Constructing spin-adiabatic states for the modeling of spin-crossing reactions. I. A shared-orbital implementation

In the modeling of spin-crossing reactions, it has become popular to directly explore the spin-adiabatic surfaces. Specifically, through constructing spin-adiabatic states from a two-state Hamiltonian (with spin-orbit coupling matrix elements) at each geometry, one can readily employ advanced geometry optimization algorithms to acquire a “transition state” structure, where the spin crossing occurs. In this work, we report the implementation of a fully-variational spin-adiabatic approach based on Kohn-Sham density functional theory spin states (sharing the same set of molecular orbitals) and the Breit-Pauli one-electron spin-orbit operator. For three model spin-crossing reactions (predissociation of N₂O, singlet-triplet conversion in CH₂, and CO addition to Fe(CO)₄), the spin-crossing points were obtained. Our results also indicated the Breit-Pauli one-electron spin-orbit coupling can vary significantly along the reaction pathway on the spin-adiabatic energy surface. On the other hand, due to the restriction that low-spin and high-spin states share the same set of molecular orbitals, the acquired spin-adiabatic energy surface shows a cusp (ie, a first-order discontinuity) at the crossing point, which prevents the use of standard geometry optimization algorithms to pinpoint the crossing point. An extension with this restriction removed is being developed to achieve the smoothness of spin-adiabatic surfaces.     

Molecular beacons with oxidized bases report on substrate specificity of DNA oxoguanine glycosylases

DNA glycosylase enzymes recognize and remove structurally distinct modified forms of DNA bases, thereby repairing genomic DNA from chemically induced damage or erasing epigenetic marks. However, these enzymes are often promiscuous, and advanced tools are needed to evaluate and engineer their substrate specificity. Thus, in the present study, we developed a new strategy to rapidly profile the substrate specificity of 8-oxoguanine glycosylases, which cleave biologically relevant oxidized forms of guanine. We monitored the enzymatic excision of fluorophore-labeled oligonucleotides containing synthetic modifications 8-oxoG and FapyG, or G. Using this molecular beacon approach, we identified several hOGG1 mutants with higher specificity for FapyG than 8-oxoG. This approach and the newly synthesized probes will be useful for the characterization of glycosylase substrate specificity and damage excision mechanisms, as well as for evaluating engineered enzymes with altered reactivities.

A three-color fluorescent molecular beacon assay for rapid profiling of substrate specificity of hOGG1 variants, and for engineering proteins to map genomic modifications.     

Mathematical Modelling of Glyphosate Molecularly Imprinted Polymer-Based Microsensor with Multiple Phenomena

The massive and careless use of glyphosate (GLY) in agricultural production raises many questions regarding environmental pollution and health risks, it is then important to develop simple methods to detect it. Electrochemical impedance spectroscopy (EIS) is an effective analytical tool for characterizing properties at the electrode/electrolyte interface. It is useful as an analytical procedure, but it can also help in the interpretation of the involved fundamental electrochemical and electronic processes. In this study, the impedance data obtained experimentally for a microsensor based on molecularly imprinted chitosan graft on 4-aminophenylacetic acid for the detection of glyphosate was analyzed using an exact mathematical model based on physical theories. The procedure for modeling experimental responses is well explained. The analysis of the observed impedance response leads to estimations of the microscopic parameters linked to the faradic and capacitive current. The interaction of glyphosate molecules with the imprinted sites of the CS-MIPs film is observed in the high frequency range. The relative variation of the charge transfer resistance is proportional to the log of the concentration of glyphosate. The capacitance decreases as the concentration of glyphosate increases, which is explained by the discharging of the charged imprinted sites when the glyphosate molecule interacts with the imprinted sites through electrostatic interactions. The phenomenon of adsorption of the ions in the CMA film is observed in the low frequency range, this phenomenon being balanced by the electrostatic interaction of glyphosate with the imprinted sites in the CS-MIPs film.     

Characterization of magnetic labels for bioassays

Magnetic nanoparticles differing by their size have been synthesized to use them for multiparametric testing, based on their differing magnetic properties. The nanoparticle has two essential roles: to act as a probe owing to its specific magnetic properties and to carry on its surface precursor groups for the covalent coupling of biological recognition molecules, such as antibodies, nucleic acids. A totally unique, newly patented, method has been used to characterize magnetic signatures using the MIAplex technology. The MIAplex reader, developed by Magnisense, measures the non-linear response of the magnetic labels when they are exposed to a multi-frequency alternating magnetic field. This specific signature based on d²B(H)/dH² was correlated to other more conventional magnetic detection methods (superconducting quantum interference devices (SQUID) and Mössbauer).     

Hierarchical Analysis of Self‐Assembled PEGylated Hexaphenylalanine Photoluminescent Nanostructures

Despite the growing literature about diphenylalanine‐based peptide materials, it still remains a challenge to delineate the theoretical insight into peptide nanostructure formation and the structural features that could permit materials with enhanced properties to be engineered. Herein, we report the synthesis of a novel peptide building block composed of six phenylalanine residues and eight PEG units, PEG₈‐F6. This aromatic peptide self‐assembles in water in stable and well‐ordered nanostructures with optoelectronic properties. A variety of techniques, such as fluorescence, FTIR, CD, DLS, SEM, SAXS, and WAXS allowed us to correlate the photoluminescence properties of the self‐assembled nanostructures with the structural organization of the peptide building block at the micro‐ and nanoscale. Finally, a model of hexaphenylalanine in aqueous solution by molecular dynamics simulations is presented to suggest structural and energetic factors controlling the formation of nanostructures.     

A Theoretical Study of ãA2 CH2

The potential energy surface and dipole moment surfaces of the ã⁴A₂ electronic state of CH₂⁺ are calculated ab initio using an augmented correlation-consistent polarized valence quadruple-ζ (aug-cc-pVQZ) basis set, with the incorporation of dynamical correlation using the coupled cluster method with single and double excitations and perturbatively connected triple excitations [CCSD(T)]. We use these surfaces in the MORBID program system to calculate rotation and rotation-vibration term values for ã-state CH₂⁺, CD⁺₂, and CHD⁺ and to simulate the rotation and rotation-vibration absorption spectrum of CH₂⁺ in the ã⁴A₂ electronic state. Our work is motivated by studies of CH₂⁺ that use the Coulomb explosion imaging technique and by the goal of predicting spectra that may be obtained from discharge sources. Although the ã state is the lowest-lying excited state above the X?/Ã ground state pair, it turns out to be relatively high-lying, and we determine that T_e(ã)=30447.5 cm⁻¹. The equilibrium bond angle for ã-state CH₂⁺ is only 77.1°; as a result the asymmetric top κ value is close to 0, and the molecule is equally far from the oblate and prolate symmetric top limits in this electronic state.