Mechanistic aspects of biological redox reactions involving NADH 2: A combined semiempirical and ab initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dihydronicotinamide,and folate and dihydrofolate analogue substrates of dihydrofolate reductase

As part of a study of factors controlling biological redox reactions of nicotinamide cofactors [nicotinamide adenine dinucleotide (phosphate) NAD(P)H], we have investigated the effect on a model reaction of the conformational state (cis or trans) of the carboxamide side chain, using quantum chemical methods. The reaction is that for the enzyme dihydrofolate reductase between the NADPH analogue, 1-methyl-dihydronicotinamide, and the protonated forms of the folate and dihydrofolate substrate analogues, pyrazine and dihydropyrazine. Some calculations on pterin and dihydropterin substrate analogues were also carried out in order to gauge the effects of inter-ring coupling. The influence of carboxamide side-chain conformation of nicotinamide on the energetics of the hydride-ion transfer, and on the structures of the transition states and stable intermolecular-interaction complexes, are examined as a function of the orientation of approach of the reactants. These approach geometries include those corresponding to the observed binding of cofactor and either substrate or inhibitor in the enzyme active site. Reactant, product, reactants-complex, and transition-state geometries were optimized at the semiempirical AM1 level, while ab initio SCF/STO-3G and SCF/3-21G single-point calculations were carried out at the AM1 optimized geometries for all species, as well as full geometry optimizations for isolated reactants and products. The results show that reactants-complex and transition-state energies are lower for the trans conformer of dihydronicotinamide than for the cis conformer, due to more favorable H-bonding or electrostatic interactions with the protonated substrate. Also, consideration of the structural parameters, including reaction coordinate bond lengths, ring geometries, and charge distributions, indicate that the trans transition states are more product-like than those for the cis. For the (trans) approaches corresponding to the enzymic orientation for substrate, the intermolecular interaction for the folate reaction lacks the stabilizing influence of the formal H-bond which is present for the dihydrofolate reaction, and consequently the reactants-complex and transition state are less stable.     

A synthesis of bredinin (Mizoribine®) from an acyclic precursor

Bredinin (4-carbamoyl-1-β-d-ribofuranosylimidazolium-5-olate, 1) was synthesised by the formation of a malonamate from 2,3-isopropylidene-d-ribofuranosylamine and ethyl malonyl chloride, followed by a sequence involving amination, via reduction of an oxime, heterocycle formation and then deprotection.     

Determination of dissociation temperature for ArO in inductively coupled plasma-mass spectrometry: Effects of excited electronic states and dissociation pathways

The method of comparing experimental and calculated ion ratios to determine a gas kinetic temperature (T_gas) characteristic of the origin of a polyatomic ion in inductively coupled plasma-mass spectrometry (ICP-MS) is applied to ArO⁺. Repeated measurements of ion ratios involving this species yield erratic T_gas values. Complications arise from the predicted presence of a low-lying excited electronic state (²Π) above the ⁴Σ ground state. Omission of this excited state yields unreasonably high temperatures (> 10,000 K) for nine out of nineteen trials. Inclusion of the excited electronic state in the partition function of ArO⁺ causes temperatures to increase further. The problem appears to be related to the prediction that ArO⁺ in the ²Π excited state dissociates into Ar⁺ and O, different products than ArO^{+ 4}Σ which dissociates into Ar and O⁺. Adjustments to the calculations to account for these different products yield reasonable temperatures (2100 to 3500 K) that are consistent from day-to-day and similar to those seen for other weakly-bound polyatomic ions.     

Solid-state NMR detection of 14N-13C dipolar couplings between amino acid side groups provides constraints on amyloid fibril architecture

Solid‐state nuclear magnetic resonance (SSNMR) is a powerful technique for the structural analysis of amyloid fibrils. With suitable isotope labelling patterns, SSNMR can provide constraints on the secondary structure, alignment and registration of β‐strands within amyloid fibrils and identify the tertiary and quaternary contacts defining the packing of the β‐sheet layers. Detection of ¹⁴N? ¹³C dipolar couplings may provide potentially useful additional structural constraints on β‐sheet packing within amyloid fibrils but has not until now been exploited for this purpose. Here a frequency‐selective, transfer of population in double resonance SSNMR experiment is used to detect a weak ¹⁴N? ¹³C dipolar coupling in amyloid‐like fibrils of the peptide H₂N‐SNNFGAILSS‐COOH, which was uniformly ¹³C and ¹⁵N labelled across the four C‐terminal amino acids. The ¹⁴N? ¹³C interatomic distance between leucine and asparagine side groups is constrained between 2.4 and 3.8 Å, which allows current structural models of the β‐spine arrangement within the fibrils to be refined. This procedure could be useful for the general structural analysis of other proteins in condensed phases and environments, such as biological membranes. Copyright © 2011 John Wiley & Sons, Ltd.     

Recovery of phosphonate surface contaminants from glass using a simple vacuum extractor with a solid-phase microextraction fiber

Recovery of chemical contaminants from fixed surfaces for analysis can be challenging, particularly if it is not possible to acquire a solid sample to be taken to the laboratory. A simple device is described that collects semi-volatile organic compounds from fixed surfaces by creating an enclosed volume over the surface, then generating a modest vacuum. A solid-phase microextraction (SPME) fiber is then inserted into the evacuated volume where it functions to sorb volatilized organic contaminants. The device is based on a syringe modified with a seal that is used to create the vacuum, with a perforable plunger through which the SPME fiber is inserted. The reduced pressure speeds partitioning of the semi-volatile compounds into the gas phase and reduces the boundary layer around the SPME fiber, which enables a fraction of the volatilized organics to partition into the SPME fiber. After sample collection, the SPME fiber is analyzed using conventional gas chromatography/mass spectrometry. The methodology has been used to collect organophosphorus compounds from glass surfaces, to provide a simple test for the functionality of the devices. Thirty minute sampling times (ΔT(vac)) resulted in fractional recovery efficiencies that ranged from 10(-3) to >10(-2), and in absolute terms, collection of low nanograms was demonstrated. Fractional recovery values were positively correlated to the vapor pressure of the compounds being sampled. Fractional recovery also increased with increasing ΔT(vac) and displayed a roughly logarithmic profile, indicating that an operational equilibrium is being approached. Fractional recovery decreased with increasing time between exposure and sampling; however, recordable quantities of the phosphonates could be collected three weeks after exposure.     

Vector Potential Theory on Nonsmooth Domains in R3 and Applications to Electromagnetic Scattering

We study boundary value problems for the time-harmonic form of the Maxwell equations, as well as for other related systems of equations, on arbitrary Lipschitz domains in the three-dimensional Euclidean space. The main goal is to develop the corresponding theory for L^p-integrable bounday data for optimal values of p’s. We also discuss a number of relevant applications in electromagnetic scattering.     

Modelling of recording system performance and its relationship to recording media properties

A recording system has been modelled which employs a peak detection scheme consisting of differentiator and cossover detector. The recording behaviours of head and tape combinations are included as variables and the effect of these on overall system error rates have been computed.