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.     

Dative sigma- and pi-bonding in boron-nitrogen compounds: molecular structures of (CH3)2NB(CH3)N(CH3)B(CH3)2 and [(CH3)2B]2NN(CH3)2 determined by gas electron diffraction and quantum chemical calculations

The molecular structures of dimethylamino[(dimethylboryl)methylamino]methylborane, Me2NBMeNMeBMe2 (1) and 1,1-bis(dimethylboryl)-2,2-dimethylhydrazine, (Me2B)2NNMe2 (2) have been determined by gas electron diffraction (GED), density functional theory calculations at the B3PW91/6-311++G** level and ab initio calculations at the MP2/6-311++G** level. 1 adopts an open structure similar to that of the isoelectronic hydrocarbon molecule permethylbutadiene; the central B-N bond distance at 148.0/149.3(7) pm (MP2/GED) corresponds to a single covalent N--B bond distance, the two terminal distances, 140.9/140.5(4) pm and 141.8/141.3(4) pm, correspond to the distance between N and B atoms joined by a covalent sigma-bond and a dative pi-bond. A closed form where the establishment of a dative bond between the terminal N and B atoms has led to the formation of a four-membered ring also corresponds to a minimum on the potential energy surface, but the energy is calculated to be 14.3 kJ mol(-1) higher at the MP2 level. This structure is also incompatible with the GED data. 2 adopts a structure in which a dative sigma-bond between the dimethylamino N atom and one of the boron atoms has led to the formation of a three-membered N(2)B ring. The dative sigma-bond distance is 165.5/164.0(13) pm, the two other bond distances in the ring are N-B=150.6/148.9(9) pm corresponding to a covalent sigma-bond and N-N=145.1/145.4(3) pm. The terminal B--N distance 139.6/138.9(9) pm is consistent with a covalent sigma-bond augmented by a dative pi-bond. An open Y-shaped structure also corresponds to a minimum on the potential energy surface, but the energy is 18.7 kJ mol(-1) higher (MP2) and it is incompatible with the GED data.     

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 equilibrium structures of Si8O12(OSiMe3)8 and Si8O12(CHCH2)8

The equilibrium molecular structure of Si(8)O(12)(OSiMe(3))(8) has been determined in the gas phase by electron diffraction (GED). With OSi-containing substituents on the cage silicon atoms, this molecule contains a moiety, which would, if reproduced in a periodic manner, yield a zeolite-type structure. Extensive ab initio calculations were used to identify two conformers of this molecule, with D(4) and D(2) point-group symmetries; the D(4)-symmetric conformer was approximately 1.2 kJ mol(-1) lower in energy. With 132 atoms in each conformer, this is one of the largest studies to be undertaken using gas electron diffraction. Semiempirical molecular-dynamics (SE-MD) calculations were used to give amplitudes of vibration, vibrational distance corrections (differences between interatomic distances in the equilibrium structure and the vibrationally averaged distances that are given directly by the diffraction data), and anharmonic constants. The structure of Si(8)O(12)(CHCH(2))(8) has also been determined by GED. Calculations showed that the vinyl groups are fairly unhindered and rotate between three minimum-energy positions. Ultimately, all possible combinations of the vinyl groups in these low-energy positions were accounted for in the GED model.     

Molecular structure of 2,5-dihydropyrrole (C4NH7), obtained by gas-phase electron diffraction and theoretical calculations

The structure of 2,5-dihydropyrrole (C4NH7) has been determined by gas-phase electron diffraction (GED), augmented by the results from ab initio calculations employing third-order M?ller-Plesset (MP3) level of theory and the 6-311+G(d,p) basis set. Several theoretical calculations were performed. From theoretical calculations using MP3/6-311+G(d,p) evidence was obtained for the presence of an axial (63%) (N-H bond axial to the CNC plane) and an equatorial conformer (37%) (N-H bond equatorial to the CNC plane). The five-membered ring was found to be puckered with the CNC plane inclined at 21.8 (38) degrees to the plane of the four carbon atoms.     

Molecular structures of free quinuclidine and its adducts with metal trihydrides, MH3 (M=B, Al or Ga), studied by gas-phase electron diffraction, X-ray diffraction and quantum chemical calculations

The structure of quinuclidine, HC(CH(2)CH(2))(3)N, has been re-investigated by quantum chemical calculations and by gas-phase electron diffraction (GED). The GED data, together with published rotational constants, have been analysed using the SARACEN method to determine the most reliable structure (r(h1)) for the gaseous molecule. The structures of two adducts of quinuclidine with group 13 trihydride molecules, MH(3) (M=B, Al), have also been determined by GED and quantum chemical calculations. The effect of the coordination of these hydrides to the quinuclidine nitrogen atom has been investigated, and the structural changes and energetics of adduct formation are discussed. We also present the crystal structure of quinuclidine borane.     

N,N-Dimethylaminopropylsilane: a case study on the nature of weak intramolecular Si...N interactions

N,N-Dimethylaminopropylsilane H(3)Si(CH(2))(3)NMe(2) was synthesised by the reaction of (MeO)(3)Si(CH(2))(3)NMe(2) with lithium aluminium hydride. Its solid-state structure was determined by X-ray diffraction, which revealed a five-membered ring with an SiN distance of 2.712(2) A. Investigation of the structure by gas-phase electron diffraction (GED), ab initio and density functional calculations and IR spectroscopy revealed that the situation in the gas phase is more complicated, with at least four conformers present in appreciable quantities. Infrared spectra indicated a possible SiN interaction in the Si-H stretching region (2000-2200 cm(-1)), as the approach of the nitrogen atom in the five-membered ring weakens the bond to the hydrogen atom in the trans position. Simulated gas-phase IR spectra generated from ab initio calculations (MP2/TZVPP) exhibited good agreement with the experimental spectrum. A method is proposed by which the fraction of the conformer with a five-membered ring can be determined by a least-squares fit of the calculated to experimental absorption intensities. The abundance of this conformer was determined as 23.7(6) %, in good agreement with the GED value of 24(6) %. The equilibrium SiN distance predicted by theory for the gas-phase structure was highly variable, ranging from 2.73 (MP2) to 3.15 A (HF). The value obtained by GED is 2.91(4) A, which could be confirmed by a scan of the potential-energy surface at the DF-LCCSD[T] level of theory. The nature of the weak dative bond in H(3)Si(CH(2))(3)NMe(2) can be described in terms of attractive inter-electronic correlation forces (dispersion) and is also interpreted in terms of the topology of the electron density.     

Tautomeric and conformational properties of malonamide, NH2C(O)-CH2-C(O)NH2: electron diffraction and quantum chemical study

The geometric structure of malonamide, NH2C(O)-CH2-C(O)NH2, has been investigated by gas electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximations with 6-311++G(3df,pd) basis sets). Both GED and quantum chemistry result in the existence of a single diketo conformer in the gas phase. According to GED refinement this conformer possesses (sc,ac) conformation with one C=O bond in synclinal orientation (dihedral angle tau(O=C-C-C)=49.0(3.0) degrees) and the other C=O bond in anticlinal orientation (dihedral angle tau(O=C-C-C)=139.5(3.3) degrees). The experimental geometric parameters are reproduced very closely by the B3LYP method.     

Hydrogen bond effect on the bonding and B2 molecular vibrations of pyrrole

The influence of the hydrogen bond on the infrared B₂ symmetry modes of pyrrole (C_2ν) has been studied. CNDO/2 calculations suggest that the most probable structure for the associated pyrrole involves the interaction NH ⋯ π. The shortest distance between the nitrogen atom and the ring of the nearest neighbor molecule is about 2.9 Å. The absorption bands of pyrrole in the gaseous state at 474, 626 and 720 and 826 cm⁻¹ have been assigned to the NH, ring and CH out-of-plane deformation modes.     

Molecular structure and relative stability of trans and cis isomers of formanilide: gas-phase electron diffraction and quantum chemical studies

Molecular structure of formanilide is determined by gas-phase electron diffraction (GED) augmented by quantum chemical calculations (B3LYP/cc-pVTZ and MP2/cc-pVTZ) and literature microwave (MW) data. The combined GED and MW data are well reproduced for the mixture of trans and cis isomers with the relative abundance of 59 ± 5 and 41 ± 5 %, respectively, at T = 410 K. The trans isomer (C _s symmetry) is planar, while the cis isomer (C ₁ symmetry) has the twisted structure with the amide group rotated by 36.7 ± 2.7° with respect to the phenyl ring. In accord with theoretical calculations, the amide bond –NH–C(O)– is planar in trans formanilide and a somewhat nonplanar in cis isomer. Accurate structural parameters were obtained by a simultaneous fit of the rotational constants reported in the literature and GED intensities obtained in this study. The N–C(O) and N–C_Ph bond dissociation energies in formanilide are calculated using Gaussian-4 method. It is revealed that the strength of N–C(O) bond in formanilide is 50 kJ/mol less than that in benzamide. On the contrary, the strength of adjacent bond (N–C_Ph) increases by 35 kJ/mol compared to aniline. It is rather unexpectedly that the bond strength weakening does not result in the bond elongating, and vice versa.     

Tautomeric and conformational properties of benzoylacetone, CH3-C(O)-CH2-C(O)-C6H5: gas-phase electron diffraction and quantum chemical study

Tautomeric and structural properties of benzoylacetone, CH(3)-C(O)-CH(2)-C(O)-C(6)H(5), have been studied by gas-phase electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximation with different basis sets up to aug-cc-pVTZ). Analysis of GED intensities resulted in the presence of 100% enol tautomer at 331(5) K. The existence of two possible enol conformers in about equal amounts is confirmed by both GED and quantum chemical results. In both conformers the enol ring possesses C(s) symmetry with a strongly asymmetric hydrogen bond. The experimental geometric parameters are reproduced very closely by the B3LYP/cc-pVTZ method.     

Monochlorogallane: physical properties and structure of the gaseous molecule H2Ga(mu-Cl)2GaH2 as determined by vibrational, electron diffraction, and ab initio studies

Monochlorogallane, synthesized by the metathesis of gallium(III) chloride with an excess of trimethylsilane at ca. 250 K, has been characterized by chemical analysis, by its IR, Raman, and 1H NMR spectra, and by the products of its reaction with trimethylamine. The vibrational spectra of the vapor species isolated in solid Ar, N2, or CH4 matrixes at ca. 12 K imply the presence of only one species, viz. the dimer with an equilibrium structure conforming to D2h symmetry. The structure of this molecule has been determined by gas-phase electron diffraction (GED) measurements augmented by the results of ab initio molecular orbital calculations. An equilibrium structure with D2h symmetry has been assumed in the analysis of the electron diffraction pattern. However, as the molecule has a very low frequency Ga(mu-Cl)2Ga ring-puckering mode, a dynamic model was used to describe it with the aid of a set of pseudoconformers spaced at even intervals (deltadelta = 5 degrees, deltamax, = 20 delta) around the ring-puckering angle delta and Boltzmann-weighted according to a quartic potential V(delta) = V4delta4 + V2delta2. The differences in bond distances and angles between the different pseudoconformers were constrained to the values derived from the ab initio calculations employing second-order Moller-Plesset (MP2) methods (with all the electrons included in the correlation calculations) and a 6-311G(d) basis set. The results for the weighted average of the principal distances (ralpha) and angles (相似文献   

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 force field of boron tribromide as determined from combined analysis of gas electron diffraction and spectroscopic data and supported by quantum-chemical density-functional calculations

The thermal-average parameters of BBr₃ at 21(1) °C were obtained from a conventional analysis of gas electron diffraction (GED) data (r_g(B---Br) = 190.0(4) pm). The equilibrium structure and the force constants were refined from a joint analysis of the GED intensities and vibrational frequencies using different approximations. The simplest approximation (quadratic potential function in rectilinear coordinates) is suitable for the refinements of the equilibrium bond length (r^h_e(B---Br) = 189.6(4) pm) and the force constants of BBr₃. The molecule is planar within the error limits. Quantum-chemical density-functional calculations supported planarity of the molecule.     

Fluoroformyl trifluoroacetyl disulfide, FC(O)SSC(O)CF3: synthesis, structure in solid and gaseous states, and conformational properties

Fluoroformyl trifluoroacetyl disulfide, FC(O)SSC(O)CF3, is prepared by quantitative reaction between FC(O)SCl and CF(3)C(O)SH. The conformational properties and geometric structure of the gaseous molecule have been studied by vibrational spectroscopy (IR(gas), Raman(liquid), IR(matrix)), gas electron diffraction (GED), and quantum chemical calculations (B3LYP and MP2 methods). The disulfide bond length derived from the GED analysis amounts 2.023(3) Angstroms, and the dihedral angle around this bond, phi(CS-SC), is 77.7(21) degrees, being the smallest dihedral angle measured for noncyclic disulfides in the gas phase. The compound exhibits a conformational equilibrium at room temperature having the most stable form C(1) symmetry with a synperiplanar (sp-sp) orientation of both carbonyl groups with respect to the disulfide bond. A second form was observed in IR spectra of the Ar matrix isolated compound at cryogenic temperatures, corresponding to a conformer that possess the carbonyl bond of the FC(O) moiety in antiperiplanar position with respect to the S-S single bond (ap-sp). A DeltaH degrees = - = 1.34(11) kcal/mol has been determined by IR(matrix) spectroscopy. The structure of single crystal of FC(O)SSC(O)CF3 was determinate by X-ray diffraction analysis at low temperature using a miniature zone melting procedure. The crystalline solid (monoclinic, P2(1)/n, a = 5.240(4)Angstroms, b = 23.319(17)Angstroms, c = 6.196(4)Angstroms, beta = 113.14(3) degrees) consists exclusively of the (sp-sp) conformation. The geometrical parameters agree with those obtained for the molecule in the gas phase.     

The molecular structure, bonding, and energetics of oxovanadium phthalocyanine: an experimental and computational study

A mass spectrometric study of saturated vapor over oxovanadium phthalocyanine showed the thermal stability and monomeric vapor composition of this compound. The molecular structure of oxovanadium phthalocyanine (VOPc) was determined using a combination of gas-phase electron diffraction (GED), mass spectrometry, and quantum chemical calculations. According to GED, the VOPc molecule has C_4v symmetry. Experimental structural parameters are in good agreement with the parameters obtained by UB3LYP/cc-pVTZ calculations. The vanadium atom has a five-coordinated square-pyramidal geometry, being shifted above the plane of the four isoindole nitrogen atoms by 0.576(14) Å. The parameters of the square pyramid VN₄ are r _h1(V–N) = 2.048(7) Å, r _h1(N···N) = 2.780(12) Å. The vanadium–oxygen bond length is r _h1(V–O) = 1.584(11) Å. NBO analysis shows polar character of coordination bonds with significant covalent contribution and pronounced direct donation. X-ray crystallography and GED give different coordination bond lengths according to the different physical meaning of the parameters obtained by these methods. The enthalpy of sublimation [?H _s ^o (593–678 K)] is 53.3 ± 0.8 kcal/mol.     

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.     

Gas electron diffraction analysis on S-methyl thioacetate, CH3C(O)SCH3

The molecular structure of S-methyl thioacetate, CH3C(O)SCH3, was determined by gas electron diffraction (GED) with the assistance of quantum chemical calculations (B3LYP/6-31G and MP2/6-31G). Experimental and theoretical methods result in a structure with syn conformation (C=O double bond syn with respect to the S-C(H3) single bond). The following skeletal geometric parameters were derived from the GED analysis (ra values with 3sigma uncertainties): C=O = 1.214(3), C-C = 1.499(5), S-C(sp2) = 1.781(6), S-C(sp3) = 1.805(6) angstroms, O=C-C = 123.4(8) degrees, O=C-S = 122.8(5) degrees and C-S-C = 99.2(9) degrees.     

Effect of fluorination: Conformation of 2,6-difluoroanisole

The geometric structure and conformation of 2,6-difluoroanisole, 2,6-C₆H₃F₂OCH₃, has been determined with gas electron diffraction (GED) and quantum chemical calculations (MP2 and B3LYP with 6-311++G(2df,pd) basis sets). The GED intensities have been analyzed with a static as well as with a dynamic model. The static model resulted in a structure with near-perpendicular orientation of the O-CH₃ bond with a thermal average dihedral angle τ(C2C1-OC) = 70 ± 3°. With the dynamic model a perpendicular equilibrium structure and a potential function for internal rotation around the C-O bond with a very flat minimum at τ(C2C1-OC) = 90° and with a barrier of 1.8 ± 0.6 kcal/mol at τ(C2C1-OC) = 0° was derived. Quantum chemical calculations predict double-minimum potential functions for the electronic energies, which become single-minimum potentials upon addition of zero-point vibrational energies. The change of conformation from planar in anisole to perpendicular in 2,6-difluoroanisole has been rationalized by orbital interactions between the oxygen electron lone pairs and benzene ring orbitals and by steric repulsion.     

Structure and conformational properties of 1,3,3-trimethyl-1,3-azasilinane: gas electron diffraction, dynamic NMR, and theoretical study

Structure and the conformational properties of 1,3,3-trimethyl-1,3-azasilinane have been studied. According to gas electron diffraction (GED), the molecule exists in a slightly distorted chair conformation with the N-Me group in equatorial position. High-level quantum chemical calculations excellently reproduce the experimental geometry. Employing variable temperature (1)H and (13)C NMR spectroscopy down to 103 K, the conformational equilibrium could be frozen and the barrier to ring inversion determined.