Sensitive Detection of Small Molecule–Protein Interactions on a Metal–Insulator–Metal Label‐Free Biosensing Platform

The need to develop label‐free biosensing devices that enable rapid analyses of interactions between small molecules/peptides and proteins for post‐genomic studies has increased significantly. We report a simple metal–insulator–metal (MIM) geometry for fabricating a highly sensitive detection platform for biosensing. MIM substrates consisting of an Au–PMMA–Ag nanolayer were extensively studied using both theoretical and experimental approaches. By monitoring reflectivity changes at the normal incidence angle, we observed molecular interactions as the thickness of the biolayer increased on the substrate surface. These interactions included the adsorption of various proteins (Mw=6–150 kD) and interactions between small molecules (Mw≤2 kD) and the immobilized proteins. The interaction of designed monosaccharide‐modified designed peptides with various lectins was also clearly detected. These interactions could not be detected by the conventional Au‐only substrate. Thus, the MIM approach affords a powerful label‐free biosensing device that will aid our understanding of protein interactions and recognition.     

Length‐Dependent Conductance of Molecular Wires and Contact Resistance in Metal–Molecule–Metal Junctions

Molecular wires are covalently bonded to gold electrodes—to form metal–molecule–metal junctions—by functionalizing each end with a ? SH group. The conductance of a wide variety of molecular junctions is studied theoretically by using first‐principles density functional theory (DFT) combined with the nonequilibrium Green′s function (NEGF) formalism. Based on the chain‐length‐dependent conductance of the series of molecular wires, the attenuation factor β is obtained and compared with the experimental data. The β value is quantitatively correlated to the molecular HOMO–LUMO gap. Coupling between the metallic electrode and the molecular bridge plays an important role in electron transport. A contact resistance of 6.0±2.0 KΩ is obtained by extrapolating the molecular‐bridge length to zero. This value is of the same magnitude as the quantum resistance.     

Molecule‐Induced Peroxide Homolysis

The homolytic cleavage of peroxide bonds, leading to the formation of free radicals, plays an important role in the (spontaneous) oxidation of a wide variety of hydrocarbons in the presence of oxygen. Such aerobic oxidations can be desired (e.g. for industrially applied autoxidations) or undesired (e.g. food deterioration). In this contribution we provide experimental and computational evidence for a molecule‐induced homolytic dissociation mechanism between alkyl peroxide and compounds featuring weakly bonded H atoms such as (di)unsaturated hydrocarbons.     

Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy

The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide‐and‐conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction‐type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre‐exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude).     

Metal–Organic‐Framework‐Templated Polyelectrolyte Nanocapsules for the Encapsulation and Delivery of Small‐Molecule–Polymer Conjugates

Herein, we report a strategy for exploiting nanoscale metal–organic frameworks (nano‐MOFs) as templates for the layer‐by‐layer (LbL) assembly of polyelectrolytes. Because small‐molecule drugs or imaging agents cannot be efficiently encapsulated by polyelectrolyte nanocapsules, we investigated two promising and biocompatible polymers (comb‐shaped polyethylene glycol (PEG) and hyperbranched polyglycerol‐based PEG) for the conjugation of model drugs and imaging agents, which were then encapsulated inside the nano‐MOF‐templated nanocapsules. Furthermore, we also systemically explored the release kinetics of the encapsulated conjugates, and examined how the encapsulation and/or release processes could be controlled by varying the composition and architecture of the polymers. We envision that our nano‐MOFs‐templated nanocapsules, through combining with small‐molecule–polymer conjugates, will represent a new type of delivery system that could open up new opportunities for biomedical applications.     

Cyano‐Functionalized Triarylamines on Coinage Metal Surfaces: Interplay of Intermolecular and Molecule–Substrate Interactions

The self‐assembly of cyano‐functionalized triarylamine derivatives on Cu(111), Ag(111) and Au(111) was studied by means of scanning tunnelling microscopy, low‐energy electron diffraction, X‐ray photoelectron spectroscopy and density functional theory calculations. Different bonding motifs, such as antiparallel dipolar coupling, hydrogen bonding and metal coordination, were observed. Whereas on Ag(111) only one hexagonally close‐packed pattern stabilized by hydrogen bonding is observed, on Au(111) two different partially porous phases are present at submonolayer coverage, stabilized by dipolar coupling, hydrogen bonding and metal coordination. In contrast to the self‐assembly on Ag(111) and Au(111), for which large islands are formed, on Cu(111), only small patches of hexagonally close‐packed networks stabilized by metal coordination and areas of disordered molecules are found. The significant variety in the molecular self‐assembly of the cyano‐functionalized triarylamine derivatives on these coinage metal surfaces is explained by differences in molecular mobility and the subtle interplay between intermolecular and molecule–substrate interactions.     

Elucidating Molecule–Plasmon Interactions in Nanocavities with 2 nm Spatial Resolution and at the Single‐Molecule Level

The fundamental understanding of the subtle interactions between molecules and plasmons is of great significance for the development of plasmon‐enhanced spectroscopy (PES) techniques with ultrahigh sensitivity. However, this information has been elusive due to the complex mechanisms and difficulty in reliably constructing and precisely controlling interactions in well‐defined plasmonic systems. Herein, the interactions in plasmonic nanocavities of film‐coupled metallic nanocubes (NCs) are investigated. Through engineering the spacer layer, molecule–plasmon interactions were precisely controlled and resolved within 2 nm. Efficient energy exchange interactions between the NCs and the surface within the 1–2 nm range are demonstrated. Additionally, optical dressed molecular excited states with a huge Lamb shift of ≈7 meV at the single‐molecule (SM) level were observed. This work provides a basis for understanding the underlying molecule–plasmon interaction, paving the way for fully manipulating light–matter interactions at the nanoscale.     

Inverting Small Molecule–Protein Recognition by the Fluorine Gauche Effect: Selectivity Regulated by Multiple H→F Bioisosterism

Fluorinated motifs have a venerable history in drug discovery, but as C(sp³)?F‐rich 3D scaffolds appear with increasing frequency, the effect of multiple bioisosteric changes on molecular recognition requires elucidation. Herein we demonstrate that installation of a 1,3,5‐stereotriad, in the substrate for a commonly used lipase from Pseudomonas fluorescens does not inhibit recognition, but inverts stereoselectivity. This provides facile access to optically active, stereochemically well‐defined organofluorine compounds (up to 98 % ee). Whilst orthogonal recognition is observed with fluorine, the trend does not hold for the corresponding chlorinated substrates or mixed halogens. This phenomenon can be placed on a structural basis by considering the stereoelectronic gauche effect inherent to F?C?C?X systems (σ→σ*). Docking reveals that this change in selectivity (H versus F) with a common lipase results from inversion in the orientation of the bound substrate being processed as a consequence of conformation. This contrasts with the stereochemical interpretation of the biogenetic isoprene rule, whereby product divergence from a common starting material is also a consequence of conformation, albeit enforced by two discrete enzymes.     

Influence of Guest Exchange on the Magnetization Dynamics of Dilanthanide Single‐Molecule‐Magnet Nodes within a Metal–Organic Framework

Multitopic organic linkers can provide a means to organize metal cluster nodes in a regular three‐dimensional array. Herein, we show that isonicotinic acid N‐oxide (HINO) serves as the linker in the formation of a metal–organic framework featuring Dy₂ single‐molecule magnets as nodes. Importantly, guest solvent exchange induces a reversible single‐crystal to single‐crystal transformation between the phases Dy₂(INO)₄(NO₃)₂?2 solvent (solvent=DMF (Dy₂‐DMF), CH₃CN (Dy₂‐CH₃CN)), thereby switching the effective magnetic relaxation barrier (determined by ac magnetic susceptibility measurements) between a negligible value for Dy₂‐DMF and 76 cm^?1 for Dy₂‐CH₃CN. Ab initio calculations indicate that this difference arises not from a significant change in the intrinsic relaxation barrier of the Dy₂ nodes, but rather from a slowing of the relaxation rate of incoherent quantum tunneling of the magnetization by two orders of magnitude.