Discovery of linear receptors for multiple dihydrogen phosphate ions using dynamic combinatorial chemistry

We describe the use of dynamic combinatorial chemistry to discover a new series of linear hydrazone-based receptors that bind multiple dihydrogen phosphate ions. Through the use of a template-driven, selection-based approach to receptor synthesis, dynamic combinatorial chemistry allows for the identification of unexpected host structures and binding motifs. Notably, we observed the unprecedented selection of these linear receptors in preference to competing macrocyclic hosts. Furthermore, linear receptors containing up to nine building blocks and three different building blocks were amplified in the dynamic combinatorial library. The receptors were formed using a dihydrazide building block based on an amino acid-disubstituted ferrocene scaffold. A detailed study of the linear pentamer revealed that it forms a helical ditopic receptor that employs four acylhydrazone hydrogen-bond donor motifs to cooperatively bind two dihydrogen phosphate ions.     

On-chip multi-electrochemical sensor array platform for simultaneous screening of nitric oxide and peroxynitrite

In this work we report on the design, microfabrication and analytical performances of a new electrochemical sensor array (ESA) which allows for the first time the simultaneous amperometric detection of nitric oxide (NO) and peroxynitrite (ONOO(-)), two biologically relevant molecules. The on-chip device includes individually addressable sets of gold ultramicroelectrodes (UMEs) of 50 μm diameter, Ag/AgCl reference electrode and gold counter electrode. The electrodes are separated into two groups; each has one reference electrode, one counter electrode and 110 UMEs specifically tailored to detect a specific analyte. The ESA is incorporated on a custom interface with a cell culture well and spring contact pins that can be easily interconnected to an external multichannel potentiostat. Each UME of the network dedicated to the detection of NO is electrochemically modified by electrodepositing thin layers of poly(eugenol) and poly(phenol). The detection of NO is performed amperometrically at 0.8 V vs. Ag/AgCl in phosphate buffer solution (PBS, pH = 7.4) and other buffers adapted to biological cell culture, using a NO-donor. The network of UMEs dedicated to the detection of ONOO(-) is used without further chemical modification of the surface and the uncoated gold electrodes operate at -0.1 V vs. Ag/AgCl to detect the reduction of ONOOH in PBS. The selectivity issue of both sensors against major biologically relevant interfering analytes is examined. Simultaneous detection of NO and ONOO(-) in PBS is also achieved.     

Frontier residues lining globin internal cavities present specific mechanical properties

The internal cavity matrix of globins plays a key role in their biological function. Previous studies have already highlighted the plasticity of this inner network, which can fluctuate with the proteins breathing motion, and the importance of a few key residues for the regulation of ligand diffusion within the protein. In this Article, we combine all-atom molecular dynamics and coarse-grain Brownian dynamics to establish a complete mechanical landscape for six different globins chain (myoglobin, neuroglobin, cytoglobin, truncated hemoglobin, and chains α and β of hemoglobin). We show that the rigidity profiles of these proteins can fluctuate along time, and how a limited set of residues present specific mechanical properties that are related to their position at the frontier between internal cavities. Eventually, we postulate the existence of conserved positions within the globin fold, which form a mechanical nucleus located at the center of the cavity network, and whose constituent residues are essential for controlling ligand migration in globins.     

Direct selected multireference configuration interaction calculations for large systems using localized orbitals

A selected multireference configuration interaction (CI) method and the corresponding code are presented. It is based on a procedure of localization that permits to obtain well localized occupied and virtual orbitals. Due to the local character of the electron correlation, using local orbitals allows one to neglect long range interactions. In a first step, three topological matrices are constructed, which determine whether two orbitals must be considered as interacting or not. Two of them concern the truncation of the determinant basis, one for occupied/virtual, the second one for dispersive interactions. The third one concerns the truncation of the list of two electron integrals. This approach permits a fine analysis of each kind of approximation and induces a huge reduction of the CI size and of the computational time. The procedure is tested on linear polyene aldehyde chains, dissociation potential energy curve, and reaction energy of a pesticide-Ca(2+) complex and finally on transition energies of a large iron system presenting a light-induced excited spin-state trapping effect.     

Raman active jagged-shaped gold-coated magnetic particles as a novel multimodal nanoprobe

The creation of novel engineered multimodal nanoparticles (NPs) is a key focus in bionanotechnology and can lead to deep understanding of biological processes at the molecular level. Here, we present a multi-component system made of gold-coupled core-shell SPIONs, as a new nanoprobe with signal enhancement in surface Raman spectroscopy, due to its jagged-shaped gold shell coating.     

Theoretical and experimental studies of CH3X-Y2 rotational line shapes for atmospheric spectra modelling: application to room-temperature CH3Cl-O2

The case of symmetric tops CH(3)X (X = Br, Cl, F, …) perturbed by non-polar diatoms Y(2) (Y = N(2), O(2), …) is analysed from the viewpoint of theoretical collisional broadening of their rotational lines observed in atmospheric spectra. A semi-classical approach involving an exponential representation of the scattering operator and exact trajectories governed by the isotropic potential is presented. For the first time the active molecule is strictly treated as a symmetric top and the atom-atom interactions are included in the intermolecular potential model. It is shown for the CH(3)Cl-O(2) system that these interactions contribute significantly to the line width for all values of the rotational quantum numbers J and K. Additional testing of modifications required in the semi-classical formalism for a correct application of the cumulant expansion is performed and it is shown that the use of the cumulant average on the rotational states of the perturbing molecule leads to entirely negligible effects for the not very strongly interacting CH(3)Cl-O(2) system. In order to check the theoretical predictions and to extend the scarce experimental data available in the literature to higher values of the rotational quantum numbers, new measurements of room-temperature O(2)-broadened CH(3)Cl rotational lines are carried out by a photomixing continuous-wave terahertz spectrometer. The experimental line widths extracted with a Voigt profile model demonstrate an excellent agreement with theoretical results up to very high J-values (J = 31, 37, 40, 45, 50).     

The relationship between redox enzyme activity and electrochemical potential-cellular and mechanistic implications from protein film electrochemistry

In protein film electrochemistry a redox protein of interest is studied as an electroactive film adsorbed on an electrode surface. For redox enzymes this configuration allows quantification of the relationship between catalytic activity and electrochemical potential. Considered as a function of enzyme environment, i.e., pH, substrate concentration etc., the activity-potential relationship provides a fingerprint of activity unique to a given enzyme. Here we consider the nature of the activity-potential relationship in terms of both its cellular impact and its origin in the structure and catalytic mechanism of the enzyme. We propose that the activity-potential relationship of a redox enzyme is tuned to facilitate cellular function and highlight opportunities to test this hypothesis through computational, structural, biochemical and cellular studies.     

Algorithmic Approach to the Extinction Probability of Branching Processes

The extinction probability of a branching process is characterized as the solution of a fixed-point equation which, for a fairly general class of Markovian branching processes, is vector quadratic. We address the question of solving that equation, using a mixture of algorithmic and probabilistic arguments. We compare the relative efficiency of three iterative methods based on functional iteration, on the basis of the probabilistic interpretation of the successive iterations as well as on the basis of traditional rate of convergence analysis. We illustrate our findings through a few numerical examples and conclude by showing how they extend to more complex systems.