An improved replica-exchange sampling method: temperature intervals with global energy reassignment

In a molecular dynamics (MD) simulation, representative sampling over the entire phase space is desired to obtain an accurate canonical distribution at a given temperature. For large molecules, such as proteins, this is problematic because systems tend to become trapped in local energy minima. The extensively used replica-exchange molecular dynamics (REMD) simulation technique overcomes this kinetic-trapping problem by allowing Boltzmann-weighted configuration exchange processes to occur between numerous thermally adjacent and compositionally identical simulations that are thermostated at sequentially higher temperatures. While the REMD method provides much better sampling than conventional MD, there are two substantial difficulties that are inherent in its application: (1) the large number of replicas that must be used to span a designated temperature range and (2) the subsequent long time required for configurations sampled at high temperatures to exchange down for potential inclusion within the low-temperature ensemble of interest. In this work, a new method based on temperature intervals with global energy reassignment (TIGER) is presented that overcomes both of these problems. A TIGER simulation is conducted as a series of short heating-sampling-quenching cycles. At the end of each cycle, the potential energies of all replicas are simultaneously compared at the same temperature using a Metropolis sampling method and then globally reassigned to the designated temperature levels. TIGER is compared with regular MD and REMD methods for the alanine dipeptide in water. The results indicate that TIGER increases sampling efficiency while substantially reducing the number of central processing units required for a comparable conventional REMD simulation.     

Template- and surfactant-free synthesis of ultrathin CeO2 nanowires in a mixed solvent and their superior adsorption capability for water treatment

Ultrathin CeO₂ nanowires with a diameter of 5 nm and an aspect ratio of more than 100 can be prepared by a one-step refluxing approach in a mixed solvent composed of water and ethanol without using any templates or surfactants. The formation mechanism of the as-synthesized ultrathin nanowires has been investigated. The as-synthesized CeO₂ nanowires with a high surface area of 125.31 m² g^–1 exhibited excellent wastewater treatment performance with high removal capacities towards organic dyes and heavy metal ions. In addition, the as-synthesized CeO₂ nanowires can adsorb Congo red selectively from a mixed solution composed of several dyes. Successful access to high quality ultrathin nanowires will make it possible for their potential application in catalysis and other fields.     

Reductive dechlorination of atrazine using sodium-borohydride catalysed by cobalt(II) phthalocyanines

A series of functional metallophthalocyanines have been synthesized to study their role as a catalyst towards the reductive dechlorination of atrazine using sodium borohydride as a mild reducing agent. The cobalt(II) phthalocyanine bearing nitro groups at the peripheral position is the most efficient catalyst with exceptionally high catalytic activity in comparison to other functional cobalt(II) phthalocyanines.     

Enhancing the growth,photosynthetic capacity and artemisinin content in Artemisia annua L. by irradiated sodium alginate

Degrading the natural bioactive agents by ionizing radiation and then using them as growth promoting substances is a novel emerging technology to exploit the genetic potential of crops in terms of growth, yield and quality. Polysaccharides, such as sodium alginate, have proven to be wonderful growth promoting substances in their depolymerized form for various plants. The effect of depolymerized form of sodium alginate, produced by irradiating the latter by ⁶⁰Co gamma rays, was studied on Artemisia annua L. with regard to growth attributes, physiological and biochemical parameters and artemisinin content. The study revealed that the irradiated sodium alginate (ISA), applied as leaf-sprays at a concentration of 20–120 mg L^?1, improved the growth attributes, photosynthetic capability, enzyme activities and artemisinin content of the plant significantly. Application of ISA at 80 mg L^?1 increased the values of the attributes studied to the maximum extent. The enhancement of leaf-artemisinin content was ascribed to the ISA-enhanced H₂O₂ content in the leaves.     

Synthesis of nickel nanoparticles in silica by alcogel electrolysis

We report a novel technique for the formation of metal nanoparticles, based on electrolysis of the alcogels containing metal chlorides. The alcogel was formed from TEOS, water, ethanol, and nickel chloride, and subjected to galvanostatic electrolysis. This resulted in successful formation of Ni nanoparticles inside the silica gel. Average particle size of FCC Ni lies between 18 and 20 nm. The formation of tetragonal nickel (a sub-oxide of nickel) as well as NiO were also detected by XRD and SAED. The resistivity measurements showed that the nickel nanoparticles were separated from each other by Ni(O) present between them. Magnetic studies based on ZFC and FC measurements below room temperature (up to 5 K) and above room temperature (up to 700 K) were conducted using SQUID and Magnetic TGA, respectively, which showed strong magnetic irreversibility as attributable to exchange interaction between metallic and oxide phases and mutual interactions among metallic particles in the network structure. The blocking temperature (~600 K) of the samples was above room temperature. M–H studies based on VSM showed an increase in magnetic coercivity with the formation of NiO. A magnetic transition associated with tetragonal nickel was seen at 10 K.     

Synthesis and characterization of palladium(II) complexes of thioureas. X-ray structures of [Pd( N , N ′-dimethylthiourea)4]Cl2?·?2H2O and [Pd(tetramethylthiourea)4]Cl2

Palladium(II) complexes of thiones having the general formula [Pd(L)₄]Cl₂, where L = thiourea (Tu), methylthiourea (Metu), N,N′-dimethylthiourea (Dmtu), and tetramethylthiourea (Tmtu) were prepared by reacting K₂[PdCl₄] with the corresponding thiones. The complexes have been characterized by elemental analysis, IR and NMR spectroscopy, and two of these, [Pd(Dmtu)₄]Cl₂ · 2H₂O (1) and [Pd(Tmtu)₄]Cl₂ (2), by X-ray crystallography. An upfield shift in the >C=S resonance of thiones in ¹³C NMR and downfield shift in N–H resonance in ¹H NMR are consistent in showing sulfur coordination with palladium(II). The crystal structures of the complexes show a square-planar coordination environment around the Pd(II) ions with the average cis and trans S–Pd–S bond angles of 89.64° and 173.48°, respectively. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. An erratum to this article can be found at     

Homo‐ and Heterovalent Polynuclear Cerium and Cerium/Manganese Aggregates

Reactions of Ce^III(NO₃)₃?6 H₂O or (NH₄)₂[Ce^IV(NO₃)₆] with Mn‐containing starting materials result in seven novel polynuclear Ce or Ce/Mn complexes with pivalato (^tBuCO ) and, in most cases, auxiliary N,O‐ or N,O,O‐donor ligands. With nuclearities ranging from 6–14, the compounds present aesthetically pleasing structures. Complexes [Ce^IV₆(μ₃‐O)₄(μ₃‐OH)₄(μ‐O₂C^tBu)₁₂] ( 1 ), [Ce^IV₆Mn^III₄(μ₄‐O)₄(μ₃‐O)₄(O₂C^tBu)₁₂(ea)₄(OAc)₄]?4 H₂O?4 MeCN (ea^?=2‐aminoethanolato; 2 ), [Ce^IV₆Mn^III₈(μ₄‐O)₄(μ₃‐O)₈(pye)₄(O₂C^tBu)₁₈]₂[Ce^IV₆(μ₃‐O)₄(μ₃‐OH)₄(O₂C^tBu)₁₀(NO₃)₄] [Ce^III(NO₃)₅(H₂O)]?21 MeCN (pye^?=pyridine‐2‐ethanolato; 3 ), and [Ce^IV₆Ce^III₂Mn^III₂(μ₄‐O)₄(μ₃‐O)₄(^tbdea)₂(O₂C^tBu)₁₂(NO₃)₂(OAc)₂]?4 CH₂Cl₂ (^tbdea^2?=2,2′‐(tert‐butylimino]bis[ethanolato]; 4 ) all contain structures based on an octahedral {Ce^IV₆(μ₃‐O)₈} core, in which many of the O‐atoms are either protonated to give (μ₃‐OH)^? hydroxo ligands or coordinate to further metal centers (Mn^III or Ce^III) to give interstitial (μ₄‐O)^2? oxo bridges. The decanuclear complex [Ce^IV₈Ce^IIIMn^III(μ₄‐O)₃(μ₃‐O)₃(μ₃‐OH)₂(μ‐OH)(bdea)₄(O₂C^tBu)_9.5(NO₃)_3.5(OAc)₂]?1.5 MeCN (bdea^2?=2,2′‐(butylimino]bis[ethanolato]; 5 ) contains a rather compact Ce^IV₇ core with the Ce^III and Mn^III centers well‐separated from each other on the periphery. The aggregate in [Ce^IV₄Mn^IV₂(μ₃‐O)₄(bdea)₂(O₂C^tBu)₁₀(NO₃)₂]?4 MeCN ( 6 ) is based on a quasi‐planar {Mn^IV₂Ce^IV₄(μ₃‐O)₄} core made up of four edge‐sharing {Mn^IVCe^IV₂(μ₃‐O)} or {Ce^IV₃(μ₃‐O)} triangles. The structure of [Ce^IV₃Mn^IV₄Mn^III(μ₄‐O)₂(μ₃‐O)₇(O₂C^tBu)₁₂(NO₃)(furan)]?6 H₂O ( 7 ?6 H₂O) can be considered as {Mn^IV₂Ce^IV₂O₄} and distorted {Mn^IV₂Mn^IIICe^IVO₄} cubane units linked through a central (μ₄‐O) bridge. The Ce₆Mn₈ equals the highest nuclearity yet reported for a heterometallic Ce/Mn aggregate. In contrast to most of the previously reported heterometallic Ce/Mn systems, which contain only Ce^IV and either Mn^IV or Mn^III, some of the aggregates presented here show mixed valency, either Mn^IV/Mn^III (see 7 ) or Ce^IV/Ce^III (see 4 and 5 ). Interestingly, some of the compounds, including the heterovalent Ce^IV/Ce^III 4 , could be obtained from either Ce^III(NO₃)₃?6 H₂O or (NH₄)₂[Ce^IV(NO₃)₆] as starting material.     

Photoinduced Remote Functionalization of Amides and Amines Using Electrophilic Nitrogen Radicals

The selective functionalization of C(sp³)?H bonds at distal positions to functional groups is a challenging task in synthetic chemistry. Reported here is a photoinduced radical cascade strategy for the divergent functionalization of amides and protected amines. The process is based on the oxidative generation of electrophilic amidyl radicals and their subsequent transposition by 1,5‐H‐atom transfer, resulting in remote fluorination, chlorination and, for the first time, thioetherification, cyanation, and alkynylation. The process is tolerant of most common functional groups and delivers useful building blocks that can be further elaborated. The utility of this strategy is demonstrated through the late‐stage functionalization of amino acids and a dipeptide.     

Dramatic specific-ion effect in supramolecular hydrogels

We report on a pronounced specific-ion effect on the intermolecular and chiral organization, supramolecular structure formation, and resulting materials properties for a series of low molecular weight peptide-based hydrogelators, observed in the presence of simple inorganic salts. This effect was demonstrated using aromatic short peptide amphiphiles, based on fluorenylmethoxycarbonyl (Fmoc). Gel-phase materials were formed due to molecular self-assembly, driven by a combination of hydrogen bonding and π-stacking interactions. Pronounced morphological changes were observed by atomic force microscopy (AFM) for Fmoc-YL peptide, ranging from dense fibrous networks to spherical aggregates, depending on the type of anions present. The gels formed had variable mechanical properties, with G'?values between 0.8?kPa and 2.4?kPa as determined by rheometry. Spectroscopic analysis provided insights into the differential mode of self-assembly, which was found to be dictated by the hydrophobic interactions of the fluorenyl component, with comparable H-bonding patterns observed in each case. The efficiency of the anions in promoting the hydrophobic interactions and thereby self-assembly was found to be consistent with the Hofmeister anion sequence. Similar effects were observed with other hydrophobic peptides, Fmoc-VL and Fmoc-LL. The effect was found to be less pronounced for a less hydrophobic peptide, Fmoc-AA. To get more insights into the molecular mechanism, the effect of anions on sol-gel equilibrium was investigated, which indicates the observed changes result from the specific-ion effects on gels structure, rather than on the sol-gel equilibrium. Thus, we demonstrate that, by simply changing the ionic environment, structurally diverse materials can be accessed providing an important design consideration in nanofabrication via molecular self-assembly.