Anharmonic IR and Raman spectra and electronic and vibrational (hyper)polarizabilities of barbituric, 2-thiobarbituric and 2-selenobarbituric acids.

Infrared, Raman and electronic absorption spectra, electronic and vibrational (hyper)polarizabilities, of barbituric, 2-thiobarbituric and 2-selenobarbituric acids were studied in gas using ab initio and density functional theory levels. The vibrational spectra were computed using harmonic and anharmonic methods. Anharmonic contributions improve the agreement between calculated and available experimental wavenumbers, especially in the highest-energy spectral region (wavenumbers >1700 cm(-1)). Vibrational and electronic transitions potentially useful to identify the investigated compounds were explored. The electronic and vibrational hyperpolarizabilities for the IDRI nonlinear optical (NLO) process at the λ value of 790 nm were computed. Supported by spectroscopic results, electronic and vibrational polarizabilities and second-order hyperpolarizabilities increase progressively in the order barbituric acid<2-thiobarbituric acid<2-selenobarbituric acid. The seleno-derivative is predicted to be ca. three/four times more hyperpolarizable than the barbituric acid. The Se→O or Se→S substitutions can be practical strategies to enhances the NLO properties of barbituric and thiobarbituric acid-based materials.

Static and dynamic electronic (hyper)polarizabilities of dimethylnaphthalene isomers: characterization of spatial contributions by density analysis.

Static and frequency-dependent electronic (hyper)polarizabilities of the dimethylnaphthalene (DMN) isomers were computed in vacuum using the Coulomb-attenuating Density Functional Theory method. The nonlinear optical Second Harmonic Generation (SHG) and Electro-Optical Pockels Effect (EOPE) were investigated at the characteristic Nd:YAG laser wavelength of 1064 nm. The response electric properties especially the longitudinal polarizability, polarizability anisotropy, and first-order hyperpolarizability are significantly affected by the position of the methyl groups. The SHG and EOPE techniques can be potentially useful to discriminate the α,α-DMN isomers (2,6-DMN < 2,7-DMN < 2,3-DMN) as well as the ß,ß-DMN isomers (1,5-DMN < 1,4-DMN < 1,8-DMN). The (hyper)polarizability differences among the investigated DMNs were elucidated through density analysis calculations. The predicted polarizabilities exhibit good linear relationships with the experimental first-order biomass-normalized rate coefficient, a physicochemical property connected to the rates of biodegradation processes of polycyclic aromatic hydrocarbons.

The effect of secondary structures on the NLO properties of single chain oligopeptides: a comparison between ß-strand and α-helix polyglycines.

The evolution of the electronic first-order longitudinal hyperpolarizability (ßzzz) and the hyperpolarizability aligned along the direction of the dipole moment (ßµ) of the α-helix and ß-strand single chain H2N-(CH2-CO-NH)n-CH2-COOH (n = 1-9) oligoglycines, were investigated. For this purpose we have used Hartree-Fock, second-order Møller-Plesset perturbation theory and Coulomb-attenuating Density Functional Theory computations. For the longest chain, ßµ(ß-strand) is one order of magnitude greater than ßµ(α-helix), due to the cooperative effect of the α-helices being unfavourable for the NLO properties. The ßzzz and ßµ values per unit cell of the ß-strand conformation were determined, extrapolating the properties in the limit of the polymer. The calculated ßzzz values were elucidated using the two-state model involving the characteristic π-π* NV1 electronic transition of peptides. Single chain ß-strand polyglycines can be discriminated from the α-helices using second-order NLO effects.

Evolution of electric dipole (hyper)polarizabilities of ß-strand polyglycine single chains: an ab initio and DFT theoretical study.

Ab initio and density functional theory calculations have been carried out on dipole moments (µ), polarizabilities (α), and second-order hyperpolarizabilities (γ) of single chain ß-strand oligoglycines in the gas phase. Basis set and electron correlation effects have been investigated. The long-range corrected CAM-B3LYP and ωB97X-D functionals furnish satisfactory results in agreement with correlated ab initio computations. The dependence of µ, α, and γ values per unit cell on chain length has been explored, extrapolating the properties in the limit of the polymer. The increase of the response electronic properties with the number of glycine units has been rationalized through the two-state model involving the typical π-π* NV1 electronic transition of peptides. The effect of the secondary structure on the electric properties has been discussed. At variance from the dipole moments, the γ values increase on going from the α-helices to the ß-strands, whereas the α values are little influenced by the conformation of the oligoglycines.

Electron correlation effects and density analysis of the first-order hyperpolarizability of neutral guanine tautomers.

Dipole moments (µ), charge distributions, and static electronic first-order hyperpolarizabilities (ß(µ)) of the two lowest-energy keto tautomers of guanine (7H and 9H) were determined in the gas phase using Hartree-Fock, Møller-Plesset perturbation theory (MP2 and MP4), and DFT (PBE1PBE, B97-1, B3LYP, CAM-B3LYP) methods with Dunning's correlation-consistent aug-cc-pVDZ and d-aug-cc-pVDZ basis sets. The most stable isomer 7H exhibits a µ value smaller than that of the 9H form by a factor of ca. 3.5. The ß µ value of the 9H tautomer is strongly dependent on the computational method employed, as it dramatically influences the ß(µ) (9H)/ß(µ) (7H) ratio, which at the highest correlated MP4/aug-cc-pVDZ level is predicted to be ca. 5. The Coulomb-attenuating hybrid exchange-correlation CAM-B3LYP method is superior to the conventional PBE1PBE, B3LYP, and B97-1 functionals in predicting the ß(µ) values. Differences between the largest diagonal hyperpolarizability components were clarified through hyperpolarizability density analyses. Dipole moment and first-order hyperpolarizability are molecular properties that are potentially useful for distinguishing the 7H from the 9H tautomer.

Prediction of mutagenic activity of nitrophenanthrene and nitroanthracene isomers by simulated IR and Raman spectra.

This paper expands upon our original work on nitroanthracenes in (Alparone, A., Librando, V., 2012. Spectrochim. Acta A 89, 129-136) on the series of nitrophenanthrene isomers. Geometries, electric properties, IR and Raman spectra of 1-, 2-, 3-, 4- and 9-nitrophenanthrene (1-NP, 2-NP, 3-NP, 4-NP and 9-NP) were obtained and analyzed using Density Functional Theory calculations. The balance between steric and π-conjugative interactions determines the order of stability 4-NP<1-NP~9-NP<2-NP∼3-NP. IR and Raman spectral zones between 1000 and 1600 cm(-1) show intense bands noticeably affected by the position of the substituent, being potentially useful to discriminate and monitor the investigated isomers. Dipole moments, summations of IR intensity (ΣI(IR)) and Raman activity (ΣA(Raman)) over the 3N-6 vibrational modes are sensitive to the structure, increasing steadily from the non-planar to the planar isomers. Good linear relationships between the ΣI(IR) (r=0.90) and ΣA(Raman) (r=0.99) against the Salmonella typhimurium strain TA98 mutagenic activity of nitrophenanthrenes and isomeric nitroanthracenes are found. On the basis of the structural and vibrational properties, 4-NP seems to have not mutagenic activity, while the unknown TA98 mutagenic potency of 1-nitroanthracene is predicted to be between that of 9-NP and 3-NP. Calculated ΣI(IR) and ΣA(Raman) values could be used as molecular descriptors for QSARs applications of series of isomers.

Solvation effects on the static and dynamic first-order electronic and vibrational hyperpolarizabilities of uracil: a polarized continuum model investigation.

Electronic (ß(e)) and vibrational (ß(v)) first-order hyperpolarizabilities of uracil were determined in gas and water solution using the Coulomb-attenuating Density Functional Theory level with the Dunning's correlation-consistent aug-cc-pVDZ basis set. Frequency-dependent ß(e) values were computed for the Second Harmonic Generation (SHG) and Electric Optical Pockels Effect (EOPE) nonlinear optical phenomena. The Polarized Continuum Model was employed to study the solvent effects on the electronic and vibrational properties. The introduction of solvation contributions increases the ß(e) (static) value by ca. 110%. In comparison, smaller enhancements are found for the ß(e) (EOPE) and ß(e) (SHG) data evaluated at the typical wavelength of 694 nm (by 40-50%). The gas-water hyperpolarizability difference was rationalised through a density analysis study. The magnitudes of the vibrational first-order hyperpolarizabilities are comparable to their electronic counterparts and noticeably increase in solution: ß(v) (EOPE) ~ ß(e) (EOPE) in aqueous phase at λ = 694 nm. Analysis of the IR and Raman spectra is useful to elucidate the most important contributing modes to the vibrational first-order hyperpolarizabilities.

Comment on: "FT-IR, FT-Raman and UV spectral investigation; computed frequency estimation analysis and electronic structure calculations on 1-nitronaphthalene" by M. Govindarajan and M. Karabacak [Spectrochim. Acta A 85 (2012) 251-260].

The title paper [1] incorrectly establishes that, in gas phase the global minimum energy structure of 1-nitronaphthalene is planar (C(s) symmetry). By contrast, present calculations indicate that the planar C(s) form is an unstable structure on the potential energy surface, exhibiting an imaginary vibrational wavenumber value corresponding to the torsional mode of the nitro group around the C-N bond. At the B3LYP/6-311++G(d,p) level of calculation the global minimum energy structure of 1-nitronaphthalene in gas phase has a non-planar geometry, characterized by O-N-C-C dihedral angles of ca. 30° and lying 0.35 kcal/mol below the C(s) form.

IR and Raman spectra of nitroanthracene isomers: substitional effects based on density functional theory study.

Structure, IR and Raman spectra of 1-, 2- and 9-nitroanthracene isomers (1-NA, 2-NA and 9-NA) were calculated and analyzed through density functional theory computations using the B3LYP functional with the 6-311+G** basis set. Steric and π-conjugative effects determine the characteristic ONCC dihedral angles, which vary from 0° (2-NA) to 28-29° (1-NA) and 59° (9-NA), influencing the relative order of stability along the series 9-NA<1-NA<2-NA. The spectral regions at wavenumber values>3000 cm(-1) and <1000 cm(-1) little depend on the substituent position. The Raman and IR intensity values of the characteristic symmetric nitro group stretching transition, appearing between 1310 and 1345 cm(-1), are rather sensitive to the position of the substituent, decreasing regularly on passing from the planar to the NO2-rotated isomers (9-NA<1-NA<2-NA). In the medium-energy spectral region (1000-1700 cm(-1)), the number and the relative position of the strongest Raman bands are of potential utility to discriminate the NA isomers. Structural and spectroscopic results suggest that the unknown mutagenic activity of 1-NA is expected to be between that of 9-NA and 2-NA.

Spectroscopic properties of neuroleptics: IR and Raman spectra of Risperidone (Risperdal) and of its mono- and di-protonated forms.

Structures and IR and Raman spectra of Risperidone in its neutral, mono- and di-protonated forms were calculated in gas phase by DFT-B3LYP/6-31G* level. Mono-protonation occurs at the nitrogen atom of the piperidine ring, while nitrogen atom of the pyrimidine ring is the preferred site for the second protonation. The lowest-energy structure of the mono-protonated Risperidone is characterized by formation of a strong seven-membered O(pyrimidine ring)⋯(+)H-N(piperidine ring) intramolecular hydrogen-bonded cycle. In the high-energy spectral region (3500-2500 cm(-1)), the bands of the N-H(+) stretches and the changes in wavenumbers and IR intensities of the C-H stretches near to the piperidine nitrogen atom (Bohlmann effect) are potentially useful to discriminate conformations and protonation states. Di-protonated structures can be identified by the presence of an isolated absorption peak located in the low-energy IR region (660-690 cm(-1)), attributed to the out-of-plane N-H(+)(pyrimidine ring) bending deformation. The most intense Raman band of neutral Risperidone placed at ca. 1500 cm(-1), assigned to C=C(pyrimidine ring) stretch + C=N(pyrimidine ring) stretch, can be a useful vibrational marker to distinguish the neutral from the protonated forms.

Electronic properties of neuroleptics: ionization energies of benzodiazepines.

Vertical ionization energies (VIEs) of medazepam, nordazepam and their molecular subunits have been calculated using the electron propagator method in the P3/CEP-31G* approximation. Vertical electron affinities (VEAs) have been obtained with a ∆SCF procedure at the DFT-B3LYP/6-31+G* level of theory. Excellent correlations have been achieved between IE(calc) and IE(exp), allowing reliable assignment of the ionization processes. Our proposed assignment differs in many instances from that previously reported in the literature. The electronic structure of the frontier Dyson orbitals shows that the IE and EA values of the benzodiazepines can be modulated by substitution at the benzene rings. Hardness values, evaluated as (IE - EA)/2, follow the trend of the experimental singlet transition energies. Medazepam is a less hard (i.e., less stable) compound than nordazepam.

The role of electronic properties to the mutagenic activity of 1,6- and 3,6-dinitrobenzo[a]pyrene isomers.

Equilibrium geometries, infrared spectra, vertical first ionization potential (IP), electronic affinity (EA), dipole moment (mu) and electronic dipole polarizability (alpha) of 1,6- and 3,6-dinitrobenzo[a]pyrene isomers (1,6-DNBaP and 3,6-DNBaP) were evaluated by means of Density Functional Theory (DFT) and recent semiempirical PM6 method. Structural, energetic and vibrational properties of DNBaP isomers are substantially similar to each other. Calculated IP, EA and alpha values of these isomers are practically identical, while mu of 3,6-DNBaP (8.2 D at DFT level) is predicted to be ca. 4 times the value of 1,6-DNBaP isomer (1.9 D at DFT level), owing to favorable mutual orientation of the individual nitro group vectors. Higher direct-mutagenic activities of 3,6-DNBaP with respect to 1,6-DNBaP isomer by 1-2 orders of magnitude might be determined by its peculiar electronic charge distribution, which through stronger electrostatic and inductive interactions, can promote much more effectively binding to active-site of enzymes involved in mutagenic pathways. On the other hand, orientation of the nitro substituents relatively to the plane of the aromatic moiety, molecular sizes, as well as nitroreduction and oxidation reactions seem not to have a key role in the determination of the different mutagenic behaviour of these isomers.

Electronic properties of some nitrobenzo[a]pyrene isomers: a possible relationship to mutagenic activity.

Ionization potential (IP), electron affinity (EA), dipole moment (mu) and electronic polarizability (alpha) of 1-, 3- and 6-nitrobenzo[a]pyrene isomers (1-NBaP, 3-NBaP, 6-NBaP) were determined by using density functional theory (DFT) and recent semiempirical PM6 methods. Calculated IP value remains almost constant along the series of isomers, while EA value depends on the nitro group position, increasing by ca. 0.2 eV on passing from 6- to 1-NBaP (or 3-NBaP) isomer. Stability, mu and alpha values decrease in the order 6-NBaP < 1-NBa approximately 3-NBaP, the largest mu variation being predicted to be 1.5 D (30%) by DFT computations. The results obtained herein are consistent with the observed greater mutagenic activity of 3- and 1-NBaP in comparison to 6-NBaP isomer, suggesting that both binding to enzyme, which depends on electric properties, and reduction process, which is related to EA value may be crucial steps in the mutagenic mechanism of this series of isomers.

Prediction of mutagenic activity of nitronaphthalene isomers by infrared and Raman spectroscopy.

IR and Raman spectra of 1- and 2-nitronaphthalene isomers (1-NN and 2-NN) have been investigated to obtain more insight into the effect of the structure on mutagenic properties. To this purpose we have performed density functional theory calculations using B3LYP functional with cc-pVDZ basis set. The results have shown that IR and Raman spectra of nitronaphthalene isomers are somewhat similar to each other. A notable exception regards the symmetrical NO bonds stretching +CN bond stretching vibration (nusNO2+nuCN), which appears as very intense peak near 1350 cm(-1) in IR and Raman spectra of both isomers. Present calculations predict that for 2-NN isomer IR and Raman absorptions of this vibration are more intense by ca. 50 and 60%, respectively, than those of 1-NN isomer. The noticeably higher IR and Raman intensity values of the nusNO2+nuCN mode for 2-NN originate, respectively, from large dipole moment and polarizability changes with respect to the normal mode, suggesting that intermolecular interactions are especially favoured along this coordinate. These results are consistent with higher mutagenic activities of 2-NN in comparison to 1-NN isomer, supporting the binding to enzyme mechanism as a determining step in mutagenic pathways for this series of nitroaromatic compounds.

Electronic and vibrational polarizabilities of the twenty naturally occurring amino acids.

The geometries, relative energies, gas-phase static and dynamic dipole polarizabilities of the two most stable neutral forms and of the zwitterionic form of the twenty naturally occurring amino acids have been obtained by Density Functional and conventional ab initio Hatree-Fock theories using correlation consistent basis sets. Mean electronic polarizabilities (s) are encompassed in the 40-160 a.u. range and are little dependent on the amino acid framework conformation and structure. The relation between and the number of electrons in the molecule makes to classify the amino acids as one of the most polarizable family of compounds. Calculated values of the neutral forms linearly relate to the molecular volume and molecular hardness as well as, rather unexpectedly, with the experimental values in water solution, where amino acids are known to be in a zwitterionic form. Vibrational polarizabilities amount to 15-45 a.u.. They come essentially from the low-frequency angular deformation modes of the -OH and -NH(2) groups.

Electronic polarizability as a predictor of biodegradation rates of dimethylnaphthalenes. an ab initio and density functional theory study.

Geometries, relative stabilities, electronic excited states, atomic charges, and electronic dipole polarizabilities of dimethylnaphthalene (DMN) isomers have been calculated in gas and aqueous phases by ab initio and DFT methods. At the highest levels of calculation, alpha,alpha-DMN (2,6-DMN, 2,7-DMN, and 2,3-DMN) are the lowest energy isomers, while 1,8-DMN is the less stable by 7-8 kcal mol(-1). The averaged electronic polarizability, , is dependent on the position of the methyl substituents, increasing in the order alpha, alpha-DMN < (a, beta-DMN < beta, beta-DMN, with the largest values being obtained for 2,6-DMN and 2,7-DMN, while the lowest value is calculated for 1,8-DMN isomer. Polarizability differences among the isomers have been related to their spectroscopic properties. The computed value of DMN isomers, with the notable exception of 2,7-DMN, is in excellent linear relationship with the observed first-order biomass-normalized rate coefficient, a parameter related to the rate of biodegradation of polycyclic aromatic hydrocarbons (PAHs). This result suggests that electronic polarizability may be a useful tool for prediction of biodegradation trends of series of compounds, and inductive and dispersive interactions play a fundamental role in the biodegradation process of DMNs. The present approach is potentially suitable for applications on PAHs with higher molecular weight.

Theoretical investigation of the (hyper)polarizabilities of pyrrole homologues C4H4XH (X = N, P, As, Sb, Bi). A coupled-cluster and density functional theory study.

Geometries, inversion barriers, static and dynamic electronic and vibrational dipole polarizability (alpha), and first (beta) and second (gamma) hyperpolarizability of the pyrrole homologues C(4)H(4)XH (X = N, P, As, Sb, Bi) have been calculated by Hartree-Fock, Møller-Plesset second-order perturbation theory, coupled-cluster theory accounting for singles, doubles, and noniterative triple excitations methods, as well as density functional theory using B3LYP and PBE1PBE functionals and Sadlej's Pol and 6-311G basis sets. Relativistic effects on the heavier homologues stibole and bismole have been taken into account within effective core potential approximation. The results show that the electronic (hyper)polarizabilities monotonically increase with the atomic number of the heteroatom, consistent with the decrease in the molecular hardness. Ring planarization reduces the carbon-carbon bond length alternation of the cis-butadienic unit, enhancing the electronic polarizability values (alpha(e)) by 4-12% and the (hyper)polarizability values (and gamma(e)) by 30-90%. Pure vibrational and zero-point vibrational average contributions to the (hyper)polarizabilities have been determined within the clamped nucleus approach. In the static limit, the pure vibrational hyperpolarizabilities have a major contribution. Anharmonic corrections dominate the pure vibrational hyperpolarizabilities of pyrrole, while they are less important for the heavier homologues. Static and dynamic electronic response properties of the pyrrole homologues are comparable to or larger than the corresponding properties of the furan and cyclopentadiene homologue series.