O. E. Grikina

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.

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.

Analysis of electron diffraction data for several symmetric coordinates of large-amplitude motions in the case of the 1,3,5-trinitrobenzene molecule

A brief description of a solution of the problem on electron diffraction analysis using the potential procedure for nonrigid molecules with large-amplitude motions along several symmetric internal coordinates was given. The efficiency of the approach was demonstrated for determination of the equilibrium geometry of the 1,3,5-trinitrobenzene molecule with three equivalent internal rotation coordinates of NO2 groups. The results of the electron diffraction experiment and quantum-chemical calculation at the MP2(full)/cc-pVTZ level were considered along with the vibrational spectra of 1,3,5-trinitrobenzene and a planar equilibrium D3hsymmetry conformation for the molecule was found reliably for the first time. The geometrical parameters of the molecule were determined (re, the bond lengths are given in Å, the angles in deg): CC 1.387(2), CN 1.474(4), NO 1.220(1), CH 1.072(31), ONO 125.8(2), CC(H)C 116.6(3), HCC* 121.7(1), CC(N)C* 123.4(3), NCC* 118.3(1), and CNO* 117.1(1); the asterisk marks the dependent parameters.

Flexibility of the Saturated Five-Membered Ring in 2,5-Pyrrolidinedione (Succinimide): Electron Diffraction and Quantum-Chemical Studies with Use of Vibrational Spectroscopy Data

The flexibility of succinimide molecule has been studied for the first time by quantum-chemical (at the MP2 level with up to the 6-311G(3df,2p) basis sets) and gas-phase electron diffraction (GED) methods using vibrational spectroscopy data from literature. The analysis of vibrational spectra, performed for the molecular model of C(2v) symmetry (predicted by high-level ab initio calculations) using the scaling procedure, has shown that the two out-of-plane ring motions, that is, ring-bending and ring-twisting, are practically pure modes of different symmetry types and can be considered separately. The one-dimensional potential curves for the ring-bending and ring-twisting vibrations calculated at the MP2(full)/6-311G(3df,2p) level could be approximated by harmonic and anharmonic functions, respectively. The diverged energy levels for the ring-twisting vibration and the constant transition frequencies for the bending motion, obtained by the solution of the direct one-dimensional problem for the nonrigid model, demonstrate this statement. In the GED analysis, the succinimide molecule with a large-amplitude ring-twisting motion was described by a dynamic model with the distribution of pseudoconformers according to the calculated potential function taking into account structural relaxation effects from the MP2(full)/6-311G(3df,2p) calculations. This model greatly improved the fit of the GED intensities (R factor decreased from 4.6% for static model to 2.8%). The equilibrium molecular parameters r(e) determined in the dynamic approximation are very close to the corresponding values from the ab initio calculations. At the same time, the parameters of the -CH(2)-CH(2)- fragment involved in the ring-twisting motion deviate considerably from those obtained for the static model (C-C bond length by 0.027 A, =C-C-H, C-C-H, and H-C-C-N angles by up to 7 degrees). The flexibility influence on the C-C bond length is several times larger than the calculated vibrational correction (r(e) - r(a)) as well as the experimental uncertainty.

Interpretation of the vibrational spectra of nitramines on the basis ofab initio calculations

It is shown that, unlike conventional methods of vibrational spectroscopy, the use ofab initia harmonic force fields, IR and Raman intensities, and depolarizations makes possible a rigorous interpretation of the experimental spectra of the simplest aliphatic nitramines (CH3)2NNO2, CH3NHNO2, H2NNO2, and their isotopomers. The scale factors, which were introduced for each compound to remove the systematic errors of the SCF MO LCAO calculation by fitting the parameters to the observed frequencies, were mutually adjusted during the solution of the inverse vibrational problem. The set of transferable scale factors established in this work can be used directly to analyze spectra of larger molecules. Some common patterns of the force fields and vibrational spectra of nitramines are discussed.

Hexamethylenetetramine (urotropine) C6H12N2: Interpreting the vibrational spectra of -d0 and -d12 isotopomers by scaling the quantum-chemical force field

The equilibrium structure and quadratic and cubic force fields of the urotropine molecule are calculated at the MP2 (full)/cc-pVTZ level. Pulay scaling of the quadratic force field allows unambiguous interpretation of the vibrational spectra of -d0 and -d12 urotropines. A reliable matrix for the quadratic force constants of urotropine is obtained which may be used to determine the parameters of the equilibrium structure of the urotropine molecule by means of gas-phase electron diffraction.

Interpreting the vibrational spectra of uracil molecules and their deuterated isotopomers using a scaled quantum-chemical quadratic force field

The quadratic force field of the uracil molecule is obtained by MP2(full) calculations using the cc-pVTZ and cc-pVQZ basis sets. Under the assumption that the most stable diketone form of the uracil molecule has a flat configuration with Cs symmetry, the available vibrational gas-phase spectra of uracil and the matrix isolation spectra of its seven N-, C-, and mixed N,C-deuterated derivatives are analyzed jointly for the first time by using Pulay’s force field scaling. Band assignments suggested earlier are corrected. It is shown that sets of 14 scaling factors allow us to reproduce the adjusted interpretation of the spectra and to obtain the most reliable quadratic force constant matrix for uracil among those available, based on joint consideration of the experimental and quantum-chemical calculation results.

Molecular structures of acetylene derivatives of tin

The geometry and force fields of the bis(trimethylstannyl)acetylene molecule (a conformer withD3d symmetry corresponding to a minimum of the total energy of the molecule) were calculated by the RHF and MP2(fc) methods. The effective core potential in SBK form with the optimized 31G* valence basis set was employed in the case of Sn atoms. The 6–31G** and 6–311G** basis sets were used for carbon and hydrogen atoms. Vibrational spectra of the light and perdeuterated isotopomers of bis(trimethylstannyl)acetylene were interpreted using the procedure of scaling the quantum-chemical force fields.

Molecular structures of acetylene derivatives of tin: 7. Bis(trimethylstannyl)acetylene: analysis of electron diffraction data taking into account nonlinear relations between Cartesian and internal vibrational coordinates

The electron diffraction data on bis(trimethylstannyl)acetylene, Me3SnC≡CSnMe3, were analyzed in the framework of the one-dimensional dynamic model of free internal rotation of the SnMe3 group about the axis of the Sn−C≡C−Sn linear fragment. The root-mean-square amplitudes and harmonic shrinkage corrections used in the analysis were calculated from the scaled quantum-chemical force field (i) taking into account nonlinear relations between Cartesian and internal vibrational coordinates at the first-order level of perturbation theory (h1) and (ii) using a conventional approach (h0). Therh1 parameters of internuclear distances describe the equilibrium geometry of the Me3SnC≡CSnMe3 molecule much better than the commonly accepted parametersrα≡rh0. Substituent effects on the geometry of the acetylene fragment are discussed.