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 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...     

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 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.     

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

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Molecular structure of carphedon as studied by gas electron diffraction and quantum chemical calculations

The gas-phase structure and conformational properties of carphedon (C₁₂H₁₄N₂O₂, phenylpiracetam, 2-oxo-4-phenyl-1-pyrrolidineacetamide) have been determined by gas electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 with 6-31G and cc-pVDZ basis sets). Since quantum chemical calculations demonstrate that the orientation of the acetamide group is fixed by a strong intramolecular N–H(amide)···O(pyrrolidone) hydrogen bond, the number of possible conformers is reduced considerably. Depending on the conformation of the pyrrolidine ring, envelope with out-of-plane C4 atom and acetamide group on the same side of the plane (“+”) or envelope with C4 and acetamide group on opposite sides (“?”), and on the orientation of the phenyl ring, axial (Ax), or equatorial (Eq), four relevant conformations, Ax?, Ax+, Eq?, and Eq+, exist. According to both quantum chemical methods (B3LYP and MP2 with cc-pVDZ basis sets) these four conformers differ by less than 2 kcal/mol in free energies. However, the two methods predict different relative free energies. The GED data were analyzed with different models. With a single-conformer model the best fit of the experimental GED intensities (agreement factor R _f = 4 %) is obtained with the Ax+ conformer. Using a two-conformer model the fit improves considerable for a 50(11):50(11) mixture of Ax? and Eq+ conformers (R _f = 2.7 %). No further improvement is obtained with a three-conformer model and large uncertainties for relative contributions occur. The geometric parameters of gaseous carphedon are compared with those in the crystal phase, where two molecules are connected by two intermolecular N–H···O hydrogen bonds, and with gas-phase values of piracetam.     

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 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 conformation of chloronitromethane as determined by gas-phase electron diffraction and theoretical calculations

The molecular structure of chloronitromethane was studied in the gas phase at a nozzle-tip temperature of 373 K. The experimental data were interpreted using a dynamic model where the molecules are undergoing torsional motion governed by a potential function: V = V2/2x(1 - cos 2tau) + V4/2x(1 - cos 4tau) with V2 = 0.81(30) and V4 = 0.12(40) kcal/mol (tau is the dihedral angle between the C-Cl and N-O bond). The conformer with a zero degree dihedral angle is the most stable conformer. Comparison with results from HF/MP2/B3LYP 6-311G(d,p) calculations were made. The important geometrical parameter values (for the eclipsed form) obtained from least-squares refinements are the following: r(C-H) = 1.061(18)A, r(C-N) = 1.509 (5)A, r(N-O) = 1.223(1)A, r(C-Cl) = 1.742(2)A, angleClCN = 115.2(7) degrees, angleO4NC = 118.9(10) degrees, angleO5NC = 114.9(16) degrees, and angleClCH 115(4) degrees.     

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.     

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.     

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

Structural Chemistry - The molecular structure of tris-2,2,6,6-tetramethyl-heptane-3,5-dione aluminium, or Al(thd)3, has been determined by quantum chemical (DFT) calculations, X-ray...     

Molecular structure of N-chlorosuccinimide studied by gas-phase electron diffraction and quantum-chemical methods

The molecular structure of N-chlorosuccinimide has been studied by GED method at the nozzle temperature of 116 °C. Vibrational corrections to the r _a parameters, Δ(r _a − r _e), have been calculated using the scaled quadratic and cubic force constants from B3LYP/6-31G(df,p) calculations. The force field scaling has been carried out using the IR and Raman spectra of the solid N-chlorosuccinimide. The molecular skeleton and the bond conformation around nitrogen were found to be planar within large experimental errors. The equilibrium geometrical parameters derived from the experimental data assuming C _2v molecular symmetry and those from MP2(fc)/6-311G(3df,2pd) calculations are in a good agreement.     

Molecular structure and conformation of nitrobenzene reinvestigated by combined analysis of gas-phase electron diffraction,rotational constants,and theoretical calculations

The molecular structure and conformation of nitrobenzene has been reinvestigated by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) spectroscopic data, and quantum chemical calculations. The equilibrium r _e structure of nitrobenzene was determined by a joint analysis of the GED data and rotational constants taken from the literature. The necessary anharmonic vibrational corrections to the internuclear distances (r _e ? r _a) and to rotational constants (B _e ⁽ⁱ⁾  ? B ₀ ⁽ⁱ⁾ ) were calculated from the B3LYP/cc-pVTZ quadratic and cubic force fields. A combined analysis of GED and MW data led to following structural parameters (r _e) of planar nitrobenzene (the total estimated uncertainties are in parentheses): r(C–C)_av = 1.391(3) Å, r(C–N) = 1.468(4) Å, r(N–O) = 1.223(2) Å, r(C–H)_av = 1.071(3) Å, \({\angle}\)C2–C1–C6 = 123.5(6)°, \({\angle}\)C1–C2–C3 = 117.8(3)°, \({\angle}\)C2–C3–C4 = 120.3(3)°, \({\angle}\)C3–C4–C5 = 120.5(6)°, \({\angle}\)C–C–N = 118.2(3)°, \({\angle}\)C–N–O = 117.9(2)°, \({\angle}\)O–N–O = 124.2(4)°, \({\angle}\)(C–C–H)_av = 120.6(20)°. These structural parameters reproduce the experimental B ₀ ⁽ⁱ⁾ values within 0.05 MHz. The experimental results are in good agreement with the theoretical calculations. The barrier height to internal rotation of nitro group, 4.1±1.0 kcal/mol, was estimated from the GED analysis using a dynamic model. The equilibrium structure was also calculated using the experimental rotational constants for nitrobenzene isotopomers and theoretical rotation–vibration interaction constants.     

Molecular structure of (cyanomethoxy)(dimethylamino)methane as studied by gas-phase electron diffraction and quantum-chemical calculations

The molecular structure of (cyanomethoxy)(dimethylamino)methane in the gas phase is investigated by means of gas-phase electron diffraction and quantum-chemical studies for the first time. It is shown that in the gaseous state, (cyanomethoxy)(dimethylamino)methane is a mixture of gauche-anti (65%) and anti-gauche (35%) conformers. The slight influence of the anomeric effect on the compound’s structural parameters was noted.     

Molecular structure of Hf(BH4)4 investigated by quantum mechanical calculations and gas-phase electron diffraction

The structure of the gaseous hafnium tetrakis(tetrahydroborate) molecule, Hf(BH4)4, has been investigated by detailed quantum mechanical calculations and by analysis of its gas electron-diffraction (GED) pattern. The ground-state geometry possesses T symmetry with all of the triply-bridged BH4 groups twisted equally about the Hf...B-H axes. Salient structural parameters (ra distances, r angles) deduced from the GED pattern by the SARACEN method were: r(Hf...B) 231.4(2), r(Hf-Hb) 221.5(7), r(B-Hb) 127.6(5), r(B-Ht) 121(1) pm, Hf...B-Hb 69.4(3), Hb-B-Hb 108.4(4), Hb-B-Ht 110.6(3), B...Hf...B-Hb 166(1) degrees. A notable feature is the large magnitude of the Hf...B and Hf-Hb anharmonicity parameters, attributed to the fluxional hydrogen atom exchange process. The properties are compared with those of related tetrahydroborates..     

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.     

Molecular structure of the trans and cis isomers of metal-free phthalocyanine studied by gas-phase electron diffraction and high-level quantum chemical calculations: NH tautomerization and calculated vibrational frequencies

The molecular structure of the trans isomer of metal-free phthalocyanine (H2Pc) is determined using the gas electron diffraction (GED) method and high-level quantum chemical calculations. B3LYP calculations employing the basis sets 6-31G**, 6-311++G**, and cc-pVTZ give two tautomeric isomers for the inner H atoms, a trans isomer having D2h symmetry and a cis isomer having C2v symmetry. The trans isomer is calculated to be 41.6 (B3LYP/6-311++G**, zero-point corrected) and 37.3 kJ/mol (B3LYP/cc-pVTZ, not zero-point corrected) more stable than the cis isomer. However, Hartree-Fock (HF) calculations using different basis sets predict that cis is preferred and that trans does not exist as a stable form of the molecule. The equilibrium composition in the gas phase at 471 degrees C (the temperature of the GED experiment) calculated at the B3LYP/6-311++G** level is 99.8% trans and 0.2% cis. This is in very good agreement with the GED data, which indicate that the mole fraction of the cis isomer is close to zero. The transition states for two mechanisms of the NH tautomerization have been characterized. A concerted mechanism where the two H atoms move simultaneously yields a transition state of D2h symmetry and an energy barrier of 95.8 kJ/mol. A two-step mechanism where a trans isomer is converted to a cis isomer, which is converted into another trans isomer, proceeds via two transition states of C(s) symmetry and an energy barrier of 64.2 kJ/mol according to the B3LYP/6-311++G** calculation. The molecular geometry determined from GED is in very good agreement with the geometry obtained from the quantum chemical calculations. Vibrational frequencies, IR, and Raman intensities have been calculated using B3LYP/6-311++G**. These calculations indicate that the molecule is rather flexible with six vibrational frequencies in the range of 20-84 cm(-1) for the trans isomer. The cis isomer might be detected by infrared matrix spectroscopy since the N-H stretching frequencies are very different for the two isomers.