobenzene. In particular, gas-phase electron diffraction and MP2 or B3LYP calculations show a small but consistent increase in the mean length of the ring CC bonds for each cyano group and a further increase in 1,2,4,5-tetracyanobenzene. Comparison with accurate results from X-ray and neutron crystallography indicates that in p-dicyanobenzene the internal ring angle at the place of substitution opens slightly as the molecule is frozen in the crystal. The small geometrical change, about 0.6 degrees , is shown to be real and to originate from intermolecular C identical withN...HC interactions in the solid state.     

Molecular structure of phthalocyaninatotin(II) studied by gas-phase electron diffraction and high-level quantum chemical calculations

The molecular structure of phthalocyaninatotin(II), Sn(II)Pc, is determined by density functional theory (DFT/B3LYP) calculations using various basis sets and gas-phase electron diffraction (GED). The quantum chemical calculations show that Sn(II)Pc has C4V symmetry, and this symmetry is consistent with the structure obtained by GED at 427 degrees C. GED locates the Sn atom at h(Sn) ) 112.8(48) pm above the plane defined by the four isoindole N atoms, and a N-Sn bond length of 226.0(10) pm is obtained. Calculation at the B3LYP/ccpVTZ/cc-pVTZ-PP(Sn) level of theory gives h(Sn) ) 114.2 pm and a N-Sn bond length of 229.4 pm. The phthalocyanine (Pc) macrocycle has a slightly nonplanar structure. Generally, the GED results are in good agreement with the X-ray structures and with the computed structure; however, the comparability between these three methods has been questioned. The N-Sn bond lengths determined by GED and X-ray are significantly shorter than those from the B3LYP predictions. Similar trends have been found for C-Sn bonds for conjugated organometallic tin compounds. Computed vibrational frequencies give five low frequencies in the range of 18-54 cm-1, which indicates a flexible molecule.     

Molecular structure of propargylgermane (2-propynylgermane) determined by gas-phase electron diffraction and quantum chemical calculations

The molecular structure of propargylgermane, HCCCH₂GeH₃, has been determined by gas-phase electron diffraction. The electron-diffraction investigation has been supported by density functional theory and ab initio calculations. The r_a value of the bond lengths (pm) are: r(C–Ge)=197.2(1); r(C–C)=143.9(2); r(CC)=123.1(1); r(H–C_acetylene)=108.5(3); r(C–H)=111.6(3) and r(Ge–H_average)=153.7(2). The Ge–C–C angle is 111.7(1)° and the C–CC angle is 178.3(4)°. The uncertainties are one standard deviation from the least-squares refinement.     

Molecular structure and internal rotation in 2,3,5,6-tetrafluoroanisole as studied by gas-phase electron diffraction and quantum chemical calculations

The geometric structure of 2,3,5,6-tetrafluoroanisole and the potential function for internal rotation around the C(sp2)-O bond were determined by gas electron diffraction (GED) and quantum chemical calculations. Analysis of the GED intensities with a static model resulted in near-perpendicular orientation of the O-CH3 bond relative to the benzene plane with a torsional angle around the C(sp2)-O bond of tau(C-O) = 67(15) degrees. With a dynamic model, a wide single-minimum potential for internal rotation around the C(sp2)-O bond with perpendicular orientation of the methoxy group [tau(C-O) = 90 degrees] and a barrier of 2.7 +/- 1.6 kcal/mol at planar orientation [tau(C-O) = 0 degrees] was derived. Calculated potential functions depend strongly on the computational method (HF, MP2, or B3LYP) and converge adequately only if large basis sets are used. The electronic energy curves show internal structure, with local minima appearing because of the interplay between electron delocalization, changes in the hybridization around the oxygen atom, and the attraction between the positively polarized hydrogen atoms in the methyl group and the fluorine atom at the ortho position. The internal structure of the electronic energy curves mostly disappears if zero-point energies and thermal corrections are added. The calculated free energy barrier at 298 K is 2.0 +/- 1.0 kcal/mol, in good agreement with the experimental determination.     

Molecular structures of phthalocyaninatozinc and hexadecafluorophthalocyaninatozinc studied by gas-phase electron diffraction and quantum chemical calculations

The molecular structures of phthalocyaninatozinc (HPc-Zn) and hexadecafluorophthalocyaninatozinc (FPc- Zn) are determined using the gas electron diffraction (GED) method and high-level density functional theory (DFT) quantum chemical calculations. Calculations at the B3LYP/6-311++G** level indicate that the equilibrium structures of HPc-Zn and FPc-Zn have D4h symmetry and yield structural parameters in good agreement with those obtained by GED at 480 and 523 degrees C respectively. The calculated force fields indicate that both molecules are flexible. Normal coordinate calculations on HPc-Zn yield five vibrational frequencies (one degenerate) in the range 22-100 cm(-1), and ten vibrational frequencies ranging from 13 to 100 cm(-1) (three degenerate) for FPc-Zn. The high-level force field calculations confirm most of the previous vibrational assignments, and some new ones are suggested. The out-of-plane vibration of the Zn atom in HPc-Zn was studied in detail optimizing models in which the distance from the Zn atom to the two symmetry equivalent diagonally opposed N atoms (h) was fixed. The calculations indicate that the vibrationally activated vertically displacement of the Zn atom is accompanied by distortion of the ligand from D4h to C2v symmetry. The average height, h, at the temperature of the GED experiment was calculated to be 14.5 pm. Small structural changes indicate that a full F substitution on the benzo-subunits do not significantly alter the geometry, however there are indications that the benzo-subunits may shrink slightly with perfluorination.     

The molecular structure of fluoromalononitrile as determined by gas-phase electron diffraction and ab initio calculations

The molecular structure of fluoromalononitrile was studied by means of gas-phase electron diffraction and quantum mechanical methods using HF/6-31G(d), MP2/6-311++G(2df,2pd) and DFT/B3LYP/6-31G(d), B3PW91/6-31G(d), B3LYP/6-311++G(2df,2pd) and B3PW91/6-311++G(2df,2pd). The r(g) and angle(alpha) structural parameters we obtained from the present analysis are: CC=1.487(5) A, CN=1.157(3) A, CF=1.386(5) A, CH=1.096 A (ass.), angleCCC=106.7(1.0) degrees , angleCCF=108.0(0.7) degrees , angleCCN=177.6(2.0) degrees . Uncertainties in parenthesis are 3sigma.     

The molecular structure of PrI3 and GdI3 as determined by synchronous gas-phase electron diffraction and mass spectrometric experiment assisted by quantum chemical calculations

A gas electron diffraction study of PrI₃ and GdI₃ has been carried out in combination with mass spectrometric vapour monitoring at 1110(10) K and 1100(10) K, respectively. Up to 3 mol.% of dimeric species was observed in addition to the dominating monomeric molecules. The change of the thermal-averaged r _g configuration parameters of the molecules in the series LaI₃ → LuI₃ reflects the lanthanide contraction. A low value of the shrinkage δ(I···I) even at such a high temperatures may be considered due to vibration effects in molecule whose equilibrium geometric nuclear structure is planar and which correspond to configurationally averaged 4f ⁿ electronic state. B3LYP calculations performed in this study with large core potential for lanthanide atoms also resulted in equilibrium geometry of D _3h symmetry. According to the quantum chemical calculations, the potential function the non-planar vibration is essentially anharmonic, which is therefore to be taken into account to correctly describe nuclear dynamics in molecules such as LnI₃.     

Molecular structure,conformation, and large amplitude motion of barbituric acid as studied by gas-phase electron diffraction and quantum chemical calculations

Structural Chemistry - B3LYP and MP2(Full) calculations with large basis sets predict the planar equilibrium structure of barbituric acid and reveal large amplitude ring puckering motion which is...     

The molecular structure of selenium dibromide as determined by combined gas-phase electron diffraction-mass spectrometric experiments and quantum chemical calculations

The vapour over solid SeBr(4) at 10 degrees C was investigated with a combined gas-phase electron diffraction/mass spectrometric (GED/MS) method. The composition of the vapour derived from the mass spectra (43% SeBr(2), 56.7% Br(2) and 0.3% Se(2)Br(2)) was in agreement with the composition obtained from the analysis of the simultaneously recorded GED intensities (41(3)% SeBr(2), 59(3)% Br(2)). The GED study results in the following geometric parameters (r(g), angle(g) values with total uncertainties): Se-Br = 2.306(5) A and Br-Se-Br = 101.6(6) degrees . Most quantum chemical approximations (B3LYP, MP2, CCSD and CCSD(T) with relativistic effective core potentials and cc-pVTZ as well as aug-cc-pVTZ basis sets for the outer shells) overestimate the Se-Br bond length by 0.01 to 0.03 A. All methods reproduce the bond angle correctly, except for the B3LYP method. Gas phase vibrational frequencies estimated from experimental vibrational amplitudes agree well with those measured by Raman spectroscopy in acetonitrile solutions. All computational methods overestimate vibrational frequencies, especially that for the symmetric stretch vibration, by about or 8 to 13%.     

The molecular structure and conformation of trichloronitromethane as determined by gas-phase electron diffraction and theoretical calculations

The molecular structure of trichloronitromethane has been studied in the gas phase using electron diffraction data. The molecules are found to undergo low barrier rotation about the CN bond with a planar CNO₂ moiety in agreement with HF/MP2/B3LYP/6-311G(d,p) calculations. The experimental data are consistent with a dynamic model using a potential function for the torsion of V = (V₆/2)(1 − cos 6τ). The major geometrical parameters (r_g and ) for the eclipsed form, obtained from least squares analysis of the data are as follows: r(NO₃) = r(NO₄) = 1.213(2) Å, r(CN) = 1.592(6) Å, r(CCl)_av = 1.749(1) Å, Cl₅CN/Cl₆CN = 109. 6°/106.3°(2), O₃NC/O₄NC = 117. 6°/114.1°(4), τCl₅C₁N₂O₃ = 0.0°, and V₆ = 0.20(25) kcal/mol.     

Equilibrium molecular structure of orotic acid from gas-phase electron diffraction data and quantum-chemical calculations

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Molecular structure and conformations of benzenesulfonamide: gas electron diffraction and quantum chemical calculations

The molecular structure and conformational properties of benzenesulfonamide, C6H5SO2NH2, were studied by gas electron diffraction (GED) and quantum chemical methods (MP2 and B3LYP with different basis sets). The calculations predict the presence of two stable conformers with the NH2 group eclipsing or staggering the SO2 group. The eclipsed form is predicted to be favored by about 0.5 kcal/mol. According to GED, the saturated vapor over solid benzenesulfonamide at a temperature of 150(5) degrees C consists of the eclipsed conformer. The GED intensities, however, possess a very low sensitivity toward the vapor composition, and contributions of the anti conformer of up to 75% (at the 0.05 level of significance) or up to 55% (at the 0.25 level of significance) cannot be excluded. The molecule possesses C(sS) symmetry with the S-N bond perpendicular to the ring plane.     

The gas-phase molecular structure of 1-fluorosilatrane from electron diffraction

The molecular geometry of 1-fluorosilatrane has been determined by gas-phase electron diffraction. The distance between the nitrogen and silicon atoms is much longer in the gas phase, viz., 2.324±0.014 Å, than in the crystal, 2.042 (1) Å [5]. This indicates a weakened donor-acceptor interaction possibly as a consequence of the absence of intermolecular interactions in the gas phase. The five-membered rings take envelope conformations with the carbon atoms adjacent to nitrogen at the envelope tips. The following bond distances ( _g , Å) and bond angles (°) were obtained with their estimated total errors: N-C, 1.481±0.008; C-C, 1.514±0.011; O-C, 1.392±0.004; Si-O, 1.652±0.003; Si-F, 1.568±0.006; C-H, 1.118±0.005; N-C-C, 104.5±0.6; C-C-O, 117.0±0.7;C-O-Si, 123.7±0.6; O-Si-F, 98.7±0.3; O-Si-O, 117.8±0.1; C-N-C, 115.0±0.3.