Low‐memory iterative density fitting

A new low‐memory modification of the density fitting approximation based on a combination of a continuous fast multipole method (CFMM) and a preconditioned conjugate gradient solver is presented. Iterative conjugate gradient solver uses preconditioners formed from blocks of the Coulomb metric matrix that decrease the number of iterations needed for convergence by up to one order of magnitude. The matrix‐vector products needed within the iterative algorithm are calculated using CFMM, which evaluates them with the linear scaling memory requirements only. Compared with the standard density fitting implementation, up to 15‐fold reduction of the memory requirements is achieved for the most efficient preconditioner at a cost of only 25% increase in computational time. The potential of the method is demonstrated by performing density functional theory calculations for zeolite fragment with 2592 atoms and 121,248 auxiliary basis functions on a single 12‐core CPU workstation. © 2015 Wiley Periodicals, Inc.     

Molecular characterization and first report of Cryptosporidium genotypes in human population in the Slovak Republic

In our study, we examined 91 fecal samples from five different groups of people containing HIV patients, hemodialysis patients, kidney transplant recipients, immunocompetent humans without clinical signs, and humans with suspected cryptosporidiosis. The purpose of our study was to determine species and genotype composition of representatives of Cryptosporidium spp. using PCR analysis of small subunit ribosomal RNA gene and 60‐kDa glycoprotein gene and examine their phylogenetic relationship. In HIV‐positive/AIDS‐infected group of patients and in hemodialysis patients, no presence of Cryptosporidium species was detected. In two kidney transplant recipients, we detected species/genotypes Cryptosporidium parvum IIaA13G1T1R1 (KT355488) and Cryptosporidium hominis IaA11G2R8 (KT355489) and in two immunocompetent patients with clinical symptoms, we identified Cryptosporidium muris and C. hominis IbA10G2T1 (KT355490). In the group of healthy immunocompetent individuals without clinical signs, we identified species/genotype C. hominis IbA11G2 (KT355491) in one sample.     

In-line coupling of microextractions across polymer inclusion membranes to capillary zone electrophoresis for rapid determination of formate in blood samples

Polymer inclusion membranes (PIMs) have several important features, i.e., PIMs are dry and non-porous membranes, which can be prepared ahead of use and stored without noticeable deterioration in extraction performance. In this contribution, in-line coupling of microextractions across PIMs to a separation method for clinical purposes was demonstrated for the first time. Formate (the major metabolite in methanol poisoning) was determined in undiluted human serum and whole blood by capillary zone electrophoresis (CZE) with simultaneous capacitively coupled contactless conductivity detection (C⁴D) and UV–Vis detection. A purpose-made microextraction device with PIM was coupled to a commercial CZE instrument in order to ensure complete automation of the entire analytical procedure, i.e., of formate extraction, injection, CZE separation and quantification. PIMs for formate extractions consisted of 60% (w/w) cellulose triacetate as base polymer and 40% (w/w) Aliquat™ 336 as anion carrier. The method was characterized by good repeatability of peak areas (≤7.0%) and migration times (≤0.8%) and by good linearity of calibration curves (r² = 0.993–0.999). Limits of detection in various matrices ranged from 15 to 54 μM for C⁴D and from 200 to 635 μM for UV–Vis detection and were sufficiently low to clearly distinguish between endogenous and toxic levels of formate in healthy and methanol intoxicated individuals. In addition, PIMs proved that they may act as phase interfaces with excellent long-term stability since once prepared, they retained their extractions properties for, at least, two months of storage.     

Synthesis of potential inhibitors of glycosyltransferases representing UDP-GlcNAc

Based on rational design of the transition state analog inhibitors of glycosyltransferases, four model glycomimetics of this type, viz. benzyl 2-thio-α-dfructofuranoside 1-diethylphosphate (XIa), its β-anomer (XIb), and their ethyl 2-thio analogs — α-anomer (XIIa) and β-anomer (XIIb), were synthesized. In addition, fourteen precursors arising during the synthesis of the desired final model compounds (XI and XII), partially or fully acetylated benzyl and/or ethyl 2-thiofructofuranoside 1-diethyl phosphates, were isolated and characterized with the aim to prepare complete series of glycomimetics, representing donor UDP-GlcNAc designated for biological assays on human GnT’s, viz. GnT-I, Core2GnT, and GnT-V.     

Determination of acid volatile sulphur in river sediments by ICP-OES coupled with purge and trap method

The developed and tested method is based on the acid volatile sulphur (AVS) releasing from a sample of sediment by acidification with hydrochloric acid and sequential absorption of released hydrogen sulphide into the absorption solution of sodium hydroxide. Total sulphur absorbed in the absorption solution is subsequently determined by inductively coupled plasma optical emission spectrometry (ICP-OES) technique. The method was tested using both model and real samples of the river sediment. Obtained results were compared with the results of iodometric determination as the method routinely used for the AVS determination. In case of using ICP-OES with purge and trap, there is no spectral interference of calcium; therefore for the determination of sulphur, it is possible to use atomic emission line of sulphur S I 180.7 nm. The tested method provides the results comparable with the iodometric method within the range of tested concentrations. The detection limit (LOD) of this method is 0.09 mg· S^2? ? L^?1 in the absorption solution which corresponds to 0.23 mg S^2?·kg^?1 in a sediment. Value of LOD is comparable with the iodometric determination.     

Robust model-based predictive control of exothermic chemical reactor

A case study of the robust model-based predictive control (MPC) of an exothermic continuous stirred tank reactor (CSTR) with uncertain parameters is presented. Three robust MPC approaches are considered and the simulation results are compared in terms of quality of control performance and total consumption of coolant. The results reveal the main benefits of the considered approaches and confirm that the robust MPC can bring about a reduction in consumption of the coolant.     

Formation of a vanillic Mannich base — theoretical study

One-pot anti-Mannich reaction of vanillin, aniline and cyclohexanone was successfully catalyzed by ionic liquid triethanolammonium chloroacetate, at room temperature. Yield of the obtained Mannich base was very good and excellent diastereoselectivity was achieved. Mechanism of the reaction was investigated using the density functional theory. The reaction started with a nucleophilic attack of aniline nitrogen at the carbonyl group of vanillin. The intermediate α-amino alcohol formed in this way was further subjected to protonation by the triethanolammonium ion yielding the imminium ion. Theoretically, the obtained imminium ion and the enol form of cyclohexanone can build the protonated Mannich base via the anti and syn pathways. The chloroacetic anion spontaneously abstracts the proton yielding the final product of the reaction anti 2-[1-(N-phenylamino)-1-(4-hydroxy-3-methoxyphenyl)]methylcyclohexanone (MB-H). The syn pathway requires lower activation energy but the anti pathway yields a thermodynamically more stable product, which implies that the examined Mannich reaction is thermodynamically controlled.