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 C _s 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.     

Gas-phase Raman spectra of s-trans- and s-gauche-1,3-butadiene and their deuterated isotopologues

The gas-phase Raman spectra of 1,3-butadiene and its 2,3-d(2),1,1,4,4-d(4) and d(6) isotopologues have been recorded using intense (6 W) green laser excitation and sensitive CCD detection. Hundreds of bands have been observed and assigned for each isotopologue. These spectra provide the best data to date for the s-trans conformer and also provide the first direct observation of the gas-phase Raman bands of the s-gauche conformer. Spectra recorded at elevated temperatures up to 250 °C for the d(0) and d(6) species help confirm the assignment of bands for the gauche rotamer. DFT computations were utilized to complement the studies. For the most part, the observed gas-phase gauche bands are in good agreement with previous matrix isolation studies. A best set of frequencies are reported for the fundamentals of the gauche rotamer of the d(0) and d(6) species.     

Ab initio structures for 90 degrees -twisted s-trans-1,3-butadiene and cyclooctatetraene: the naked sp2-sp2 bond

The bond length of a carbon-carbon sp2-sp2 sigma-bond without the perturbing effects of pi-interactions has been estimated by high level calculations on two prototypical systems: a 90 degrees -twisted form of butadiene and the tub conformer of cyclooctatetraene. The former system yields a value of 1.4818 A, considerably longer than previous estimates. The corresponding bond length in the latter is slightly shorter due to some pi-electron delocalization.     

Structure, force fields, and vibrational spectra of cerium tetrahalides

The geometrical structure, force fields, and vibrational spectra of CeX₄ (X = F, Cl, Br, I) were investigated by second, third, and fourth order Möller-Plesset perturbation theory, CISD+Q configuration interaction method, and the CCSD(T) coupled cluster method. Calculations on CeF₄ were also performed by multiconfiguration second order perturbation theory MCQDPT2/CASSCF. The wave function of the ground state of CeX₄ molecules was found to be appreciably non-one-configurational; this property increases from cerium fluorides to iodides and leads to the divergence of the series of Möller-Plesset perturbation theory. The calculated data point to a tetrahedral equilibrium nuclear configuration in CeX₄ molecules. The energy barriers to the inversion of the tetrahedral CeX₄ molecules via the square configurations are high enough, 74–89 kJ/mol. The calculated vibration frequencies, effective internuclear distances, and mean amplitudes of nuclear vibrations in CeF₄ agree with IR and Raman spectroscopic and high-temperature gas-phase electron diffraction data.     

Interpretation of the vibrational spectra of matrix-isolated uracil from scaled ab initio quantum mechanical force fields

The vibrational spectrum of uracil trapped in an argon matrix has been interpreted based on ab initio Hartree–Fock SCF calculations with a split-valence 4?21 basis set. The directly computed theoretical general valence force field was scaled with empirical scale factors in order to correct for the systematic errors originating in the limitation of the theoretical model. Scale factors transferred from related molecules provided a priori prediction of fundamental frequencies and intensities, permitting several corrections to be proposed for earlier assignments. Using the observed spectrum with the few altered assignments, a new set of scale factors was optimized to give the best force field available from combined consideration of the experimental and the theoretical data. For unknown reasons, the out-of-plane force field predicted a spectrum agreeing slightly less well with experiment than did the in-plane force field. However, the overall agreement between theory and experiment provided additional support for the assumptions involved in the method. The computed force fields were compared with others available from previous work. The comparison demonstrated the importance of expanding the energy surface around the true energy minimum and of using a proper scaling procedure. Previous scaled CNDO /2 calculations were found to be surprisingly good despite the large corrections required and the fact that they were made at an incorrect geometry.     

Simulation of IR and Raman spectra of p-hydroxyanisole and p-nitroanisole based on scaled DFT force fields and their vibrational assignments

This work deals with the vibrational spectroscopy of p-hydroxyanisole (PHA) and p-nitroanisole (PNA) by means of quantum chemical calculations. The mid and far FT-IR and FT-Raman spectra were recorded in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-31G* method and basis set combination and were scaled using various scale factors which yield a good agreement between observed and calculated frequencies. The vibrational spectra were interpreted with the aid of normal coordinate analysis based on scaled density functional force field. The results of the calculations were applied to simulate infrared and Raman spectra of the title compounds, which showed excellent agreement with the observed spectra.     

The vibrational spectra of cis,cis-,trans,trans- and cis,trans-1,4-dichloro-1,3-butadiene

The i.r. spectra of cis,cis,trans,_trans and cis,trans-1,4-dichloro-1,3-butadiene were recorded in cyclohexane solution in the region 600-40 cm⁻¹. Raman spectra, including polarization measurements of the neat liquids were obtained. Some previously unobserved fundamentals, particularly in the low frequency region, were assigned, and a few revisions in the earlier interpretations were made.Force fields containing 21 parameters for the cis,cis and the trans,trans compounds were constructed by transferring force constants from cis- and trans-1-chloro-1,3-butadiene. By mixing the force constants from these monochlorobutadienes a 29 parameter force field was derived for the cis,trans compound. The calculated r.m.s. amplitudes of vibration and perpendicular amplitude correction coefficients are presented.     

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.     

The vibrational spectra, molecular structure and conformation of organic azides Part II. 2-Azido-1,3-butadiene

A sample of 2-azido-1,3-butadiene was synthesized from 4-bromo-1,2-butadiene and tetramethylguanidinium azide. Although the sample is highly explosive, we succeeded in making a structure determination by gaseous electron diffraction. IR spectra of the vapour, of the matrix isolated species in argon at 15 K, and of an amorphous and crystalline solid at 90 K were recorded. A Raman spectrum of the liquid, including semiquantitative polarization data, was obtained at 240 K.

The title compound was found to be planar with the CNN angle 117° oriented syn to the adjacent C=C double bond, the NNN angle was ca. 177° oriented anti to the C---N bond. The following bond distances (r_a) were obtained: N---N(N), 114.3; N---N(C), 125.3; C---N, 143.4; C=C, 135.0; and C---C, 146.7 pm.

No additional conformers were observed in the vapour, liquid, amorphous or crystalline states.     

The vibrational spectra, molecular structure and conformation of organic azides Part III. 2,3-Diazido-1,3-butadiene

A sample of 2,3-diazido-1,3-butadiene has been synthesized from 1,4-dibromo-2-butyne and tetramethylguanidinium azide. The highly explosive sample has been studied by gaseous electron diffraction and by IR spectroscopy. Only incomplete Raman spectra have been recorded due to sample decomposition in the laser beam. The title compound is found to be planar with the CNN angle equal to 114.5°, oriented syn to the adjacent C=C double bond; the NNN angle is ca. 167°, oriented anti to the C---N bond. The following bond distances (r_a) are obtained: N---N(N), 114.1; N---N(C), 124.2; C---N, 143.2; C=C 134.8; and C---C, 148.5 pm. The vibrational spectra are tentatively assigned in terms of C_2h molecular symmetry, supported by force constant calculations.     

Theoretical prediction of vibrational spectra. The a priori scaled quantum mechanical (SQM) force field and vibrational spectra of pyrimidine

The complete harmonic force field of pyrimidine has been computed at the ab initio Hartree—Fock level using a 4–21 Gaussian basis set. In order to compensate the systematic overestimations of the force constants at the aforementioned level of quantum mechanical approximation, the theoretical force constants were empirically scaled by using nine scale factors. (The values of all these scale factors were previously determined by fitting the theoretical force field of benzene to the observed vibrational spectra of benzene.) The resulting a priori scaled quantum mechanical (SQM) force field is regarded as the most accurate and physically the most correct harmonic force field for pyrimidine. This force field was then used to predict the vibrational spectra of pyrimidine-h₄ and pyrimidine-d₄. On the basis of these a priori vibrational spectra uncertain assignments have been confidently resolved. After a few reassignments, the mean deviations between the experimental and calculated frequencies are below 9 and 18 cm⁻¹ for the non-CH stretching in-plane and the out-of-plane vibrations, respectively. Computed IR intensities are generally in agreement with experiments at a qualitative level.     

A quantum-chemical study of nitroguanidine and tetramethyl nitroguanidine: Stable structures,force fields,and the interpretation of the vibrational spectrum

Stable structures of nitroguanidine and tetramethyl nitroguanidine were searched by the MP2 and B3LYP methods with the use of the 6–31G(d,p) and 6–311G(d,p) basis sets. For nitroguanidine, the force fields calculated by these methods were scaled using the experimental spectra for seven isotopomers. The obtained scaling factors made it possible to theoretically evaluate and assign the frequencies in the spectrum of tetramethyl nitroguanidine.     

The conformation and vibrational spectra of 2-ethynyl-1,3-butadiene (3-methylene-4-pentene-yne)

A sample of 2-ethynyl-1,3-butadiene was synthesized by a thermal rearrangement of 1,2-hexadiene-5-yne at ca. 770 K. Infrared spectra were recorded of the vapour, the liquid and of the amorphous and crystalline solids at 90 K in the region 4000-50 cm⁻¹. Raman spectra were obtained of the cooled liquid, including semiquantitative polarization measurements, and of the crystalline solid at 90 K. The spectral data indicate that 2-ethynyl-1,3-butadiene exists as the s-trans conformer in the various states of aggregation but the possibility of small amounts of a second conformer cannot be excluded.     

Predictive abilities of scaled quantum mechanical molecular force fields: application to 2,3-dimethylbuta-1,3-diene

In connection with the appearance of new experimental vibrational data on the high-energy rotational isomer of 2,3-dimethylbuta-1,3-diene (I) in a low-temperature matrix and in neat crystals, the ab initio-based vibrational analysis of this molecule has been re-evaluated. Calculated wavenumbers derived from a scaled quantum-mechanical force field analysis at the MP2(FC)/aug-cc-pVDZ//MP2(FC)/aug-cc-pVDZ computational level are compared with experimental data. Several reassignments of the fundamental wavenumbers for I have been suggested in the course of the current analysis, and the existence of a high-energy non-planar s-gauche conformer of 2,3-dimethylbuta-1,3-diene has been confirmed.     

Simulations of vibrational spectra from classical trajectories: calibration with ab initio force fields

An algorithm allowing simulating vibrational spectra from classical time-dependent trajectories was applied for infrared absorption, vibrational circular dichroism, Raman, and Raman optical activity of model harmonic systems. The implementation of the theory within the TINKER molecular dynamics (MD) program package was tested with ab initio harmonic force fields in order to determine the feasibility for more extended MD simulations. The results suggest that sufficiently accurate frequencies can be simulated with integration time steps shorter than about 0.5 fs. For a given integration time step, lower vibrational frequencies ( approximately 0-2000 cm(-1)) could be reproduced with a higher accuracy than higher-frequency vibrational modes (e.g., O-H and C-H stretching). In principle, the algorithm also provides correct intensities for ideal systems. In applied simulations, however, the intensity profiles are affected by an unrealistic energy distribution between normal modes and a slow energy relaxation. Additionally, the energy fluctuations may cause weakening of the intensities on average. For ab initio force fields, these obstacles could be overcome by an arbitrary normal mode energy correction. For general MD simulations, averaging of many shorter MD trajectories started with randomly distributed atomic velocities provided the best spectral shapes. alpha-pinene, D-gluconic acid, formaldehyde dimer, and the acetylprolineamide molecule were used in the tests.     

Ab initio study of the structure, force fields, and vibrational spectra of alkali metal tellurites

The equilibrium geometrical parameters, force fields, vibration frequencies, and intensities in the IR molecular spectra of M₂TeO₃ (M-Li, Na, K) are found by the Hartree — Fock ab initio method in the bases complemented with polarization and diffusion functions using relativistic effective core potentials. The relative energies of alternative molecular configurations and the energies of the dissociation M₂TeO₃→ M2O + TeO2 are refined using Möller — Plessett second-order perturbation theory. It is found that the chemical bond in these molecules can be approximated by the scheme (M⁺)₂[TeO₃]^2- The equilibrium nuclear configuration has C_s symmetry and corresponds to the bis-bidentate coordination of M₊ cations by the pyramidal anion [TeO₃]^2-. The mono-bidentate structures of C_s symmetry correspond to the saddle points on the potential energy surface of the molecules. The calculated IR molecular spectrum of K₂TeO₃ agrees with the experimental spectrum obtained by the matrix isolation method by J. Ogden et al. [J. Chem. Soc. Dalton Trans., 1957 (1997)]. Based on the results of the previous ab initio studies of alkali metal sulfites and selenites, the barrier of the intramolecular rearrangement (bb)→(mb)→(bb)’ was found to lower in the series Li₂XO₃→Na₂XO₂→K₂XO₃ (X = S, Se, Te) and M₂TeO₃→M₂SeO₃→M₂SO₃. The degree of deformation of the XO fragment in the M₂XO₃ molecules decreases when the M atom is replaced by its heavier analog (Li→Na→K).     

Mechanism of thermal reactions of dimerization and trimerization of hexafluoro-1,3-butadiene: A quantum-chemical study

The mechanism of thermal oligomerization of hexafluoro-l,3-butadiene was examined using RHF, ROHF, and GVB/DH, and by B3LYP/6-31G* and /6-311G* quantum-chemical methods. The energies of highly reactive excited states of the monomer and of intermediate biradical species were estimated. Isomeric biradicals (excited monomers and dimers) with the free valences localized on two carbon atoms were shown to coexist in the reaction mixture. Recombination of such biradicals and their reactions with neutral stable molecules give rise to diverse products, depending on the reaction temperature.     

Predictive abilities of scaled quantum-mechanical molecular force fields: application to 2-methylbuta-1,3-diene (isoprene)

The ab initio-based, scaled quantum-mechanical molecular force field (SQM-FF) analysis of the vibrational spectra of the s-trans and s-gauche conformers of 2-methylbuta-1,3-diene (isoprene), reported previously at the HF/6-31G//HF/6-31G computational level [Bock, et al. J Mol Struct 160: 337, 1987], has been updated in this article using a more complete set of experimental data on the s-gauche conformer along with revised results for the s-trans conformer obtained in the gas phase, in a low-temperature matrix, and in neat crystals. Geometrical parameters and the calculated wavenumbers derived from the SQM-FF at the MP2(FC)/aug-cc-pVDZ//MP2(FC)/aug-cc-pVDZ level are compared to experiment. The analyses performed are consistent with the presence of a twisted high-energy s-gauche conformer of isoprene.