Secretory phospholipase A2 hydrolysis of phospholipid analogues is dependent on water accessibility to the active site

A new and unnatural type of phospholipids with the head group attached to the 2-position of the glycerol backbone has been synthesized and shown to be a good substrate for secretory phospholipase A2 (sPLA2). To investigate the unexpected sPLA2 activity, we have compared three different phospholipids by using fluorescence techniques and HPLC, namely: (R)-1,2-dipalmitoyl-glycero-3-phosphocholine (hereafter referred to as 1R), (R)-1-O-hexadecyl-2-palmitoyl-glycero-3-phoshocholine (2R), and (S)-1-O-hexadecyl-3-palmitoyl-glycero-2-phosphocholine (3S). Furthermore, to understand the underlying mechanisms for the observed differences, we have performed molecular dynamics simulations to clarify on a structural level the substrate specificity of sPLA2 toward phospholipid analogues with their head groups in the 2-position of the glycerol backbone. We have studied the lipids above 1R, 2R, and 3S as well as their enantiomers 1S, 2S, and 3R. In the simulations of sPLA2-1S and sPLA2-3R, structural distortion in the binding cleft induced by the phospholipids showed that these are not substrates for sPLA2. In the case of the phospholipids 1R, 2R, and 3S, our simulations revealed that the difference observed experimentally in sPLA2 activity might be caused by reduced access of water molecules to the active site. We have monitored the number of water molecules that enter the active site region for the different sPLA2-phospholipid complexes and found that the probability of a water molecule reaching the correct position such that hydrolysis can occur is reduced for the unnatural lipids. The relative water count follows 1R > 2R > 3S. This is in good agreement with experimental data that indicate the same trend for sPLA2 activity: 1R > 2R > 3S.     

Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: Applications to solvated water and formaldehyde

A combined quantum mechanics/molecular mechanics (QM/MM) method is described, where the polarization between the solvent and solute is accounted for using a self-consistent scheme linear in the solvent polarization. The QM/MM method is implemented for calculation of energies and molecular response properties including the calculation of linear and quadratic response functions using the density-functional theory (DFT) and the Hartree-Fock (HF) theory. Sample calculations presented for ground-state energies, first-order ground-state properties, excitation energies, first-order excited state properties, polarizabilities, first-hyperpolarizabilities, and two-photon absorptions strengths of formaldehyde suggests that DFT may in some cases be a sufficiently reliable alternative to high-level theory, such as coupled-cluster (CC) theory, in modeling solvent shifts, whereas results obtained with the HF wave function deviate significantly from the CC results. Calculations carried out on water gives results that also are comparable with CC calculations in accuracy for ground-state and first-order properties. However, to obtain such accuracy an exchange-correlation functional capable of describing the diffuse Rydberg states must be chosen.     

Petasis three-component coupling reactions of hydrazides for the synthesis of oxadiazolones and oxazolidinones

An application of readily available hydrazides in the Petasis 3-component coupling reaction is presented. An investigation of the substrate scope was performed to establish a general, synthetically useful protocol for the formation of hydrazido alcohols, which were selectively converted to oxazolidinone and oxadiazolone ring systems through triphosgene-mediated cyclization reactions.     

All-silica nanofluidic devices for DNA-analysis fabricated by imprint of sol-gel silica with silicon stamp

We present a simple and cheap method for fabrication of silica nanofluidic devices for single-molecule studies. By imprinting sol-gel materials with a multi-level stamp comprising micro- and nanofeatures, channels of different depth are produced in a single process step. Calcination of the imprinted hybrid sol-gel material produces purely inorganic silica, which has very low autofluorescence and can be fusion bonded to a glass lid. Compared to top-down processing of fused silica or silicon substrates, imprint of sol-gel silica enables fabrication of high-quality nanofluidic devices without expensive high-vacuum lithography and etching techniques. The applicability of the fabricated device for single-molecule studies is demonstrated by measuring the extension of DNA molecules of different lengths confined in the nanochannels.     

Microdroplet-etched highly birefringent low-loss fiber tapers

We use hydrofluoric acid microdroplets to directly etch highly birefringent biconical fiber tapers from standard single-mode fibers. The fiber tapers have micrometer-sized cross sections, which are controlled by the etching condition. The characteristic teardrop cross section leads to a high group birefringence of B(G)≈0.017 and insertion losses <0.7 dB over waist lengths of about 2.1 mm.     

Synthesis of Ozone at Atmospheric Pressure by a Quenched Induction-Coupled Plasma Torch

The technical feasibility of using an induction-coupled plasma (ICP) torch to synthesize ozone at atmospheric pressure is explored. Ozone concentrations up to ~250 ppm were achieved using a thermal plasma reactor system based on an ICP torch operating at 2.5 MHz and ~11 kVA with an argon/oxygen mixture as the plasma-forming gas. The corresponding production rate and yield were ~20 g ozone/hr and ~2g ozone/kWh, respectively. A gaseous oxygen quench formed ozone by rapid mixing of molecular oxygen with atomic oxygen produced by the torch. The ozone concentration in the reaction chamber was measured by Fourier Transform infrared (FTIR) spectroscopy over a wide range of experimental conditions and configurations. The geometry of the quench gas flow, the quench flow velocity, and the quench flow rate played important roles in determining the ozone concentration. The ozone concentration was sensitive to the torch RF power, but was insensitive to the torch gas flow rates. These observations are interpreted within the framework of a simple model of ozone synthesis.     

Acetate formation during the ethanol oxidation on Rh(1 1 1)

The catalytic cracking of ethanol on clean and oxygen precovered Rh(1 1 1) surfaces has been studied by a combination of synchrotron based high-resolution core level spectroscopy and surface infrared spectroscopy. On the clean surface the decomposition of ethanol occurs without any formation of atomic oxygen. The presence of oxygen on the surface changes the reactivity significantly and acetate (CH₃COO) was identified as an important surface intermediate in the ethanol oxidation.     

Theoretical investigation of the coexistence of α and β-nitric acid trihydrates (NAT) molecular conformations

In this letter we document the possibility of the existence of a second molecular configuration for nitric acid trihydrates. Density functional theory (DFT) methods have been used for studying the nitric acid trihydrates α and β-NAT conformations, their spectroscopic and thermodynamics properties and dipole moments have been calculated. This study describes the gas–solid phase transition of the NAT and provides two possible pathways for the molecular structure transformation between α and β-NAT.     

Post-necking behaviour modelled by a gradient dependent plasticity theory

The delay of the onset of localization and the post-necking behaviour for stretched thin sheets are determined by three-dimensional effects. Thus, a 2-D finite element analysis based on a local plasticity theory will give a physically unrealistic mesh dependent solution. This, in spite of the fact that the stress state, is essentially two-dimensional. By incorporating a length scale with relation to the thickness of the sheet, it is demonstrated how a 2-D finite element analysis based on a gradient dependent plasticity theory can give a good approximation of the post-necking behaviour. This is illustrated by numerical comparison of results from a full 3-D finite element analysis, with results from a 2-D finite element model based on a finite strain version of a gradient dependent J₂-flow theory. Some numerical problems in the modeling will be discussed briefly.