The B3LYP hybrid density functional study on solids

The B3LYP hybrid density functional method, which is very successful in the study of thermochemistry of atoms and molecules, has been applied to some periodic systems recently. The applications to solids and surfaces show that the B3LYP hybrid functional reproduces the experimental energy gaps and magnetic moments for a variety of materials.     

Enthalpies of formation of olefinic ethers by G3(MP2)//B3LYP calculations

The gas‐phase enthalpies of formation at 298.15 K of a number of acyclic and cyclic olefinic ethers (mainly α,β‐unsaturated ethers), together with those of a few cyclic mono‐ and dienes, have been estimated by G3(MP2)//B3LYP calculations. In most cases, the computational and experimental data (if available) are in good mutual agreement. Whenever significant deviations between the experimental and computational data were found, the experimental enthalpies of formation arise from a single data source, and it appears that small experimental errors are embedded therein. A marked error was found in the experimental enthalpy of formation of 2‐chloroethyl ethyl ether, used in this work as a reagent for estimation of the enthalpy of formation of 2‐chloroethyl vinyl ether by an isodesmic reaction. Moreover, significant errors were also found in the literature values for the computational (B3LYP/6‐311G**) enthalpies of formation of several Me‐substituted derivatives of methyl vinyl ether. The present computational method, besides providing acceptable enthalpies of formation for unsaturated ethers, was also found to give accurate Δ_fH(g) values for cyclic mono‐ and dienes. Thus, the G3(MP2)//B3LYP computational method proved to be a valuable tool for investigating the energetics of olefinic ethers and hydrocarbons. Copyright © 2008 John Wiley & Sons, Ltd.     

Enthalpies of formation and isomerization of aromatic hydrocarbons and ethers by G3(MP2)//B3LYP calculations

A computational method for estimation of the gas‐phase enthalpies of formation of aromatic hydrocarbons and ethers has been developed. The method is based on high‐level G3(MP2)//B3LYP calculations, atomization reactions, and structure‐dependent correction terms. By this method, enthalpies of formation Δ_fH_m°(g, 298.15 K) of 86 aromatic compounds were evaluated. The calculated enthalpies of formation raise questions of the reliability of several experimental enthalpies of formation reported in the literature. As an application of the computational enthalpies of formation, reaction enthalpies for several types of isomerization reactions of aromatic compounds were calculated. In cases in which experimental reaction enthalpies were available for comparison, the agreement between the computational and experimental data proved to be excellent. Copyright © 2008 John Wiley & Sons, Ltd.     

Vibrational spectra and quantum chemical calculations of uracilyl–pyridinium mesomeric betaine

Modified nucleobases (MNs) are promising molecules with potential application in non‐linear optic (NLO) and drug design against a wide number of diseases. In the present paper we report studies on a cross‐conjugated mesomeric betaine, which can act as a MN, formed by the covalent union of a 4‐dimethylamino pyridinium and a uracilyl groups. The molecule thus formed must be presented by a dipolar canonical formulae in which positive and negative charges are delocalized within separated moieties. Quantum chemistry density functional theory (DFT) calculations, at the B3PW91/6‐31G** level, and Fourier transform (FT) infrared and Raman spectra of this molecule and its N‐deuterated derivative were performed. The calculated structural properties over the ground state optimized structure evidenced a strong separation between the two conjugated systems. Comparison with previous results obtained for the cationic species indicated that N‐protonation clearly affects the degree of conjugation. Assignments of the FT‐IR and FT‐Raman spectra were supported by the DFT wavenumbers, intensities and normal modes, which also evidenced the separation of the two conjugated systems. Significant deviations were found for the stretching force constants of the inter‐ring and the uracilyl skeletal bonds when comparing this molecule with its N‐protonated species. Copyright © 2007 John Wiley & Sons, Ltd.     

Enthalpies of formation and isomerization of cis‐ and trans‐decalin,and their oxa‐analogs by G3(MP2)//B3LYP calculations

G3(MP2)//B3LYP calculations have been carried out on trans‐ and cis‐decalin, and their mono‐, di‐, tri‐, and tetraoxa‐analogs. The main purpose of the work was to obtain enthalpies of formation for these compounds, and to study the relative stabilities of the cis–trans and positional isomers of the various (poly)oxadecalins. Comparison of the computational enthalpies of formation with the respective experimental ones, known only for the decalins and 1,3,5,7‐tetraoxadecalins, shows that in both cases the computational values are more negative than the experimental ones, the deviations being ?5 to ?7 kJ mol^?1 for the decalins and ?12 to ?17 kJ mol^?1 for the 1,3,5,7‐tetraoxadecalins. The respective computational enthalpies of cis–trans isomerization, however, are in excellent to satisfactory agreement with the experimental data. The cis–trans enthalpy differences vary from +11.0 kJ mol^?1 for decalin to ?15.4 kJ mol^?1 for 1,4,5,8‐tetraoxadecalin. Low relative enthalpy values were also calculated for the cis isomers of 1,8‐dioxadecalin (?3.7 kJ mol^?1), 1,3,6‐trioxadecalin (?4.6 kJ mol^?1), 1,3,8‐trioxadecalin (?9.7 kJ mol^?1), 1,4,5‐ trioxadecalin (?5.6 kJ mol^?1), 1,3,5,8‐tetraoxadecalin (?7.3 kJ mol^?1), and 1,3,6,8‐tetraoxadecalin (?14.5 kJ mol^?1). Copyright © 2009 John Wiley & Sons, Ltd.     

Low-frequency vibrational modes of glutamine

High-resolution terahertz absorption and Raman spectra of glutamine in the frequency region 0.2 THz-2.8 THz are obtained by using THz time domain spectroscopy and low-frequency Raman spectroscopy. Based on the experimental and the computational results, the vibration modes corresponding to the terahertz absorption and Raman scatting peaks are assigned and further verified by the theoretical calculations. Spectral investigation of the periodic structure of glutamine based on the sophisticated hybrid density functional B3LYP indicates that the vibrational modes come mainly from the inter-molecular hydrogen bond in this frequency region.     

Systematic investigations of anthocyanin–metal interactions by Raman spectroscopy

The FT‐Raman spectra of the chloride salts of pelargonidin‐3‐glucoside, cyanidin‐3‐glucoside and delphinidin‐3‐glucoside, their structures at pH 5.0 and their interaction with aluminium and ferric ions are presented for the first time and discussed with regard to their spectroscopic response. Two marker bands at approximately 1510 and 1330/1350 cm⁻¹ and one band at approximately 1330/1350 cm⁻¹ were identified being characteristic for the formation of ferric and aluminium chelates, respectively, of cyanidin‐3‐glucoside and delphinidin‐3‐glucoside. In contrast, pelargonidin‐3‐glucoside, exhibiting one single hydroxyl group in the B‐ring, did not form metal chelates, which could be clearly demonstrated by missing marker bands. The formation of anthocyanin–metal chelates was also verified in model systems containing commercial sugar beet pectin and a pectic polysaccharide fraction isolated thereof, respectively. In addition, the absence of anthocyanin–metal chelates in systems prepared with citrate buffer was confirmed, and the effects of low and high methoxylated citrus pectins on chelate formation were studied. Copyright © 2012 John Wiley & Sons, Ltd.     

Conformations and enthalpies of formation of methylenecyclohexane, 1,4‐dimethylenecyclohexane,cyclohexanone, 4‐methylenecyclohexanone, 1,4‐cyclohexanedione,and their mono‐ and dioxa derivatives by G3(MP2)//B3LYP calculations

A computational study of the stable conformations and gas‐phase enthalpies of formation at 25 °C of the title compounds has been carried out by G3(MP2)//B3LYP calculations. The work stems from our early observations on the thermodynamic and NMR spectroscopic properties of 2‐methylenetetrahydropyran and related compounds suggesting a dominating chair conformation, with poor p–π overlap in the ? O? C?C moiety, for these compounds. Besides computational verification of the chair conformation of 2‐methylenetetrahydropyran, the work was extended to find out the stable conformations of a number of other related compounds and to evaluate the relative stabilities of the various conformers. Another important goal of the work was the estimation of the gas‐phase enthalpies of formation of the present compounds, for which such literature data are scarce. A significant error in the literature value of the enthalpy of formation of methylenecyclohexane was found. Finally, the relative enthalpy levels of the isomeric compounds of this work are discussed. The high thermodynamic stability of the compounds containing an ester functional group, ? O? C?O, relative to the stability of isomeric compounds with an ? O? C?C moiety in place of the ester function, is demonstrated. Copyright © 2009 John Wiley & Sons, Ltd.     

FT-IR and Raman spectra and vibrational investigation of bis (4-acetylanilinium) hexachlorostannate using DFT (B3LYP) calculation

4-acetylanilinium was used as a ligand for the synthesis of the organic/inorganic compound bis (4-acetylanilinium) hexachlorostannate. Vibrational study in the solid state was performed by FT-Raman of the free 4-acetylanilinium ligand C₈H₉ON⁺ and by FT-IR and FT-Raman spectroscopies of the [C₈H₁₀NO]₂ SnCl₆ compound. The comparative analysis of the Raman spectra of the title compound with that of the free ligand was discussed. The structure of the [C₈H₁₀NO]₂SnCl₆ was optimized by density functional theory (DFT) using B3LYP method and shows that the calculated values obtained by B3LYP/LanL2DZ basis are in a better agreement with the experimental data reported by Song et al. (2011) [1] than those obtained by B3LYP/LanL2MB basis. The vibrational frequencies are calculated using density functional theory (DFT) with the B3LYP/LanL2DZ basis, and scaled by various factors. Root mean square (RMS) value was calculated and the small difference between experimental and calculated modes has been interpreted by intermolecular interactions in the crystal.     

Energy calculations of 6-mercaptopurine riboside adsorbed on a silver electrode surface using density functional theory

The normal Raman and surface enhanced Raman scattering spectra were obtained for 6-mercaptopurine riboside. The mode of interaction between 6-MPR and an adatom on a silver electrode surface was studied using density functional theory calculations. Two functionals, B3LYP and DVWN, were used in the analysis. The calculations were performed on the ionized and non-ionized forms of 6-MPR, with the silver ions attached to the three possible coordination sites, N1, N3 and N7 of the molecule. The analysis was performed based on the zero-point-energy as well as adsorption and solvation energies. Results of the B3LYP and DVWN calculations were consistent and established that coordination through the N7 of 6-MPR was the most energetically favorable of the three coordination sites. The analysis was unable to determine, with a high degree of accuracy, whether the molecule adsorbs on the surface in its non-ionized or ionized form.     

Structure and vibrational analysis of 1‐hydroxy naphthalene based on density functional theory calculations

The solid phase mid‐FTIR and FT‐Raman spectra of 1‐hydroxy naphthalene (HNP) were recorded in the regions 4000–400 and 4000–50 cm, respectively. The spectra were interpreted with the help of normal coordinate analysis following full structure optimization and force field calculations based on the density functional theory (DFT) using the standard B3LYP/6‐31G** method and basis set combination. The results of the calculations were applied to simulate infrared and Raman spectra of the title compound which showed excellent agreement with the observed spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Detailed analysis of the charge transfer complex N,N‐dimethylaniline–SO2 by Raman spectroscopy and density functional theory calculations

Although the amine sulfur dioxide chemistry was well characterized in the past both experimentally and theoretically, no systematic Raman spectroscopic study describes the interaction between N,N‐dimethylaniline (DMA) and sulfur dioxide (SO₂). The formation of a deep red oil by the reaction of SO₂ with DMA is an evidence of the charge transfer (CT) nature of the DMA–SO₂ interaction. The DMA–SO₂ normal Raman spectrum shows the appearance of two intense bands at 1110 and 1151 cm⁻¹, which are enhanced when resonance is approached. These bands are assigned to ν_s(SO₂) and ν(ϕ N) vibrational modes, respectively, confirming the interaction between SO₂ and the amine via the nitrogen atom. The dimethyl group steric effect favors the interaction of SO₂ with the ring π electrons, which gives rise to a π–π* low‐energy CT electronic transition, as confirmed by time‐dependent density functional theory (TDDFT) calculations. In addition, the calculated Raman DMA–SO₂ spectrum at the B3LYP/6‐311 + + g(3df,3pd) level shows good agreement with the experimental results (vibrational wavenumbers and relative intensities), allowing a complete assignment of the vibrational modes. A better understanding of the intermolecular interactions in this model system can be extremely useful in designing new materials to absorb, detect, or even quantify SO₂. Copyright © 2009 John Wiley & Sons, Ltd.     

FT‐IR and FT‐Raman investigations of the chemosensing material para‐hexafluoroisopropanol aniline

As an important chemosensing material involving hexafluoroisopropanol (HFIP) for detecting nerve agents, para‐HFIP aniline (p‐HFIPA) has been firstly synthesized through a new reaction approach and then characterized by nuclear magnetic resonance and mass spectrometry experiments. Fourier transform infrared absorption spectroscopy (FT‐IR) and FT‐Raman spectra of p‐HFIPA have been obtained in the regions of 4000–500 and 4000–200 cm⁻¹, respectively. Detailed identifications of its fundamental vibrational bands have been given for the first time. Moreover, p‐HFIPA has been optimized and vibrational wavenumber analysis can be subsequently performed via density functional theory (DFT) approach in order to assist these identifications in the experimental FT‐IR and FT‐Raman spectra. The present experimental FT‐IR and FT‐Raman spectra of p‐HFIPA are in good agreement with theoretical FT‐IR and FT‐Raman spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman spectroscopy of 3‐(pent‐1‐enyl) methyl ether and selected deuterium‐labelled analogues

The Raman spectra of 3‐(pent‐1‐enyl) methyl ether (3‐methoxypent‐1‐ene) and four deuterium‐labelled analogues are reported and discussed. Correlations between specific structural features and the associated Raman bands are developed, with a view to enhancing the analytical application of Raman spectroscopy in investigating materials containing an alkenyl group. Particular attention is given to developing means of distinguishing the methyl group attached to the carbon skeleton from that of the methoxy group, to maximize the analytical utility of the signals associated with ν(sp² CH), ν(sp² CH₂) and ν(CC) stretching vibrations, and to interpreting in more detail certain δ(sp² CH) and δ(sp² CH₂) vibrations of the atoms of the double bond. These results establish a definitive spectroscopic protocol for differentiating a methoxy group from a methyl substituent attached directly to a carbon atom in unsaturated ethers. Copyright © 2007 John Wiley & Sons, Ltd.     

Temperature‐dependent Raman spectroscopy of BaTiO3 nanorods synthesized by using a template‐assisted sol–gel procedure

In the present work, multiphase polycrystalline BTO nanorods were synthesized using template‐assisted sol–gel deposition and their structural evolution was studied using thermo Raman spectroscopy, X‐ray diffractometry and high‐resolution transmission electron microscopy (HRTEM). In the BTO nanorods, the tetragonal phase was the dominant one, while both Raman and HRTEM indicated a coexistence with the high‐temperature hexagonal polymorph. This phase was stable across the whole of the investigated temperature range (from −95 °C to 200 °C). The investigated nanorods underwent a diffuse phase transition from tetragonal to cubic with respect to the temperature, whereas the final phase‐transition temperature was shifted to higher values compared to that expected for BTO. The low‐temperature orthorhombic‐to‐rhombohedral phase transition was also shifted to higher temperatures. These differences could be explained by the strain induced by the presence of hexagonal nanolamellas intergrown within the tetragonal nanocrystals. This result indicates that the temperature of the ferroelectric phase transition in polycrystalline BTO nanorods can be manipulated by introducing a stable hexagonal phase. Copyright © 2012 John Wiley & Sons, Ltd.     

UV resonance Raman study of cation–π interactions in an indole crown ether

UV resonance Raman (UVRR) spectroscopy is used to probe changes in vibrational structure associated with cation–π interactions for the most prevalent amino acid π–donor, tryptophan. The model compound studied here is a diaza crown ether with two indole substituents. In the presence of sodium or potassium sequestered in the crown ether, or a protonated diaza group on the compound, the indole moieties participate in a cation–π interaction in which the pyrrolo group acts as the primary π‐donor. Systematic shifts in relative intensity in the 760–780 cm⁻¹ region are observed upon formation of this cation–π interaction; we propose that these modifications reflect shifts of the delocalized, ring‐breathing W18 and hydrogen‐out‐of‐plane (HOOP) vibrational modes in this spectral region. The observed changes are attributed to perturbations of the π‐electron density as well as of normal modes that involve large displacement of the hydrogen atom on the C2 position of the pyrrole ring. Modest variations in the UVRR spectra for the three complexes studied here are correlated to differences in cation–π strength. Specifically, the UVRR spectrum of the sodium‐bound complex differs from those of the potassium‐bound or protonated‐diaza complexes, and may reflect the observation that the C2 hydrogen atom in the sodium‐bound complex exhibits the greatest perturbation relative to the other species. Normal modes sensitive to hydrogen‐bonding, such as the tryptophan W10, W9, and W8 modes, also undergo shifts in the presence of the salts. These shifts reflect the strength of interaction of the indole N H group with the iodide or hexafluorophosphate counteranion. The current observation that the W18 and HOOP normal mode regions of the indole crown ether compound are sensitive to cation–pyrrolo π interactions suggests that this region may provide reliable spectroscopic evidence of these important interactions in proteins. Copyright © 2010 John Wiley & Sons, Ltd.     

Study of asymmetric wavenumber shift of the Fermi doublet ν1 − 2ν2 in the Raman spectrum of liquid carbon disulfide

The Raman spectra of liquid carbon disulfide (CS₂) diluted with benzene (C₆H₆) have been measured. By changing the CS₂, the concentration, we found an asymmetric wavenumber shift phenomenon. With decreasing concentration of CS₂, the position of the ν₁ (655 cm⁻¹) band remains practically unchanged, and the 2ν₂ (796 cm⁻¹) band shifts toward higher wavenumbers. To interpret this asymmetric wavenumber shift phenomenon of the Fermi doublet ν₁ − 2ν₂ in the Raman spectra satisfactorily, we propose a modified Bertran model. The values of the Fermi resonance (FR) parameters of CS₂ at different concentrations were calculated using the Bertran equations. In addition, we found the fundamental ν₂, which should be independent of the FR interaction, shifted to higher wavenumbers as the concentration decreased. This shift was probably driven by the tuning of the FR. Copyright © 2009 John Wiley & Sons, Ltd.     

Density functional theory calculations and vibrational spectra of 3,5 dichloro hydroxy benzaldehyde and 2,4 dichloro benzaldehyde

The solid‐phase Fourier transform infrared (FT‐IR) and FT‐Raman spectra of 3,5 dichloro hydroxy benzaldehyde (DHB) and 2,4 dichloro benzaldehyde (DB) have been recorded in the regions 4000–400 and 4000–0 cm⁻¹, respectively. Theoretical information on the optimized geometry, harmonic vibrational wavenumbers as well as infrared and Raman intensities were obtained by means of density functional theory (DFT) using standard B3LYP/6–31G** level. This information was used in the assignment of the various fundamentals. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Copyright © 2008 John Wiley & Sons, Ltd.     

Effect of signal intensity normalization on the multivariate analysis of spectral data in complex ‘real‐world’ datasets

Spectral signal intensities, especially in ‘real‐world’ applications with nonstandardized sample presentation due to uncontrolled variables/factors, commonly require additional spectral processing to normalize signal intensity in an effective way. In this study, we have demonstrated the complexity of choosing a normalization routine in the presence of multiple spectrally distinct constituents by probing a dataset of Raman spectra. Variation in absolute signal intensity (90.1% of total variance) of the Raman spectra of these complex biological samples swamps the variation in useful signals (9.4% of total variance), degrading its diagnostic and evaluative potential. Using traditional spectral band choices, it is shown that normalization results are more complex than generally encountered in traditionally designed sample sets investigating limited chemical species. We demonstrate that no choice of a single band proves to be appropriate for predicting all the reference parameters, instead requiring a tailored normalization routine for each parameter. Of the reference parameters studied in the chosen system, signals from pathogenic adducts in ocular tissues called advanced glycation endproducts were most prominent when normalizing about the 1550–1690 cm⁻¹ region of the spectrum (17.5% of total variance, compared with 0.3% for unnormalized), while prediction of pentosidine and gender were optimized by normalization about the 1570 (R² = 0.97 vs 0.57 for unnormalized) and 1003 cm⁻¹ (p < 0.0000001 vs p < 0.01 for unnormalized) bands, respectively. The data obtained point to the extreme sensitivity of multivariate analysis to signal intensity normalization. Some general guidelines for making appropriate band choices are given, including the use of peak‐finding routines. Copyright © 2008 John Wiley & Sons, Ltd.