Wave‐function frozen‐density embedding: Approximate analytical nuclear ground‐state gradients

We report the derivation of approximate analytical nuclear ground‐state uncoupled frozen density embedding (FDEu) gradients for the resolution of identity (RI) variant of the second‐order approximate coupled cluster singles and doubles (RICC2) as well as density functional theory (DFT), and an efficient implementation thereof in the KOALA program. In order to guarantee a computationally efficient treatment, those gradient terms are neglected which would require the exchange of orbital information. This approach allows for geometry optimizations of single molecules surrounded by numerous molecules with fixed nuclei at RICC2‐in‐RICC2, RICC2‐in‐DFT, and DFT‐in‐DFT FDE level of theory using a dispersion correction, required due to the DFT‐based treatment of the interaction in FDE theory. Accuracy and applicability are assessed by the example of two case studies: (a) the Watson‐Crick pair adenine‐thymine, for which the optimized structures exhibit a maximum error of about 0.08 Å for our best scheme compared to supermolecular reference calculations, (b) carbon monoxide on a magnesium oxide surface model, for which the error amount up to 0.1 Å for our best scheme. Efficiency is demonstrated by successively including environment molecules and comparing to an optimized conventional supermolecular implementation, showing that the method is able to outperform conventional RICC2 schemes already with a rather small number of environment molecules, gaining significant speed up in computation time. © 2016 Wiley Periodicals, Inc.     

CpPEt2As4—An Organic‐Substituted As4 Butterfly Compound

Cp^PEt₂As₄ (Cp^PEt=C₅(4‐EtC₆H₄)₅) ( 1 ) is synthesized by the reaction of Cp^PEt. radicals with yellow arsenic (As₄). In solution an equilibrium of the starting materials and the product is found. However, 1 can be isolated and stored in the solid state without decomposition. As₄ can be easily released from 1 under thermal or photochemical conditions. From powder samples of Cp^PEt₂As₄, yellow arsenic can be sublimed under rather mild conditions (T=125 °C). A similar behavior for the P₄‐releasing agent was determined for the related phosphorus compound Cp^BIG₂P₄ ( 2 ; Cp^BIG=C₅(4‐nBuC₆H₄)₅). DFT calculations show the importance of dispersion forces for the stability of the products.     

Polyhedral approximation of ellipsoidal uncertainty sets via extended formulations: a computational case study

Robust optimization is an important technique to immunize optimization problems against data uncertainty. In the case of a linear program and an ellipsoidal uncertainty set, the robust counterpart turns into a second-order cone program. In this work, we investigate the efficiency of linearizing the second-order cone constraints of the latter. This is done using the optimal linear outer-approximation approach by Ben-Tal and Nemirovski (Math Oper Res 26:193–205, 2001) from which we derive an optimal inner approximation of the second-order cone. We examine the performance of this approach on various benchmark sets including portfolio optimization instances as well as (robustified versions of) the MIPLIB and the SNDlib.     

Interactive simulation of aircraft noise in aural and visual virtual environments

This paper describes a novel aircraft noise simulation technique developed at RWTH Aachen University, which makes use of aircraft noise auralization and 3D visualization to make aircraft noise both heard and seen in immersive Virtual Reality (VR) environments. This technique is intended to be used to increase the residents’ acceptance of aircraft noise by presenting noise changes in a more directly relatable form, and also aid in understanding what contributes to the residents’ subjective annoyance via psychoacoustic surveys. This paper describes the technique as well as some of its initial applications. The reasoning behind the development of such a technique is that the issue of aircraft noise experienced by residents in airport vicinities is one of subjective annoyance. Any efforts at noise abatement have been conventionally presented to residents in terms of noise level reductions in conventional metrics such as A-weighted level or equivalent sound level L_eq. This conventional approach however proves insufficient in increasing aircraft noise acceptance due to two main reasons – firstly, the residents have only a rudimentary understanding of changes in decibel and secondly, the conventional metrics do not fully capture what the residents actually find annoying i.e. characteristics of aircraft noise they find least acceptable. In order to allow least resistance to air-traffic expansion, the acceptance of aircraft noise has to be increased, for which such a new approach to noise assessment is required.     

Enzymatic assay of marine bacterial phosphatases by capillary electrophoresis with laser-induced fluorescence detection

Microbial ectoenzyme activities in aquatic environments are important determinants of polymer hydrolysis and indicators of the state of microbial carbon, nitrogen, and phosphorus nutrition. Marine ectoenzymes are found on the cell surface or in the periplasmic space of gram-negative heterotrophic bacteria. Phosphatases, which remove phosphate groups from substrates, are one example of an ectoenzyme. Enzyme assays based on-capillary electrophoresis (CE) take advantage of CE's high-efficiency separation, extremely low sample volume requirements, and its ability to electrophoretically mix and separate zones of enzymes, substrates, and products all in one experimental run. CE has better resolving power and, when utilized with laser-induced fluorescence (LIF) detection, it is more sensitive than chromatography. CE-LIF is a promising tool for determining different phosphatases within a single microbial strain as well as the functional diversity between strains. In this study, four bacterial strains were studied (Shewanella sp., TW7, BB2AT2, and Vibrio alginolyticus) with each yielding at least one phosphatase that was kinetically characterized. K(m) values were calculated and found to be in the range of 0.0725-3.35 microM, whereas V(max) values ranged from 1.02 x 10(-3) to 1.05 x 10(-2) microM/min. The large range of values demonstrates differences among the phosphatases, suggesting different roles for each phosphatase not only between the species but also within a single bacterial species. This can have the important implications for organic matter processing in the sea.     

Analysis of pure copper – a comparison of analytical methods

The reliability and performance of various analytical methods for the determination of 22 trace elements in pure copper is compared and discussed. The work was performed in the framework of an interlaboratory comparison for the preparation of four pure copper reference materials with graded element mass fractions of Ag, Al, As, Bi, Cd, Co, Cr, Fe, Mg, Mn, Ni, P, Pb, S, Sb, Se, Si, Sn, Te, Ti, Zn, and Zr. Special analytical results (ET-AAS, ICP-MS) obtained by the authors were described in more detail and were compared to the certified values. Special regard was paid to the influence of the copper matrix on performance and sensitivity of each analytical method and to the dissolution procedure of copper matrix and interferences from insoluble residues. For a generalized evaluation of the figures of merit for each applied elemental analytical method results from several independent laboratories were included in the discussion. Correspondence: Britta Lange, Department of Analytical Chemistry, Reference Materials, Federal Institute for Materials Research and Testing (BAM), Richard-Willstaetter-Str. 11, D-12489 Berlin, Germany     

High yield protection of alcohols, including tertiary and base sensitive alcohols, as benzhydryl ethers by heating with diphenyldiazomethane in the absence of any other reagent

A protecting group that can be introduced efficiently without the need for any acid or base catalysis and which is not prone to acid or base catalysed migration is a significant advantage for many syntheses. Benzhydryl [diphenylmethyl] ethers of sugar lactones are formed in high yield under neutral conditions when the corresponding alcohol is heated with diphenyldiazomethane in an inert solvent such as acetonitrile or toluene; this allows the easy protection of base sensitive and highly hindered tertiary alcohols in the absence of any other reagents.     

A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres

We describe a novel synthetic small molecule which shows an unprecedented stabilization of the human telomeric G-quadruplex with high selectivity relative to double-stranded DNA. We report that this compound can be used in vitro to inhibit telomerase activity and to uncap human POT1 (protection of telomeres 1) from the telomeric G-overhang. We also show that the small molecule G-quadruplex binder induces a partial alteration of shelterin through POT1 uncapping from telomeres in human HT1080 cancer cells and the presence of gammaH2AX foci colocalized at telomeres.     

Development of a library of N-substituted maleimides for the local functionalization of linear polymer chains

A novel kinetic process was investigated for functionalizing "on-demand" local regions of well-defined linear polystyrene chains. This concept relies on the atom transfer radical copolymerization (ATRP) of functional N-substituted maleimides with styrene. This copolymerization is a controlled radical process, which combines two unique kinetic features: i) all the polymers chains are growing simultaneously and ii) the cross-propagation of the comonomers is highly-favored as compared to homopolymerization. Thus, discrete amounts of N-substituted maleimides (e.g., 1 equiv as compared to initiator) are consumed extremely fast in the copolymerization process and are therefore locally incorporated in narrow regions of the growing polystyrene chains. MALDI-TOF analysis of model copolymers indicated that this kinetic concept is efficient. Although a sequence distribution is observed, well-defined polymer chains having only one or two functional maleimide units per chain were found to be the most abundant species. Furthermore, the position of the functional groups in the polystyrene chains can be kinetically-controlled by adding the N-substituted maleimides at desired times during the course of the polymerization. This method is very versatile and can be applied to a wide variety of N-substituted maleimides. Herein, a library of 20 different maleimides bearing various functional groups (e.g., aromatic moieties, fluorinated groups, hydroxy functions, protected esters, protected amines, light-responsive moieties, fluorophores and biorelevant functions such as short poly(ethylene glycol) segments or biotin moieties) was investigated. In most cases, the functional N-substituted maleimides could be efficiently incorporated in the polystyrene chains.     

Determination of disulfide bond patterns in laminin beta1 chain N-terminal domains by nano-high-performance liquid chromatography/matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry

The disulfide bonding patterns in the N-terminal (LN) domains of the basement membrane protein laminin beta1 have not been investigated so far. We report an in-depth mass spectrometric analysis using offline nano-high-performance liquid chromatography/matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (nano-HPLC/MALDI-TOF/TOF-MS) for determining the disulfide bond patterns in the LN-domain of recombinant mouse laminin beta1 chain for the first time. Mass spectra were recorded and the putatively disulfide-linked peptides were subjected to LIFT-TOF/TOF-MS to confirm the disulfide bond. Screening the fragment ion mass spectra of disulfide-linked peptides for characteristic 66-amu patterns (34 u +32 u), arising from symmetric and asymmetric cleavage of disulfide bonds, facilitated their identification. Using various enzymes for proteolytic digestion of a recombinant laminin beta1 chain N-terminal protein fragment, a linear bonding pattern of the eight cysteine residues in the LN-domain of the laminin beta1 chain was observed with a (1-2, 3-4, 5-6, 7-8) connectivity of cysteines. The identical disulfide-bonding pattern was found in E4, the N-terminal laminin beta1 chain fragment derived by elastase digestion of mouse tumor laminin-111, confirming that this pattern also occurs in native laminin.