Improving the performance of molecular dynamics simulations on parallel clusters

In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds.     

Synthesis,Spectral and Magnetic Properties,and Crystal Structures of Copper(II) Pyridinecarboxylate Adducts with N‐Heterocyclic Ligands

Synthesis and characterization of seven new complexes [Cu(2‐MeSnic)₂(CH₃OH)]₂ (where 2‐MeSnic is 2‐methylthionicotinate), [Cu(2‐MeSnic)₂L₂]₂ (where L is pyridine — py, ethylnicotinate — Etnic and butylnicotinate — Bunic), [Cu(2‐MeSnic)₂L₂(H₂O)₂] (where L is py and nicotinamide — nia) and [Cu(2‐MeSnic)₂(N‐Menia)₂(H₂O)₂]·2H₂O (where N‐Menia is N‐methylnicotinamide) are reported. The characterization were based on elemental analysis, infrared, electronic and EPR spectra, and magnetic susceptibility measurements over a temperature range of 1.8 — 300 K or 70 — 300 K. Three complexes of different type were studied by X‐ray analysis. The molecule of [Cu(2‐MeSnic)₂(CH₃OH)]₂ has dimeric paddle‐wheel cage structure with a tetragonal pyramidal arrangement around Cu^II. The dimer results from the fact that carboxyl groups of four 2‐MeSnic anions function as bridging in a syn‐syn arrangement. On the other hand [Cu(2‐MeSnic)₂(py)₂]₂ forms dimers with hexacoordinated Cu^II atoms in highly distorted coordination octahedra, each with two oxygen atoms of bridging carboxyl groups in an anti‐anti arrangement of two 2‐MeSnic anions, with two oxygen atoms of one asymmetrically chelating 2‐MeSnic anion and with two nitrogen atoms of two pyridine ligands. The temperature independent EPR spectrum for this complex exhibits an axial signal which corresponds to almost isolated S = ¹/₂ magnetic ions. Magnetic data for the dimer show a weak antiferromagnetic interaction between the two metal ions with J = —0.65 cm^—1. The Cu^II atom in complex [Cu(2‐MeSnic)₂(py)₂(H₂O)₂] is hexacoordinated in an elongated centrosymmetrical tetragonal‐bipyramidal arrangement (4 + 2). Based on the molecular structure the electronic, infrared, electron paramagnetic resonance spectra and magnetic properties are discussed and stereochemistry as well as the mode of ligand coordination in new solid complexes under study have been determined.     

5,10:13,14-Disecosteroids: novel modified steroids containing 10- and 9-membered rings

In this paper a synthetic pathway to the modified 5,10:13,14-bisfragmentation cholestane derivatives 8-14 is described. The synthesis involves introduction of the 5α- and 14α-hydroxyl groups in the cholestane molecule and subsequent cleavage of the C(5)-C(10) bond in 5α,14α-dihydroxycholestan-3β-yl acetate (4) with the HgO/I₂ reagent and the C(13)-C(14) bond in the stereoisomeric 14α-hydroxy-5,10-secosteroids 5 and 6 with the Pb(OAc)₄/I₂ reagent. Complete and unambiguous ¹H and ¹³C NMR resonance assignments of the obtained secosteroids, as well as the solution conformations of their 10- and 9-membered rings were determined by extensive analysis of 1D and 2D NMR spectral data. The structures and the solid-state conformations of 5,10-secosteroids 5-7 were confirmed by X-ray analysis. All diseco-compounds have a novel 5,10:13,14-disecocholestane skeleton.     

Gas phase and solution state stability of complexes L…M, where M = Cu, Ni, or Zn and L = R−C(O)NHOH (R = H, NH2, CH3, CF3, or Phenyl)

The structure and gas-phase metal affinities (M = Cu²⁺, Ni²⁺, and Zn²⁺) of formohydroxamic acid derivatives R–C(O)NHOH (R = H, NH₂, CH₃, CF₃ and Phenyl) were studied using the B3LYP/6-311+G(d,p) method of DFT theory. In order to evaluate the conformational behavior of these systems in water, we carried out CPCM-SCRF optimization calculations at the B3LYP/6-311+G(d,p) levels of theory. The obtained optimized geometries and interaction affinities of the gas and solution phase were compared. The following order of stability was found for ionic complexes of the transition metals: Cu²⁺ > Ni(t)²⁺ > Zn²⁺. The same stability order would be expected according to the Irving–Williams order of stability constants. The high-spin complexes of the Ni²⁺ were more stable than the low-spin complexes. The solvent effect reduced the observed relative stability of individual metallic complexes of substituted hydroxamic acids.     

Incorporating glycidyl methacrylate into block copolymers using poly(methacrylate‐ran‐styrene) macroinitiators synthesized by nitroxide‐mediated polymerization

Methyl methacrylate/styrene (MMA/S), ethyl methacrylate/styrene (EMA/S) and butyl methacrylate/styrene (BMA/S) feeds (>90 mol % methacrylate) were copolymerized in 50 wt % p‐xylene at 90 °C with 10 mol % of additional SG1‐free nitroxide mediator relative to unimolecular initiator (BlocBuilder^®) to yield methacrylate rich copolymers with polydispersities _w/ _n = 1.23–1.46. k_pK values (k_p = propagation rate constant, K = equilibrium constant) for MMA/S copolymerizations were comparable with previous literature, whereas EMA/S and BMA/S copolymerizations were characterized by slightly higher k_pK's. Chain extensions with styrene at 110 °C initiated by the methacrylate‐rich macroinitiators (number average molecular weight _n = 12.9–33.5 kg mol^?1) resulted in slightly broader molecular weight distributions with _w/ _n = 1.24–1.86 and were often bimodal. Chain extensions with glycidyl methacrylate/styrene/methacrylate (GMA/S/XMA where XMA = MMA, EMA or BMA) mixtures at 90 °C using the same macroinitiators resulted frequently in bimodal molecular weight distributions with many inactive macroinitiators and higher _w/ _n = 2.01–2.48. P(XMA/S) macroinitiators ( _n = 4.9–8.9 kg mol^?1), polymerized to low conversion and purified to remove “dead” chains, initiated chain extensions with GMA/MMA/S and GMA/EMA/S giving products with _w/ _n ～ 1.5 and much fewer unreacted macroinitiators (<5%), whereas the GMA/BMA/S chain extension was characterized by slightly more unreacted macroinitiators (～20%). © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2574–2588, 2009     

Supramolecular dimer formation through hydrogen bond extensions of carboxylate ligands – Path for magnetic exchange

A new complex of unusual composition [Cu(3-O₂Nbz)₂(nia)(H₂O)₂] (1) (nia = nicotinamide, 3-O₂Nbz = 3-nitrobenzoate) has been prepared and studied together with two other complexes of composition [Cu(4-O₂Nbz)₂(nia)₂(H₂O)₂] (2) and [Cu(4-O₂Nbz)₂(nia)₂]?(4-O₂NbzH)₂ (3) (4-O₂Nbz = 4-nitrobenzoate). The composition of all complexes has been determined by elemental analysis, the complexes have been studied by electronic, infrared and EPR spectroscopy, as well as by magnetization measurements over the temperature range 1.8–300 K, and their structures have been solved. The structure of complex (1) consists of molecules, where Cu(II) atom is monodentately coordinated by the pair of 3-nitrobenzoato anions in trans  -positions together with water and nicotinamide molecules, forming nearly tetragonal basal plane, and by another water molecule in axial position of tetragonal-pyramidal coordination polyhedron. The neighboring molecule coordination polyhedron basal planes are coplanar and allow formation of supramolecular dimers with strong H-bonds between hydrogen atoms from equatorially coordinated water molecules and uncoordinated carboxylate oxygen atoms thus giving the nearest Cu?$?$Cu distance of 4.886(2) Å. Magnetization measurements showed that complex (1) exhibits maximum of magnetic susceptibility at 6.5 K and a fit to Bleaney-Bowers equation gave singlet–triplet energy gap 2J = −6.25 cm⁻¹, and zJ′ = −0.03 cm⁻¹. This might be an experimental proof that the carboxylate bridges extended with hydrogen bonds are the pathway of the spin–spin interactions. The temperature dependence of changes in EPR spectra of (1) and the spectrum at 4.2 K have confirmed its hydrogen bonded dimeric structure. The calculated Cu?$?$Cu distance 4.8 Å is in very good agreement with the value obtained from crystal structure. The complexes (2) and (3) at 300 K exhibit magnetic moment μ_eff = 1.98 B.M. and μ_eff = 1.84 B.M., respectively. These values practically do not change with lowering the temperature up to 5 K and only small drops to μ_eff = 1.87 B.M. (for (2)) and μ_eff = 1.79 B.M. (for (3)) at 1.8 K have been observed. The EPR spectra of complex (2) at room temperature as well as at 77 K are of axial type with g_⊥ = 2.062 and g_|| = 2.285 and exhibit resolved parallel hyperfine splitting with A_|| = 160 Gauss. The EPR spectra of complex (3) at room temperature as well as at 77 K are of axial type with g_⊥ = 2.065 and g_|| = 2.235 and exhibit unresolved parallel hyperfine splitting. EPR spectra of (2) and (3) are consistent with the X-ray structure.     

On‐line flow‐through extraction–preconcentration‐large volume injection‐RP LC for trace determination of pyrethroids in Slovak soil

A rapid micro‐analytical multiresidue method was developed for analysis of pyrethroids (kadethrin K, cypermethrin C and permethrin P) in soil micro‐sample (200 mg). It uses on‐line flow‐through extraction of soil micro‐samples (packed into a short glass column) with a methanol‐aqueous citric acid buffer mixture, successive on‐line SPE preconcentration of analytes from the extract and on‐line RP‐HPLC analysis with UV photometric detection. The separation of pyrethroids is performed on a Purospher RP‐18e column with methanol/water as mobile phase. Effects of sorbent placed at the bottom of a short column holding the soil sample and different kinds of on‐line SPE columns were tested. Besides, the influence of volume of the effluent on the pyrethroids recovery was also studied. Calibration curves were linear over the range assayed from 0.01 to 0.2 μg/mL with correlation coefficients of linear regression (least‐squares method) in the range 0.998–0.999. Recovery studies were carried out at 0.25–1.00 μg/g dry soil fortification level and obtained recoveries were for K 81–84%, C 56–59% and for P 58–63%. Achieved LOD (confidence band) of studied pyrethroids were for large‐volume injection (1 mL) 4.5 ng K, 3.7 ng C, 3.6 ng P or 27 ng/g K, 32 ng/g C and 29 ng/g P in dry soil “solid sampling HPLC”.     

Dibenzo[b,f]oxepin‐10(11H)‐one and dibenzo[b,f]thiepin‐10(11H)‐one as useful synthons in the synthesis of various dibenzo[e,h]azulenes

The present review focuses on dibenzo[b,f]oxepin‐10(11H)‐one ( I , X = O) and dibenzo[b,f]thiepin‐10(11H)‐one ( I , X = S) as common synthons in the efficient synthesis of various dibenzoxepino[4,5‐ and dibenzothiepino[4,5]‐fused five‐membered heterocycles: [2,3] fused thiophene ( II ), [3,4] fused thiophene ( III ), furan ( IV ), pyrrole ( V ), imidazole ( VI ), pyrazole ( VII ), oxazole ( VIII ), and thiazole ( IX ). The potential of I to be converted into reactive intermediates that readily undergo heteroaromatic annulation reactions by cyclocondensation with proper binucleophiles allows formation of a range of enumerated functionalized dibenzo[e,h]azulene [4] structures ( II , III , IV , V , VI , VII , VIII , IX ). Dibenzo[e,h]azulenes as heterotetracyclic scaffold can be exploited in further modifications to obtain compounds with altered physicochemical and biological profile. J. Heterocyclic Chem., (2012).     

Immobilization in biotechnology and biorecognition: from macro- to nanoscale systems

Biological molecules such as enzymes, cells, antibodies, lectins, peptide aptamers, and cellular components in an immobilized form are extensively used in biotechnology, in biorecognition and in many medicinal applications. This review provides a comprehensive summary of the developments in new immobilization materials, techniques, and their practical applications previously developed by the authors. A detailed overview of several immobilization materials and technologies is given here, including bead cellulose, encapsulation in ionotropic gels and polyelectrolyte complexes, and various immobilization protocols applied onto surfaces. In addition, the review summarises the screening and design of an immobilization protocol, practical applications of immobilized biocatalysts in the industrial production of metabolites, monitoring, and control of fermentation processes, preparation of electrochemical/optical biosensors and biofuel cells.