DFT study of structure and vibrational spectra of ceramide 3: comparison to experimental data

The Fourier transform Raman and infrared (IR) spectra of the Ceramide 3 (CER3) have been recorded in the regions 200–3500 cm^? 1 and 680–4000 cm^? 1, respectively. We have calculated the equilibrium geometry, harmonic vibrational wavenumbers, electrostatic potential surfaces, absolute Raman scattering activities and IR absorption intensities by the density functional theory with B3LYP functionals having extended basis set 6-311G. This work is undertaken to study the vibrational spectra of CER3 completely and to identify the various normal modes with better wavenumber accuracy. Good consistency is found between the calculated results and experimental data for the IR and Raman spectra.     

Vibrational spectral assignments of paraldehyde by ab initio and density functional methods

The FTIR and Laser-Raman spectra of paraldehyde have been recorded in the regions 4000–400 cm⁻¹ and 3500–250 cm⁻¹ respectively. Molecular electronic energy, geometrical structure, harmonic vibrational spectra, infrared intensities and Raman scattering activities have been computed at the HF/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory. The results were compared with experimental values with the help of scaling procedures. The observed wave numbers in FTIR and Laser-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wave numbers in the expected range and are in good agreement with computed values.     

Structure and vibrational frequencies of 6-chloro-8-thia-1,4-epoxybicyclo[4.3.0]non-2-ene: density functional theory study

The Fourier transform infrared (FT-IR) spectrum of 6-chloro-8-thia-1,4-epoxybicyclo[4.3.0]non-2-ene has been recorded in the region 4000–525 cm^? 1. The optimised geometry, frequency and intensity of the vibrational bands of the title compound have been calculated using the ab initio Hartree–Fock and the density functional theory method with 6-31G(d,p) and 6-311G(d,p) basis set levels. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR spectrum. The observed and the calculated frequencies are found to be in good agreement. The theoretical vibrational spectrum of the title compound were interpreted by means of potential energy distributions using VEDA 4 program.     

FTIR,FT-Raman spectra and quantum chemical studies of nebivolol

Fourier transform infrared and Raman spectra of nebivolol have been recorded. The structure, conformational stability, geometry optimisation, and vibrational wave numbers have been investigated. Satisfactory vibrational assignments were made for the stable conformer of the molecule using Restricted Hartree–Fock (RHF) and density functional theory (DFT) calculation (B3LYP) with the 6-31G(d,p) basis set. Comparison of the observed fundamental vibrational wave numbers of the molecule and calculated results by RHF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. The RHF and DFT-based NMR calculation procedure was also done. It was used to assign the ¹³C NMR chemical shift of nebivolol.     

Spectroscopic investigation on glutamic acid by Coulomb-attenuating and double hybrid density functional theory methods

This study deals with the identification of glutamic acid by means of quantum chemical approach. FT-IR, FT-Raman and UV–vis spectra were recorded in the region 4000–400, 4000–50 cm^? 1 and 200–600 nm, respectively. CAM-B3LYP/6-31G(d,p) and B2PLYP/6-31G(d,p) calculations were performed to obtain the optimised molecular structures, vibrational frequencies and corresponding vibrational assignment, thermodynamic properties and natural bonding orbital (NBO) analysis. The results show that the obtained optimised geometric parameters (bond lengths, bond angles and bond dihedrals) and vibrational frequencies were found to be in good agreement with the experimental results. The calculations of the electronic spectra were compared with the experimental ones. Furthermore, highest occupied molecular orbital and lowest unoccupied molecular orbital analyses and UV–vis spectral analysis were also performed to determine the energy band gaps and transition states. NBO analysis, calculated using density functional theory methods (CAM-B3LYP/6-31G(d,p) and B2PLYP/6-31G(d,p)), was induced to find inter-molecular atoms. ¹³C and ¹H NMR isotropic chemical shifts were calculated and the assignments made were compared with the ChemDraw Ultra values.     

Quantum chemical insight on vibration spectra of silica systems

A set of silicate ions and corresponding lithium salts have been quantum chemically (QC) simulated in a “free molecule” approach. The infrared (IR), inelastic neutron scattering (INS), and Raman spectra have been simulated and fitted to the experimentally registered ones. The complete assignment of the vibrational bands along with the intensities and potential energy distribution has been performed. The applicability of the traditionally used quasimolecule Si–O–Si model to the interpretation of bands near 440–480 cm^? 1 and so-called “Boson” peak near 50 cm^? 1 has been critically discussed.     

Molecular structure and vibrational spectra of 4-nitrobenzylchloride by ab initio Hartree–Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra 4-nitrobenzylchloride of (NBC) were recorded in the solid phase. The Fourier transform gas phase infrared spectrum of NBC was also recorded. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF/DFT (B3LYP and BLYP) and SVWN methods with the 6-31G(d,p) basis set. The scaled theoretical wave numbers by B3LYP showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of NBC is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.     

Characterisation of DNA methylation status using spectroscopy (mid‐IR versus Raman) with multivariate analysis

Methylation status plays important roles in the regulation of gene expression and significantly influences the dynamics, bending and flexibility of DNA. The aim of this study was to determine whether attenuated total reflection Fourier‐transform infrared (ATR‐FTIR) or Raman spectroscopy with subsequent multivariate analysis could determine methylation patterning in oligonucleotides variously containing 5‐methylcytosine, cytosine and guanine bases. Applied to Low‐E reflective glass slides, 10 independent spectral acquisitions were acquired per oligonucleotide sample. Resultant spectra were baseline‐corrected and vector normalised over the 1750 cm^–1–760 cm^–1 (for ATR‐FTIR spectroscopy) or the 1750 cm^–1–600 cm^–1 (for Raman spectroscopy) regions. Data were then analysed using principal component analysis (PCA) coupled with linear discriminant analysis (LDA). Exploiting this approach, biomolecular signatures enabling sensitive and specific discrimination of methylation patterning were derived. For DNA sequence and methylation analysis, this approach has the potential to be an important tool, especially when material is scarce. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Characteristic Studies on the Pyrolysis Products from Hydrolyzed Canadian Lignocellulosic Feedstocks

Lignocellulosic feedstocks are utilized for the production of fuel ethanol and butanol through dilute acid/enzymatic hydrolysis and fermentation. Hydrolysis residue, a major by-product of biomass hydrolysis, is rich in recalcitrant carbon as majority of cellulosic and hemicellulosic components are released during pretreatment. With the intention of their effective utilization, hydrolysis residues from forestry (pinewood), energy crop system (timothy grass), and agriculture (wheat straw) were pyrolysed in a fixed-bed reactor at 600 °C with slow heating rate of 5 °C/min for 4 h. In order to understand the product (biochar, bio-oil, and gases) properties and advocate their energy and environmental values, chemical characterizations such as carbon–hydrogen–nitrogen–sulfur analysis, inductively coupled plasma-mass spectrometry, pH, electrical conductivity, scanning electron microscopy, porosity analysis, thermogravimetric analysis, X-ray diffraction, Fourier transform infrared (FTIR) and Raman spectroscopy, nuclear magnetic resonance (NMR) and gas chromatography–mass spectrometry (GC-MS) were employed. The yield of biochar, bio-oil and gases was 38.9–41.7, 18.6–22.3, and 24.9–28.8 wt%, respectively. The high pH and electrical conductivity of biochars with substantial amounts of Na, Mg, K, and Ca indicated their alkaline and saline nature, which would necessitate proper agronomical soil applications. Variable intensities of C–C, C–H, C–O, O–H, and C–N functional groups were detected in the FTIR spectra of residues, biochars, and bio-oils. Raman spectroscopy showed the development of graphite (1,580–1,610 cm^?1) and defect (1,325–1,380 cm^?1) carbon structures in biochars. ¹H NMR of bio-oils indicated aromatics, olefinics, and aliphatics, whereas ¹³C NMR indicated carbonyls, aromatics, carbohydrates, alkyls, methoxy, and hydroxy carbon. GC studies of pyrolysis gases identified chiefly H₂ and CO with traces of CH₄, CO₂, and C₂+ components.     

Normal coordinate analysis and vibrational spectra of 9-β-D-arabinofuranosyladenine hydrochloride (ara-A.HCl)

The vibrational spectra of a synthetic purine nucleoside with known antiviral activity, 9--D-arabino-furanosyladenine hydrochloride (ara-A.HCl) are reported. The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra were recorded in the 4000-30 cm^–1 spectral region. The harmonic frequencies and potential energy distributions (PED) of the vibrational modes of ara-A.HCI were calculated by two different methods: a classical molecular mechanics method and a semiempirical molecular orbital (MO) method, PM3. The results of both computational methods, based on the Wilson GF method, are compared with observed spectra, and an assignment of the vibrational modes of ara-A.HCl is proposed on the basis of the potential energy distributions (PED). It is found that the wavenumbers can be calculated with remarkable accuracy (1% deviation in most cases), with the classical mechanics method, by transferring a sufficiently large set of available harmonic force constants, thus permitting a reliable assignment. The semiempirical MO method, PM3, is found to be useful for the assignment of experimental frequencies although it is less accurate (10% deviation). IR intensities calculated by this method did not coincide with the experimental values. Certain out-of-plane vibrations in the base, not reported in previous studies, have been observed. The performance of both methods was related to the crystallographic and ab initio data available. Previous normal coordinate calculations for the adenine base and the nucleoside 5-dGMP are compared with our results and discussed, in relation to the crystal structure of Ara-A.HCl. Correspondence to: A. Hernanz     

Vibrational spectroscopy of seaweed galactans

Information from classical infrared spectroscopy studies has been of significance for characterizing seaweed galactans. The development of Fourier transform infrared spectroscopy and of Fourier transform laser Raman spectroscopy has produced great advances in the application of vibrational spectroscopy to the structural study of polysaccharides. Computational facilities in the spectrometers allow the arithmetic manipulations of the spectra. The second-derivative mode in the FT IR spectrocopy provided more information by increasing the number and resolution of the bands in the spectra as compared to the parent ones. A review of literature data on vibrational spectroscopy of sulfated polysaccharides and new results are presented. Agar-type polymers showed two diagnostic bands in the second-derivative mode in the region 800–700 cm^–1. Carrageenans exhibited a number of bands in the region 1600–1000 cm^–1. Fourier transform laser Raman spectroscopy in the solid state gave well-defined characteristic spectra of agar and carrageenans. Both techniques can be applied to small samples in the solid state and allow differentiation in a few minutes between agar and carrageenan-type seaweed galactans. The second-derivative mode of the FT IR spectra can be applied to distinguish agar-producing from carrageenan-producing seaweeds. The spectra on KBr pellets of dried, ground agarophyte and carrageenophyte seaweed samples showed the same bands as the corresponding polysaccharides.     

Synthesis of cubic ZnS microspheres exhibiting broad visible emission for bioimaging applications

Biocompatible ZnS microspheres with an average diameter of 3.85 µm were grown by solvo‐hydrothermal (S‐H) method using water–acetonitrile–ethylenediamine (EDA) solution combination. ZnS microspheres were characterized by X‐ray diffraction (XRD), scanning electron microscopy (SEM), high‐resolution transmission electron microscopy (HRTEM), Fourier transform (FT)‐Raman spectroscopy and Fourier transform infrared spectroscopy (FTIR) techniques. The broad photoluminescence (PL) emissions from 380–580 nm that were seen from the ZnS microspheres attributed to the increase in carrier concentration, as understood from the observed intense Raman band at 257 cm^–1. Cytotoxicity and haemocompatibility investigations of these ZnS microspheres revealed its biocompatibility. ZnS microspheres, along with biological cell lines, were giving visible light emission and could be used for bioimaging applications. Copyright © 2015 John Wiley & Sons, Ltd.     

Molecular structure and spectroscopic (FT-IR,FT-Raman, 13C, 1H NMR and UV) studies of 3,4-dihydroxy-l-phenylalanine using density functional theory

Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 3,4-dihydroxy-l-phenylalanine (3,4-DPA) in solid phase were recorded and analysed in this research. Along with this, the IR spectra in CHCl₃ and the use of acetone as solvents of 3,4-DPA were also recorded. The equilibrium geometry, bonding features and harmonic vibrational frequencies were investigated with the help of density functional theory (DFT) method. The ¹H and ¹³C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge including atomic orbital method and compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation was analysed using natural bond orbital analysis. The results show that charge in electron density (E _D) in the σ* and π* antibonding orbitals and second-order delocalisation energies E(2) confirms the occurrence of intramolecular charge transfer within the molecule. UV–vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were analysed using the time-dependent (TD)-DFT approach. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound, which showed good agreement with the observed spectra.     

Direct discrimination of different plant populations and study on temperature effects by Fourier transform infrared spectroscopy

Fourier transform infrared spectroscopy was used to characterise highland and lowland populations of Polygonum minus Huds. grown in different controlled environments. A thermal perturbation technique of two-dimensional correlation infrared spectroscopy (2D-IR) correlation spectra was applied to establish differences between the populations. The absorption peaks at 3,480 cm^?1 (hydroxyl group), 2,927 cm^?1 (methyl group), 1,623 cm^?1 (carbonyl group), and 1,068 cm^?1 (C–O group) were particularly powerful in separating the populations. These peaks, which indicate the presence of carbohydrate, terpenes, amide and flavonoids were more intense for the highland populations than lowland populations, and increased in environments with a higher temperature. Wavenumbers (1,634, 669 cm^?1) and (1,634, 1,555 cm^?1) in the 2D-IR correlation spectra provided fingerprint signals to differentiate plants grown at different temperatures. This study demonstrates that IR fingerprinting, which combines mid-IR spectra and 2D-IR correlation spectra, can directly discriminate different populations of P. minus and the effects of temperature.     

Molecular structure,spectroscopic (FT-IR,FT-Raman,UV–vis), NBO,thermochemistry analysis of bis(thiourea)zinc(II) chloride crystals

The experimental and theoretical studies on the molecular structure and vibrational spectra of bis(thiourea)zinc(II) chloride (BTZC) crystals were investigated. The Fourier transform infrared, Fourier transform Raman and UV–vis spectra of BTZC were recorded. The molecular geometry and vibrational frequencies of BTZC in the ground state were calculated by using B3LYP with LANL2DZ as basis set. Comparison of the observed structural parameters of BTZC with single-crystal X-ray studies yields a good agreement. Vibrational analysis of the simultaneous IR and Raman activation of the Zn–Cl stretching mode in the molecule provides the evidence for the charge transfer interaction taking place within the molecule. The energy and oscillator strength are calculated by time-dependent density functional theory. The simulated spectra satisfactorily coincide with the experimental spectra.     

Molecular Structure Evaluation of Wheat Gluten during Frozen Storage

The effects of frozen storage (0–120 day) on the secondary structure and molecular chain conformation of hydrated gluten were investigated using Fourier transform infrared spectroscopy (FTIR) and atomic force microscopy (AFM). After frozen storage, no changes were observed in the secondary structure of the 60% hydrated gluten; spectra were consistent with a tight ordered structure with many interchain hydrogen bond interactions. For the dehydrated gluten, more complex changes took place: during frozen storage for up to 60 days, there were distinctive changes in the low-frequency region of the amide I band (1618–1633 cm^?1) which were attributed to changes in the β-sheet structure. However, with the increase of frozen storage from 60 to 120 days, a band near 1614 cm^?1 replaced that at 1659 cm^?1 illustrate that the formation of protein aggregates during the long-time frozen storage, which along with the establishment of new intermolecular non-covalent bonds within the protein molecule or between two neighboring molecules. AFM images showed that the gluten chain formed a fibril-like branched network, and this network was weakened with increasing frozen storage time.     

Electronic structure simulations of 2,6-dimethyl-2,5-heptadien-4-one by FTIR,FT-Raman,NMR, UV–vis,NBO and density functional theory

Density functional theory (DFT) (B3LYP and B3PW91) calculations have been carried out for 2,6-dimethyl-2,5-heptadien-4-one (DMHD4O) using 6–311++ G** basis set. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out from the FTIR and FT-Raman spectral data. The theoretical electronic absorption has been calculated by using time-dependent DFT (TD-DFT) methods and compared with the experimental spectra. The theoretically computed Frontier energy gaps and TD-DFT calculations are in good agreement with the experimental UV–vis spectral absorption. The chemical hardness measured from the Frontier molecular orbital energies of DMHD4O is 0.0693 eV. Electronic stability of the compound arising from hyperconjugative interactions and charge delocalisation were also investigated based on the natural bond orbital (NBO) analysis. Effective stabilisation energy E ⁽²⁾ associated with the interactions of the π and the lone pair of electrons was determined by the NBO analysis. ¹³C and ¹H NMR chemical shifts of the compound have been calculated by means of Gauge-Invariant Atomic Orbital using B3LYP/6–311++ G** method. The partial ionic character of the carbonyl group due to resonance render a partially positive charge to the carbonyl carbon, and thus C4 chemical shift lie in the very downfield 191.6 ppm. Comparison between the experimental and the theoretical results indicates that B3LYP method is able to provide satisfactory results for predicting vibrational, electronic and NMR properties.     

FT-IR,FT-Raman spectra and DFT vibrational analysis of 2-aminobiphenyl

In this work, the Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 2-aminobiphenyl (2ABP) were recorded in the solid phase. The optimised geometry, frequency and intensity of the vibrational bands of 2ABP were obtained by the density functional theory (BLYP and B3LYP) methods with complete relaxation in the potential energy surface using 6-31G(d) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectrograms.     

Barrier potentials,molecular structure,force filed calculations and quantum chemical studies of some bipyridine di-carboxylic acids using the experimental and theoretical using (DFT,IVP) approach

ABSTRACT

FT-IR and FT-Raman spectra of 2,2′-bipyridine-3,3′-dicarboxylic acid (B3DA), 2,2′-bipyridine-4,4′-dicarboxylic acid (B4DA) and 2,2′-bipyridine-5,5′-dicarboxylic acid (B5DA) were recorded and analysed. The quantum chemical calculations of the title compounds begin with barrier potentials at different rotation angles around the C–C′ and C–Cα bonds in order to arrive conformation of lowest energy using DFT employing B3LYP functional with 6-311++G(d,p) basis set. This confirmation was further optimised to get the global minimum geometry. The vibrational frequencies along with IR, Raman intensities were computed, the rms error between observed and calculated frequencies were 11.2 cm^?1, 10.2 cm^?1 and 12.2 cm^?1 for B3DA, B4DA, and B5DA. An 87-element modified valence force field is derived by solving the inverse vibrational problem using Wilson’s GF matrix method. This force field is refined using 163 observed fundamentals employing in overlay least-squares technique. The average error between computed and experimental frequencies was found as 12.85 cm^?1 using potential energy distribution (PED) and eigenvectors. By using the gauge-independent atomic orbital (GIAO) method calculate the ¹H and ¹³C NMR chemical shifts of the molecules and compared with experimental results. The first-order hyperpolarisability, HOMO and LUMO energies, molecular electrostatic potential (MESP) and natural orbital analysis (NBO) of titled compounds were evaluated using DFT.     

The manifestation of hydrogen bonding in the IR spectra of dl-threitol and erythritol (300–20 K)

The infrared (4000–400 cm⁻¹) and, in part, Raman spectra were recorded for the two isomeric polycrystalline sugar alcohols, dl-threitol and erythritol. Samples were pure substances and isotopically diluted OH/OD compounds. IR spectra were recorded in the 300–20 K range. Assignment of hydrogen bond structure sensitive out-of-plane bending vibrational modes for OH/OD-groups of different H-bond systems is based on isotope exchange and temperature variations. At least seven bands for threitol and two for erythritol correspond to differently H-bonded OH/OD-groups. Relative strengths and quantity of different H-bonds were evaluated. Unlike erythritol, threitol contains over 5% of weak H-bonds. The formation from the melt of a crystalline racemate as a molecular compound of d- and l-forms is suggested. Comparisons with previous neutron scattering results are discussed. In solution, all four OH-groups of both tetritols form H-bonds of equal strength in accord with the basicity of the solvent.