Preparative isolation of (+)-beta-eudesmol fromAmyris balsamifera

Summary Optically pure (+)-beta-eudesmol is a possible starting material for the synthesis of several termite defense compounds. A two step procedure for the isolation of gram quantities of (+)-beta-eudesmol from commercially availableAmyris balsamifera oil (syn. West Indian sandalwood oil), containing 8% beta-eudesmol, was developed. Step one consisted of an efficient vacuum distillation of the total oil. Step two was a medium pressure LC separation with an AgNO₃ impregnated silica gel stationary phase. Several other separation procedures failed due to the presence of many closely related sesquiterpene alcohols (75% of the oil).     

Chiral separations of basic drugs and quantitation of bupivacaine enantiomers in serum by capillary electrophoresis with modified cyclodextrin buffers.

Modified cyclodextrin derivatives were evaluated as the buffer additives in capillary electrophoresis of several racemic pharmaceutical bases. Uncoated and polyacrylamide-modified silica capillaries were compared for their effectiveness in the enantiomeric resolution and migration reproducibility of model solutes. Using cationic detergents in the mixed-micellar mode, optimized separations of the racemic drug bupivacaine are demonstrated in a spiked serum sample at the therapeutic level. Precision, linearity and sensitivity of the method appear adequate for reliable quantitation required in pharmacokinetic and clinical studies.     

Dipyrrylmetheneboron Difluorides as Labels in Two-Photon Excited Fluorometry. Part II–Nucleic Acid Hybridization Assays

Five two-photon excitable dipyrrylmetheneboron difluoride labels (dipyrrylmethene-BF₂ labels) with fluorescence emission maximum between 530 and 590 nm, and a frequently used rhodamine label, TAMRA, were conjugated to aminomodified oligonucleotides. The performance of the labeled oligonucleotides was studied in a separation-free nucleic acid hybridization assay using ArcDia^™ TPX bioaffinity assay technology. The results show that oligonucleotide conjugates of dipyrrylmethene-BF₂ labels provide higher two-photon excited fluorescence yield and better assay sensitivity than corresponding TAMRA conjugate. The effect of conjugation on photophysical properties of the labels and performance of the labeled oligonucleotides in separation-free hybridization assay is discussed.     

Hydrophilic Labeling Reagents of Dipyrrylmethene-BF2 Dyes for Two-Photon Excited Fluorometry: Syntheses and Photophysical Characterization

Recently introduced bioaffinity assay technology, ArcDia TPX, is based on two-photon excited fluorescence (TPE) and it enables separation-free ultra-sensitive immunoassays from microvolumes. Here we present syntheses of novel two-photon excitable fluorescent labeling reagents which have been specially designed to be used as label molecules in the ArcDia TPX assay technique. The labeling reagents are based on dipyrrylmetheneboron difluoride (dipyrrylmethene-BF2) chromophore, which have been substituted with aryl, heteroaryl or arylalkenyl chemical groups to extend the pi-electron conjugation. These substitutions results in a series of dipyrrylmethene-BF2 fluorophores with different photophysical properties. Dipyrrylmethene-BF2 fluorophores have been further substituted with a dipeptide linker unit and finally activated as succinimidyl esters to enable specific coupling with primary amino groups. The dipeptide linker serves as a spacer arm between the label and a target, and enhances the solubility of the label in aqueous solutions. Study of the chemical and photophysical performance of the new labeling reagents is described. The new labeling reagents exhibit high fluorescence quantum yields, and molar absorption coefficients. The results show that the new labels with the hydrophilic dipeptide linker unit provide large two-photon excitation cross-sections, high fluorescence quantum efficiency and good solubility in aqueous solutions. The results suggest that the novel dipyrrylmethene-BF2 labels are highly applicable to bioaffinity assays based on two-photon excitation of fluorescence.     

Retention mechanisms and selectivity in internal-surface reversed-phase liquid chromatography. Studies with cyanobacterial peptide toxins

Summary Microcystins-LA,-LR,-RR,-YR and nodularin, cyanobacterial peptide toxins, were separated by internal-surface reversed-phase (ISRP), high-performance liquid chromatography. The capacity factors of the toxins were measured in the range pH 2–8 using acetonitrile, isopropanol or tetrahydrofuran in potassium dihydrogenphosphate mobile phase. The main retention mechanism of the ISRP column was reversed-phase interaction but cation-exchange offered additional selectivity at neutral and slightly acidic pH. At neutral pH (10% modifier, 0.1 M buffer) the elution order was microcystin-LA (two nonpolar residues leucine and alanine as the variable amino acids), nodularin, microcystin-LR,-YR and-RR (two basic arginines as the variable amino acids). The retention times of all toxins except microcystin-RR were substantially longer at acidic pH. At pH 2 (10% modifier, 0.1 M buffer) where the cation-exchange mechanism was inoperative the elution order was changed to microcystin-RR, nodularin, microcystin-LR,-YR and-LA. The best separation was achieved at pH 2 where even two desmethylated microcystin-RR analogs could be separated from microcystin-RR.     

PyFrag 2019—Automating the exploration and analysis of reaction mechanisms

We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Load balancing by work–stealing in quantum chemistry calculations: Application to hybrid density functional methods

Parallel implementations of quantum chemistry programs targeting supercomputers are challenging applications of dynamic load balancing algorithms. The implementation of work stealing (WS) algorithms is discussed and their usefulness is demonstrated. Evaluation of the four‐center integrals of a Cu₁₀ cluster requires 25 core‐hours overall, achieving 88% efficiency with simple WS for 2048 cores, and 97% with task presorting based on a cost estimate. Limitations of cost sorting become noticeable for larger systems. When spatial symmetry is exploited together with integral screening, bundling the original tasks yields an efficiency of 98% for Cu₇₉ in O_h symmetry on 512, 1204, and 2048 cores. The advantage of WS algorithms described in this work is not limited to the evaluation of four‐center integrals. © 2014 Wiley Periodicals, Inc.     

The photometric determination of silicon as α-silicomolybdic acid

A photometric method for the determination of silicon based on the yellow color of α-silicomolybdic acid is described. The pH must be kept within the range 3.0–3.7, and the equilibrium state is established by beating the solution. Since the color of this modification is remarkably stable and reproducible, a high degree of precision can be attained.