Structural,vibrational spectra and normal coordinate analysis for two tautomers of 4(5)‐(2′‐furyl)‐imidazole

We have synthesized both the 4 and 5 tautomeric forms of 4(5)‐(2′‐furyl)‐imidazole (1) and investigated their molecular vibrations by infrared and Raman spectroscopies as well as by calculation based on the density functional theory (DFT) approach. Examination of the temperature dependence of IR intensity revealed the band characteristics of the 4 and 5 tautomers of (1). Comparison of experimental and calculated chemical shifts in nuclear magnetic resonance (NMR) spectroscopy was made in order to identify the two tautomeric forms. The assignment of vibrational normal modes was performed, and the force field obtained reproduced the experimental vibrational wavenumbers with a root mean‐square deviation (RMSD) value of ca. 13 cm⁻¹ for both tautomers. The natural bond orbital (NBO) study reveals the characteristics of the electronic delocalization of the two tautomeric structures. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectroscopy and DFT calculations of di‐amino acid peptides: α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu in the solid state

Experimental vibrational spectroscopic studies and density functional theory (DFT) calculations of the di‐amino acid peptide derivatives α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu have been undertaken. Raman and infrared spectra have been recorded for samples in the solid state. DFT simulations were conducted using the B3‐LYP correlation functional and the cc‐pVDZ basis set to determine energy minimized/geometry optimized structures (based on a single isolated molecule in the gaseous state). Normal coordinate calculations have provided vibrational assignments for fundamental modes, including their potential energy distributions. Significant differences are observed between α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu both in the computed structures and in the vibrational spectra. The combination of experimental and calculated spectra provide an insight into the structural and vibrational spectroscopic properties of di‐amino acid peptide derivatives. Copyright © 2009 John Wiley & Sons, Ltd.     

Identification of hydrogen bond modes in polarized Raman spectra of single crystals of α‐oxalic acid dihydrate

Polarized Raman spectra of single crystals of the α‐polymorphs of protonated and deuterated oxalic acid dihydrate were recorded. The interpretation of the spectra is assisted by periodic DFT calculations using the CRYSTAL06 program and by comparison with the infrared spectra of the polycrystalline material. The agreement between the calculated and observed band wavenumbers is fair in the case of low‐anharmonicity modes, but marked differences appear for the stretching modes that are strongly anharmonic. A very broad feature, extending between ∼2000 and 1200 cm⁻¹, is attributed to OH stretching. Notable is the topping of this feature by distinct bands that can be attributed to CO stretching, H₂O scissoring and COH bending coupled to C O stretching. The assignments are supported by isotope effects. However, deuteration does not notably affect the wavenumber limits of the broad OH stretching band, which suggests that the potential governing the proton dynamics is of the asymmetric double‐minimum type with a very low barrier. The calculated normal coordinates show a strong participation of the bending modes of water molecules in almost all internal acid motions, as well as in the external phonons. Copyright © 2009 John Wiley & Sons, Ltd.     

Analysis of vibrational spectra of 2‐fluoro‐6‐nitrotoluene based on density functional theory calculations

The conformational behavior and structural stability of 2‐fluoro‐6‐nitrotoluene (FNT) were investigated by utilizing density functional theory (DFT) with the standard B3LYP/6‐311 + G** method and basis set combinations. The vibrational wavenumbers of FNT were computed at DFT levels and complete vibrational assignments were made on the basis of normal coordinate calculations. Normal coordinate analysis (NCA) has been carried out to support the vibrational analysis. The results were compared with the experimental values. The observed Fourier transform infrared (FTIR) and Fourier transform (FT) Raman vibrational wavenumbers were analyzed and compared with the theoretically predicted vibrational spectra. The results of vibrational spectra of FNT were also compared with the vibrational spectra of some toluene derivatives. The assignments of bands to various normal modes of the molecules were also carried out. Copyright © 2008 John Wiley & Sons, Ltd.     

Analysis of structure and vibrational spectra of 2,5‐dihydroxybenzoicacid based on density functional theory calculations

The spectra of 2,5‐dihydroxybenzoic acid (DHBA) have been recorded using Fourier transform‐infrared spectroscopy (FT‐IR) and FT‐Raman measurements. The total energy calculations of DHBA were evaluated for various possible conformers. The spectra were interpreted with the help of normal coordinate analysis based on density functional theory (DFT) using standard B3LYP/6–31G* method for the most optimized geometry. The effect of intramolecular hydrogen bonding was discussed. Normal coordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors, yielding fairly good agreement between observed and calculated frequencies. On the basis of the comparison between calculated and experimental results, assignments of fundamental modes were examined. Copyright © 2009 John Wiley & Sons, Ltd.     

Solvent‐dependent structural dynamics of 2(1H)‐pyridinone in light absorbing S4(ππ*) state

The B‐band resonance Raman spectra of 2(1H)‐pyridinone (NHP) in water and acetonitrile were obtained, and their intensity patterns were found to be significantly different. To explore the underlying excited state tautomeric reaction mechanisms of NHP in water and acetonitrile, the vibrational analysis was carried out for NHP, 2(1D)‐pyridinone (NDP), NHP–(H₂O)_n (n = 1, 2) clusters, and NDP–(D₂O)_n (n = 1, 2) clusters on the basis of the FT‐Raman experiments, the B3LYP/6‐311++G(d,p) computations using PCM solvent model, and the normal mode analysis. Good agreements between experimental and theoretically predicted frequencies and intensities in different surrounding environments enabled reliable assignments of Raman bands in both the FT‐Raman and the resonance Raman spectra. The results indicated that most of the B‐band resonance Raman spectra in H₂O was assignable to the fundamental, overtones, and combination bands of about ten vibration modes of ring‐type NHP–(H₂O)₂ cluster, while most of the B‐band resonance Raman spectra in CH₃CN was assigned to the fundamental, overtones, and combination bands of about eight vibration modes of linear‐type NHP–CH₃CN. The solvent effect of the excited state enol‐keto tautomeric reaction mechanisms was explored on the basis of the significant difference in the short‐time structural dynamics of NHP in H₂O and CH₃CN. The inter‐molecular and intra‐molecular ESPT reaction mechanisms were proposed respectively to explain the Franck–Condon region structural dynamics of NHP in H₂O and CH₃CN.Copyright © 2015 John Wiley & Sons, Ltd.     

UV‐induced transformations of matrix‐isolated 1,3,4‐thiadiazole‐2‐thiones

Monomers of 5‐mercapto‐1,3,4‐thiadiazole‐2‐thione (bismuthiol) were studied using an experimental matrix‐isolation technique as well as by carrying out theoretical quantum chemical calculations. The calculations, performed using the quadratic configuration interaction method with single and double excitations (QCISD)/6‐31++G(d,p)//DFT(B3LYP)/6‐311++G(2d,p), predict that the thione–thiol tautomer of bismuthiol should be significantly (by more than 19 kJ mol^?1) more stable than other tautomeric forms. Accordingly, only the signatures of the thione–thiol tautomer were observed in the FT‐IR spectrum of bismuthiol, recorded directly after deposition of an Ar matrix. UV (λ > 320 nm) irradiation induced the conversion of the thione–thiol tautomer into the dithiol form. Analogous investigations were carried out for two related compounds: 5‐methyl‐1,3,4‐thiadiazole‐2‐thione and 5‐methylthio‐1,3,4‐thiadiazole‐2‐thione. For these two species, only the thione tautomeric forms were observed after deposition of Ar matrices. These tautomers were predicted (by QCISD calculations) to be more stable (by at least 19 kJ mol^?1) than other tautomeric forms. Upon UV irradiation, the most stable thione forms of these compounds were transformed into the corresponding thiol tautomers. Direct observation of the thione → thiol phototautomeric processes provides a clear proof that intramolecular proton transfer reaction can occur in molecules, such as bismuthiol, in spite of the increased NH···S distance, in comparison to other phototautomerizing species studied so far. All the isomers of the studied compounds (substrates and products of the photoreactions) were identified by comparison of their IR spectra with the spectra calculated at the DFT(B3LYP)/6‐311++G(2d,p) level of theory for possible isomeric structures. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectroscopy and crystal structure analysis of two polymorphs of the di‐amino acid peptide cyclo(L‐Glu‐L‐Glu)

Cyclo(L ‐Glu‐L ‐Glu) has been crystallised in two different polymorphic forms. Both polymorphs are monoclinic, but form 1 is in space group P2₁ and form 2 is in space group C2. Raman scattering and FT‐IR spectroscopic studies have been conducted for the N,O‐protonated and deuterated derivatives. Raman spectra of orientated single crystals, solid‐state and aqueous solution samples have also been recorded. The different hydrogen‐bonding patterns for the two polymorphs have the greatest effect on vibrational modes with N H and CO stretching character. DFT (B3‐LYP/cc‐pVDZ) calculations of the isolated cyclo(L ‐Glu‐L ‐Glu) molecule predict that the minimum energy structure, assuming C₂ symmetry, has a boat conformation for the diketopiperazine ring with the two L ‐Glu side chains being folded above the ring. The calculated geometry is in good agreement with the X‐ray crystallographic structures for both polymorphs. Normal coordinate analysis has facilitated the band assignments for the experimental vibrational spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

FT‐Raman,FT‐IR spectra and DFT calculations on monomeric and dimeric structures of 5‐fluoro‐ and 5‐chloro‐salicylic acid

The experimental and theoretical study on the structures and vibrations of 5‐fluoro‐salicylic acid and 5‐chloro‐salicylic acid (5‐FSA and 5‐ClSA, C₇H₅FO₃ and C₇H₅ClO₃) is presented. The Fourier transform infrared spectra (4000–400 cm⁻¹) and the Fourier transform Raman spectra (4000–50 cm⁻¹) of the title molecules in the solid phase were recorded. The molecular structures, vibrational wavenumbers, infrared intensities, Raman intensities and Raman scattering activities were calculated for a pair of molecules linked by the intermolecular O H···O hydrogen bond. The geometrical parameters and energies of 5‐FSA and 5ClSA were obtained for all eight conformers/isomers from density functional theory (DFT) (B3LYP) with 6‐311++G(d,p) basis set calculations. The computational results identified the most stable conformer of 5‐FSA and 5‐ClSA as the C1 form. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The spectroscopic and theoretical results were compared with the corresponding properties for 5‐FSA and 5‐ClSA monomers and dimer of C1 conformer. The optimized bond lengths, bond angles and calculated wavenumbers showed the best agreement with the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.     

Theoretical study on the molecular tautomerism of the 3-hydroxy-pyridin-4-one system

3-hydroxy-pyridin-4-one is a parent molecule for the family of hydroxypyridinones that are known in coordination chemistry as efficient metal ions chelators. In this work, relative stabilities of some possible tautomers were investigated using several quantum chemical methods: CBS (complete basis set methods), Gn, DFT (density functional theory), Hartree–Fock and MP2. Performed calculations show that the system under consideration exists as a mixture of two tautomers with comparable energies. Among them, the hydroxypyridinone structure of the studied molecular system seems to be a bit more stable than the o-dihydroxypyridine one, by a few kJ/mol only. Aromaticity and intra-molecular hydrogen bonding are the main effects influencing the stability of the studied tautomeric structures. Consequently, aromatic effects were calculated using several indices of aromaticity: HOMA (harmonic oscillator model of aromaticity), NICS (nucleus independent chemical shift), H, PDI (para delocalisation index), MCI (multi-centre index) and ASE (aromatic stabilisation energy). The strength of possible intra-molecular hydrogen bonds (H-bonds) was determined by means of the AIM (atoms-in-molecules) method and by calculating enthalpies for theoretical reactions that do or do not involve H-bonds. The AIM method was employed to understand how variations in atomic energies influence the stability of different tautomeric structures.     

FTIR and FT‐Raman spectra and density functional computations of the vibrational spectra,molecular geometry and atomic charges of the biomolecule: 5‐bromouracil

FTIR and FT‐Raman spectra of 5‐bromouracil in the powder form were recorded in the region 400–4000 cm⁻¹ and 50–4000 cm⁻¹, respectively. The observed wavenumbers were analysed and assigned to different normal modes of vibration of the molecule. Quantum chemical calculations were performed to support the assignments of the observed wavenumbers. The performance of the B3LYP hybrid density functional (DFT) method was compared with other methods. With the 6–31 G** and 6–311 + G(2d,p) basis sets, the calculated geometry, dipole moments and harmonic vibrations were determined. A comparison with the uracil molecule was made, and specific scale factors were deduced and employed in the predicted wavenumbers of 5‐bromouracil. The total atomic charges and thermodynamic parameters were calculated, and are discussed briefly. Structure and harmonic vibrations of 5‐bromouracil were also calculated in the presence of water within a simple model with one molecule. It is observed that the bromine atom at position 5 exhibits smaller inductive effects than the fluorine atom, producing a small distortion of the electrostatic potential around the ring and a reduction of the molecular dipole moment. Copyright © 2007 John Wiley & Sons, Ltd.     

Experimental (FT‐IR) and theoretical (DFT) studies on prototropy and H‐bond formation for pyrazine‐2‐amidoxime

The results of the first structural studies (with the use of both experimental and theoretical methods) on pyrazine‐2‐amidoxime (PAOX) were shown and discussed. FT‐IR spectra were recorded in different concentrations of the PAOX in apolar solvent to check the possibility of the inter‐ or intramolecular hydrogen‐bond formation. All possible tautomers–rotamers of PAOX were then theoretically considered at the DFT(B3LYP)/6‐311+G** level in vacuo. For selected isomers, calculations were also performed at higher levels of theory {B3LYP/6‐311+G(3df,2p) and G3B3}. Based on the results of DFT calculations, the most stable isomers were found, and their total free energies and infrared spectra were calculated. The energy variation plots for the N8?C7?N9?O10 and N1?C2?C7?N9 dihedral angles were also computed to find two energy barriers, one for E/Z isomerization around the C7?N9 double bond and the other one for rotation of the pyrazinyl ring around the C2?C7 single bond. The results show that the stability of the PAOX isomers strongly depend on their configuration and orientation of the substituents. The possibilities of inter‐ and intramolecular hydrogen bonds were also experimentally and theoretically checked. Finally, a potential of mean force was determined in CHCl₃ for a dimer of PAOX with hexamethylphosphoramide. Both, experimental and theoretical results are in agreement. Copyright © 2016 John Wiley & Sons, Ltd.     

Vibrational spectroscopic studies of the structure of di‐amino acid peptides. Part II: cyclo(L‐Asp‐L‐Asp) in the solid state and in aqueous solution

Solid‐state protonated and N,O‐deuterated Fourier transform infrared (IR) and Raman scattering spectra together with the protonated and deuterated Raman spectra in aqueous solution of the cyclic di‐amino acid peptide cyclo(L ‐Asp‐L ‐Asp) are reported. Vibrational band assignments have been made on the basis of comparisons with previously cited literature values for diketopiperazine (DKP) derivatives and normal coordinate analyses for both the protonated and deuterated species based upon DFT calculations at the B3‐LYP/cc‐pVDZ level of the isolated molecule in the gas phase. The calculated minimum energy structure for cyclo(L ‐Asp‐L ‐Asp), assuming C₂ symmetry, predicts a boat conformation for the DKP ring with both the two L ‐aspartyl side chains being folded slightly above the ring. The CO stretching vibrations have been assigned for the side‐chain carboxylic acid group (e.g. at 1693 and 1670 cm⁻¹ in the Raman spectrum) and the cis amide I bands (e.g. at 1660 cm⁻¹ in the Raman spectrum). The presence of two bands for the carboxylic acid CO stretching modes in the solid‐state Raman spectrum can be accounted for by factor group splitting of the two nonequivalent molecules in a crystallographic unit cell. The cis amide II band is observed at 1489 cm⁻¹ in the solid‐state Raman spectrum, which is in agreement with results for cyclic di‐amino acid peptide molecules examined previously in the solid state, where the DKP ring adopts a boat conformation. Additionally, it also appears that as the molecular mass of the substituent on the C^α atom is increased, the amide II band wavenumber decreases to below 1500 cm⁻¹; this may be a consequence of increased strain on the DKP ring. The cis amide II Raman band is characterized by its relatively small deuterium shift (29 cm⁻¹), which indicates that this band has a smaller N H bending contribution than the trans amide II vibrational band observed for linear peptides. Copyright © 2009 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.     

The revision of intermolecular interactions in 1,3‐dinitrobenzene crystal—the role of nitro groups in optical nonlinearity

Polarized Fourier transform‐infrared (FT‐IR) reflectance spectra and powder Raman spectra have been measured for 1,3‐dinitrobenzene crystal in order to revise the assignments of bands by means of the oriented gas model reinforced with quantum chemical [density functional theory (DFT)] calculations. Longitudinal optical/transverse optical (LO‐TO) splitting of some bands is observed indicating medium strong, long‐range, dipole–dipole interactions. The analysis of overtones in the polarized FT‐NIR spectra has allowed us to estimate the anharmonicity of vibrations in the crystal. The molecular motions of the nitro groups are analyzed on the basis of temperature‐dependent polycrystalline IR spectra. Based on the values of the energy difference (Δν_el) between the forbidden A_1g→B_2u transition in the benzene molecule in the gas phase and the first electronic transition in 1,3‐dinitrobenzene, it has been concluded that the intermolecular interactions are medium strong. The nitro group interactions are proposed to play the main role in the optical nonlinearity. Copyright © 2010 John Wiley & Sons, Ltd.     

Crystal → nematic phase transition in the liquid crystalline system 1‐isothiocyanato‐4‐(trans‐4‐propylcyclohexyl) benzene (3CHBT) probed by temperature‐dependent micro‐Raman study and DFT calculations

Raman spectra of 3CHBT in unoriented form were recorded at 14 different temperature measurements in the range 25–55 °C, which covers the crystal → nematic (N) phase transition, and the Raman signatures of the phase transition were identified. The wavenumber shifts and linewidth changes of Raman marker bands with varying temperature were determined. The assignments of important vibrational modes of 3CHBT were also made using the experimentally observed Raman and infrared spectra, calculated wavenumbers, and potential energy distribution. The DFT calculations using the B3LYP method employing 6‐31G functional were performed for geometry optimization and vibrational spectra of monomer and dimer of 3CHBT. The analysis of the vibrational bands, especially the variation of their peak position as a function of temperature in two different spectral regions, 1150–1275 cm⁻¹ and 1950–2300 cm⁻¹, is discussed in detail. Both the linewidth and peak position of the ( C H ) in‐plane bending and ν(NCS) modes, which give Raman signatures of the crystal → N phase transition, are discussed in detail. The molecular dynamics of this transition has also been discussed. We propose the co‐existence of two types of dimers, one in parallel and the other in antiparallel arrangement, while going to the nematic phase. The structure of the nematic phase in bulk has also been proposed in terms of these dimers. The red shift of the ν(NCS) band and blue shift of almost all other ring modes show increased intermolecular interaction between the aromatic rings and decreased intermolecular interaction between two  NCS groups in the nematic phase. Copyright © 2009 John Wiley & Sons, Ltd.     

Surface‐enhanced Raman scattering assessment of DNA from leaf tissues adsorbed on silver colloidal nanoparticles

In this work, the surface‐enhanced Raman scattering (SERS) spectra of seven genomic DNAs from leaves of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.), respectively, have been analyzed in the wavenumber range 200–1800 cm⁻¹. The surface‐enhanced Raman vibrational modes for each of these cases, spectroscopic band assignments and structural interpretations of genomic DNAs are reported. A high molecular structural information content can be found in the SERS spectra of these DNAs from leaf tissues. Based on this work, specific plant DNA–ligand interactions or accurate local structure of DNA might be further investigated using surface‐enhanced Raman spectroscopy. Besides, this study will generate information which is valuable in the development of label‐free DNA detection for chemical probing in living cell. Copyright © 2013 John Wiley & Sons, Ltd.     

Photofragmentation mechanisms of nickel methyl xanthate—resonance Raman and density functional theory investigation

The C‐, D‐, and E‐band resonance Raman spectra were obtained for nickel methyl xanthate (NMX) in acetonitrile solution. Density functional calculations were carried out to help elucidate its ultraviolet electronic transitions and vibrational assignments of the resonance Raman spectra associated with the C‐, D‐, and E‐band absorptions. The Franck–Condon region photodissociation dynamics of NMX in C, D, and E‐band absorptions were revealed to have multidimensional characters and to be significantly different from one another in terms of the resonance Raman intensity patterns. The photofragmentation mechanism associated with C‐, D‐, and E‐band absorptions are briefly discussed. Copyright © 2010 John Wiley & Sons, Ltd.     

Experimental vibrational spectra (Raman,infrared) and DFT calculations on monomeric and dimeric structures of 2‐ and 6‐bromonicotinic acid

In this work, the Fourier transform infrared and Raman spectra of 2‐bromonicotinic acid and 6‐bromonicotinic acid (abbreviated as 2‐BrNA and 6‐BrNA, C₆H₄BrNO₂) have been recorded in the region 4000–400 and 3500–50 cm⁻¹. The optimum molecular geometry, normal mode wavenumbers, infrared intensities and Raman scattering activities, corresponding vibrational assignments and intermolecular hydrogen bonds were investigated with the help of B3LYP density functional theory (DFT) method using 6‐311++G(d,p) basis set. Reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. From the calculations, the molecules are predicted to exist predominantly as the C1 conformer. Copyright © 2009 John Wiley & Sons, Ltd.     

FT‐IR,FT‐Raman,and computational calculations of 4‐chloro‐2‐(3‐chlorophenyl carbamoyl)phenyl acetate

FT‐IR and FT‐Raman spectra of 4‐chloro‐2‐(3‐chlorophenylcarbamoyl) phenyl acetate were studied. Vibrational wavenumbers and corresponding vibrational assignments were examined theoretically using the Gaussian03 set of quantum chemistry codes and the normal modes are assigned by potential energy distribution (PED) calculations. Simultaneous IR and Raman activation of the CO stretching mode shows the charge transfer interaction through a π‐conjugated path. Optimized geometrical parameters of the title compound are in agreement with the reported values. Analysis of the phenyl ring modes shows that C C stretching mode is equally active as strong bands in both IR and Raman, which can be interpreted as the evidence of intramolecular charge transfer via conjugated ring path and is responsible for hyperpolarizability enhancement leading to nonlinear optical activity. The red‐shift of the NH‐stretching wavenumber in the infrared spectrum from the computed wavenumber indicates the weakening of the NH bond resulting in proton transfer to the neighboring oxygen atom. Copyright © 2009 John Wiley & Sons, Ltd.