Danuta Michalska

Electronic structures, vibrational spectra, and revised assignment of aniline and its radical cation: Theoretical study

Comprehensive studies of the molecular and electronic structures, vibrational frequencies, and infrared and Raman intensities of the aniline radical cation, C6H5NH2+ have been performed by using the unrestricted density functional (UB3LYP) and second-order Moller–Plesset (UMP2) methods with the extended 6-311++G(df,pd) basis set. For comparison, analogous calculations were carried out for the closed-shell neutral aniline. The studies provided detailed insight into the bonding changes that take place in aniline upon ionization. The natural bond orbital (NBO) analysis has revealed that the pπ-radical conjugative interactions are of prime importance in stabilizing the planar, quinoid-type structure of the aniline radical cation. It is shown that the natural charges calculated for aniline are consistent with the chemical properties of this molecule (an ortho- and para-directing power of the NH2 group in electrophilic substitutions), whereas Mulliken charges are not reliable. The theoretical vibrational freque...

The performance of different density functional methods in the calculation of molecular structures and vibrational spectra of platinum(II) antitumor drugs: cisplatin and carboplatin

A comparison of eight density functional models for predicting the molecular structures, vibrational frequencies, infrared intensities, and Raman scattering activities of platinum(II) antitumor drugs, cisplatin and carboplatin, is reported. Methods examined include the pure density functional protocols (G96LYP, G96PW91, modified mPWPW and original PW91PW91), one‐parameter hybrid approaches (mPW1PW and mPW1LYP), and three‐parameter hybrid models (B3LYP and B3PW91), as well as the HF and MP2 levels of theory. Different effective core potentials (ECPs) and several basis sets are considered. The theoretical results are discussed and compared with the experimental data. It is remarkable that the mPW1PW protocol introduced by Adamo and Barone [J Chem Phys 1998, 108, 664], is clearly superior to all the remaining density functional methods (including B3LYP). The geometry and vibrational frequencies of cisplatin and carboplatin calculated with the mPW1PW method, and the ECP of Hay and Wadt (LanL2DZ basis set) are in better agreement with experiment than those obtained with the MP2 method. The use of more elaborated ECP and the enlargements of basis sets do not significantly improve the results. A clear‐cut assignments of the platinum‐ligand vibrations in cisplatin and carboplatin are presented. It is concluded that mPW1PW is the new reliable method, which can be used in predicting molecular structures and vibrational spectra of large coordination compounds containing platinum(II).

Theoretical infrared spectrum and revised assignment for para-nitrophenol. Density functional theory studies

The harmonic vibrational frequencies and infrared intensities of p-nitrophenol as well as geometries of ortho- and para-nitrophenol, are calculated with density functional theory (DFT), using BLYP functional and 6-31G(d,p) basis set. The calculated (unscaled) spectra are in very good agreement with the gas phase and solid IR spectra of p-nitrophenol. A detailed interpretation of the infrared spectra of p-nitrophenol is reported on the basis of the calculated potential energy distribution (PED). Several reassignments have been made.

Study of the Nature of Improper Blue‐Shifting Hydrogen Bonding and Standard Hydrogen Bonding in the X3CH⋅⋅⋅OH2 and XH⋅⋅⋅OH2 Complexes (X=F, Cl, Br, I): A Correlated Ab Initio Study

Weak hydrogen bonding was studied in the XH...OH2 and X3CH...OH2 complexes (X = F, Cl, Br, I) using the correlated MP2 ab initio method with relativistic Stuttgart/Dresden pseudopotentials and basis set (SDD). The accuracy of the method was tested for selected nonrelativistic complexes by performing MP2 calculations with all-electron basis sets (6-311G** and TZVPP). The characteristics of bonding in the hydrogen halide complexes correspond to the standard H-bonding (an elongation of the X-H bond and red shift of its stretch frequency), whereas those in the X3CH...OH2 complexes (X = F, Cl) are typical of improper blue-shifting H-bonding (a contraction of the CH bond and blue shift of the respective stretch frequency). A natural bond orbital analysis revealed some important differences between both classes of complexes: a) the electron density transfer (EDT) in the former complexes is considerably larger than that in the latter complexes: b) the EDT in the former complexes is almost completely directed to the sigma*-antibonding orbital of the XH bond, which causes a weakening of this bond, its elongation, and a concomitant decrease of the XH stretch frequency. In the latter complexes, only a small portion of the EDT goes to the sigma*-antibonding orbital of the CH bond of the proton donor and a larger part is transferred to the remote (nonparticipating) part of the proton donor. As a consequence, the structural reorganization of the proton donor occurred, leading to the contraction of the C-H bond. The fact that a small red shift of the C-H stretch frequency was found in bromoform-water and iodoform-water complexes was explained by the competition of both the above-mentioned mechanisms with dominating passage of electron density to the sigma*-antibonding orbital of the C-H bond. For an explanation of all the geometric features of both types of complexes, it is however necessary to consider both charge transfer and electrostatic effects. The electrostatic effects fail sometimes to interpret the geometry changes in the proton donor.

INFRARED MATRIX ISOLATION SPECTRA OF 1-METHYLURACIL. REVISED ASSIGNMENT BASED ON THE HARTREE-FOCK AND POST-HARTREE-FOCK STUDIES

Abstract Ab initio calculations of the infrared spectra of 1-methyluracil have been carried out with the Hartree–Fock and the second order Moller–Plesset perturbation (MP2) methods using the D95V** basis set. Theoretical harmonic frequencies and absolute infrared intensities reproduce well the experimental infrared spectra of the Ar matrix isolated species. The revised assignment of the infrared spectra of monomeric 1-methyluracil isolated in Ar and N2 matrices is presented.

Fourier Transform Infrared Spectroscopy as a Powerful Tool for the Study of Carbohydrates in Aqueous Solutions

FT-IR spectral investigations on carbohydrates were undertaken in aqueous media in order to facilitate the assignments of vibrational bands. For pure anomeric forms of glucose, FT-IR spectra obtained as a function of time revealed many changes in spectral content, providing new information about anomer characteristic bands in aqueous media. It was also found that fructose, which is known to undergo complex mutarotation, exhibits two types of spectral changes, whereas glucose, which undergoes simple mutarotation, shows a single type of spectral change. Thus FT-IR spectral investigations in aqueous carbohydrates should be able to distinguish between simple and complex mutarotation cases. As a vibrational spectroscopic technique, the importance of FT-IR spectroscopy is further emphasized by showing that Raman spectroscopy is not sensitive enough to reveal the structural changes of carbohydrates in aqueous media.

The amino group in adenine: MP2 and CCSD(T) complete basis set limit calculations of the planarization barrier and DFT/B3LYP study of the anharmonic frequencies of adenine.

The amino group in adenine plays a key role in formation of hydrogen bonds in nucleic acids and in other molecular systems. Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. Ab initio MP2 and density functional B3LYP methods with various basis sets have been used to calculate the optimized structure and the infrared spectrum of adenine (the N9-H tautomer). Calculations at the MP2 level with larger basis sets tend to decrease the degree of pyramidalization of the C-NH2 group, whereas the B3LYP method consistently yields the planar or nearly planar structure of adenine. MP2 complete basis set (CBS) limit method with the aug-cc-pVTZ --> aug-cc-pVQZ (aTZ --> aQZ) extrapolation scheme has predicted very small planarization barrier of adenine, 0.015 kcal/mol, which is in very good agreement with the MP2-predicted planarization barrier of 0.020 kcal/mol, reported by S. Wang and H. F. Schaefer III, J. Chem. Phys. 2006, 124, 044303. Similar results were obtained in calculations by the coupled cluster CCSD(T) CBS method. Thus, it can be concluded that the amino group in adenine, in the gas phase, is very flexible with a small degree of nonplanarity. Extremely low planarization barrier implies that adenine requires very little energy to conform the structure of the amino group to formation of the complementary hydrogen bonds with other molecules. This fact is very important for base pairing in nucleic acids or other polymers containing adenine residues. The anharmonic frequencies of adenine have been calculated at the B3LYP/6-311++G(df,pd) level of theory. The theoretical results show excellent agreement with the available experimental data. The revised assignment of the infrared spectrum of adenine in Ar matrix has been made. The predicted anharmonic frequency of the NH2 inversion, 181 cm(-1), is supported by the experimental data. It is demonstrated that the vibrational frequencies and potential energy distribution (PED) obtained from the B3LYP calculations are more reliable than those obtained at the MP2 level.

Ab initio second-order Møller-Plesset calculation of the vibrational spectra of C4 clusters☆

Abstract Second-order Moller-Plesset calculations on the C 4 potential surface yielded three isomers, a linear triplet and rhombic and tetrahedral singlets. A large discrepancy between observed and calculated frequencies of the Σ u + vibration of linear 12 C 4 is outside the expected range of error. It is tentatively suggested that an observed absorption at 1544 cm −1 previously assigned to C 5 might belong instead to C 4 .

Vibrational properties and DFT calculations of the perovskite metal formate framework of [(CH3)2NH2][Ni(HCOO3)] system.

Experimental Raman and IR spectra of multiferroic [(CH3)2NH2][Ni(HCOO)3] were recorded at room temperature. The three-parameter hybrid B3LYP density functional method has been used with the 6-31G(d, p) basis set to derive the equilibrium geometry, atomic spin densities, vibrational wavenumbers, infrared intensities and Raman scattering activities. Based on these calculations, the assignment of the observed bands to the respective internal and lattice modes is proposed. The performed calculations revealed that the ν(NH2) stretching, ρ(NH2) rocking and τ(CH3) torsional modes are very sensitive to formation of the hydrogen bond between the DMA(+) cation and Ni-formate framework. Therefore, these modes are suitable probes for strength of hydrogen bonds in this family of metal-formate frameworks and study of their temperature dependence may provide significant information on a role of the hydrogen bonds in mechanism of the ferroelectric phase transition occurring in these compounds at low temperatures.

Theoretical investigation of the conformation, acidity, basicity and hydrogen bonding ability of halogenated ethers

MP2/6-311++G(d,p) calculations have been carried out to investigate the conformation, protonation and the hydrogen bonding interactions with water of several halogenated ethers (CH(3)OCH(2)Cl, CH(2)ClOCH(2)Cl, CH(3)OCHCl(2), CHFClOCHF(2)). The optimized geometries, ν(CH) harmonic vibrational frequencies and the SAPT decomposition of the interaction energies are studied. The interaction with one water molecule gives several stable structures characterized by O(w)H(w)...O and CH...O(w) hydrogen bonds or by O...Cl halogen bonding. The MP2/CBS calculated binding energies of different complexes between the halogenated ethers and water vary between 1.7 and 7.7 kcal mol(-1). The energies of these structures are discussed as a function of the proton affinity of the ethers and the deprotonation enthalpy of the CH bonds. The contraction of the CH bonds and blue shifts of the corresponding stretching vibrations in the O-protonated ethers and their O...H(w)O(w) complexes are compared. A natural bond orbital analysis has revealed that substitution of the H atoms by one or several halogen atoms has a great influence on the hyperconjugative effects from the two non-equivalent O lone pairs to relevant antibonding orbitals, and the subsequent geometry of the hydrogen bonded complexes.