Quantum chemistry in parallel with PQS

This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux‐based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large—by ab initio standards—molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high‐level calculations (DFT, MP2, CI, and Coupled‐Cluster) can be performed on systems with up to several thousand basis functions on small (4‐32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post‐job visualization and display. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

2-Acetamino-1,2-dideoxynojirimycin—lysine hybrids as hexosaminidase inhibitors

Cyclisation by double reductive amination of 2-acetamino-2-deoxy-d-xylo-hexos-5-ulose with N-2 protected l-lysine derivatives provided 2-acetamino-1,2-dideoxynojirimycin derivatives without any observable epimer formation at C-5. Modifications on the lysine moiety gave access to lipophilic derivatives that exhibited improved hexosaminidase inhibitory activities.     

Factors Affecting the Production of Aromatic Immonium Ions in MALDI 157 nm Photodissociation Studies

Immonium ions are commonly observed in the high energy fragmentation of peptide ions. In a MALDI-TOF/TOF mass spectrometer, singly charged peptides photofragmented with 157 nm VUV light yield a copious abundance of immonium ions, especially those from aromatic residues. However, their intensities may vary from one peptide to another. In this work, the effect of varying amino acid position, peptide length, and peptide composition on immonium ion yield is investigated. Internal immonium ions are found to have the strongest intensity, whereas immonium ions arising from C-terminal residues are the weakest. Peptide length and competition among residues also strongly influence the immonium ion production. Quantum calculations provide insights about immonium ion structures and the fragment ion conformations that promote or inhibit immonium ion formation.

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Comparison of capillary electrophoresis with traditional methods to analyse bovine whey proteins

The separation of the four major whey proteins by sodium dodecyl sulphate (SDS)-capillary gel electrophoresis (CGE) is described. Whilst commercially purified whey proteins could be analysed using the recommended protocol, the more complex nature of an acid whey and a reconstituted whey protein concentrate (WPC) powder necessitated considerable refinement of the CGE sample buffer. Individual whey proteins in the acid whey and WPC samples were then also separated and quantitated using capillary zone electrophoresis, polyacrylamide gel electrophoresis (PAGE) and HPLC methods and the results were compared. The values obtained for -lactalbumin (-Lac) and β-lactoglobulin (β-Lg) were consistent throughout the various methods, although size-exclusion HPLC, SDS-PAGE and SDS-CGE could not separate the two β-Lg variants or the glycosylated form of -Lac from the β-Lg. There was considerable variation in the values for the bovine serum albumin and immunoglobulin determined by the different methods and it was concluded that none of the methods could satisfactorily quantitate all four whey proteins.     

Depolymerization and chemical modification of lignite coal byPseudomonas cepacia strain DLC-07

Applied Biochemistry and Biotechnology - Coal metabolizingPseudomonas cepacia DLC-07 was isolated from soil and shown to use soluble lignite coal as a carbon/energy source.Pseudomonas modified coal...     

Cationic iridium complexes of the Xantphos ligand. Flexible coordination modes and the isolation of the hydride insertion product with an alkene

Reaction of the Ir(I)-Xantphos complex [Ir(κ²-Xantphos)(COD)][BAr^F₄] (Xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene, Ar^F = C₆H₃(CF₃)₂) with H₂ in acetone or CH₂Cl₂/MeCN affords the Ir(III)-hydrido complexes [Ir(κ³-Xantphos)(H)₂(L)][BAr^F₄], L = acetone or MeCN, whereas in non-coordinating CH₂Cl₂ solvent dimeric [Ir(κ³-Xantphos)(H)(μ-H)]₂[BAr^F₄]₂ is formed. A common intermediate in these reactions that invokes a (σ, η²-C₈H₁₃) ligand is reported. Addition of excess tert-butylethene (tbe) to [Ir(κ³-Xantphos)(H)₂(MeCN)][BAr^F₄] results in insertion of a hydride into the alkene to form [Ir(κ³-Xantphos)(MeCN)(CH₂CH₂C(CH₃)₃)(H)][BAr^F₄], an Ir(III) alkyl-hydrido-Xantphos complex. This reaction is reversible, and heating (80 °C) results in the reformation of [Ir(κ³-Xantphos)(H)₂(MeCN)][BAr^F₄] and tbe. These complexes have been characterised by NMR spectroscopy, ESI-MS and single-crystal X-ray diffraction. They show variable coordination modes of the Xantphos ligand: cis-κ²-P,P, fac-κ³-P,O,P and mer-κ³-P,O,P with the later coordination mode like that found in related PNP-pincer complexes.     

Coupling asymmetric flow-field flow fractionation and fluorescence parallel factor analysis reveals stratification of dissolved organic matter in a drinking water reservoir

Using asymmetrical flow field-flow fractionation (AF4) and fluorescence parallel factor analysis (PARAFAC), we showed physicochemical properties of chromophoric dissolved organic matter (CDOM) in the Beaver Lake Reservoir (Lowell, AR) were stratified by depth. Sampling was performed at a drinking water intake structure from May to July 2010 at three depths (3-, 10-, and 18-m) below the water surface. AF4-fractograms showed that the CDOM had diffusion coefficient peak maximums between 3.5 and 2.8 × 10⁻⁶ cm² s⁻¹, which corresponded to a molecular weight range of 680–1950 Da and a size of 1.6–2.5 nm. Fluorescence excitation–emission matrices of whole water samples and AF4-generated fractions were decomposed with a PARAFAC model into five principal components. For the whole water samples, the average total maximum fluorescence was highest for the 10-m depth samples and lowest (about 40% less) for 18-m depth samples. While humic-like fluorophores comprised the majority of the total fluorescence at each depth, a protein-like fluorophore was in the least abundance at the 10-m depth, indicating stratification of both total fluorescence and the type of fluorophores. The results present a powerful approach to investigate CDOM properties and can be extended to investigate CDOM reactivity, with particular applications in areas such as disinfection byproduct formation and control and evaluating changes in drinking water source quality driven by climate change.     

Macroscopic wall number analysis of single-walled, double-walled, and few-walled carbon nanotubes by X-ray diffraction

The layer number is of great importance for nanocarbon materials, such as carbon nanotubes (CNTs) and graphene. While simple optical methods exist to evaluate few-layer graphene, equivalent analysis for CNTs is limited to transmission electron microscopy. We present a simple macroscopic method based on the (002) X-ray diffraction peak to evaluate the average wall number of CNTs in the range from single- to few-walled. The key was the finding that the (002) peak could be decomposed into two basic components: the intertube structure (outer-wall contacts) and the intratube structure (concentric shells). Decomposition of the peaks revealed a linear relationship between the average wall number and the ratio of the intertube and intratube contributions to the (002) peak. Good agreement with CNTs having average wall numbers ranging from 1 to ～5 demonstrated this as a macroscopic method for average wall number analysis.     

Simultaneous multiresidue determination of 48 pesticides in Yeongsan and Sumjin River water using GC-NPD and confirmation via GC-MS

In a continuation of our earlier work, a multiresidual analytical method using 48 frequently used neutral pesticides in a water matrix was developed and validated in this study. The samples were extracted with dichloromethane and the pesticides were analyzed via GC-NPD followed by confirmation with GC-MS. Good linearity was detected over a concentration range of 0.01-1.0 microg/mL with correlation coefficients (r(2) ) in excess of 0.982. The recoveries were measured between 70.7 and 111.4% for the majority of the targeted pesticides with relative standard deviations (RSDs) of less than 20%. The LODs and LOQs were in ranges of 0.1-2 and 0.33-6.6 microg/L, respectively. A total of 66 water samples were collected from different locations in Yeongsan and the Sumjin River, Republic of Korea, and were analyzed in accordance with the developed method. None of the water samples were determined to contain any of the targeted pesticides. The method has been shown to be simpler, faster, and more cost-effective than the method established by the Environmental Protection Agency (EPA).