Molecular dynamics simulation of ferronanofluid behavior in a nanochannel in the presence of constant and time-dependent magnetic fields

Journal of Thermal Analysis and Calorimetry - For the first time, double phosphates(V) Zn3Cr4(PO4)6 and Mg3Cr4(PO4)6 were synthesized by non-waste solid-state reaction, performed in the temperature...     

Interactions between a dsDNA Oligonucleotide and Imidazolium Chloride Ionic Liquids: Effect of Alkyl Chain Length,Part I

Ionic liquids (ILs) have become nearly ubiquitous solvents and their interactions with biomolecules has been a focus of study. Here, we used the fluorescence emission of DAPI, a groove binding fluorophore, coupled with molecular dynamics (MD) simulations to report on interactions between imidazolium chloride ([Im_n,1]⁺) ionic liquids and a synthetic DNA oligonucleotide composed entirely of T/A bases (7(TA)) to elucidate the effects ILs on a model DNA duplex. Spectral shifts on the order of 500–1000 cm⁻¹, spectral broadening (~1000 cm⁻¹), and excitation and emission intensity ratio changes combine to give evidence of an increased DAPI environment heterogeneity on added IL. Fluorescence lifetimes for DAPI/IL solutions yielded two time constants 0.15 ns (~80% to 60% contribution) and 2.36–2.71 ns for IL up to 250 mM. With DNA, three time constants were required that varied with added IL (0.33–0.15 ns (1–58% contribution), ~1.7–1.0 ns (~5% contribution), and 3.8–3.6 ns (94–39% contribution)). MD radial distribution functions revealed that π-π stacking interactions between the imidazolium ring were dominant at lower IL concentration and that electrostatic and hydrophobic interactions become more prominent as IL concentration increased. Alkyl chain alignment with DNA and IL-IL interactions also varied with IL. Collectively, our data showed that, at low IL concentration, IL was primarily bound to the DNA minor groove and with increased IL concentration the phosphate regions and major groove binding sites were also important contributors to the complete set of IL-DNA duplex interactions.     

Surface Interaction of Ionic Liquids: Stabilization of Polyethylene Terephthalate-Degrading Enzymes in Solution

The effect of aqueous solutions of selected ionic liquids solutions on Ideonella sakaiensis PETase with bis(2-hydroxyethyl) terephthalate (BHET) substrate were studied by means of molecular dynamics simulations in order to identify the possible effect of ionic liquids on the structure and dynamics of enzymatic Polyethylene terephthalate (PET) hydrolysis. The use of specific ionic liquids can potentially enhance the enzymatic hydrolyses of PET where these ionic liquids are known to partially dissolve PET. The aqueous solution of cholinium phosphate were found to have the smallest effect of the structure of PETase, and its interaction with (BHET) as substrate was comparable to that with the pure water. Thus, the cholinium phosphate was identified as possible candidate as ionic liquid co-solvent to study the enzymatic hydrolyses of PET.     

A First-Passage Kinetic Monte Carlo algorithm for complex diffusion–reaction systems

We develop an asynchronous event-driven First-Passage Kinetic Monte Carlo (FPKMC) algorithm for continuous time and space systems involving multiple diffusing and reacting species of spherical particles in two and three dimensions. The FPKMC algorithm presented here is based on the method introduced in Oppelstrup et al. [10] and is implemented in a robust and flexible framework. Unlike standard KMC algorithms such as the n-fold algorithm, FPKMC is most efficient at low densities where it replaces the many small hops needed for reactants to find each other with large first-passage hops sampled from exact time-dependent Green’s functions, without sacrificing accuracy. We describe in detail the key components of the algorithm, including the event-loop and the sampling of first-passage probability distributions, and demonstrate the accuracy of the new method. We apply the FPKMC algorithm to the challenging problem of simulation of long-term irradiation of metals, relevant to the performance and aging of nuclear materials in current and future nuclear power plants. The problem of radiation damage spans many decades of time-scales, from picosecond spikes caused by primary cascades, to years of slow damage annealing and microstructure evolution. Our implementation of the FPKMC algorithm has been able to simulate the irradiation of a metal sample for durations that are orders of magnitude longer than any previous simulations using the standard Object KMC or more recent asynchronous algorithms.     

Integrated photonic crystal spectrometers for sensing applications

A combination of negative refraction and diffraction compensation in a superprism-based photonic crystal structure is used to demonstrate a compact on-chip photonic crystal spectrometer. This structure provides strong dispersion and signal isolation, which are essential for forming an efficient and compact spectrometer. Performance of these spectrometers as spectral pattern detectors is discussed. The experimental results show that a PC structure with 80 μm × 220 μm dimension can locate a single spectral feature with better than 10 pm accuracy over a bandwidth of 50 nm around 1550 nm center wavelength at an output signal-to-noise ratio of 13 dB.     

Investigation of avalanche photocurrent at the edge of fundamental absorption band in Schottky diodes

The relative importance of the contribution of two mechanisms, that of the change in the collection of photocurrent carriers and that of the shift of the edge of fundamental absorption of light in strong electric fields in Schottky photodiodes, to the observed spectral dependence of the avalanche photocurrent is asessed.Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 12, pp. 83–86, December, 1985.     

The selective aerobic oxidation of methylaromatics to benzaldehydes using a unique combination of two heterogeneous catalysts

A unique combination of a supported cobalt complex and the first example of supported NHPI in acetic acid gives a surprisingly stable heterogeneous catalytic system for the selective aerobic oxidation of methylaromatics to benzaldehydes at atmospheric pressure.     

Ritter-enabled catalytic asymmetric chloroamidation of olefins

Intermolecular asymmetric haloamination reactions are challenging due to the inherently high halenium affinity (HalA) of the nitrogen atom, which often leads to N-halogenated products as a kinetic trap. To circumvent this issue, acetonitrile, possessing a low HalA, was used as the nucleophile in the catalytic asymmetric Ritter-type chloroamidation of allyl-amides. This method is compatible with Z and E alkenes with both alkyl and aromatic substitution. Mild acidic workup reveals the 1,2-chloroamide products with enantiomeric excess greater than 95% for many examples. We also report the successful use of the sulfonamide chlorenium reagent dichloramine-T in this chlorenium-initiated catalytic asymmetric Ritter-type reaction. Facile modifications lead to chiral imidazoline, guanidine, and orthogonally protected 1,2,3 chiral tri-amines.

Intermolecular haloamination reactions are challenging due to the high halenium affinity of the nitrogen atom. This is circumvented by using acetonitrile as an attenuated nucleophile, resulting in an enantioselective halo-Ritter reaction.     

Prediction of sound velocity and compressibility via molecular simulation at fixed entropy

A molecular-level simulation route is proposed to compute the isentropic thermodynamic properties in a fluid system by Monte Carlo simulation at fixed entropy. The method involves computation of the pressure response of a system to an infinitesimal change in system density by introduction of a single molecule, while retaining the system volume as well as the absolute molar entropy. The probability for accepting a change in temperature during the Monte Carlo moves was weighted against the argument proposed by Smith et al. [W.R. Smith, M. Lísal, I. Nezbeda, Chem. Phys. Lett. 426 (2006) 436–440]. Application to fluid argon has confirmed superior accuracy for the technique within the gas state to yield results within 1.2% of the measured values for the range of thermodynamic conditions investigated.     

‘Fixed charge’ chemical derivatization and data dependant multistage tandem mass spectrometry for mapping protein surface residue accessibility

Protein surface accessible residues play an important role in protein folding, protein-protein interactions and protein-ligand binding. However, a common problem associated with the use of selective chemical labeling methods for mapping protein solvent accessible residues is that when a complicated peptide mixture resulting from a large protein or protein complex is analyzed, the modified peptides may be difficult to identify and characterize amongst the largely unmodified peptide population (i.e., the ‘needle in a haystack’ problem). To address this challenge, we describe here the development of a strategy involving the synthesis and application of a novel ‘fixed charge’ sulfonium ion containing lysine-specific protein modification reagent, S,S′-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS), coupled with capillary HPLC-ESI-MS, automated CID-MS/MS, and data-dependant neutral loss mode MS³ in an ion trap mass spectrometer, to map the surface accessible lysine residues in a small model protein, cellular retinoic acid binding protein II (CRABP II). After reaction with different reagent:protein ratios and digestion with Glu-C, modified peptides are selectively identified and the number of modifications within each peptide are determined by CID-MS/MS, via the exclusive neutral loss(es) of dimethylsulfide, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility) of the peptide. The observation of these characteristic neutral losses are then used to automatically ‘trigger’ the acquisition of an MS³ spectrum to allow the peptide sequence and the site(s) of modification to be characterized. Using this approach, the experimentally determined relative solvent accessibilities of the lysine residues were found to show good agreement with the known solution structure of CRABP II.