Molecular dynamics simulation of poly(3‐hexylthiophene) helical structure In Vacuo and in amorphous polymer surrounding

The stability of poly(3‐hexylthiophene) (P3HT) helical structure has been investigated in vacuo and in amorphous polymer surrounding via molecular dynamics‐based simulations at temperatures below and above the P3HT melting point. The results show that the helical chain remains stable at room temperature both in vacuo and in amorphous surrounding, and promptly loses its structure at elevated temperatures. However, the amorphous surrounding inhibits the destruction of the helix at higher temperatures. In addition, it is shown that the electrostatic interactions do not significantly affect the stability of the helical structure. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2448–2456     

N‐bromo‐hydantoin grafted polystyrene beads: Synthesis and nano‐micro beads characteristics for achieving controlled release of active oxidative bromine and extended microbial inactivation efficiency

N‐bromo‐hydantoin and N‐bromo‐5,5′‐dimethylhydantoin conjugated polystyrene beads were synthesized from chloromethyl polystyrene beads which differ in their particles size, crosslinking, nano‐micro porosity, and tunnels size on the surface, in order to study the effect of these parameters on oxidative halogen release and resultant activity, for water purification applications. The synthesized beads were characterized using elemental analysis, FT‐IR, solid state ¹³C‐NMR, and scanning electron microscope (SEM). The conjugation yield and kinetics in different solvents and bromine loading capacity were studied. The N‐bromoamine polystyrene beads were tested for water decontamination according to NSF 231 protocol. The release of active bromine was analyzed by spectrophotometer using a DPD‐1 kit and also studied the antimicrobial activity against Escherichia coli and MS2 phages. Bead's nano‐micro characteristics were found critical for oxidative halogen release control: rate stabilization and modulation, extension and also influences antimicrobial activity. The synthesized beads exhibited extended and stable release of bromine, 6 and 4 log reduction for E. coli and MS2, respectively for 250 L of passing contaminated water. Thus, N‐halamine hydantoins conjugated polystyrenes, chemically or kinetically release modified should have applications as disinfectants in water purification systems as well as medical field. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 596–610     

Synthesis,structure and properties of N-aminosaccharin – A selective inhibitor of human carbonic anhydrase I

Previously unknown N-aminosaccharin was prepared in good yield via the one-step direct amination of saccharin sodium salt with hydroxylamine-O-mesitylenesulfonic acid (MSH) and its reactivity investigated. N-aminosaccharin and its derivatives were tested against hCA isoforms and the parent compound was identified to be a selective, low micromolar inhibitor (K_i = 8.8 μM) of hCA I. These findings provide a ligand-efficient starting point for the design of potent hCA I inhibitors – a promising drug target for retinal/cerebral edema treatment.     

Density functional theory investigation of the binding interactions between phosphoryl,carbonyl, imino,and thiocarbonyl ligands and the pentaaqua nickel(II) complex: Coordination affinity and associated parameters

Density Functional Theory (UB3LYP/6‐311++G(d,p)) calculations of the affinity of the pentaaqua nickel(II) complex for a set of phosphoryl [O?P(H)(CH₃)(PhR)], imino [HN?C(CH₃)(PhR)], thiocarbonyl [S?C(CH₃)(PhR)] and carbonyl [O?C(CH₃)(PhR)] ligands were performed, where R?NH₂, OCH₃, OH, CH₃, H, Cl, CN, and NO₂ is a substituent at the para‐position of a phenyl ring.The affinity of the pentaaqua nickel(II) complex for these ligands was analized and quantified in terms of interaction enthalpy (ΔH), Gibbs free energy (ΔG²⁹⁸), geometric and electronic parameters of the resultant octahedral complexes. The ΔH and ΔG²⁹⁸ results show that the ligand coordination strength increases in the following order: carbonyl < thiocarbonyl < imino < phosphoryl. This coordination strength order is also observed in the analysis of the metal‐ligand distances and charges on the ligand atom that interacts with the Ni(II) cation. The electronic character of the substituent R is the main parameter that affects the strength of the metal‐ligand coordination. Ligands containing electron‐donating groups (NH₂, OCH₃, OH) have more exothermic ΔH and ΔG²⁹⁸ than ligands with electron‐withdrawing groups (Cl, CN, NO₂). The metal‐ligand interaction decomposed by means of the energy decomposition analysis (EDA) method shows that the electronic character of the ligand modulates all the components of the metal‐ligand interaction. The absolute softness of the free ligands is correlated with the covalent contribution to the instantaneous interaction energy calculated using the EDA method. © 2013 Wiley Periodicals, Inc.     

129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: Essential role of the relativity,dynamics, and explicit solvent

The isotropic ¹²⁹Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C₆₀ dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimental conditions and to evaluate the role of different physical factors influencing the ¹²⁹Xe NMR CS. The ¹²⁹Xe shielding constant was obtained by averaging the ¹²⁹Xe nuclear magnetic shieldings calculated for snapshots obtained from the molecular dynamics trajectory of the Xe@C₆₀ system embedded in a periodic box of benzene molecules. Relativistic corrections were added at the Breit–Pauli perturbation theory (BPPT) level, included the solvent, and were dynamically averaged. It is demonstrated that the contribution of internal dynamics of the Xe@C₆₀ system represents about 8% of the total nonrelativistic NMR CS, whereas the effects of dynamical solvent add another 8%. The dynamically averaged relativistic effects contribute by 9% to the total calculated ¹²⁹Xe NMR CS. The final theoretical value of 172.7 ppm corresponds well to the experimental ¹²⁹Xe CS of 179.2 ppm and lies within the estimated errors of the model. The presented computational protocol serves as a prototype for calculations of ¹²⁹Xe NMR parameters in different Xe atom guest–host systems. © 2013 Wiley Periodicals, Inc.     

Towards Polyoxometalate‐Cluster‐Based Nano‐Electronics

We explore the concept that the incorporation of polyoxometalates (POMs) into complementary metal oxide semiconductor (CMOS) technologies could offer a fundamentally better way to design and engineer new types of data storage devices, due to the enhanced electronic complementarity with SiO₂, high redox potentials, and multiple redox states accessible to polyoxometalate clusters. To explore this we constructed a custom‐built simulation domain bridge. Connecting DFT, for the quantum mechanical modelling part, and mesoscopic device modelling, confirms the theoretical basis for the proposed advantages of POMs in non‐volatile molecular memories (NVMM) or flash‐RAM.     

Unusual Structure,Fluxionality, and Reaction Mechanism of Carbonyl Hydrosilylation by Silyl Hydride Complex [(ArN)Mo(H)(SiH2Ph)(PMe3)3]

The reactions of bis(borohydride) complexes [(RN?)Mo(BH₄)₂(PMe₃)₂] ( 4 : R=2,6‐Me₂C₆H₃; 5 : R=2,6‐iPr₂C₆H₃) with hydrosilanes afford new silyl hydride derivatives [(RN?)Mo(H)(SiR′₃)(PMe₃)₃] ( 3 : R=Ar, R′₃=H₂Ph; 8 : R=Ar′, R′₃=H₂Ph; 9 : R=Ar, R′₃=(OEt)₃; 10 : R=Ar, R′₃=HMePh). These compounds can also be conveniently prepared by reacting [(RN?)Mo(H)(Cl)(PMe₃)₃] with one equivalent of LiBH₄ in the presence of a silane. Complex 3 undergoes intramolecular and intermolecular phosphine exchange, as well as exchange between the silyl ligand and the free silane. Kinetic and DFT studies show that the intermolecular phosphine exchange occurs through the predissociation of a PMe₃ group, which, surprisingly, is facilitated by the silane. The intramolecular exchange proceeds through a new non‐Bailar‐twist pathway. The silyl/silane exchange proceeds through an unusual Mo^VI intermediate, [(ArN?)Mo(H)₂(SiH₂Ph)₂(PMe₃)₂] ( 19 ). Complex 3 was found to be the catalyst of a variety of hydrosilylation reactions of carbonyl compounds (aldehydes and ketones) and nitriles, as well as of silane alcoholysis. Stoichiometric mechanistic studies of the hydrosilylation of acetone, supported by DFT calculations, suggest the operation of an unexpected mechanism, in that the silyl ligand of compound 3 plays an unusual role as a spectator ligand. The addition of acetone to compound 3 leads to the formation of [trans‐(ArN)Mo(OiPr)(SiH₂Ph)(PMe₃)₂] ( 18 ). This latter species does not undergo the elimination of a Si? O group (which corresponds to the conventional Ojima′s mechanism of hydrosilylation). Rather, complex 18 undergoes unusual reversible β‐CH activation of the isopropoxy ligand. In the hydrosilylation of benzaldehyde, the reaction proceeds through the formation of a new intermediate bis(benzaldehyde) adduct, [(ArN?)Mo(η²‐PhC(O)H)₂(PMe₃)], which reacts further with hydrosilane through a η¹‐silane complex, as studied by DFT calculations.     

2DE‐based approach for estimation of number of protein species in a cell

Insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of human proteome. But to go further, we need at least to know the proteome size, or how many different protein species compose this proteome. This is the task that could be at least partially realized by the method described in this article. The approach used in our study is based on detection of protein spots in 2DE after staining by protein dyes with various sensitivities. As the different protein spots contain different protein species, counting the spots opens a way for estimation of number of protein species. The function representing the dependence of the number of protein spots on sensitivity or LOD of protein dyes was generated. And extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) allowed to counting the number of different molecules (polypeptide species) at the concentration level of a single polypeptide per proteome. Using this approach, it was estimated that the minimal numbers of protein species for model objects, Escherichia coli and Pirococcus furiosus, are 6200 and 3400, respectively. We expect a single human cell (HepG2) to contain minimum 70 000 protein species.