Examination of complex oligosaccharides by matrix-assisted laser desorption/ionization mass spectrometry on time-of-flight and magnetic sector instruments

Matrix-assisted laser desorption/ionization (MALDI) spectra of underivatized oligosaccharides of the type attached to asparagine in glycoproteins (N-linked oligosaccharides) were examined with linear time-of-flight (TOF) and magnetic sector instruments using 2,5-dihydroxybenzoic acid (2,5-DHB), α-cyano-4-hydroxycinnamic acid, sinapinic acid, 1,4-dihydroxynaphthalene-2-carboxylic acid or 2-(4-hydroxyphenylazo)benzoic acid (HABA) as the matrices. All compounds formed abundant [M + Na]⁺ ions with the strongest signals being obtained from 2,5-DHB after recrystallization of the initially dried sample spot from ethanol. Only traces of fragmentation were detected from neutral oligosaccharides on the TOF system but more abundant fragment ions (about 5% relative abundance) were present in the spectra from the magnetic sector instrument. Fragmentation was dominated by Y-type glycosidic cleavages (Domon and Costello nomenclature) between all sugar residues yielding sequence and branching information. Sialic acid-containing oligosaccharides generally produced the sodium adduct of the sodium salt and gave much weaker signals than the neutral sugars in the positive-ion mode. There was also considerable loss of the sialic acid moleties as the result of fragmentation on the magnetic sector instrument. The least fragmentation of both neutral and acidic sugars was caused by 2.5 DHB, which proved to be the most appropriate matrix for examination of oligosaccharide mixtures. Much better resolution of the oligosaccharides was obtained than by traditional methods such as the use of Bio-Gel P-4 gel filtration column chromatography. It is worth noting also that the measurements were considerably faster (a few minutes as opposed to about 16 h). In addition, no radiolabelling was necessary as required for detection on the P-4 columns. Mixtures of oligosaccharides from several glycoproteins (ribonuclease B, human immunoglobulin G (IgG) transferrin, bovine fetuin and chicken ovalbumin) were examined and the patterns of the identified oligosaccharides were found to agree closely with the known compositions of the sugar mixtures. The mass spectrometric resolution on the magnetic sector instrument was very much better (up to 3000, FWHM) than could be obtained with the linear TOF systems (200–400). The technique was used as a detection system for the products of exoglycosidase digestion in experiments to determine the detailed structure of the oligosaccharide chains from human IgG.     

Spin-forbidden ligand binding to the ferrous-heme group: ab initio and DFT studies

The potential energy surfaces (PESs) and associated energy barriers that characterize the spin-forbidden recombination reactions of the gas-phase ferrous deoxy-heme group with CO, NO, and H2O ligands have been calculated using density functional theory (DFT). The bond energy for binding of O2 has also been calculated. Extensive large basis set CCSD(T) calculations on two small models of the heme group have been used to calibrate the accuracy of different DFT functionals for treating these systems. Pure functionals are shown to overestimate the stability of the low-spin forms of the deoxy-heme model, and to overestimate the binding energy of H2O and CO, whereas hybrid functionals such as B3PW91 and B3LYP yield accurate results. Accordingly, the latter functionals have been used to explore the PESs for binding. CO binding is found to involve a significant barrier of ca. 3 kcal mol-1 due to the need to change from the deoxy-heme quintet ground state to the bound singlet state. Binding of water does not involve a barrier, but the resulting bond is weak and may be further weakened in the protein environment, which should explain why water binding is not usually observed in heme proteins such as myoglobin. NO binding involves a low barrier, which is consistent with observed rapid geminate recombination. The calculated bond energies are in good agreement with previous reported values and in fair agreement with experiment for CO and O2. The value for NO is significantly lower than the experimentally derived bond energy, suggesting that B3LYP is less accurate in this case.     

Substituent effects and the mechanism of alkene metathesis catalyzed by ruthenium dichloride catalysts

Density functional theory calculations are reported concerning the dissociative mechanism for alkene metathesis by ruthenium dichloride catalysts, including both bisphosphine and diaminocarbene/phosphine complexes. The calculations use a hierarchy of models, ranging from [(L)(PH(3))Ru(Cl)(2)(CH(2))](L=PH(3) or diaminocarbene) through the larger [(L)(PMe(3))Ru(Cl)(2)(CHPh)] to the "real"[(L)(PCy(3))Ru(Cl)(2)(CHPh)]. Calculations show that the rate-limiting step for metathesis is either ring closing from an alkene complex to form a ruthena-cyclobutane, or ring-opening of the latter intermediate to form an isomeric alkene complex. The higher efficiency of the diaminocarbene based catalysts is due to the stabilization of the formal +iv oxidation state of the ruthenium centre in the metallacycle. This effect is partly masked in the smaller model systems due to a previously unnoticed stereoelectronic effect. The calculations do not reproduce the experimental observation whereby the initiation step, phosphine dissociation, is more energetically demanding and hence slower for the diaminocarbene-containing catalyst system than for the bisphosphine. Further calculations on the corresponding bond energies using a variety of DFT and hybrid DFT/molecular mechanics methods all find instead a larger phosphine dissociation energy for the bisphosphine catalyst. This reversed order of binding energies would in fact be the one expected based on the stronger trans influence of the diaminocarbene ligand. The discrepancy with experiment is small and could have a number of causes which are discussed here.     

Role of polarization and alignment in photoactuation of nematic elastomers

Changing the orientational order in liquid-crystal elastomers leads to internal stresses and changes of the sample shape. When this effect is induced by light, due to photoisomerization of constituent molecular moieties, the photomechanical actuation results. We investigate quantitatively how the intensity and the polarization of light affect photoactuation. By studying dissolved, as well as covalently bonded azo-dyes, we determine the changes in absorption and the response kinetics. For the first time we compare the response of aligned monodomain, and randomly disordered polydomain nematic elastomers, and demonstrate that both have a comparable photoresponse, strongly dependent on the polarization of light. Polarization-dependent photoactuation in polydomain elastomers gives an unambiguous proof of its mechanism since it is the only experiment that distinguishes from the associated thermal effects.     

Random walks on lattices. IV. Continuous-time walks and influence of absorbing boundaries

The general study of random walks on a lattice is developed further with emphasis on continuous-time walks with an asymmetric bias. Continuous time walks are characterized by random pauses between jumps, with a common pausing time distribution(t). An analytic solution in the form of an inverse Laplace transform for P(l, t), the probability of a walker being atl at timet if it started atl _o att=0, is obtained in the presence of completely absorbing boundaries. Numerical results for P(l, t) are presented for characteristically different (t), including one which leads to a non-Gaussian behavior for P(l, t) even for larget. Asymptotic results are obtained for the number of surviving walkers and the mean l showing the effect of the absorption at the boundary.This study was partially supported by ARPA and monitored by ONR(N00014-17-0308).     

Multiplexing fibre optic near infrared (NIR) spectroscopy as an emerging technology to monitor industrial bioprocesses

The application of near infrared spectroscopy in bioprocessing has been limited by its dependence on calibrations derived from single bioreactor at a given time. Here, we propose a multiplexed calibration technique which allows calibrations to be built from multiple bioreactors run in parallel. This gives the flexibility to monitor multiple vessels and facilitates calibration model transfer between bioreactors. Models have been developed for the two key analytes: glucose and lactate using Chinese hamster ovary (CHO) cell lines and using analyte specific information obtained from the feasibility studies. We observe slight model degradation for the multiplexed models in comparison to the conventional (single probe) models, decrease in r² values from 89.4% to 88% for glucose whereas for lactate from 92% to 91.8% and a simultaneous increase in the number of factors as the model incorporates the inter-probe variability, nevertheless the models were fit for purpose. The results of this particular application of implementing multiplexed-NIRS to monitor multiple bioreactor vessels are very encouraging, as successful models have been built on-line and validated externally, which proffers the prospect of reducing timelines in monitoring the vessels considerably, and in turn, providing improved control.     

Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways?

Prediction of tandem mass spectrometric (MS/MS) fragmentation for non‐peptidic molecules based on structure is of immense interest to the mass spectrometrist. If a reliable approach to MS/MS prediction could be achieved its impact within the pharmaceutical industry could be immense. Many publications have stressed that the fragmentation of a molecular ion or protonated molecule is a complex process that depends on many parameters, making prediction difficult. Commercial prediction software relies on a collection of general heuristic rules of fragmentation, which involve cleaving every bond in the structure to produce a list of ‘expected’ masses which can be compared with the experimental data. These approaches do not take into account the thermodynamic or molecular orbital effects that impact on the molecule at the point of protonation which could influence the potential sites of bond cleavage based on the structural motif. A series of compounds have been studied by examining the experimentally derived high‐resolution MS/MS data and comparing it with the in silico modelling of the neutral and protonated structures. The effect that protonation at specific sites can have on the bond lengths has also been determined. We have calculated the thermodynamically most stable protonated species and have observed how that information can help predict the cleavage site for that ion. The data have shown that this use of in silico techniques could be a possible way to predict MS/MS spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Dielectric constants of fluid mixtures over a wide range of temperature and density

A new expression is presented for estimating the dielectric constant of a fluid mixture as a function of temperature, density and composition. The estimated dielectric constants (and their derivatives) are required for phase-equilibrium calculations, based on an equation of state, for systems containing electrolytes and nonelectrolytes. The new expression holds for the entire range of fluid densities, from zero to liquid-like densities. Mixing of components is performed on a volume-fraction basis at constant temperature and constant reduced density. For polar components where data are not available at the temperature and/or reduced density of interest, the well-characterized behavior of water is used to extrapolate the available pure-component data. The importance of using the correct density of the mixture is shown. Using one adjustable parameter for each nonideal binary subsystem, predicted results can be significantly improved.