Study on the structure and vibrational spectra of efavirenz conformers using DFT: Comparison to experimental data

Efavirenz, (S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3 ,1-benzoxazin-2-one, is an anti HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. A systematic quantum chemical study of the possible conformations, their relative stabilities and vibrational spectra of efavirenz has been reported. Structural and spectral characteristics of efavirenz have been studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for potential energy curve, optimized geometries and vibrational spectra have been carried out using 6-311++G(d,p) basis sets and B3LYP functionals. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of efavirenz. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The infrared and the Raman spectra of the molecule based on OFT calculations show reasonable agreement with the experimental results. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. (C) 2011 Elsevier B.V. All rights reserved.

Selective double quantum resolved correlation experiment for the complete separation of entire proton NMR spectra of enantiomers

The present study reports a two dimensional NMR experiment which separates single quantum spectra of enantiomers from that of a racemic mixture. This is a blend of selective double quantum refocusing, for resolving couplings and chemical shift interactions along two dimensions followed by correlation of the selectively excited protons to the entire coupled spin network. The concept is solely based on the presence of distinct intra methyl dipolar couplings of different enantiomers when dissolved in chiral orienting media. The analysis of single enantiomer spectrum obtained from respective F-2 cross sections yield all the spectral information. (C) 2011 Elsevier Inc. All rights reserved.

Fermi-edge singularity in photoluminescence spectra of modulation-doped AlGaAs/InGaAs/GaAs quantum wells

The photoluminescence study of Fermi-edge singularity (FES) in modulation-doped pseudomorphic AlxGa1-xAs/InyGa1-yAs/GaAs quantum well (QW) heterostructures is presented. In the above QW structures the optical transitions between n = 1 and n = 2 electronic subband to the n = 1 heavy hole subband (E-11 and E-21 transitions, respectively) are observed with FES appearing as a lower energy shoulder to the E-21 transition. The observed FES is attributed to the Fermi wave vector in the first electronic subband under the conditions of population of the second electronic subband. The FES appears at about 10 meV below E-21 transition around 4.2 K. Initially it gets stronger with increasing temperature and becomes a distinct peak at about 20 K. Further increase in temperature quenches FES and reaches the base line at around 40 K.

Study of molecular structure and vibrational spectra of poly (beta,-1-malic acid) PMLA] using DFT approach

Poly (beta-L-malic acid) (PMLA) is a biodegradable polymer and it has various important applications in the biomedical field. In the present work the structural and spectral characteristics of PMLA have been studied by methods of infrared. Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) using oligomeric approach employing B3LYP with complete relaxation in the potential energy surface using 6-311++G (d, p) basis set. Based on results, we have discussed the correlation between the vibrational modes and the structure of the PMLA. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The calculated infrared and the Raman spectra of the polymer based on DFT calculations show reasonable agreement with the experimental results. (c) 2012 Elsevier Ltd. All rights reserved.

Infrared Spectra of Dimethylphenanthrenes in the Gas phase

Infrared spectra of atmospherically and astronomically important dimethylphenanthrenes (DMPs), namely 1,9-DMP, 2,4-DMP, and 3,9-DMP, were recorded in the gas phase from 400 to 4000 cm(-1) with a resolution of 0.5 cm(-1) at 110 degrees C using a 7.2 m gas cell. DFT calculations at the B3LYP/6-311G** level were carried out to get the harmonic and anharmonic frequencies and their corresponding intensities for the assignment of the observed bands. However, spectral assignments could not be made unambiguously using anharmonic or selectively scaled harmonic frequencies. Therefore, the scaled quantum mechanical (SQM) force field analysis method was adopted to achieve more accurate assignments. In this method force fields instead of frequencies were scaled. The Cartesian force field matrix obtained from the Gaussian calculations was converted to a nonredundant local coordinate force field matrix and then the force fields were scaled to match experimental frequencies in a consistent manner using a modified version of the UMAT program of the QCPE package. Potential energy distributions (PEDs) of the normal modes in terms of nonredundant local coordinates obtained from these calculations helped us derive the nature of the vibration at each frequency. The intensity of observed bands in the experimental spectra was calculated using estimated vapor pressures of the DMPs. An error analysis of the mean deviation between experimental and calculated intensities reveal that the observed methyl C-H stretching intensity deviates more compared to the aromatic C-H and non C-H stretching bands.

The 27-plet contributions to the CP-conserving K -> pi l(+)l(-) decays

We revisit the rare kaon decays K -> pi l(+)l(-) which are of special interest due to the recent measurements of the charged kaon decay spectra. We compute the contribution of the 27-plet to the decay amplitudes in one loop SU(3) chiral perturbation theory. We estimate the resulting impact to be similar to 10% to the branching ratios of the charged kaon decays, and also noticeably influence the shape of the spectra. With current values of the constants G(8) associated with the octet and G(27) associated with the 27-plet, the contribution of the latter pushes the spectrum in the correct direction, towards the charged lepton spectra. We also discuss the impact for neutral decay rates and spectra.

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.

Novel ATPase activity of the polyprotein intermediate, Viral Protein genome-linked-Nuclear Inclusion-a protease, of Pepper vein banding potyvirus

Potyviruses temporally regulate their protein function by polyprotein processing. Previous studies have shown that VPg (Viral Protein genome-linked) of Pepper vein banding virus interacts with the NIa-Pro (Nuclear Inclusion-a protease) domain, and modulates the kinetics of the protease. In the present study, we report for the first time that VPg harbors the Walker motifs A and B, and the presence of NIa-Pro, especially in cis (cleavage site (E191A) VPg-Pro mutant), is essential for manifestation of the ATPase activity. Mutation of Lys47 (Walker motif A) and Asp88:Glu89 (Walker motif B) to alanine in E191A VPg-Pro lead to reduced ATPase activity, confirming that this activity was inherent to VPg. We propose that potyviral VPg, established as an intrinsically disordered domain, undergoes plausible structural alterations upon interaction with globular NIa-Pro which induces the ATPase activity. (C) 2012 Elsevier Inc. All rights reserved.

SuSeFLAV: A program for calculating supersymmetric spectra and lepton flavour violation

The program SuSeFLAV is introduced for computing supersymmetric mass spectra with flavour violation in various supersymmetric breaking scenarios with/without see-saw mechanism. A short user guide summarizing the compilation, executables and the input files is provided.

Nuclear targeting terpyridine iron(II) complexes for cellular imaging and remarkable photocytotoxicity

Iron(II) complexes Fe(L)(2)](2+) as perchlorate (1-3) and chloride (1a-3a) salts, where L is 4'-phenyl-2,2':6',2 `'-terpyridine (phtpy in 1, 1a), 4'-(9-anthracenyl)-2,2':6',2 `'-terpyridine (antpy in 2, 2a) and 4'-(1-pyrenyl)-2,2':6',2 `'-terpyridine (pytpy in 3, 3a), were prepared and their photocytotoxicity studied. The diamagnetic complexes 1-3 having an FeN6 core showed an Fe(III)-Fe(II) redox couple near 1.0 V vs. saturated calomel electrode in MeCN-0.1 M tetrabutylammonium perchlorate. Complexes 2 and 3, in addition, displayed a quasi-reversible ligand-based redox process near 0.0 V. The redox and spectral properties are rationalized from the theoretical studies. The complexes bind to DNA in a partial intercalative mode. The pytpy complex efficiently photo-cleaves DNA in green light via superoxide and hydroxyl radical formation. The antpy and pytpy complexes exhibited a remarkable photocytotoxic effect in HeLa cancer cells (IC50, similar to 9 mu M) in visible light (400-700 nm), while remaining essentially nontoxic in dark (IC50, similar to 90 mu M). Formation of reactive oxygen species (ROS) inside the HeLa cells was evidenced from the fluorescence enhancement of dichlorofluorescein upon treatment with the pytpy complex followed by photo-exposure. The antpy and pytpy complexes were used for cellular imaging. Confocal imaging and dual staining study using propidium iodide (PI) showed nuclear localization of the complexes. (c) 2012 Elsevier Inc. All rights reserved.

Influence of annealing temperature on Raman and photoluminescence spectra of electron beam evaporated TiO2 thin films

Titanium dioxide (TiO2) thin films were deposited on fused quartz substrates by electron beam evaporation method at room temperature. The films were annealed at different temperatures in ambient air. The surface morphology/roughness at different annealing temperatures were analyzed by atomic force microscopy (AFM). The crystallinity of the film has improved with the increase of annealing temperature. The effect of annealing temperature on optical, photoluminescence and Raman spectra of TiO2 films were investigated. The refractive index of TiO2 films were studied by envelope method and reflectance spectra and it is observed that the refractive index of the films was high. The photoluminescence intensity corresponding to green emission was enhanced with increase of annealing temperature. The peaks in Raman spectra depicts that the TiO2 film is of anatase phase after annealing at 300 degrees C and higher. The films show high refractive index, good optical quality and photoluminescence characteristics suggest that possible usage in opto-electronic and optical coating applications. (C) 2012 Elsevier B.V. All rights reserved.

Time-Temperature Scaling of Conductivity Spectra of Organic Plastic Crystalline Conductors

Organic plastic crystalline soft matter ion conductors are interesting alternatives to liquid electrolytes in electrochemical storage devices such as Lithium-ion batteries. The solvent dynamics plays a major role in determining the ion transport in plastic crystalline ion conductors. We present here an analysis of the frequency-dependent ionic conductivity of succinonitrile-based plastic crystalline ion conductors at varying salt composition (0.005 to 1 M) and temperature (-20 to 60 degrees C) using time-temperature superposition principle (TTSP). The main motivation of the work has been to establish comprehensive insight into the ion transport mechanism from a single method viz, impedance spectroscopy rather than employing cluster of different characterization methods probing various length and time scales. The TTSP remarkably aids in explicit identification of the extent of the roles of solvent dynamics and ion-ion interactions on the effective conductivity of the orientationally disordered plastic crystalline ion conductors.

Two-Dimensional Correlation Analysis of Temperature-Dependent FT-IR Spectra of Oleic Acid

In the present study, variable temperature FT-IR spectroscopic investigations were used to characterize the spectral changes in oleic acid during heating oleic acid in the temperature range from -30 degrees;C to 22 degrees C. In order to extract more information about the spectral variations taking place during the phase transition process, 2D correlation spectroscopy (2DCOS) was employed for the stretching (C?O) and rocking (CH2) band of oleic acid. However, the interpretation of these spectral variations in the FT-IR spectra is not straightforward, because the absorption bands are heavily overlapped and change due to two processes: recrystallization of the ?-phase and melting of the oleic acid. Furthermore, the solid phase transition from the ?- to the a-phase was also observed between -4 degrees C and -2 degrees C. Thus, for a more detailed 2DCOS analysis, we have split up the spectral data set in the subsets recorded between -30 degrees C to -16 degrees C, -16 degrees C to 10 degrees C, and 10 degrees C to 22 degrees C. In the corresponding synchronous and asynchronous 2D correlation plots, absorption bands that are characteristic of the crystalline and amorphous regions of oleic acid were separated.