DFT simulations and vibrational analysis of FTIR and FT‐Raman spectra of 2‐amino‐4,6‐dihydroxypyrimidine

This work deals with the vibrational spectroscopy of 2‐amino‐4,6‐dihydroxy pyrimidine (ADHP) by means of quantum chemical calculations. The mid‐ and far FTIR and FT‐Raman spectra were measured in the condensed state. The fundamental vibrational wavenumbers and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6‐311 + G** methods and basis set combinations, and were scaled using various scale factors, which yielded good agreement between the observed and calculated wavenumbers. The vibrational spectra were interpreted with the aid of normal coordinate analysis based on the scaled density functional force field. The results of the calculations were applied to simulate the infrared and Raman spectra of the title compound, which showed excellent agreement with the observed spectra. Copyright © 2008 John Wiley & Sons, Ltd.     

Surface‐enhanced Raman scattering of protoberberine alkaloids

Quaternary protoberberine alkaloids are a class of natural dyes characterized by bright colors ranging from yellow to orange. As they present a strong fluorescence emission, their analysis by Raman spectroscopy is limited to specific techniques such as Fourier transform (FT)‐Raman and spectral shift Raman techniques such as shifted subtracted Raman difference spectroscopy (SSRDS) and shifted excitation Raman difference spectroscopy (SERDS). In a previous article, we successfully used surface‐enhanced Raman scattering (SERS) in the analysis of the alkaloid dye berberine in an ancient textile. The examination of the Raman and SERS spectra of berberine in combination with density functional theory (DFT) calculations indicated a flat adsorption geometry of the molecule on the Ag surface. In this article we extend that work to the study of related protoberberine alkaloids, palmatine, jatrorrhizine, and coptisine. The same adsorption geometry as in berberine was deduced. We found that the four alkaloids, although minimally different in their chemical structures, could be differentiated by the position of marker bands. Those bands are the most enhanced ones in the SERS spectra, which appear in the 700–800 cm⁻¹ region. Copyright © 2008 John Wiley & Sons, Ltd.     

Adsorption of 1,2,4‐triazole on a silver electrode: surface‐enhanced Raman spectroscopy and density functional theory studies

The pH‐dependent surface‐enhanced Raman scattering (SERS) of 1,2,4‐triazole adsorbed on silver electrode and normal Raman (NR) spectra of this compound in the aqueous solutions were investigated. The observed bands in the NR and SERS spectra were assigned with the help of density functional theory calculations for model molecules in the neutral, anionic, and cationic forms and their complexes with silver. The Raman wavenumbers and intensities were computed at the optimized molecular geometry. Vibrational assignments of the SERS and NR spectra are provided by calculated potential energy distributions. The combination of experimental SERS results and density functional theory calculations provide an insight into the molecular structure of adlayers formed by 1,2,4‐triazole on a silver surface at varying pH values and enable the determination of molecular orientation with respect to the surface. Copyright © 2012 John Wiley & Sons, Ltd.     

Resonance Raman spectroscopic and density functional theory investigation of the excited state structural dynamics of 2‐mercapto‐1‐methylimidazole

The resonance Raman spectroscopy in conjunction with the density functional theory calculations were used to study the excited state structural dynamics of 2‐mercapto‐1‐methylimidazole (MMI). The experimental UV absorption bands were assigned according to the time‐dependent density functional calculations. The vibrational assignments were done for the A‐band resonance Raman spectra of MMI in water and acetonitrile on the basis of the Fourier transform infrared (FT‐IR) and FT‐Raman measurements in solid, in water and in acetonitrile and the corresponding B3LYP/6‐311+G(d, p) computations. The dynamic structures of MMI were obtained by analysis of the resonance Raman intensity pattern and normal mode analysis. The differences in the dynamic structures of MMI and thiourea were revealed and explained. The structural dynamic of MMI was found to be similar to that of 2‐thiopyrimidone in terms of major reaction coordinates and thus favored the intra‐molecular proton transfer reaction. Copyright © 2012 John Wiley & Sons, Ltd.     

Raman and SERS study of metoclopramide at different pH values

Conjugate acid–base forms of the drug metoclopramide were investigated by Raman spectroscopy in aqueous solutions and by surface‐enhanced Raman scattering (SERS), when the molecules were adsorbed on colloidal silver surfaces. Raman spectra were recorded at pH values below 8, metoclopramide being poorly water soluble at higher pH values. The SERS spectra of metoclopramide were recorded in the 3–11 pH range, even in spite of its low solubility at basic pH values. The Raman and SERS spectra were assigned by means of density functional theory (DFT) calculations. By monitoring several SERS marker bands, the protonated, neutral or the coexistence of both molecular species adsorbed on the colloidal silver particles could be evidenced. The adsorbate orientation was deduced to be perpendicular to the metal surface for the protonated molecular species and tilted for the neutral metoclopramide molecular species. Copyright © 2009 John Wiley & Sons, Ltd.     

Molecular structure and vibrational spectra of 3 (or 4 or 6)‐methyl‐5‐nitro‐2‐pyridinethiones: FT‐IR,FT‐Raman and DFT quantum chemical calculations

IR and Raman spectra (RS) of polycrystalline 3‐(or 4 or 6)‐methyl‐5‐nitro‐2‐pyridinethione have been measured and analyzed by means of density functional theory (DFT) quantum chemical calculations. The B3LYP/6‐311G(2d,2p) approach has been applied for both the thiol and thione tautomers due to the possibility of the formation of these two thiole forms. Molecular structures of these compounds have been optimized starting from different molecular geometries of the thiol group and thione group. Two conformations of the 2‐mercaptopyridine, trans and cis, have been taken into account. It was shown that the studied compounds appear in the solid state in the thione form. The effect of the hydrogen‐bond formation in the studied compounds has been considered. Copyright © 2008 John Wiley & Sons, Ltd.     

Can Raman spectroscopy detect cumulenic structures of linear carbon chains?

The molecular and vibrational structures of cumulenic carbon chains are investigated by density functional theory calculations and compared with that of hydrogen‐capped polyynes. The small value of bond length alternation (BLA) along the CC bonds sequence obtained by geometry optimization of uncapped C_n chains and vinyl‐capped carbon chains confirms their cumulenic structure. It is demonstrated that for finite length chains the structural parameters are determined by end effects as far as the Peierls distortion, expected for very long molecules, does not occur. The Raman spectra of such molecules are calculated to verify the possibility of identifying markers of cumulenic chains by means of vibrational spectroscopy. As expected, the longitudinal mode consisting of the BLA oscillation, which is responsible for the strongest Raman transition of polyynes, becomes very weak for cumulenes; this behaviour is rationalized in terms of local polarizability derivatives. However, other longitudinal modes can be observed in the Raman spectra of C_n chains. The wavenumber behaviour and the optical activity of these modes are interpreted on the basis of the phonon dispersion branch of an ideally infinite cumulenic polymer. Raman intensities computed for chains of different lengths allow to conclude that cumulenic molecules could be detected and identified by means of Raman spectroscopy. Copyright © 2009 John Wiley & Sons, Ltd.     

The autooxidation process in linoleic acid screened by Raman spectroscopy

The chemical changes associated to the autooxidation process of linoleic acid (LA) were detected by Raman spectroscopy and interpreted in the light of density functional theory (DFT) calculations performed for both the fatty acid and its main oxidation products. The present methodology, applied for a six‐day period upon induction of oxidation (through heating), allowed to understand the chemical modifications occurring during the oxidation process. Raman spectroscopy was shown to be a suitable and reliable technique for assessing the oxidation degree of fatty acid samples, particularly pure fatty acids, mainly when computational methods are used alongside to predict the spectral features of the distinct chemical entities involved. Screening of the oxidation process was mostly based on the loss of intensity of the bands assigned to LA cis‐double bonds. Copyright © 2012 John Wiley & Sons, Ltd.     

In situ analysis of chiral components of pichtae essential oil by means of ROA spectroscopy: experimental and theoretical Raman and ROA spectra of bornyl acetate

In this paper, a novel approach to analyze in situ (−)‐bornyl acetate (BA) in pichtae essential oil (Siberian fir needle oil, Abies sibirica oil) by means of Raman optical activity (ROA) is reported. As part of this approach, a conformational study in the gas phase of (+)‐ and (−)‐BA has been carried out, predicting the presence of three conformers for each enantiomer at 298.15 K. The structures of these conformers were optimized with density functional theory with the Becke 3LYP functional and 6–311 + + g** basis set. Subsequently, the Raman and ROA spectra were simulated in order to compare them with the experimentally measured spectra of the neat enantiomers of BA. Finally, the combination of Raman and ROA spectroscopy as well as DFT calculations was successfully applied not only for the detection of BA but also for the determination of the specific enantiomer of BA present in the investigated pichtae essential oil samples. Thus, the ROA technique described here has the potential to be used as a fast and easy commercial method to control the quality of essential oils. Copyright © 2011 John Wiley & Sons, Ltd.     

Molecular structure,NMR and vibrational spectral analysis of 2,4‐difluorophenol by ab initio HF and density functional theory

Quantum chemical calculations of energies, geometries and vibrational wavenumbers of 2,4‐difluorophenol (2,4‐DFP) were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6‐311G(d,p) as basis set. The optimized geometrical parameters obtained by HF and DFT calculations are in good agreement with related molecules. The best level of theory in order to reproduce the experimental wavenumbers is the B3LYP method with the 6‐311G(d,p) basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of 2,4‐DFP is also reported. The entropy of the title compound was also performed at HF/6‐311G(d,p) and B3LYP/6‐311G(d,p) levels of theory. The isotropic chemical shift computed by ¹H, ¹³C NMR analyses also shows good agreement with experimental observations. The theoretical spectrograms for FT‐IR and FT‐Raman spectra of the title molecule have been constructed. Copyright © 2009 John Wiley & Sons, Ltd.     

Theoretical investigation and computational evaluation of overtone and combination features in resonance Raman spectra of polyenes and carotenoids

We review the theory for overtones and combinations in resonant Raman spectroscopy introduced by Nafie, Stein and Peticolas in 1971 on the basis of time‐ordered diagrams, and we apply it to β‐carotene with the support of density functional theory calculations. Comparison with experimental results obtained by Tasumi's group in 1994 is provided. The theory here presented allows a prompt evaluation of resonant Raman intensities with presently available quantum chemistry tools. Copyright © 2014 John Wiley & Sons, Ltd.     

Synthesis and Raman spectroscopic investigation of a new self‐assembly monolayer material 4‐[N‐phenyl‐N‐(3‐methylphenyl)‐amino]‐benzoic acid for organic light‐emitting devices

We have synthesized 4‐[N‐phenyl‐N‐(3‐methylphenyl)‐amino]‐benzoic acid (4‐[PBA]) and investigated its molecular vibrations by infrared and Raman spectroscopies as well as by calculations based on the density functional theory (DFT) approach. The Fourier transform (FT) Raman, dispersive Raman and FT‐IR spectra of 4‐[PBA] were recorded in the solid phase. We analyzed the optimized geometric structure and energies of 4‐[PBA] in the ground state. Stability of the molecule arising from hyperconjugative interactions and charge delocalization was studied using natural bond orbital analysis. The results show that change in electron density in the σ* and π* antibonding orbitals and E₂ energies confirm the occurrence of intramolecular charge transfer within the molecule. Theoretical calculations were performed at the DFT level using the Gaussian 09 program. Selected experimental bands were assigned and characterized on the basis of the scaled theoretical wavenumbers by their total energy distribution. The good agreement between the experimental and theoretical spectra allowed positive assignment of the observed vibrational absorption bands. Finally, the calculation results were applied to simulate the Raman and IR spectra of the title compound, which show agreement with the observed spectra. Copyright © 2011 John Wiley & Sons, Ltd.     

Modeling red coral (Corallium rubrum) and African snail (Helixia aspersa) shell pigments: Raman spectroscopy versus DFT studies

Pigments from red coral (Corallium rubrum) and African snail (Helixia aspersa) shell were studied non‐invasively using Raman spectroscopy with 1064‐nm laser beam. The two observed bands because of organic pigments confined in biomineralized CaCO₃ matrix at about 1500 and 1100 cm⁻¹ were assigned to ν(CC) and ν(C―C), respectively. Both signals originate from polyene(s) of largely unknown structure, containing several conjugated CC bonds. The small peak at 1016 cm⁻¹ in the Raman spectrum of coral pigment was assigned to in‐plane ―CH₃ rocking or structural deformation of polyene chain because of spatial confinement in the mineral matrix. The organic pigments in red coral and snail shell were present in inorganic matrix containing aragonite (shell) and calcite (coral). In addition, using Raman spectroscopy, it was observed that aragonite was replaced by calcite as result of healing damaged parts of snail shell. This is an important finding which indicates a great potential of nondestructive Raman spectroscopy instead of X‐ray technique, as a diagnostic tool in environmental studies. To support analysis of the observed Raman spectra detailed calculations using density functional theory (DFT with B3LYP and BLYP density functionals) on structure and vibrations of model all‐trans polyenes were undertaken. DFT calculated CC and C―C stretching frequencies for all‐trans polyenes containing from 2 to 14 CC units were compared with the observed ν(CC) and ν(C―C) band positions of the studied coral and shell. Individual correction factors were used to better match theoretical wavenumbers with observed band positions in red coral and African snail. It was concluded that all‐trans polyene pigments of red coral and dark parts of African snail shell contain 11–12 and 14 CC double bond units, respectively. However, Raman spectroscopy cannot produce any clear information on the presence and nature of the end‐chain substituents in the studied pigments. Copyright © 2016 John Wiley & Sons, Ltd.     

Surface‐enhanced Raman scattering of N‐acetylneuraminic acid on silver nanoparticle surface

N‐Acetylneuraminic acid (sialic acid, Neu5Ac) has recently gained interest as a potential marker for a variety of pathophysiological processes, although no Raman study has been reported for this important biomolecule. In this paper, the vibrational properties of Neu5Ac were studied by means of Raman, surface‐enhanced Raman scattering (SERS), and density functional theory calculations. By adsorption of Neu5Ac on silver nanoparticle surface, strongly enhanced Raman intensities are obtained, allowing easy measurement of small amounts of aqueous Neu5Ac (10 µl of a 10⁻⁷ m solution) utilizing low laser power and short exposure time. The mechanism of adsorption of Neu5Ac on the silver surface is discussed on the basis of the experimental and theoretical results. This study demonstrates that SERS can provide an effective tool for development of a label‐free, rapid, and sensitive optical platform for identification of Neu5Ac. Copyright © 2014 John Wiley & Sons, Ltd.     

Raman spectrum of monobromoindigo

Monobromoindigo is a component of Tyrian purple, a purple–red natural colorant extracted from various species of sea snails, which was possibly first produced by the ancient Phoenicians and has been employed as a symbol of royalty and power by several civilizations over the centuries. Raman spectroscopy has proved to be an effective analytical technique to detect historical dyes, as it allows rapid and accurate identification of unknowns in a nondestructive way. Although other constituents of Tyrian purple have been comprehensively investigated by Raman spectroscopy, the Raman bands of 6‐bromoindigo, a molecule that has been correlated with a specific snail species, Hexaplex trunculus (also known as Murex trunculus), have been reported but not previously assigned. This paper includes a complete assignment of the Raman spectrum of the 6‐bromoindigo isomer, including experimental spectra recorded at 488 and 785 nm, which were compared with those collected from indigo under the same conditions. 1 1 This article was first published online 03 November 2011. Errors were subsequently identified. This notice is included in both print and online versions to indicate that both have been corrected 07 December 2011.
Theoretical Raman spectra for both molecules were obtained using density functional theory calculations. Copyright © 2011 John Wiley & Sons, Ltd.     

Probing the structure and Franck–Condon region of protochlorophyllide a through analysis of the Raman and resonance Raman spectra

The structure and Franck–Condon region of protochlorophyllide a, a precursor in the biosynthesis of chlorophyll and substrate of the light‐regulated enzyme protochlorophyllide oxidoreductase (POR), were investigated by Raman and resonance Raman (RR) spectroscopy. The spectroscopic results are compared to the spectra of the structurally closely related porphyrin model compound magnesium octaethylporphyrin (MgOEP), and interpreted on the basis of density functional theory (DFT) calculations. It is shown that the electronic properties of the two porphyrin macrocycles are affected by different vibrational coupling modes, resulting in a higher absorption cross section of protochlorophyllide a in the visible spectral region. Furthermore, a comparison of the Fourier transform (FT)‐Raman and RR spectra of protochlorophyllide a indicates the modes that are resonantly enhanced upon excitation. Based on vibrational normal mode calculations, these modes include C C ring‐breathing and CC stretching vibrations of the porphyrin macrocycle. In particular, the strong band at 1703 cm⁻¹ can be attributed to the CO carbonyl vibration of the cyclopentanone ring, which is attached in conjugation to the π‐electron path of the porphyrin ring system. The enhancement of that mode upon electronically resonant excitation is discussed in the light of the reaction model suggested for the photoreduction of protochlorophyllide a in the POR. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectroscopy of a compound with a CS7 ring

The product of the Asinger reaction between elemental sulfur, n‐butylamine and acetophenone is 8‐(n‐butylaminophenylmethyliden)‐1,2,3,4,5,6,7‐heptathiocane which contains a CS₇ ring. A combination of infrared, Raman and inelastic neutron scattering spectroscopies with periodic density functional theory calculations is used to provide a complete assignment of the vibrational spectra of this unusual species. The similarity between the Raman spectra of the compound and that of elemental sulfur is particularly striking. Copyright © 2009 John Wiley & Sons, Ltd.     

In‐situ Raman spectroscopy of current‐carrying graphene microbridge

In‐situ Raman spectroscopy was performed on chemical vapor deposited graphene microbridge (3 μm × 80 μm) under electrical current density up to 2.58 × 10⁸ A/cm² in ambient conditions. We found that both the G and the G′ peak of the Raman spectra do not restore back to the initial values at zero current, but to slightly higher values after switching off the current through the microbridge. The up‐shift of the G peak and the G′ peak, after switching off the electrical current, is believed to be due to p‐doping by oxygen adsorption, which is confirmed by scanning photoemission microscopy. Both C–O and C=O bond components in the C1s spectra from the microbridge were found to be significantly increased after high electrical current density was flown. The C=O bond is likely the main source of the p‐doping according to our density functional theory calculation of the electronic structure. Copyright © 2014 John Wiley & Sons, Ltd.     

Irbesartan: FTIR and Raman spectra. Density functional study on vibrational and NMR spectra

Arterial hypertension is a very common disease, which is treated with different medications such as Irbesartan. This compound is a nonpeptide antagonist of the receptor of the enzyme angiotensin II. The infrared and Raman spectra of this compound were recorded and discussed assisted with density functional theory using the 6‐31G** basis set and animated pictures. Irbesartan exists in two tautomeric forms which can be isolated in the solid state. The vibrational study has been recorded using a mixture of both forms. ¹³C, ¹⁵N and ¹H NMR theoretical studies have been performed and compared with previously reported experimental data. Theoretical calculations allowed the determination of the main features of the A and B tautomers of Irbesartan both in the vibrational studies and in the NMR spectroscopy. Copyright © 2009 John Wiley & Sons, Ltd.     

The Raman spectrum of the γ′‐V2O5 polymorph: a combined experimental and DFT study

Structure and vibrational dynamics of γ′‐V₂O₅ synthesized from a pristine γ‐LiV₂O₅ sample via a chemical oxidation route was studied by means of Raman spectroscopy and quantum‐chemical calculations. The calculations based on density functional theory reliably reproduce the experimental structure of the γ′‐V₂O₅ lattice. The calculated Raman spectrum agrees remarkably well with the experimental one. Making use of the agreement, a complete assignment of Raman bands to vibrations of particular structural units is proposed. The comparison of Raman spectra and structural features of α‐V₂O₅ and γ′‐V₂O₅ polymorphs allowed establishing reliable ‘structure–spectrum’ correlations and identifying Raman peaks characteristic for different structural units. Copyright © 2015 John Wiley & Sons, Ltd.