L. S. Khaikin

The structure of nitrobenzene and the interpretation of the vibrational frequencies of the CNO2 moiety on the basis of ab initio calculations

Abstract The vibrational spectra of nitrobenzene and its para - d 1 , d 5 , 16 O 18 O, 18 O 2 and 15 N isotopic modifications are evaluated using the RHF/6-31G* ab initio harmonic force field. A rigorous interpretation of the experimental CNO 2 moiety bands is carried out. Systematic deficiencies of the SCF method are effectively removed by applying scale factors optimized previously for a number of aliphatic nitro compounds. Fully optimized geometries are also reported for planar and orthogonal nitrobenzene conformations at the RHF and MP2 computational levels using the standard 6-31G* and 6-31G** basis sets. Theoretical geometries and barriers to internal rotation are compared with available experimental data. The calculations suggest that steric factors affect appreciably the structural parameters of the CNO 2 fragment in the equilibrium planar conformation and consequently the potential function for internal rotation in nitrobenzene.

Study of the Thymine Molecule: Equilibrium Structure from Joint Analysis of Gas-Phase Electron Diffraction and Microwave Data and Assignment of Vibrational Spectra Using Results of Ab initio Calculations

Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1), angle e (N1-C6=C5) = 123.1 (5), angle e (C2-N1-C6) = 123.7 (5), angle e (N1-C2-N3) = 112.8 (5), angle e (C2-N3-C4) = 128.0 (5), angle e (N3-C4-C5) = 114.8 (5), angle e (C6=C5-C9) = 124.4 (9). The experimental structural parameters are in good agreement with those from MP2 (full) calculations with use of cc-pVTZ and cc-pVQZ basis sets.

Gas phase electron diffraction study of trimethylstannylacetylene

Abstract Trimethylstannylacetylene has been studied by gas phase electron diffraction. The bond lengths, r a (A), and valence angles (degrees) determined with errors represented by three times standard deviation values are as follows: .The results are compared with the structural data on organotin compounds studied earlier. The bond lengths are shown subject to different substituent effects.

Molecular structures of acetylene derivatives of tin: Part II. Gas phase electron diffraction study ofbis(trimethylstannyl)acetylene, Me3SnCCSnMe3

Abstract A gas phase electron diffraction study of bis(trimethylstannyl)acetylene is reported. The ra structure refines to the following parameters (bond lengths in nm, valence angles in degrees): The numbers in parentheses are three times the standard deviation values. The difference between the bond lengths in the bis(trimethyl-stannyl) acetylene molecule is less significant than with trimethylstannylacetylene. The observed departure from linearity in the Sn-CC-Sn fragment is seemingly due to the shrinkage effect.

Molecular structures of acetylene derivatives of tin: Part III. Gas phase electron diffraction study of tetrakis(trifluoropropynyl)-tin, Sn(CC-CF3)4

Abstract A gas phase electron diffraction study of tetrakis(trifluoropropynyl)tin is reported. The model, based on T d symmetry for the carbon—tin skeleton and C 3v symmetry for the CF 3 groups, refines to the following parameters (bond lengths, r a , in nm; valence angles in degrees): Sn—C0.2070(7), CC 0.1215(6), C—C 0.1460(7), C—F 0.1343(2), CCF 111.3(0.2). The uncertainties (given in parentheses) represent three times the standard deviation values. The results obtained point to practically free rotation of the CF 3 groups. The presence of electronegative CF 3 causes shortening of the Sn-C bonds in Sn(CC—CF 3 ) 4 from Me 3 SnCCH and Me 3 SnCCSnMe 3 . The triple CC bond length is larger than in hexafluoro-2-butyne and nearly the same as in dimethylacetylene.

An analysis of electron diffraction data on bis(trimethylsilyl)acetylene taking into account nonlinear relations between Cartesian and internal vibrational coordinates

Abstract The electron diffraction data on bis(trimethylsilyl)acetylene were analyzed in terms of the one-dimensional dynamic model of free Si(CH 3 ) 3 group rotations about the Si–C C–Si axis. The root-mean-square amplitudes and harmonic shrinkage corrections were calculated taking into account nonlinear relations between Cartesian and internal vibrational coordinates at the level of first-order perturbation theory ( h 1) and with the use of the traditional scheme ( h 0). The experimental r α distances were virtually independent of the approximation used to calculate vibrational effects. The r h 1 parameter values much better approximated the equilibrium geometry than the familiar r α r h 0 parameters. The r h 1 -structure of bis(trimethylsilyl)acetylene refined to Si–C(H 3 ) 1.877(4), Si–C 1.841(4), C C 1.239(3), C–H(av.) 1.108(3) A, (H 3 )C–Si–C 109.2(2)° and Si–C–H(av.) 111.3(2)°. Electron diffraction data on silylacetylenes were systematized in terms of r g parameters equal to r h 1 for bonded distances.

Gas-phase electron diffraction study of tris(trimethylstannyl)amine, N(SnMe3)3

Abstract The geometrical parameters of tris(trimethylstannyl)amine have been determined by gas-phase electron diffraction. The a structure has been refined using mean amplitude values calculated from the force fields of a number of tin derivatives. The experimental data are consistent with a planar bond configuration at the nitrogen in N(SnMe 3 ) 3 . The final set of geometrical parameters is as follows (average bond distances, r g , in A, angles in degrees): SnC 2.166(5), SnN 2.038(3), CH 1.117(17). NSnC 108.5(1.5), SnCH 112.1(1.6). Mean amplitude values have been varied for those distances which give considerable contributions to scattering. The results obtained fill a gap in the knowledge of structures of Group IV element μ-nitrido derivatives. They confirm the conclusion that lowering of ligand MR n electro-negativity weakens the tendency to deviation from planarity in the central fragment NM 3 . This tendency may be considered as a manifestation of the second-order Jahn-Teller effect.

Vibrational spectra of (CH3)3SnCCH, (Cd3)3SnCCH and (CD3)3SnCCD and force field of trimethylstannylacetylene

Abstract The IR (32–4000 cm −1 ) and polarized Raman (50–3500 cm −1 ) spectra of liquid (CH 3 ) 3 SnCCH, (Cd 3 ) 3 SnCCH and (CD 3 ) 3 SnCCD are measured at room temperature. The spectra are interpreted in terms of a model of point group C 3v . The CH (CD) methyl bonds lying in symmetry planes are assumed to be in an eclipsed arrangement with respect to the acetylene bond. The force constants of trimethylstannylacetylene are calculated by the least-squares method.

Gas phase electron diffraction study of tetravinyltin Sn(CHCH2)4

Abstract The tetravinyltin molecule has been studied by gas phase electron diffraction. The r a structure analysis is based on the assumptions that a single conformer occurs in Sn(CHCH 2 ) 4 and that tin has a tetrahedral bond configuration. The preferred model ( S 4 symmetry) predicts all four vinyl groups to be intermediate between staggered and eclipsed conformations. The structure refinement gives the following parameters (bond lengths, r a , in nm, valence angles in degrees): , SnCC = 121.9(0.6), CC = 0.1349(8), SnCH = 116.8(4.5), av. = 0.1098(14). The uncertainties given in parentheses represent three times the standard deviation values. The observed shortening of the bond in Sn(CHCH 2 ) 4 from in SnMe 4 (by 0.0027 nm) is equal to the shortening that occurs on going from in ethane to in propylene. With the corresponding Si and Ge derivatives, this effect is less pronounced.

Molecular structures of acetylene derivatives of tin: Part IV. Gas-phase electron-diffraction study of tetraethynyltin, Sn(CCH)4, and triethynyltin iodide, ISn(CCH)3

Abstract The geometrical parameters of tetraethynyltin and triethynyltin iodide have been determined by gas-phase electron diffraction. Triethynyltin iodide was present as an admixture in both the tetraethynyltin samples studied. Because the samples differed significantly in percentage of the iodide (17.4 ± 4.0 and 47.1 ± 3.5 mol %, in samples A and B, respectively), it was possible to determine the structures of both molecules to a sufficient degree of accuracy. The r α , structures were solved by the least-squares treatment of the molecular intensities, using mean amplitudes and shrinkage corrections calculated from the force fields of a number of tin derivatives. The T d -symmetry model of Sn(CCH) 4 was refined to give the following parameters: Sn-C, 2.068(5); CC, 1.228(8); CH, 1.079(51). The structural parameters for ISn(CCH) 3 (on the basis of the C 3v model with linear Sn-CC-H fragments) are as follows: Sn-I, 2.646(4); Sn-C, 2.062(17); CC, 1.226(6); ∠ISnC 108.0(2.8). (The thermal average bond distances, r g , are given in A, and the valence angle, rα, in degrees; the values in paren- theses are three times the standard deviations, 3σ.) The Sn-C bonds in Sn(CCH) 4 , and ISn(CCH) 3 are shorter than the corresponding bonds in the monoethynyltin derivatives, Me 3 SnCCH and Me 3 SnCCSnMe 3 . The SnI bond in ISn(CCH) 3 is noticeably shorter than those in stannane iodide and trimethylstannane iodide.