Anharmonic vibrational spectroscopy calculations with electronic structure potentials: comparison of MP2 and DFT for organic molecules

Density functional theory (DFT) technique is the most commonly used approach when it comes to computation of vibrational spectra of molecular species. In this study, we compare anharmonic spectra of several organic molecules such as allene, propyne, glycine, and imidazole, computed from ab initio MP2 potentials and DFT potentials based on commonly used BLYP and B3LYP functionals. Anharmonic spectra are obtained using the direct vibrational self-consistent field (VSCF) method and its correlation-corrected extension (CC-VSCF). The results of computations are compared with available experimental data. It is shown that the most accurate vibrational frequencies are obtained with the MP2 method, followed by the DFT/B3LYP method, while DFT/BLYP results are often unsatisfactory. Contribution to the Mark S. Gordon 65th Birthday Festschrift Issue.     

HF, MP2 and DFT calculations and spectroscopic study of the vibrational and conformational properties of N-diethylendiamine

The conformational stability and vibrational modes of the N-diethylendiamine organic cation (N-DD(2+)) were studied by experimental (Raman) spectroscopy combined with theoretical calculations. Various ab initio theories were used: Hartree-Fock (HF) theory, M?ller-Plesset second-order perturbation (MP2) theory and density functional theory (DFT). Three stable conformers of N-DD(2+), trans-trans, gauche-gauche and gauche-trans were calculated. A comparison between the computed structural parameters of the conformers at both levels of theory and the X-ray data was made. It is demonstrated that the N-DD(2+) cation adopts more probably the gauche-gauche conformation at room temperature. In order to make a more detailed interpretation of the low temperature phase transition of N-DDHP, the Raman spectra of N-DDHP were recorded at room and low temperature in the 200-3400 cm(-1) region. The vibrational frequencies of the different conformers of N-DD(2+) were also calculated using the DFT/B3LYP (6-31G(d)) level of theory. By comparison between the experimental and theoretical results, the conformational dynamic of the N-DD(2+) organic cation was confirmed. It is shown that the N-DD(2+) cation configuration changes from gauche-gauche conformer to gauche-trans conformer when decreasing the temperature.     

Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study

An extension of the SIBFA polarizable molecular mechanics procedure to flexible oligopeptides is reported. The procedure is evaluated by computing the relative conformational energies, deltaE(conf), of the alanine tetrapeptide in 10 representative conformations, which were originally derived by Beachy et al. (J Am Chem Soc 1997, 119, 5908) to benchmark molecular mechanics procedures with respect to ab initio computations. In the present study, a particular emphasis is on the separable nature of the components of the energy and the particular impact of the polarization energy component on deltaE(conf). We perform comparisons with respect to single-point HF, DFT, LMP2, and MP2 computations done at the SIBFA-derived energy minima. Such comparisons are made first for the 10 conformers derived from phi/psi torsional angle energy-minimization (the rigid rotor approach), and, in a second step, after allowing additional relaxation of the C(alpha) centered valence angles. In both series of energy-minimization, the SIBFA deltaE(conf) compared best with the LMP2 results using the 6-311G** basis set, the rms being 1.3 kcal/mol. In the absence of the polarization component, the rms is 3.5 kcal/mol. In both series of minimizations, the magnitudes of deltaE(conf), computed as differences with respect to the most stable conformer taken as energy zero, decrease along the series: HF > DFT > LMP2 > SIBFA > MP2, indicative of increasing stabilization of the most highly folded conformers.     

MNDO,AM1 and PM3 calculations in the study of the energy and structure of quinazolone tautomers

MNDO, AM1, and PM3 calculations were used to study the tautomeric forms of quinazolones. The relative energy of the tautomers closest to the experimental value was obtained using the AM1 and PM3 methods. The keto-enol tautomeric equilibrium of quinazolones in the gas phase is shifted toward the ketone form.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1246–1251, September, 1993.     

Structure and stability of thiourea with water, DFT and MP2 calculations

The relative stabilities of thiourea in water are investigated computationally by considering thiourea–water complexes containing up to 1–6 water molecules (CS(NH₂)₂(H₂O)_n=1–6) using density functional theory and MP2 ab initio molecular orbital theory. The results show that the thiourea complex is stable and has an unusually high affinity for incoming water molecules. The clusters are progressively stabilized by the addition of water molecules, as indicated by the increasing of the binding energy. The binding energy of the cluster to each H₂O molecule is about 33 kJ mol⁻¹ for n=1–5.The C–S bond, N–C bond distance, Mulliken populations and binding energy keep approximately constant as the clusters increase in size with an increasing number of H₂O molecules. As the solvation progresses, the C–S distance increases monotonically while the Mulliken populations on the C–S bond reduces monotonically with the addition of each H₂O molecule, indicating that the C–S bond of the thiourea unit in the clusters is de-stabilized with an increasing number of H₂O molecules. Charge transfers for the clusters are mainly found at N, S atoms of the thiourea.     

AM1, PM3, and PM5 calculations of the absorption maxima of basic organic dyes

The absorption maxima, λ_max, of various organic dyes such as indigo, azobenzene, phenylamine, hydrazone, anthraquinone, naphthoquinone, and malachite green were calculated using the AM1, PM3, and PM5 semiempirical molecular orbital theories with the configuration interaction singles (CIS) and random phase approximation (RPA) approaches. The calculated λ_max were then compared with the values obtained by CNDO/S, INDO/S, ab initio CIS, and time-dependent density functional theory (TD-DFT). We found that the λ_max values calculated by AM1, PM3, and PM5 were in good correlation with the observed λ_max values. When B3LYP/cc-pVDZ optimized geometries were used, the square of the correlation coefficients between the calculated and observed λ_max, , at the AM1-RPA, PM3-RPA, and PM5-RPA levels were 0.891, 0.897, and 0.927, respectively. In particular, at PM5-RPA//B3LYP/cc-pVDZ was the largest among those obtained from all the other calculations including TD/B3LYP/cc-pVDZ//B3LYP/cc-pVDZ . Accordingly, the standard deviation of the difference between observed and calculated λ_max by the linear regression function at PM5-RPA//B3LYP/cc-pVDZ was the smallest. It was therefore concluded that this method was the most promising for the prediction of λ_max of various dyes among the computational methods studied here. When AM1 optimized geometries were used, at the AM1-RPA, PM3-RPA, and PM5-RPA levels were 0.822, 0.841, and 0.901, respectively, and they were also comparable to that at TD/B3LYP/cc-pVDZ//B3LYP/cc-pVDZ. Therefore, although some calibration efforts may be needed for AM1 geometries, PM5-RPA(CIS)//AM1 may be a second candidate available for the prediction of the absorption maxima of dyes, especially in the case of emphasizing computational cost.     

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-d₀ (PY) and -d₁ and for N-methylpyrrolidine-d₀ (NMP), -d₂, -d₃ and -d₈. 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.     

A comparative study by AM1, PM3 and ab initio HF/3-21G methods on the structure and reactivity of monosubstituted carbanion 1,2,4-triazolium ylides

A full conformational analysis of six 1,2,4-monosubstituted carbanion 1,2,4-triazolium ylides 4 a–f was performed using AM1, PM3 and HF/3-21G methods. The C-type conformers were found as the most stable structures by these different methods. This study also includes a qualitative estimation of the chemical behavior of triazolium ylides 4 a–f as nucleophilic agents on the level of ylide carbon atoms. The ab initio 3-21G method seems to be the most suitable in the characterization of these molecular systems.     

Parameterization of charge model 3 for AM1, PM3, BLYP,and B3LYP

We have recently developed a new Class IV charge model for calculating partial atomic charges in molecules. The new model, called Charge Model 3 (CM3), was parameterized for calculations on molecules containing H, Li, C, N, O, F, Si, S, P, Cl, and Br by Hartree-Fock theory and by hybrid density functional theory (DFT) based on the modified Perdew-Wang density functional with several basis sets. In the present article we extend CM3 to semiempirical molecular orbital theory, in particular Austin Model 1 (AM1) and Parameterized Model 3 (PM3), and to the popular BLYP and B3LYP DFT and hybrid DFT methods, respectively. For the BLYP extension, we consider the 6-31G(d) basis set, and for the B3LYP extension, we consider three basis sets: 6-31G(d), 6-31+G(d), and MIDI!6D. We begin with the previous CM3 strategy, which involves 34 parameters for 30 pairs of elements. We then refine the model to improve the charges in compounds that contain N and O. This modification, involving two new parameters, leads to improved dipole moments for amides, bifunctional H, C, N, O compounds, aldehydes, ketones, esters, and carboxylic acids; the improvement for compounds not containing N results from obtaining more physical parameters for carbonyl groups when the O=C-N conjugation of amides is addressed in the parameterization. In addition, for the PM3 method, we added an additional parameter to improve dipole moments of compounds that contain bonds between C and N. This additional parameter leads to improved accuracy in the dipole moments of aromatic nitrogen heterocycles with five-membered rings.     

Semiempirical computation of homolytic O-H bond dissociation energies of alcohols: comparison of the AM1 and PM3 methods

The heats of formation of various alcohols and alkoxy radicals were calculated using the AM1 and PM3 semiempirical methods, which were then used to calculate the bond dissociation energies of the alcohols. Both restricted Hartree-Fock (RHF) and unrestricted Hartree-Fock (UHF) calculations were performed to determine which technique was most applicable to the computation of bond dissociation energies within the semiempirical frameworks. It was determined that AM1/RHF calculations gave the most accurate results for O-H bond dissociation energies of alcohols. The effect of using configuration interaction calculations to calculate bond dissociation energies within the semiempirical framework was also examined.     

Electronic and structural properties of the metalloporphyrin structural isomers: semiempirical AM1 and PM3 calculations

Semiempirical calculations using AM1 and PM3 have been performed on the zinc(II) and magnesium(II) complexes of nine structural isomers of tetrapyrrole macrocycles such as porphyrin, porphycene, corrphycene and hemiporphycene, N-confused porphyrin and other isomers that have not been synthesized. The optimized geometry and the bond parameters obtained compare favorably with results obtained from X-ray and spectral studies. Heats of formation, ionization potentials, HOMO-LUMO energy differences, dipole moments, and the splitting of HOMOs and LUMOs of the metal complexes of each of these isomers are also reported and compared with experimental results. The “four-orbital model” of Gouterman remains valid for the investigated structural isomers. The present study represents an unusually appropriate opportunity to study, via molecular orbital methods, the interaction between various metal ions, and the electronic and geometrical environment of the central cavity of the closely related isomeric macrocycles. The major outcome of this study is the verification of the expected differential behavior of metal ions employed in the present study as a sophisticated probe of cavity properties which also suggests that this procedure can be extended to other metal complexes. This study also serves as an interesting prototype for more elaborate ab initio calculations. However, such calculations on the presently investigated macrocyclic systems may have to be performed at a higher level than MP2 or DFT to account for the unusual delocalization, as suggested by a recent study by Schaefer and co-workers on delocalized [10]annulene (H.M. Sulzbach, H.F. Schaefer, W. Klopper and H.P. Luthi, J. Am. Chem. Soc., 118 (1996) 3519).     

Conformation and reactivity of α-oxo-ketenes: Ab initio and semiempirical (AM1, PM3) calculations

Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal α-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.     

Ab initio calculation of the MgO(100) interaction with He and Ne: a HF + MP2 and HF + MP2(B3LYP) comparison

Second order Rayleigh Schr?dinger perturbation theory is applied to calculate the correlation energy contribution to the London dispersion interaction to approximate the interaction of the He and Ne with the MgO(100) surface; single particle orbitals using either Hartree-Fock theory or hybrid-exchange density functional theory are used as the reference state.     

Structure and binding energy of anion-pi and cation-pi complexes: a comparison of MP2, RI-MP2, DFT, and DF-DFT methods

Several complexes of benzene with cations, hexafluorobenzene with anions, 1,3,5-trifluorobenzene with cations and anions, and s-triazine with cations and anions have been evaluated and compared at the MP2 and resolution of the identity MP2 (RI-MP2) levels. The RI-MP2 method is considerably faster than the MP2 and the interaction energies and equilibrium distances are almost identical for both methods. A similar result is found when comparing DFT and density fitting DFT (DF-DFT) levels. Therefore RI-MP2 and DF-DFT methods are well suited for the study of ion-pi interactions.     

Fourier transform infrared and Raman spectra. Semi empirical AM1 and PM3; MP2/DZV and DFT/B3LYP-6-31G(d) ab initio calculations for dimethylterephthalate (DMT)

Fourier transform infrared and Raman spectra of dimethylterephthalate (DMT), as microcrystalline powder, have been investigated. The vibrational spectra were calculated using the AM1 and PM3 semi empirical procedures, and the M?ller-Plesset (MP2/DZV), and the Becke-Lee, Yang and Parr gradient-corrected correlation functional: B3LYP/6-31G(d) ab initio calculations. On this basis, and assisted with the FT-IR and Raman spectra of the terephthalic acid, an assignment of the vibrational spectra of dimethylterephthalate was proposed. In the calculations, remarkable differences concerning the assignments of the vibrational spectra were noted between the AM1 and PM3 methods. Also, the ab initio procedure shows differences in interpreting the spectra compared with the semi empiric procedures, and among themselves. Calculated geometrical parameters were compared with the experimental values of dimethylterephthalate, diethylterephthalate and terephthalic acid.     

Application of DFT and MP2 calculations on structural and water-assisted proton transfer in 3-amino-4-nitrofurazan

Density functional theory (DFT) and MP2 calculations have been employed to study of 3-amino-4-nitrofurazan molecule using the standard 6-311++G(d,p) basis set. The chemical properties of the 3-amino-4-nitrofurazan have been extensively studied. The geometries of molecules in the gas phase were optimized and compared with the crystallography of this substance. The results suggest that A form is the most stable form in the gas phase and it is the predominant tautomer in solution according to the DFT and MP2 calculations, respectively. In addition, variation of dipole moments in the gas phase, the specific solvent effects with addition of one molecule of water near the electrophilic centers of tautomers, the transition state of proton transfer assisted by a water molecule, the NBO charges of atoms and the potential energy surface were investigated. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are presented.     

A new non-symmetric N(OH)3 species: Comparison with the C3 species and thermochemistry at the HF,DFT, MP2, MP4 and CCSD(T) levels of theory

A new non-symmetric N(OH)₃ species more stable than the C₃ structure is found at Density Functional Theory (B3PW91, B3LYP), MP2, MP4 and CCSD(T) levels with extended basis sets. C₁ and C₃ structures are qualitatively different from those of the As(OH)₃ molecule. Energy differences and interconversion barriers become smaller with increasing inclusion of electronic correlation. However at the MP2, MP4 and CCSD(T) levels, these differences increase with basis set quality. ZPE corrections lead to barrier collapse but only at the CCSD(T)/AVTZ level. The C₁ and C₃ MP2/AVTZ infrared spectra are given for future studies.     

4-hydroxy-2H-1,2-benzothiazine-3-carbohydrazide 1,1-dioxide-oxalohydrazide (1:1): X-ray structure and DFT calculations

The title compound, 4-hydroxy-2H-1,2-benzothiazine-3-carbohydrazide 1,1-dioxide-oxalohydrazide (1:1), is determined using X-ray diffraction techniques and the molecular structure is also optimized at the B3LYP/6-31G(d,p) level using density functional theory (DFT). The asymmetric unit consists of four independent molecules. The oxalohydrazide molecules have the centre of symmetry at the mid-point of the central C-C bond. Each thiazine ring adopts a half-chair conformation. Intermolecular C-H...O, N-H...O and N-H...N hydrogen bonds produce R ₂ ² (10), R ₂ ² (13), R ₃ ³ (12) and R ₃ ³ (15) rings, which lead to one-dimensional polymeric chains. An extensive three-dimensional supramolecular network of N-H...N, N-H...O, C-H...O and O-H...O hydrogen bonds is responsible for crystal structure stabilization.