Assessing the performance of density functional theory for the dynamic polarizabilities of amino acids: Treatment of correlation and role of exact exchange

The theoretical determination of electric response properties of the biological systems is a field where the application of density functional theory (DFT) appears to be quite promising. In this work, the performance of 41 density functional methods is evaluated in predicting dynamic polarizabilities of an experimental benchmark set of 20 proteinogenic amino acids. The behavior of a large number of density functionals, including various types of the local spin density approximation (LSDA), generalized gradient approximation (GGA), meta‐GGA (m‐GGA), hybrid‐GGA (h‐GGA), hybrid meta‐GGA (hm‐GGA), and range‐separated hybrid‐GGA (rsh‐GGA), has been assessed for the purpose. Analyzing the results of our DFT benchmarking, we found that these computationally economical methods show very diverse predictive capability and a careful selection of DFT functionals is very important in the polarizability calculations. Considering the role of exchange, correlation, dispersion and long‐range corrections, it turned out that in the LSDA class, SVWN3 gives better results than SPL and SVWN5 toward the reference values. Of the GGA methods, OPBE outperforms all other functionals. The M06‐L is the best method of m‐GGA class. The B3LYP and TPSSh are the best functionals of h‐GGA and hm‐GGA lineages, respectively. Finally, CAM‐B3LYP is the best method of rsh‐GGA functionals that predicts the most accurate polarizability for amino acids by a large margin with respect to others. Overall, the best performing functionals turn out to be hm‐GGAs TPSSh, TPSS1KCIS, M05, tau‐HCTHhyb, and h‐GGA B3LYP. Hopefully, the results of this investigation might provide the useful guidance to propose a new exchange‐correlation functional for calculating the optical properties of biomolecular materials. © 2013 Wiley Periodicals, Inc.     

Crisp and soft multivariate methods visualize individual cell nuclei in Raman images of liver tissue sections

Raman and infrared spectroscopy have been recognized to be promising tools in clinical diagnostics because they provide molecular contrast without external stains. Here, vertex component analysis (VCA) was applied to Raman and Fourier transform infrared (FTIR) images of liver tissue sections and the results were compared with K-means cluster analysis, fuzzy C-means cluster analysis and principal component analysis. The main components of VCA from three Raman images were assigned to the central vein, periportal vein, cell nuclei, liver parenchyma and bile duct. After resonant Mie scattering correction, VCA of FTIR images identified veins, liver parenchyma, cracks, but no cell nuclei. The advantages of VCA in the context of tissue characterization by vibrational spectroscopic imaging are that the tissue architecture is visualized and the spectral information is reconstructed. Composite images were constructed that revealed a high molecular contrast and that can be interpreted in a similar way like hematoxylin and eosin stained tissue sections.     

Synthesis, characterization and crystal structures of palladium(II) complexes containing neutral, one and twofold deprotonated 1,2,4-triazine species

The synthesis and characterization of three new palladium(II) complexes of 4-amino-6-ethyl-1,2,4-triazine-3-thion-5-one (AETTO, H₃L), [PdCl₂(H₃L)]·H₂O (1), [Pd₂Cl₂(H₂L)(PPh₃)₃]NO₃·2CH₃CN (2) and [Pd(HL)(PPh₃)₂] (3), are reported. All the synthesized compounds are air-stable and were characterized by elemental analyses, IR, NMR spectroscopy and mass spectrometry. In addition, the molecular structures of the complexes have been determined by X-ray single crystal diffraction. On the basis of the crystallographic data, the neutral ligand in 1 and the deprotonated ligands in 2 and 3 act as bidentate NS donors. The singly deprotonated ligand in 2 acts as a bridging agent between two metal centers in the binuclear Pd^II-complex.     

Voltammetric Determination of Hemoglobin Using a Pencil Lead Electrode

In this paper the electrochemical behavior of hemoglobin (Hb) immobilized on a pencil lead electrode (PLE) was investigated. Immobilization of Hb on the pencil lead electrode was performed by nonelectrochemical and electrochemical methods. In phosphate buffer solution with pH 7.0 Hb showed a pair of well‐defined and nearly reversible redox waves (the anodic and cathodic peak potentials are located at ?0.18 V and ?0.22 V, respectively). The dependence of the anodic peak potential (E_pa) on the pH of the buffer solution indicated that the conversion of Hb? Fe(III)/Hb? Fe(II) is a one‐electron‐transfer reaction process coupled with one‐proton‐transfer. In addition the effect of scan rate on peak currents and peak separation potential was investigated and electrochemical parameters such as α and k_s were calculated. In the second part of this work, the ability of the electrode for determination of Hb concentration was investigated. The results showed a linear dynamic range from 0.15 to 2 µM and a detection limit of 0.11 µM. The relative standard deviation is 4.1 % for 4 successive determinations of a 1 µM Hb solution.     

Binding Studies of Isoxsuprine Hydrochloride to Calf Thymus DNA Using Multispectroscopic and Molecular Docking Techniques

In the present work, the interaction of Isoxsuprine (ISX) with Calf thymus DNA (ct-DNA) under physiological conditions (Tris–HCl buffer of pH 7.4) was investigated by using electronic absorption, circular dichroism, viscosity, electrochemical studies, fluorescence techniques, salt effect studies and computational studies. Competitive fluorimetric studies with Hoechst 33258 have shown that ISX exhibit the ability to displace the DNA-bound Hoechst 33258, indicating that it binds to ct-DNA in strong competition with Hoechst 33258 for the minor groove binding. Furthermore, the resulting data showed that ISX cannot displace methylene blue or acridine orange, which are the common intercalator molecules. The viscosity of ct-DNA solution was almost unchanged on addition of ISX and circular dichroism (CD) spectra of ct-DNA showed small changes in the presence of ISX which is in agreement with groove binding mode of interaction. Thus all above studies showed that the ISX drug binds to ct-DNA in a groove binding mode.The salt-effect studies showed the non-electrostatic nature of binding of ISX to ct-DNA. Moreover, molecular docking results support the above experimental data and suggest that ISX prefers to bind on the minor groove of ct-DNA.     

Laser Spectroscopic Characterization for the Rapid Detection of Nutrients along with CN Molecular Emission Band in Plant-Biochar

We report a quantitative analysis of various plant-biochar samples (S1, S2 and S3) by utilizing a laser-induced breakdown spectroscopy (LIBS) technique. For LIBS analysis, laser-induced microplasma was generated on the target surface by using a focused beam through a high-power Nd: YAG laser and optical emission spectra were recorded using a charged coupled device (CCD) array spectrometer, with wavelength ranges from 200 nm to 720 nm. The spectroscopical analysis showed the existence of various ingredients, including H, Li, Ca, Na, Al, Zn, Mg, Sr, Si, and Fe, along with a CN molecular emission band due to B²Σ⁺ − X²Σ⁺ electronic transition. By assuming conditions of the plasma is optically thin and in LTE, calibration-free laser-induced breakdown spectroscopy (CF-LIBS) was utilized for the compositional analysis of the ingredients present in the three plant-biochar samples. To lower the uncertainties, we used an average composition (%) of the three plant-biochar samples. The quantitative study of the plant-biochar samples was also achieved using the energy dispersive X-ray (EDX) technique, showing good agreement with the CF-LIBS technique. In addition, statistical analysis, such as principal component analysis (PCA), was performed for the clustering and classification of the three plant-biochar samples. The first three PCs explained an overall ~91% of the variation in LIBS spectral data, including PC1 (58.71%), PC2 (20.9%), and PC3 (11.4%). These findings suggest that LIBS is a robust tool for rapid measurement of heavy as well as light elements, such as H, Li, and nutritional metals in plant-biochar samples.