Density functional theory and ab initio studies of vibrational spectra of 2-bis (2-chloroethyl) aminoperhydro-1,3,2-oxazaphosphorinane-2-oxide

The Fourier transform Raman (FTR) and Fourier transform infrared (FTIR) spectra of 2-bis (2-chloroethyl) aminoperhydro-1,3,2-oxazaphosphorinane-2-oxide were recorded in the regions 4000–100 cm^? 1 and 4000–400 cm¹, respectively, in the solid phase. Molecular electronic energy, geometrical structure, harmonic vibrational spectra, infrared intensities and Raman scattering activities, highest occupied molecular orbital, lowest unoccupied molecular orbital energy, energy gaps and thermodynamical properties such as zero-point vibrational energies, rotational constants, entropies and dipole moment were computed at the Hartree–Fock/6-31G(d,p) and three parameter hybrid functional Lee–Yang–Parr/6-31G(d,p) levels of theory. The vibrational studies were interpreted in terms of potential energy distribution. The results were compared with experimental values with the help of scaling procedures. The observed wave number in FTIR and FTR spectra was analysed 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.     

Theoretical and experimental studies of vibrational spectra and thermal analysis of 2-nitroaniline and its cation

The FTIR spectrum of 2-nitroaniline was recorded in the regions 4000–400 cm⁻¹. The optimized molecular geometry, bond orders, atomic charges, harmonic vibrational wave numbers and intensities of vibrational bands of 2-nitroaniline and its cation were calculated at DFT levels invoking two different basis sets 6-31G** and 6-31+G** using Gaussian 03W program. The X-ray geometry and FTIR vibrational frequencies were compared with the results of DFT calculations. The thermal stability of 2NA is studied by the thermo gravimetric analysis (TGA). Experimental degradation process of 2-nitroaniline was interpreted with the bond order analysis. The Mulliken atomic charge analysis was also made in the present study. Based on the molecular geometry and Mulliken charge analysis, intra molecular hydrogen bonding was identified.     

Density functional theory characterisation of 4-hydroxyazobenzene

We report the structural properties, infrared (IR) and Raman spectra, dipole moment, polarisability, hardness and chemical potential of the trans and cis configurations of 4-hydroxyazobenzene calculated using the B3LYP functionals. All calculations were performed with the following basis sets: 6–31G, 6–31++G, 6–31G(d,p), 6–31++G(d,p), 6–31G(2d,2p), 6–31++G(2d,2p) and 6–311++G(2d,2p). We observed that 6–31++G(d,p) gives similar results to 6–311++G(2d,2p). Consequently, SVWN and PW91 methods were also used in association with 6–31++G(d,p) to test the influence of the different models of exchange and correlation functionals. A planar structure was obtained for all the optimised trans configuration structures. In both isomers, the presence of the hydroxyl group leads to an asymmetry in certain structural parameters. From these results, two IR or Raman active frequencies can be used to easily distinguish trans and cis configurations. The trans configuration was found to be more stable than the cis configuration by 67 ± 2 kJ mol⁻¹ at 0 K. The difference of the dipole moment between trans and cis for 4-hydroxyazobenzene was found to be lower than for trans and cis azobenzene.     

FTIR-spectral analysis of two photosynthetic H2-producing strains and their extracellular polymeric substances

The Fourier transform infrared (FTIR) spectra of the cells of two photosynthetic H₂-producing strains, Rhodoblastus acidophilus and Rhodobacter capsulatus, as well as their extracellular polymeric substances (EPS), were evaluated. The FTIR spectra of R. capsulatus and its EPS during its cultivation were also recorded. The main peaks in the spectra, including 1,080 cm⁻¹ (carbohydrates), 1,250 cm⁻¹ (nucleic acids), 2,830–2,930 cm⁻¹ (lipids), 1,660–1,535 cm⁻¹ (Amide I and II of proteins), were observed. The relative heights of these peaks in the spectra of the two strains were different, showing the difference in contents of various components in the cells or EPS. The ratios among the main components in the EPS obtained from the FTIR spectra were in good agreement with those from a conventional quantitative chemical analysis. As an easy, rapid, and direct technique, the FTIR spectroscopy could be used to characterize the components and their relative contents of EPS of photosynthetic bacteria.An erratum to this article can be found at     

ONIOM DFT/PM3 calculation on the interaction between STI-571 and abelson tyrosine kinase

The ONIOM2 (B3LYP/6–31G (d, p): PM3) and B3LYP/6–31G (d, p) methods were applied to investigate the interaction between STI-571 and abelson tyrosine kinase binding site. The complex of N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)- phenyl]-benzamide (part of STI-571) and related 16 amino acid residues were found at B3LYP/6–31G (d, p) level to have hydrogen bonds and π....π stacking interaction, their binding energy via HAF optimization was −20.4 kcal mol⁻¹. The results derived from this study agreed well with the reported observation. Figure Optimized structure of STI-571 and Thr315 in abelson tyrosine kinase based on ONIOM2 method     

Low-frequency fourier transform infrared spectroscopy of the oxygen-evolving complex in Photosystem II*

In this communication, we report our progress on the development of low-frequency Fourier transform infrared (FTIR) spectroscopic techniques to study metal-substrate and metal-ligand vibrational modes in the Photosystem II/oxygen-evolving complex (PS II/OEC). This information will provide important structural and mechanistic insight into the OEC. Strong water absorption in the low-frequency region (below 1000 cm⁻¹), a lack of suitable materials, and temperature control problems have limited previous FTIR spectroscopic studies of the OEC to higher frequencies (>1000 cm⁻¹). We have overcome these technical difficulties that have blocked access to the low-frequency region and have developed successive instruments that allow us to move deeper into the low-frequency region (down to 350 cm⁻¹), while increasing both data accumulation efficiency and S/N ratio. We have detected several low-frequency modes in the S₂/S₁spectrum that are specifically associated with these two states. Our results demonstrate the utility of FTIR techniques in accessing low-frequency modes in Photosystem II and in proteins generally. This revised version was published online in June 2006 with corrections to the Cover Date.     

Molecular structure and vibrational and chemical shift assignments of 5-(2-Hydroxyphenyl)-4-(p-tolyl)-2,4-dihydro-1,2,4-triazole-3-thione by DFT and <Emphasis Type="Italic">ab initio</Emphasis> HF calculations

The molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) ¹H and ¹³C chemical shift values and several thermodynamic parameters of 5-(2-Hydroxyphenyl)-4-(p-tolyl)-2,4-dihydro-1,2,4-triazole-3-thione in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (DFT/B3LYP) with 6–31G(d), 6–31 + G(d,p) and LANL2DZ basis sets. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the experimental bands observed. Also, calculated ¹H chemical shift values compared with the experimental ones. The data of the title compound display significant molecular structure and IR, NMR analysis provide the basis for future design of efficient materials having the of 1,2,4-triazole core.     

Coherent phenomena of charge separation in reaction centers of LL131H and LL131H/LM160H/FM197H mutants of <Emphasis Type="Italic">Rhodobacter sphaeroides</Emphasis>

Primary stage of charge separation and transfer of charges was studied in reaction centers (RCs) of point mutants LL131H and LL131H/LM160H/FM197H of the purple bacterium Rhodobacter sphaeroides by differential absorption spectroscopy with temporal resolution of 18 fsec at 90 K. Difference absorption spectra measured at 0–4 psec delays after excitation of dimer P at 870 nm with 30 fsec step were obtained in the spectral range of 935–1060 nm. It was found that a decay of P* due to charge separation is considerably slower in the mutant RCs in comparison with native RCs of Rba. sphaeroides. Coherent oscillations were found in the kinetics of stimulated emission of the P* state at 940 nm. Fourier analysis of the oscillations revealed a set of characteristic bands in the frequency range of 20–500 cm⁻¹. The most intense band has the frequency of −30 cm⁻¹ in RCs of mutant LL131H and in native RCs and the frequency of ∼100 cm⁻¹ in RCs of the triple mutant. It was found that an absorption band of bacteriochlorophyll anion B_A⁻ which is registered in the difference absorption spectra of native RCs at 1020 nm is absent in the analogous spectra of the mutants. The results are analyzed in terms of the participation of the B_A molecule in the primary electron transfer in the presence of a nuclear wave packet moving along the inharmonic surface of P* potential energy.     

Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin

Vibrational excitations of low-frequency collective modes are essential for functionally important conformational transitions in proteins. We carried out an analysis of the low-frequency modes in the G protein coupled receptors (GPCR) family of cone opsins based on both normal-mode analysis and molecular dynamics (MD) simulations. Power spectra obtained by MD can be compared directly with normal modes. In agreement with existing experimental evidence related to transmembrane proteins, cone opsins have functionally important transitions that correspond to approximately 950 modes and are found below 80 cm⁻¹. This is in contrast to bacteriorhodopsin and rhodopsin, where the important low-frequency transition modes are below 50 cm⁻¹. We find that the density of states (DOS) profile of blue opsin in a solvent (e.g. water) has increased populations in the very lowest frequency modes (<15 cm⁻¹); this is indicative of the increased thermostability of blue opsin. From our work we found that, although light absorption behaves differently in blue, green and red opsins, their low-frequency vibrational motions are similar. The similarities and differences in the domain motions of blue, red and green opsins are discussed for several representative modes. In addition, the influence of the presence of a solvent is reported and compared with vacuum spectra. We thus demonstrate that terahertz spectroscopy of low-frequency modes might be relevant for identifying those vibrational degrees of freedom that correlate to known conformational changes in opsins. An erratum to this article can be found at     

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.     

Multivariate Analysis of Phenol in Freeze-Dried and Spray-Dried Insulin Formulations by NIR and FTIR

Dehydration is a commonly used method to stabilise protein formulations. Upon dehydration, there is a significant risk the composition of the formulation will change especially if the protein formulation contains volatile compounds. Phenol is often used as excipient in insulin formulations, stabilising the insulin hexamer by changing the secondary structure. We have previously shown that it is possible to maintain this structural change after drying. The aim of this study was to evaluate the residual phenol content in spray-dried and freeze-dried insulin formulations by Fourier transform infrared (FTIR) spectroscopy and near infrared (NIR) spectroscopy using multivariate data analysis. A principal component analysis (PCA) and partial least squares (PLS) projections were used to analyse spectral data. After drying, there was a difference between the two drying methods in the phenol/insulin ratio and the water content of the dried samples. The spray-dried samples contained more water and less phenol compared with the freeze-dried samples. For the FTIR spectra, the best model used one PLS component to describe the phenol/insulin ratio in the powders, and was based on the second derivative pre-treated spectra in the 850–650 cm⁻¹ region. The best PLS model based on the NIR spectra utilised three PLS components to describe the phenol/insulin ratio and was based on the standard normal variate transformed spectra in the 6,200–5,800 cm⁻¹ region. The root mean square error of cross validation was 0.69% and 0.60% (w/w) for the models based on the FTIR and NIR spectra, respectively. In general, both methods were suitable for phenol quantification in dried phenol/insulin samples.     

Fourier transform infrared microspectroscopy as a diagnostic tool for distinguishing between normal and malignant human gastric tissue

Fourier transform infrared (FTIR) microspectroscopy can be considered to be a fast and non-invasive tool for distinguishing between normal and cancerous cells and tissues without the need for laborious and invasive sampling procedures. Gastric samples from four patients (age, 65±2 years) were analysed. Samples were obtained from the organs removed during gastrectomy and then classified as normal or cancerous. Classification was based on histopathological examinations at our institution. Formalin-fixed sections of gastric tissue were analysed by FTIR- microspectroscopy. To characterize differences between sections of normal and cancerous tissue, specific regions of the spectra were analysed to study variations in the levels of metabolites. To distinguish between two conditions (normal and cancerous), changes in the relative intensity of bands in the range 600–4000 cm⁻¹ were analysed. A FTIR spectral map of the bands in the region 2800–3100 cm^–1 and 900–1800 cm^–1 were created to analyse pathological changes in tissues. The limited data available showed that normal gastric tissue had stronger absorption than cancerous tissue over a wide region in the four patients. There was a significant decrease in total biomolecular components for cancerous tissue compared with normal tissue.     

Benthos structure on tropical tidal flats of Australia

General features of benthos communities of tropical tidal flats are defined from northeast Australia, based on surveys from 1988 to 1991 in Hinchinbrook Channel and in the Haughton River estuary. A zonation of benthic communities is described. Total abundances for macrofauna averaged 31 individuals 200 cm⁻², mesofauna (defined as infauna smaller than 0.5 mm and retained on a 0.25 mm sieve) averaged 16 individuals 10 cm⁻² and meiofauna averaged 231 individuals 5 cm⁻². The two study sites were similar in their abundance structures, but species due to a higher diversity of polychaeta in the Channel (120 species, H′=3.80 vs. 29 species and H′=1.78 in the Haughton estuary). Species densities were comparable at both sites and rather low (6 species 177 cm⁻², 2–7 species 10 cm⁻² and 5 meiobenthic Plathelminth species 5 cm⁻²). Over 50% of the species encountered were represented by less than three individuals. Deposit feeders, dominated the assemblages both in terms of individuals as well as species numbers. Tropical tidal flats are compared with their temperate counterparts and approaches for future research in tropical benthos communities are recommended.     

FTIR and Raman Spectra Compared with Ab Initio Calculated Frequency Modes for 5-Aminouracil

Infrared (IR) and Raman spectra of 5-aminouracil were recorded in the region 200–4,000 cm^− 1. Assuming under the C_s point group that the distribution of the normal mode of vibrations between the two species are planar (a′) and non-planar (a″), given by 25a′ + 11a″ of which 30 modes (21a′ + 9a″) correspond to the uracil moiety and six modes (4a′ + 2a″) correspond to the NH₂ group, with a comparison of theoretically ab initio calculated frequencies, the results are in reasonably good agreement with the experimental IR and Raman spectra. Consistent assignments have been made for the internal modes of the NH₂ group, especially for the anti-symmetric NH₂ stretching and bending modes. The non-equivalence of the two NH bonds of the NH₂ group suggests a difference in the strength of the two hydrogen bonds on the pyrimidine ring. Symmetry and anti-symmetry NH stretching modes of the NH₂ group show the invalidity of the empirical relationship. These two NH₂ stretching frequencies are distinctly separated from the CH/NH ring stretching frequencies. A strong and sharp IR band that acts at 3,380 cm^− 1 could be identified as the anti-symmetric NH₂ mode whereas the band at 3,290 cm^− 1 smaller density could be identified as the symmetric NH₂ stretching mode.     

FTIR spectroscopy as a potential tool to analyse structural modifications during morphogenesis of Candida albicans

Candida albicans is a polymorphic organism that grows under certain conditions as blastospores, hyphae or pseudohyphae. The potentials of FTIR spectroscopy for assessing structural differences in C. albicans blastospores and hyphae were investigated. The main observed differences were localised in the polysaccharide (950–1,185 cm⁻¹), protein (1,480–1,720 cm⁻¹), and the fatty acids (2,840–3,000 cm⁻¹) regions. Quantitative evaluation of differences between hyphae and blastospores by curve-fitting of these regions indicate that these modifications could be due to both changes in structure and content of components of the cell wall such as β-glucans, mannoproteins, and lipids. Furthermore, glycogen consumption could be involved during hyphae elongation. Thus, FTIR spectroscopy can be an interesting tool to investigate differences in structure and in content between blastospores and hyphae. We also demonstrate through this study that differentiation of C. albicans clinical strains using hyphae is feasible, as this has been previously shown with blastospores. This preliminary work on identification of C. albicans using hyphae is a prelude to a larger clinical study for early typing within 7 h from a pure culture.     

Theoretical 49Ti NMR chemical shifts

⁴⁹Ti chemical shifts for a total of 20 titanium complexes are reported, and several levels of theory are evaluated in order to identify a reliable approach for the calculation of titanium NMR data. The popular B3LYP/6–31G(d)//B3LYP/6–31G(d) proves to give very good agreement with experimental data over a range from 1,400 to −1,300 ppm. The MP2/6–31G(d)//MP2/6–31G(d) level computes even smaller average deviations but fails for TiI₄. This behavior together with its huge demand for computational resources requires careful handling of this theoretical level. In addition, NMR data for five titanium fulvene (or related) complexes are given. Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday     

Regulation of Caenorhabditis elegans and Pseudomonas aeruginosa machinery during interactions

The amenability of Caenorhabditis elegans against pathogen provides a valuable tool for studying host–pathogen interactions. Physiological experiments revealed that the P. aeruginosa was able to kill C. elegans efficiently. The effects of P. aeruginosa PA14, PAO1 and their isolated lipopolysaccharide (LPS) on the host system were analyzed. The LPS at higher concentrations (≥2 mg/ml) was toxic to the host animals. Kinetic studies using qPCR revealed the regulation of host-specific candidate antimicrobial genes during pathogen-mediated infections. In addition, the pathogen-specific virulent gene, exoT expression, was anlyzed and found to be varied during the interactions with the host system. Ability of the pathogens to modify their internal machinery in the presence of the host was analyzed by XRD, FTIR and PCA. LPS isolated from pathogens upon exposure to C. elegans showed modifications at their functional regions. LPS from PAO1 showed difference in d-spacing angle (Å) and °2Th position. FTIR spectra revealed alterations in polysaccharide (1,200–900 cm⁻¹) and fatty acid (3,000–2,800 cm⁻¹) regions of LPS from P. aeruginosa PAO1 exposed to the host system. These data provide additional insights on how the pathogens subvert its own and host machinery during interactions.     

FTIR spectroscopy of the reaction center of Chloroflexus aurantiacus: Photooxidation of the primary electron donor

Photochemical oxidation of the primary electron donor P in reaction centers (RCs) of the filamentous anoxygenic phototrophic bacterium Chloroflexus (C.) aurantiacus was examined by light-induced Fourier transform infrared (FTIR) difference spectroscopy at 95 K in the spectral range of 4000–1200 cm⁻¹. The light-induced P⁺Q_A⁻/PQ_A IR spectrum of C. aurantiacus RCs is compared to the well-characterized FTIR difference spectrum of P photooxidation in the purple bacterium Rhodobacter (R.) sphaeroides R-26 RCs. The presence in the P⁺Q_A⁻/PQ_A FTIR spectrum of C. aurantiacus RCs of specific low-energy electronic transitions at ∼2650 and ∼2200 cm⁻¹, as well as of associated vibrational (phase-phonon) bands at 1567, 1481, and 1294–1285 cm⁻¹, indicates that the radical cation P⁺ in these RCs has dimeric structure, with the positive charge distributed between the two coupled bacteriochlorophyll a molecules. The intensity of the P⁺ absorbance band at ∼1250 nm (upon chemical oxidation of P at room temperature) in C. aurantiacus RCs is approximately 1.5 times lower than that in R. sphaeroides R-26 RCs. This fact, together with the decreased intensity of the absorbance band at ∼2650 cm⁻¹, is interpreted in terms of the weaker coupling of bacteriochlorophylls in the P⁺ dimer in C. aurantiacus compared to R. sphaeroides R-26. In accordance with the previous (pre)resonance Raman data, FTIR measurements in the carbonyl stretching region show that in C. aurantiacus RCs (i) the 13¹-keto C=O groups of P_A and P_B molecules constituting the P dimer are not involved in hydrogen bonding in either neutral or photooxidized state of P and (ii) the 3¹-acetyl C=O group of P_B forms a hydrogen bond (probably with tyrosine M187) absorbing at 1635 cm⁻¹. Differential signals at 1757(+)/1749(−) and 1741(+)/1733(−) cm⁻¹ in the FTIR spectrum of C. aurantiacus RCs are attributed to the 13³-ester C=O groups of P in different environments.     

Pelagic occurrence of the sympagic amphipod Gammarus wilkitzkii in ice-free waters of the Greenland Sea – dead end or part of life-cycle?

The sympagic (=ice-associated) amphipod Gammarus wilkitzkii usually lives attached to the underside of Arctic sea ice. During an expedition to the Greenland Sea in May/June 1997, high numbers of this species were found in pelagic Rectangular Midwater Trawl catches (0–500 m water depth) in an ice-free area, 35–42 km away from the ice edge. The amphipods seemed to have maintained position in the water column for at least 4 days. Mean biomass data (length: 2.9 cm, organic content: 73% dry mass), gut fullness (>50% in 85% of specimens) and sex ratio (females:males = 1:1.5) of these amphipods were very similar to values for under-ice populations. Due to their relatively high body density (mean: 1.134 g cm⁻³), the energy demand for swimming was assumed to be high. Measurements of oxygen consumption of swimming and resting amphipods (8.8 and 4.0 J g wet mass⁻¹ day⁻¹, respectively) suggested that, from an energetic point of view, G. wilkitzkii would maintain position in an ice-free water column for the time period. Accepted: 11 January 1999     

Bacterioplankton of the Gdansk Basin,Baltic Sea

The numbers, biomass, and production of bacterioplankton were determined in the Russian Sector of the Gdansk Basin (Baltic Sea) in 2007–2009. Significant spatial and temporal variations were determined. During the year, bacterial activity increased with increasing water temperature and higher availability of organic substrates. The lowest bacterial production (0.01–31.63 mg C m⁻³ day⁻¹) was observed in late winter and late autumn, while the highest (0.17–341.70 mg C m⁻³ day⁻¹) occurred in spring and summer. Since bacterial numbers and biomass were found to depend on the weather conditions and the terrigenous inflow, significant variations were observed from year to year. The highest and lowest numbers and biomass of bacterioplankton determined in summer were 0.09–1.10 × 10⁶ cells mL⁻¹ and 2–22 mg C m⁻³ for July 2007 and 1.96–11.23 × 10⁶ cells mL⁻¹ and 23–123 mg C m^–3 for July 2009. The values of these parameters were the highest along the coast and decreased towards the open sea.