MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives

An algorithm for the rapid analytical determination of the accessible surface areas of solute molecules is described. The accessible surface areas as well as the derivatives with respect to the Cartesian coordinates of the atoms are computed by a program called “MSEED,” which is based in part on Connolly's analytical formulas for determining surface area. Comparisons of the CPU time required for MSEED, Connolly's numerical algorithm DOT, and a program for surface area determination (ANA) based on Connolly's analytical algorithm, are presented. MSEED is shown to be as much as 70 times faster than ANA and up to 11 times faster than DOT for several proteins. The greater speed of MSEED is achieved partially because nonproductive computation of the surface areas of internal atoms is avoided. A sample minimization of an energy function, which included a term for hydration, was carried out on MET-enkephalin using MSEED to compute the solvent-accessible surface area and its derivatives. The potential employed was ECEPP/2 plus an empirical potential for solvation based on the solvent-accessible surface area of the peptide. The CPU time required for 150 steps of minimization with the potential that included solvation was approximately twice as great as the CPU time required for 150 steps of minimization with the ECEPP/2 potential only.     

Effect of Dielectric Constant of Solvents on the Particle Size and Bandgap of La/SnO2‐TiO2 Nanoparticles and Their Catalytic Properties

Lanthanum (La) supported on tin oxide‐titanium oxide (SnO₂‐TiO₂ ) nanoparticles were prepared by a sol–gel method followed by a hydrothermal method. Effect of different solvents (ethyl acetate, benzyl alcohol, ethylene glycol) on the particle size and catalytic activity was investigated. The nanomaterial was characterized by transmission electron microscopy, powder X‐ray diffraction, scanning electron microscopy, fourier transform infrared spectroscopy, and energy dispersive X‐ray. The catalytic and optical properties were studied using solid‐phase spectrophotometry and ultraviolet–visible spectroscopy, respectively. Gas chromatography‐mass spectrometry (GC‐MS) was used to detect the intermediates during the catalytic degradation of methylene blue. It was observed that with decrease in the dielectric constant (ε) of the solvent, the bandgap and particle size decrease and catalytic efficiency increases. Hence, the highest catalytic activity was observed with the solvent having the least dielectric constant.     

Synthesis,Electrochemistry, and Spectroscopy of Blue Platinum(II) Polyynes and Diynes

The smallest band gap observed so far (1.77 eV) for an organometallic polymer is exhibited by the blue, rigid-rod polymer 2 , which is prepared by the reaction of trans-[PtCl₂(PnBu₃)₂] with one equivalent of 1 .     

Estimation of uranium in geological rock samples by beta–gamma method and its comparison with pellet fluorimetry method

Geological rock samples collected from Narwapahar uranium mines, UCIL, Jaduguda were analysed for the estimation of uranium concentration (U₃O₈) by beta–gamma method which is a physical technique and same set of samples were analysed by pellet fluorimetry technique which is a chemical technique. 28 samples were analysed by beta–gamma method and values varied between 240 and 2,500 ppm. Samples were analysed by pellet fluorimetry and values varied between 260 and 2,300 ppm. The results obtained were well comparable by both the techniques.     

Influence of Halogen Substitution in the Ligand Sphere on the Antitumor and Antibacterial Activity of Half‐sandwich Ruthenium(II) Complexes [RuX(η6‐arene)(C5H4N‐2‐CH=N‐Ar)]+

New complexes [(η⁶‐p‐cymene)Ru(C₅H₄N‐2‐CH=N–Ar)X]PF₆ [X = Br ( 1 ), I ( 2 ); Ar = 4‐fluorophenyl ( a ), 4‐chlorophenyl ( b ), 4‐bromophenyl ( c ), 4‐iodophenyl ( d ), 2,5‐dichlorophenyl ( e )] were prepared, as well as 3a – 3e (X = Cl) and the new complexes [(η⁶‐arene)RuCl(N‐N)]PF₆ (arene = C₆H₅OCH₂CH₂OH, N‐N = 2,2′‐bipyridine ( 4 ), 2,6‐(dimethylphenyl)‐pyridin‐2‐yl‐methylene amine ( 5 ), 2,6‐(diisopropylphenyl)‐pyridin‐2‐yl‐methylene amine ( 6 ); arene = p‐cymene, N‐N = 4‐(aminophenyl)‐pyridin‐2‐yl‐methylene amine ( 7 )]. X‐ray diffraction studies were performed for 1a , 1b , 1c , 1d , 2b , 5 , and 7 . Cytotoxicities of 1a – 1d and 2 were established versus human cancer cells epithelial colorectal adenocarcinoma (Caco‐2) (IC₅₀: 35.8–631.0 μM), breast adenocarcinoma (MCF7) (IC₅₀: 36.3–128.8.0 μM), and hepatocellular carcinoma (HepG2) (IC₅₀: 60.6–439.8 μM), 3a – 3e were tested against HepG2 and Caco‐2, and 4 – 7 were tested against Caco‐2. 1 – 7 were tested against non‐cancerous human epithelial kidney cells. 1 and 2 were more selective towards tumor cells than the anticancer drug 5‐fluorouracil (5‐FU), but 3a – 3e (X = Cl) were not selective. 1 and 2 had good activity against MCF7, some with lower IC₅₀ than 5‐FU. Complexes with X = Br or I had moderate activity against Caco‐2 and HepG2, but those with Cl were inactive. Antibacterial activities of 1a , 2b , 3a , and 7 were tested against antibacterial susceptible and resistant Gram‐negative and ‐positive bacteria. 1a , 2b , and 3a showed activity against methicillin‐resistant S. aureus (MIC = 31–2000 μg · mL^–1).     

A comparative study of the simulated-annealing and Monte Carlo-with-minimization approaches to the minimum-energy structures of polypeptides: [Met]-enkephalin

A comparison of two methods for surmounting the multiple-minima problem, Simulated Annealing (SA) and Monte Carlo with Minimization (MCM), is presented with applications to [Met]-enkephalin in the absence and in the presence of water. SA explores a continuous space of internal variables, while MCM explores a discrete space consisting of the local energy minima on that space. Starting from random conformations chosen from the whole conformational space in both cases, it is found that, while SA converges to low-energy structures significantly faster than MCM, the former does not converge to a unique minimum whereas the latter does. Furthermore, the behavior of the RMS deviations with respect to the apparent global minimum (for enkephalin in the absence of water) shows no correlation with the observed overall energy decrease in the case of SA, whereas such a correlation is quite evident with MCM; this implies that, even though the potential energy decreases in the annealing process, the Monte Carlo SA trajectory does not proceed towards the global minimum. Possible reasons for these differences between the two methods are discussed. It is concluded that, while SA presents attractive prospects for possibly improving or refining given structures, it must be considered inferior to MCM, at least in problems where little or no structural information is available for the molecule of interest.     

First Principles Investigation of Fluorine Based Strontium Series of Perovskites

Density functional theory is used to explore structural, elastic, and mechanical properties of SrLiF₃, SrNaF₃, SrKF₃ and SrRbF₃ fluoroperovskite compounds by means of an ab-initio Full Potential-Linearized Augmented Plane Wave (FP-LAPW) method. Several lattice parameters are employed to obtain accurate equilibrium volume (V_o). The resultant quantities include ground state energy, elastic constants, shear modulus, bulk modulus, young's modulus, cauchy's pressure, poisson's ratio, shear constant, ratio of elastic anisotropy factor, kleinman's parameter, melting temperature, and lame's coefficient. The calculated structural parameters via DFT as well as analytical methods are found to be consistent with experimental findings. Chemical bonding is used to investigate corresponding chemical trends which authenticate combination of covalent-ionic behavior. Furthermore electron density plots as well as elastic and mechanical properties are reported for the first time which reveals that fluorine based strontium series of perovskites are mechanically stable and posses weak resistance towards shear deformation as compared to resistance towards unidirectional compression while brittleness and ionic behavior is dominated in them which decreases from SrLiF₃ to SrRbF₃. Calculated cauchy's pressure, poisson's ratio and B/G ratio also proves ionic nature in these compounds. The present methodology represents an effective and influential approach to calculate the whole set of elastic and mechanical parameters which would support to understand various physical phenomena and empower device engineers for implementing these materials in numerous applications.     

Synthesis, Characterization and Photoluminescence Study of Novel Sulfobetaine Polyelectrolytes

A novel sulfobetaine copolymer is developed via polycondensation approach. The comonomers, melamine, condenses with a diketone, 5,5-dimethyl-1,3-cyclohexane (dimedone) to produce polyimine chain based on Schiff base chemistry. Dimedone-[N,N' melaminium] propane sulfonate copolymer crystals were obtained on treatment of the polyimine with sulfopropylating agent, 1,3-propane sultone with a crosslinker, di(ethylene glycol diacrylate) (DEGDA). This crosslinked sulfobetaine polymer yielded fine needle like single crystals and shows strong blue fluorescence and a week green phosphorescence. Multi-exponential fluorescence decay function indicates the presence of different conformers both in solution and crystalline phase. This easy straightforward protocol for synthesis of crystalline, soluble, and luminescent polymer could prove to be a landmark in development of next generation smart functional materials.