Precise mass measurement of a double-stranded 500 base-pair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/μL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd.     

Ciliation and lamellae in crystalline polymers

Molecular cilia, the uncrystallized portions of chains already partly attached to polymer crystals, exert a profound influence on the course of polymeric crystallization with ultimate responsibility for the divergence of adjacent lamellae which leads to spherulitic growth. Their effective size and pressure have been measured, in α-polypropylene, from electron microscopic measurements of the separation and maximum curvature of lamellae in row structures. That cilia exist and extend the effective region occupied by a lamella beyond the geometrical confines of its fold surfaces is important for crystallization theory and may well have implications for the connection of lamellae into networks and for gelation.     

Thermal decomposition products of a chlorinated aromatic polyamide

Products from the thermal decomposition of a chlorinated aromatic polyamide fabric are described for conditions of pyrolysis and flaming and nonflaming oxidative degradation. Volatile degradation products were identified by gas chromatography-mass spectrometry (GC-MS) and the condensible fraction, by infrared (IR) spectroscopy, high-pressure liquid chromatography (HPLC), and MS. Nonvolatile char was characterized by IR and elemental analysis. Twenty-one compounds were identified as volatile products from pyrolysis at 550°C; the condensible material contained ammonium chloride and at least 22 organic compounds. From volatile compounds produced in flaming oxidative degradation 21 compounds were identified, of which CO, CO₂, and H₂O were prominent. Nonflaming oxidative degradation at 400 and 550°C produced 11 and 21 volatile identifiable compounds, respectively, and results from experiments at the higher temperature compared favorably with results from the flaming experiments. By comparison of data from this work with those from unchlorinated analogs (described in an earlier article), it is concluded that the incorporation of chlorine into the polymeric structure lowers the temperature for the onset of thermal degradation and alters the type and concentration of thermolytic products. The major degradation products can be explained by a mechanism similar to that proposed for aromatic polyamides with the exception of the formation of substantial amounts of ammonium chloride. It is proposed that the latter is formed by an initial acid-catalyzed hydrolysis reaction which is followed by deammoniation or by an intermolecular process that involves an isoimide intermediate.     

Methyl dynamics in crystalline amino acids: MD and NMR

Correlation times for rotation of deuterated methyls in crystalline leucine, valine, and cyclo-L-alanyl-L-alanine are calculated with molecular dynamics and compared with NMR data. The simulations distinguish between methyls having different steric environments in the crystal, yielding correlation times differing by a factor of up to 30 for methyls within a given crystal. MD and NMR correlation times agree to within a factor of 2. However, averaging over nonequivalent methyls can yield correlation functions that, although actually multiexponential, are well fit by single exponentials. This may have significance for interpreting NMR data; previous NMR data did not distinguish between the methyls in these crystals. Adiabatic rotational barriers calculated with the X-ray structure differ from effective barriers during simulation by up to +/-1 kcal/mol; the difference indicates that dynamical effects have a significant role in determining rotational correlation times.     

Radiochemical neutron activation analysis of chromium in biological materials using ion chromatography with “on-line” yield determination

The use of ion chromatography with continuous UV detection for radiochemical separation of Cr with simultaneous yield determination is presented. The RNAA method consists of sample destruction in HNO₃+HClO₄, extraction of Cr(VI) with tribenzylamine in CHCl₃, backextraction in NaOH and chromatography of chromate. From radiotracer experiments, the ratio of signals for⁵¹Cr and Cr spike was found to be constant for a chromium mass range of 15 to 100 g. Application of the RNAA method to Cr determination in biological reference materials showed a reasonable agreement with the reference values. A relative standard deviation of 3% on the 100 g/kg level for homogeneous material was achieved.IAEA-fellow, on leave from the Philippine Nuclear Research Institute Philippine     

Analysis of the products of thermal decomposition of an aromatic polyamide fabric

The thermal degradation of an aromatic polyamide was studied under conditions of pyrolysis and oxidative degradation at 550°C and of flaming combustion. Techniques described elsewhere were used to determine the volatile compounds quantitatively by gas chromatography-mass spectrometry (GC–MS). The condensible material and the solid residue were characterized by infrared spectroscopy and MS, and in pyrolysis experiments 28 compounds were identified (CO, CO₂, H₂O, and C₆H₅CN were the primary products). Collectively, these compounds accounted for 79% of the sample weight loss. The remaining 21% was a condensible material that contained at least 17 compounds; the two major components were 1,3-dicyanobenzene and 3-cyanobenzoic acid. Most of the nitrogen content of the polymer remained as involatile residue. This study was sufficiently detailed to obtain a mass balance between the composition of the original polymer and the sum of the observed pyrolysis products. The major products observed in pyrolysis experiments supported a mechanism that involved the cleavage of an aromatic-NH bond and the loss of H₂O to form aromatic nitriles. Hydrolysis of the amide linkage, followed by decarboxylation of the product acid, accounted for the high concentrations of CO₂ observed. Oxidative degradation at 450°C yielded ten identifiable compounds and an additional 19 volatile compounds were formed at 550°C. The condensible fraction, which contained at least 20 compounds, was similar in composition to the fraction collected from the pyrolysis experiments. The sum of the carbon content from the two major volatile products of oxidative degradation (CO and CO₂) and from the solid residue quantitatively accounted for the carbon content in the original sample. Flaming combustion studies revealed a markedly different product distribution than was observed under nonflaming conditions, especially in regard to the higher-molecular-weight species.     

Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations

The application of hybrid quantum mechanical and molecular mechanical (QM/MM) potentials to the study of chemical reactions in enzymes is outlined. The discussion is general and addresses the difficulties encountered in an enzyme QM/MM study. First, general criteria for determining whether a particular enzyme is an appropriate candidate for a QM/MM approach are outlined. Methods for obtaining starting structures are detailed. The importance of choosing appropriate levels of ab initio or semiempirical theory is emphasized. Approaches for interfacing the QM and MM regions are briefly discussed, with greater detail given to describing our CHARMM-GAMESS interface. Techniques for partitioning the system into QM and MM regions are explored. Link atom placement, as distant from reacting atoms as possible within the confines of computational efficiency, is examined in some detail. Methods for determining reaction paths are also discussed. © 1996 John Wiley & Sons, Inc.     

Method ruggedness studies incorporating a risk based approach: a tutorial

This tutorial explains how well thought-out application of design and analysis methodology, combined with risk assessment, leads to improved assessment of method ruggedness. The authors define analytical method ruggedness as an experimental evaluation of noise factors such as analyst, instrument or stationary phase batch. Ruggedness testing is usually performed upon transfer of a method to another laboratory, however, it can also be employed during method development when an assessment of the method's inherent variability is required. The use of a ruggedness study provides a more rigorous method for assessing method precision than a simple comparative intermediate precision study which is typically performed as part of method validation. Prior to designing a ruggedness study, factors that are likely to have a significant effect on the performance of the method should be identified (via a risk assessment) and controlled where appropriate. Noise factors that are not controlled are considered for inclusion in the study. The purpose of the study should be to challenge the method and identify whether any noise factors significantly affect the method's precision. The results from the study are firstly used to identify any special cause variability due to specific attributable circumstances. Secondly, common cause variability is apportioned to determine which factors are responsible for most of the variability. The total common cause variability can then be used to assess whether the method's precision requirements are achievable. The approach used to design and analyse method ruggedness studies will be covered in this tutorial using a real example.     

1,3-dipolar cycloadditions of trimethylsilyldiazomethane revisited: steric demand of the dipolarophile and the influence on product distribution

The 1,3-dipolar cycloaddition of trimethylsilyldiazomethane with alpha,beta-unsaturated esters was examined. The resulting 1-pyrazolines isomerize to regioisomeric 2-pyrazolines (a or b) or undergo desilylation (c). Acrylates yield only b or c. beta-Substituted dipolarophiles may yield all three types of products. This work demonstrates that the distribution of 2-pyrazoline products is highly dependent on the relative configuration of the substituents on the 1-pyrazoline intermediate.