MOVIPAC: Vibrational spectroscopy with a robust meta‐program for massively parallel standard and inverse calculations

We present the software package MO VI PAC for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. MO VI PAC unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add‐ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta‐program design, MO VI PAC focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode‐ and Intensity‐Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π‐helix consisting of 20 (S)‐alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α‐ and 3₁₀‐helical analogs. © 2012 Wiley Periodicals, Inc.     

Successions in Words and Compositions

We consider words over the alphabet [k] = {1, 2, . . . , k}, k ?? 2. For a fixed nonnegative integer p, a p-succession in a word w ₁ w ₂ . . . w _n consists of two consecutive letters of the form (w _i , w _i ?+ p), i = 1, 2, . . . , n ? 1. We analyze words with respect to a given number of contained p-successions. First we find the mean and variance of the number of p-successions. We then determine the distribution of the number of p-successions in words of length n as n (and possibly k) tends to infinity; a simple instance of a phase transition (Gaussian-Poisson-degenerate) is encountered. Finally, we also investigate successions in compositions of integers.     

Detection and characterization of silver nanoparticles in chicken meat by asymmetric flow field flow fractionation with detection by conventional or single particle ICP-MS

A method of analysis of silver nanoparticles (AgNPs) in chicken meat was developed. The homogenized chicken meat sample, which was spiked with AgNPs, was subjected to enzymolysis by Proteinase K for 40 min at 37 °C. Transmission electron microscopy and inductively coupled plasma mass spectrometry (ICP-MS) in single particle mode were used to characterize the number-based size distribution of AgNPs in the meat digestate. Because similar size distributions were found in the meat digestate and in the aqueous suspension of AgNPs used for spiking the meat, it was shown that no detectable dissolution of the AgNPs took place during the sample preparation stage. The digestate was injected into the asymmetric flow field flow fractionation (AF⁴) -ICP-MS system, which enabled fractionation of nanoparticles from the remaining meat matrix, and resulted in one large peak in the fractograms as well as two smaller peaks eluting close to the void volume. The recovery of silver contained in the large AgNP peak was around 80 %. Size determination of AgNPs in the meat matrix, based on external size calibration of the AF⁴ channel, was hampered by non-ideal (early elution) behavior of the AgNPs. Single particle ICP-MS was applied for determination of the number-based particle size distribution of AgNPs in collected fractions. The presented work describes for the first time the coupling of AF⁴ and ICP-MS for AgNP separation in a food matrix.     

Accurate quantification of the redox-sensitive GSH/GSSG ratios in the yeast Pichia pastoris by HILIC–MS/MS

A novel method for the simultaneous quantification of both glutathione (GSH) and its oxidized form glutathione disulfide (GSSG) by hydrophilic interaction chromatography–MS/MS has been developed and is critically discussed. Internal standardization based on isotopically labeled standards for both analytes is an absolute prerequisite for accurate quantification of this redox pair. Hence, a highly efficient and selective miniaturized procedure for the synthesis of isotopically labeled GSSG from commercially available glutathione-(glycine-¹³C₂,¹⁵N) was established using H₂O₂ as oxidant and NaI as catalyst. Moreover, a tool is presented to monitor and hence uncover artifactual GSSG formation due to oxidation of GSH during sample preparation, which is the main source of systematic error in GSSG analysis. For this purpose, we propose to monitor the oxidation product formed by reaction of naturally occurring GSH with the isotopically labeled GSH used as internal standard. For the determination of GSH/GSSG ratios in yeast, different extraction methods based on (1) hot extraction with aqueous, acidic, or organic solvents, (2) mechanical cell lysis, and (3) extraction at subambient temperature were investigated in terms of recovery, extraction efficiency, and artifactual formation of GSSG. Total combined uncertainties of as low as 25–30 % (coverage factor?=?2) for the determination of GSH/GSSG ratios without derivatization were made possible by the addition of the internal standards early in the analytical procedure (before extraction) and immediate analysis of the analytes.     

Multidimensional nano-HPLC coupled with tandem mass spectrometry for analyzing biotinylated proteins

Multidimensional high-performance liquid chromatography (HPLC) is a key method in shotgun proteomics approaches for analyzing highly complex protein mixtures by complementary chromatographic separation principles. Here, we describe an integrated 3D-nano-HPLC/nano-electrospray ionization quadrupole time-of-flight mass spectrometry system that allows an enzymatic digestion of proteins followed by an enrichment and subsequent separation of the created peptide mixtures. The online 3D-nano-HPLC system is composed of a monolithic trypsin reactor in the first dimension, a monolithic affinity column with immobilized monomeric avidin in the second dimension, and a reversed phase C18 HPLC-Chip in the third dimension that is coupled to a nano-ESI-Q-TOF mass spectrometer. The 3D-LC/MS setup is exemplified for the identification of biotinylated proteins from a simple protein mixture. Additionally, we describe an online 2D-nano-HPLC/nano-ESI-LTQ-Orbitrap-MS/MS setup for the enrichment, separation, and identification of cross-linked, biotinylated species from chemical cross-linking of cytochrome c and a calmodulin/peptide complex using a novel trifunctional cross-linker with two amine-reactive groups and a biotin label.

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.