Microsecond simulations of DNA and ion transport in nanopores with novel ion–ion and ion–nucleotides effective potentials

We developed a novel scheme based on the grand‐canonical Monte Carlo/Brownian dynamics simulations and have extended it to studies of ion currents across three nanopores with the potential for single‐stranded DNA (ssDNA) sequencing: solid‐state nanopore Si₃N₄, α‐hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide‐specific ion dynamics compatible with ssDNA coarse‐grained model, we used the inverse Monte Carlo protocol, which maps the relevant ion–nucleotide distribution functions from all‐atom molecular dynamics (MD) simulations. Combined with the previously developed simulation platform for Brownian dynamics simulations of ion transport, it allows for microsecond‐ and millisecond‐long simulations of ssDNA dynamics in the nanopore with a conductance computation accuracy that equals or exceeds that of all‐atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all‐atom MD simulations. © 2014 Wiley Periodicals, Inc.     

1,4-Addition of aryl boronic acids to α,β-unsaturated ketones catalyzed by a CCC–NHC pincer rhodium complex

An air- and water-stable CCC–NHC pincer Rh complex catalyzed the 1,4-addition of aryl boronic acids to α,β-unsaturated ketones and aldehydes. This bench top method proceeds in eco-friendly solvents including methanol and water. The scope of boronic acids was expanded to include heterocyclic examples.     

Novel Poly(ester urethane urea)/Polydioxanone Blends: Electrospun Fibrous Meshes and Films

In this work, we report the electrospinning and mechano-morphological characterizations of scaffolds based on blends of a novel poly(ester urethane urea) (PHH) and poly(dioxanone) (PDO). At the optimized electrospinning conditions, PHH, PDO and blend PHH/PDO in Hexafluroisopropanol (HFIP) solution yielded bead-free non-woven random nanofibers with high porosity and diameter in the range of hundreds of nanometers. The structural, morphological, and biomechanical properties were investigated using Differential Scanning Calorimetry, Scanning Electron Microscopy, Atomic Force Microscopy, and tensile tests. The blended scaffold showed an elastic modulus (~5 MPa) with a combination of the ultimate tensile strength (2 ± 0.5 MPa), and maximum elongation (150% ± 44%) in hydrated conditions, which are comparable to the materials currently being used for soft tissue applications such as skin, native arteries, and cardiac muscles applications. This demonstrates the feasibility of an electrospun PHH/PDO blend for cardiac patches or vascular graft applications that mimic the nanoscale structure and mechanical properties of native tissue.     

Droplets evaporation: Problems and solutions

The evaporation of single droplets and sprays into gaseous atmosphere and the evaporation of sessile liquid droplets on solid substrates are here considered. We argue that if thermodynamics is augmented with Derjaguin’s (disjoining/conjoining) pressure to handle phenomena in a vicinity of the three-phase contact line, problems like the singularity of the evaporation flux and of the viscous stress at the three-phase contact line of a sessile droplet are ruled out.     

Beta and gamma decays of J π = 1+, 24mAl state

A β-γ spectroscopy of the J ^π , 426 keV isomeric state of ²⁴Al (^24m Al) has been carried out by using a ²⁴Al secondary beam with high purity and high isomeric ratio. From the absolute γ-ray and β-particle intensities observed in the decay of the isomeric state, the branching ratio R _B of the isomeric γ decay from ^24m Al to the J ^π = 4⁺, ground state of ²⁴Al have been derived. The obtained R _B value of 69.6(7)% is much smaller than the previously accepted value of 82.5(30)%. The precise half-life for the isomer decay, T _1/2 ^m = 130.9(13) ms, has been also determined in this experiment. Accordingly, the M3 γ-decay strength B(M3) of the ^24m Al decay becomes smaller and the total β-decay branching ratio becomes larger. In particular, the β-decay branching ratio to the ground state of ²⁴Mg becomes 24.3(9)%, which is 2.4 times larger than the previous value of 10.1(28)%. By combining the branching ratio and the half-life, the Gamow-Teller (GT) transition strength B(GT) of 0.0194(7) is deduced for the GT transition from ^24m Al to the J ^π = 0⁺, ground state of ²⁴Mg. This value is in good agreement with the values derived from charge-exchange reactions.     

Selective and efficient quantum process tomography without ancilla

Several methods, known as quantum process tomography, are available to characterize the evolution of quantum systems, a task of crucial importance. However, their complexity dramatically increases with the size of the system. Here we present a new method for quantum process tomography. We describe a new algorithm that can be used to selectively estimate any parameter characterizing a quantum process. Unlike any of its predecessors this new quantum tomographer combines two virtues: it requires investing a number of physical resources scaling polynomially with the number of qubits and at the same time it does not require any ancillary resources. We present the results of the first implementation of this quantum device, characterizing quantum processes affecting two qubits encoded in heralded single photons. Even for this small system our method displays clear advantages over the other existing ones.     

Main group multiple C-H/N-H bond activation of a diamine and isolation of a molecular dilithium zincate hydride: experimental and DFT evidence for alkali metal-zinc synergistic effects

The surprising transformation of the saturated diamine (iPr)NHCH(2)CH(2)NH(iPr) to the unsaturated diazaethene [(iPr)NCH═CHN(iPr)](2-) via the synergic mixture nBuM, (tBu)(2)Zn and TMEDA (where M = Li, Na; TMEDA = N,N,N',N'-tetramethylethylenediamine) has been investigated by multinuclear NMR spectroscopic studies and DFT calculations. Several pertinent intermediary and related compounds (TMEDA)Li[(iPr)NCH(2)CH(2)NH(iPr)]Zn(tBu)(2) (3), (TMEDA)Li[(iPr)NCH(2)CH(2)CH(2)N(iPr)]Zn(tBu) (5), {(THF)Li[(iPr)NCH(2)CH(2)N(iPr)]Zn(tBu)}(2) (6), and {(TMEDA)Na[(iPr)NCH(2)CH(2)N(iPr)]Zn(tBu)}(2) (11), characterized by single-crystal X-ray diffraction, are discussed in relation to their role in the formation of (TMEDA)M[(iPr)NCH═CHN(iPr)]Zn(tBu) (M = Li, 1; Na, 10). In addition, the dilithio zincate molecular hydride [(TMEDA)Li](2)[(iPr)NCH(2)CH(2)N(iPr)]Zn(tBu)H 7 has been synthesized from the reaction of (TMEDA)Li[(iPr)NCH(2)CH(2)NH(iPr)]Zn(tBu)(2)3 with nBuLi(TMEDA) and also characterized by both X-ray crystallographic and NMR spectroscopic studies. The retention of the Li-H bond of 7 in solution was confirmed by (7)Li-(1)H HSQC experiments. Also, the (7)Li NMR spectrum of 7 in C(6)D(6) solution allowed for the rare observation of a scalar (1)J(Li-H) coupling constant of 13.3 Hz. Possible mechanisms for the transformation from diamine to diazaethene, a process involving the formal breakage of four bonds, have been determined computationally using density functional theory. The dominant mechanism, starting from (TMEDA)Li[(iPr)NCH(2)CH(2)N(iPr)]Zn(tBu) (4), involves the formation of a hydride intermediate and leads directly to the observed diazaethene product. In addition the existence of 7 in equilibrium with 4 through the dynamic association and dissociation of a (TMEDA)LiH ligand, also provides a secondary mechanism for the formation of the diazaethene. The two reaction pathways (i.e., starting from 4 or 7) are quite distinct and provide excellent examples in which the two distinct metals in the system are able to interact synergically to catalyze this otherwise challenging transformation.     

Preparative treatment with NaOH to selectively concentrate iron oxides of a Chilean volcanic soil?material to produce effective heterogeneous Fenton catalyst

A Chilean volcanic Ultisol material was first size-fractionated so as to obtain the fraction with mean particle sizes ??<?53 ??m. This sample was then sequentially treated three or five times with 5 mol L^???1 NaOH, in an attempt to evaluate the effectiveness of the selective chemical dissolution to concentrate iron oxides, as a preparation procedure before using the materials as heterogeneous Fenton catalysts. The effects of those treatments on the iron oxides mineralogy were monitored with Mössbauer spectroscopy. The NaOH-treated samples were tested as catalysts towards the H₂O₂ decomposition. Three or five sequential NaOH treatments were found to be comparably effective, by concentrating nearly the same proportion of iron oxides in the remaining solid phase (25.1 ± 0.4 and 23.3 ± 0.2 mass%, respectively). 298 K-Mössbauer patterns were similar for both samples, with a central (super)paramagnetic Fe^3?+? doublet and a broad sextet, assignable to several closely coexisting magnetically ordered forms of iron oxides. Despite of this nearly similar effect of the two treatments, the Ultisol material treated three times with NaOH presents higher heterogeneous catalytic efficiency and is more suitable to decompose H₂O₂ than that with five treatments.     

Regio‐ and stereospecific assembly of dispiro[indoline‐3,3′‐pyrrolizine‐1′,5′′‐thiazolidines] from simple precursors using a one‐pot procedure: synthesis,spectroscopic and structural characterization,and a proposed mechanism of formation

The synthesis and characterization of three new dispiro[indoline‐3,3′‐pyrrolizine‐1′,5′′‐thiazolidine] compounds are reported, together with the crystal structures of two of them. (3RS,1′SR,2′SR,7a′SR)‐2′‐(4‐Chlorophenyl)‐1‐hexyl‐2′′‐sulfanylidene‐5′,6′,7′,7a′‐tetrahydro‐2′H‐dispiro[indoline‐3,3′‐pyrrolizine‐1′,5′′‐thiazolidine]‐2,4′′‐dione, C₂₈H₃₀ClN₃O₂S₂, (I), (3RS,1′SR,2′SR,7a′SR)‐2′‐(4‐chlorophenyl)‐1‐benzyl‐5‐methyl‐2′′‐sulfanylidene‐5′,6′,7′,7a′‐tetrahydro‐2′H‐dispiro[indoline‐3,3′‐pyrrolizine‐1′,5′′‐thiazolidine]‐2,4′′‐dione, C₃₀H₂₆ClN₃O₂S₂, (II), and (3RS,1′SR,2′SR,7a′SR)‐2′‐(4‐chlorophenyl)‐5‐fluoro‐2′′‐sulfanylidene‐5′,6′,7′,7a′‐tetrahydro‐2′H‐dispiro[indoline‐3,3′‐pyrrolizine‐1′,5′′‐thiazolidine]‐2,4′′‐dione, C₂₂H₁₇ClFN₃O₂S₂, (III), were each isolated as a single regioisomer using a one‐pot reaction involving l ‐proline, a substituted isatin and (Z)‐5‐(4‐chlorobenzylidene)‐2‐sulfanylidenethiazolidin‐4‐one [5‐(4‐chlorobenzylidene)rhodanine]. The compositions of (I)–(III) were established by elemental analysis, complemented by high‐resolution mass spectrometry in the case of (I); their constitutions, including the definition of the regiochemistry, were established using NMR spectroscopy, and the relative configurations at the four stereogenic centres were established using single‐crystal X‐ray structure analysis. A possible reaction mechanism for the formation of (I)–(III) is proposed, based on the detailed stereochemistry. The molecules of (I) are linked into simple chains by a single N—H…N hydrogen bond, those of (II) are linked into a chain of rings by a combination of N—H…O and C—H…S=C hydrogen bonds, and those of (III) are linked into sheets by a combination of N—H…N and N—H…S=C hydrogen bonds.