Density Functional Theory Force Field Research Articles

Ab initio and DFT studies of the molecular structures and vibrational spectra of succinonitrile

The Molecular structure, conformational stability and vibrational frequencies of succinonitrile NCCH 2CH 2CN have been investigated with ab initio and density functional theory (DFT) methods implementing the standard 6–311++G * basis set. The potential energy surfaces (PES) have been explored at DFT-B3LYP, HF and MP2 levels of theory. In agreements with previous experimental results, the molecule was predicted to exist in equilibrium mixture of trans and gauche conforms with the trans form being slightly lower in energy. The vibrational frequencies and the corresponding vibrational assignments of succinonitrile in both C 2h and C 2 symmetry were examined theoretically and the calculated Infrared and Raman spectra of the molecule were plotted. Observed frequencies for normal modes were compared with those calculated from normal mode coordinate analysis carried out on the basis of ab initio and DFT force fields using the standard 6–311++G * basis set of the theoretical optimized geometry. Theoretical IR intensities and Raman activities are reported.

Vibrational spectra and structure of 5,6-diamino uracil and 5,6-dihydro-5-methyl uracil by density functional theory calculations

The molecular vibrations of 5,6-diamino uracil and 5,6-dihydro-5-methyl uracil were investigated in polycrystalline sample, at room temperature, by FT-IR and FT-Raman spectroscopies. The spectra were interpreted with the aid of normal coordinate analysis following a full structure optimization and force field calculations based on the density functional theory (DFT) using standard B3LYP/6-31G * and B3LYP/6-311+G ** methods and basis set combinations. The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compounds. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.

Theoretical investigation of the structure and vibrational spectra of carbamoyl azide

Molecular structure and vibrational frequencies of carbamoyl azide NH 2CO–NNN have been investigated with ab initio and density functional theory (DFT) methods. The molecular geometries for all the possible conformers of the molecule were optimized using DFT–B3LYP, DFT–BLYP and MP2 applying the standard 6-311++G ** basis set. From the calculations, the molecule was predicted to exist predominantly in cis conformation with the cis– trans rotational barrier of about 7.91–9.10 kcal/mol depending on the level of theory applied. The vibrational frequencies and the corresponding vibrational assignments of carbamoyl azide in C s symmetry were examined theoretically and the calculated Infrared and Raman spectra of the molecule in the cis conformation were plotted. Observed frequencies for normal modes were compare with those calculated from normal mode coordinate analysis carried out on the basis of ab initio and DFT force fields using the standard 6-311++G ** basis set of the theoretical optimized geometry. Theoretical IR intensities and Raman activities are reported.

Ab initio and density functional calculations of the structures and vibrational spectra of formaldoxime

Molecular structure and vibrational frequencies of formaldoxime, CH 2 NOH, have been investigated with ab initio and density functional theory (DFT) methods. The molecular geometries for all the possible conformers of the molecule were optimized using DFT-B3LYP, DFT-BLYP and MP2 applying the standard 6-311+G** basis set. From the calculations, the molecule was predicted to exit predominantly in trans conformation with the trans– cis rotational barrier of about 9.2–9.7 kcal/mol depending on the level of theory applied. The vibrational frequencies and the corresponding vibrational assignments of formaldoxime in C s symmetry were examined theoretically and the calculated infrared and Raman spectra of the molecule in the trans conformation were plotted. Observed frequencies for normal modes were compared with those calculated from normal mode coordinate analysis carried out on the basis of ab initio and DFT force fields using the standard 6-311+G** basis set of the theoretical optimized geometry. Theoretical IR intensities and Raman activities are reported.

Density functional theory study on the structure and vibrational spectra for cyanuric chloride

The molecular structure and vibrational spectra of cyanuric chloride have been investigated by density functional theory (DFT) using standard B3LYP/6-31G* and B3LYP/6-311+G** method and basis set combinations. The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. Both the calculated structural parameters and vibrational frequencies are in good agreement with the available experimental data.

Vibrational spectra and potential energy distributions for 4,5-dichloro-3-hydroxypyridazine by density functional theory and normal coordinate calculations

The solid phase FT-IR and FT-Raman spectra of 4,5-dichloro-3-hydroxypyridazine have been recorded in the regions 4000–400 cm −1 and 3500–100 cm −1, respectively. The spectra were interpreted with the aid of normal coordinate analysis following a full structure optimization and force field calculations based on the density functional theory (DFT) using the standard B3LYP/6-31G* and B3LYP/6-311+G** method and basis set combinations. The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. The IR and Raman spectra were predicted theoretically and compared with the experimental spectra.

DFT studies, vibrational spectra and conformational stability of 4-hydroxy-3-methylacetophenone and 4-hydroxy-3-methoxyacetophenone

The FT-IR and FT-Raman spectra of 4-hydroxy-3-methylacetophenone (HMA) and 4-hydroxy-3-methoxyacetophenone (HMOA) have been recorded. The total energy calculations of HMA and HMOA were tried for various possible conformers. The spectra were interpreted with the aid of normal coordinate analysis based on density functional theory (DFT) using standard B3LYP/6-31G * and B3LYP/6-311 + G ** methods and basis sets combinations for the most optimized geometries. Normal coordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. On the basis of the comparison between calculated and experimental results, assignments of fundamental modes were examined.

Simulation of IR and Raman spectra based on scaled DFT force fields: a case study of 2-(methylthio)benzonitrile, with emphasis on band assignment

The solid phase FT-IR and FT-Raman, solution phase linear dichroism IR (in nematic liquid crystal), and vapor phase GC/IR spectra of 2-(methylthio)benzonitrile have been recorded in the regions 4000–50, 3500–100, 4000–400, and 4000–650 cm −1, respectively. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimizations and force field calculations based on density functional theory (DFT) using standard B3LYP/6-31G* and B3LYP/6-311+G** method and basis set combinations. Normal coordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. IR dichroism data revealed an error in band assignment associated with a νCS vibration, which could be eliminated only by introducing independent scaling factors for sulfur, whereas the overall frequency fit was further improved. Simulation of infrared and Raman spectra utilizing the results of these calculations led to excellent overall agreement with the observed spectral patterns, especially with the higher level basis set. The SQM approach applying selective scaling of the DFT force field was shown to be superior to the uniform scaling method in its ability to allow for making modifications in the band assignment, resulting in more accurate simulation of IR and Raman spectra including band polarizations and intensity patterns.

Surface-enhanced Raman scattering of pyridine and p-nitrophenol studied by density functional theory calculations

A new methodology based on density functional theory (DFT) calculation to simulate surface-enhanced Raman scattering (SERS) spectra has been proposed, improving the theoretical approach by Aroca et al. This methodology aims at predicting differences in the enhancement factors among Raman bands in a SERS spectrum, thereby, helping one to interpret the SERS spectrum. A SERS spectrum of pyridine was simulated using Hartree–Fock, Møller–Plesset, and DFT methods. It has been found that the adsorption of pyridine is ascribed to a dipole–dipole interaction and that the DFT calculation is more efficient than the others from the viewpoints of the accuracy and computation time. A SERS spectrum of p-nitrophenol (PNP), which is a charge-separated molecule, was measured in a silver colloidal solution and simulated with the DFT calculation. The DFT calculation suggests that the adsorption of p-nitrophenol is attributed to a Coulombic interaction. In addition, the normal coordinate analysis of p-nitrophenol was performed on the basis of GF matrix method using the DFT force field, and the Raman bands that showed the strong SERS effect were assigned. It has been found from the assignments that an adsorption site cannot be specified when there are more than two adsorption sites even if the adsorption orientation of a molecule on a colloid is determined by surface selection rules, as defined by Moskovits et al. Consequently, the new methodology based on the DFT calculation is useful to predict the SERS effect for each band and will cut new path to apply SERS spectroscopy to quantitative microanalyses.

New developments in the calculation of metalloporphyrin Raman spectra via density functional theory

The recent development of density functional theory (DFT) makes it possible to calculate accurately metalloporphyrin structures and potential surfaces. This is illustrated for nickel porphine, the vibrations of which are reliably assigned from extensive spectroscopic studies. With a minimal set of scaling factors, the DFT force field reproduces the experimental wavenumbers to higher accuracy than the best available empirical force field. Moreover, the calculated intensities are in good accord with experiment, including the surprisingly large off-resonant Raman intensities of non-totally symmetric (B1g) modes. DFT also predicts a slight ruffling distortion of the porphyrin, and accurately reproduces the IR intensity of a distortion-induced out-of-plane mode. In the case of iron porphine, DFT correctly predicts an intermediate-spin (3A2g) ground state, with short Fe—N bonds, and a high-spin (5A1g) excited state with a planar geometry but an expanded porphyrin core. When the Fe is displaced from the plane, the potential rises faster for the 3A2g than the 5A1g state, which becomes the ground state beyond a 0.4 Å displacement. The doming mode is predicted to be at 71 cm-1, close to the 75 cm-1 wavenumber determined from coherent reaction dynamics in myoglobin. The vibrational wavenumbers of CO bound to heme are correctly calculated, and the potential for distorting the CO away from the heme normal is found to be surprisingly soft. Also, the transition dipole for the CO stretching mode is calculated to lag significantly behind the CO bond vector, thereby resolving an apparent discrepancy between crystallography and polarized IR spectroscopy with regard to the CO geometry in its adduct with myoglobin. Finally, the DFT force field was used successfully in conjunction with INDO calculations of the excited states, to reproduce resonance Raman intensities for NiP, both for Soret and Q-band resonances. These results give promise for developing a quantitative modeling capability for heme protein vibrational spectra. Copyright © 1998 John Wiley & Sons, Ltd.

Vibrational spectra and harmonic force fields of pyrrolidine derivatives: comparison between HF, MP2 and DFT force fields

Infrared and Raman spectra are reported for the isotopic species of pyrrolidine-d 0 (PY) and -d 1 and for N-methylpyrrolidine-d 0 (NMP), -d 2, -d 3 and -d 8. A complete assignment of the experimentally observed bands to normal modes is presented and discussed in particular in the CH/CD stretching region. The molecular structures and harmonic force fields were calculated ab initio at the Hartree–Fock (HF), the second order Møller–Plesset (MP2) and the density functional theory (DFT) level with the 6-31G* basis set. The force fields were fitted by use of 7 (PY) and 4 (NMP) independent scale factors. The spectra calculated with the DFT force fields are in better agreement with the experiment than those calculated by the MP2 and HF force fields. Though some scaled fundamental frequencies show larger deviations from the experimental ones, the mean percentage deviations of calculated frequencies from experimental fundamentals are less than 2.6% for all isotopic species of PY and NMP under study. The results indicate that density functional theory is a reliable tool to get a deeper insight in the assignment of vibrational spectra and the nature of normal modes of pyrrolidine derivatives.

Vibrational analysis of the spectra of 1,3,4-oxadiazole, 1,3,4-thiadiazole, 1,2,5-oxadiazole and 1,2,5-thiadiazole: comparison between DFT, MP2 and HF force fields

Ab initio harmonic force fields were calculated at the corresponding optimized geometries for 1,3,4-oxadiazole, (OD3), 1,3,4-thiadiazole (TD3), 1,2,5-oxadiazole (OD2) and 1,2,5-thiadiazole (TD2) with the Becke3LYP (B3LYP) density functional theory (DFT) using the 6-31G∗∗ basis set. The DFT force fields were scaled where the experimental frequencies were assigned to the calculated frequencies similar to that previously reported for the studied molecules with the second order Møller-Plesset (MP2) and the Hartree-Fock (HF) force fields using the same basis set, 6-31G∗∗. The calculated spectra with the DFT/6-31G∗∗ force fields were in better agreement with the experimental spectra than those calculated with the MP2/6-31G∗∗ or HF/6-31G∗∗ force fields. In addition, the scale factors obtained with DFT force fields are better correlated and less divergent than those obtained with the MP2 or HF force fields. The optimized geometries at the DFT/6-31G∗∗ level have poor prediction of the S-C and N-S bond lengths and CSC and NSN bond angles which is reflected such that the root-mean-square (rms) deviation of the calculated frequencies from the experimental frequencies are worse for TD3 and TD2 than for OD3 and OD2 but generally better than those obtained with the MP2/6-31G∗∗ or HF/6-31G∗∗ force fields. The rms deviations obtained with the DFT force fields are about half those obtained with the HF force fields. In the view of the excellent results obtained by the scaled DFT force fields for the four molecules, scaled force fields calculated with the DFT method are preferred to be used for vibrational analysis rather than with the HF or MP2 methods.

Vibrational Optical Activity of (3S,6S)-3,6-Dimethyl-1,4-dioxane-2,5-dione

Vibrational circular dichroism (VCD), absorption, Raman, and Raman optical activity (ROA) spectra for the title compound, a cyclic dimer, were measured in non-aqueous solution. The vibrational normal modes are assigned based on the result from ab initio force field calculation. Harmonic frequencies and atomic polar tensors for simulation of IR absorption were calculated both on the (Hartree−Fock SCF) HF/6-31G** level and using density functional theory (DFT) methods with the Becke3/LYP hybrid functional. Magnetic transition dipole derivatives were calculated on the HF/6-31G level, and the ROA polarizability tensors were calculated on the HF/4-31G level. Excellent agreement between the DFT calculated and experimental frequencies was obtained without a need for scaling. Furthermore, using the DFT force field, the correct VCD sign and intensity patterns were reproduced as compared to the experimental mid-IR spectra. Reasonable near-IR VCD and mid-IR ROA sign patterns for the intense peaks were also calculated. The excellent agreement for the mid-IR VCD results shows that medium-sized, biologically relevant molecules can have their spectra simulated using quantum mechanical techniques to a high level, certainly one suitable for conformational analyses by direct comparison of theory to experimental results. Comparison of DFT and HF level calculations suggests that the improvement found using DFT methods is primarily due to the force field and not to the intensity parameters. DFT atomic polar tensors were systematically weaker than the HF generated ones. Weak coupling between the subunits of this dimer implies dominance by local interactions which suggests that useful extension of these calculational techniques to larger oligomers might be accomplished by transfer of parameters.