Nonlocal Interaction Equations in Environments with Heterogeneities and Boundaries

We study well-posedness of a class of nonlocal interaction equations with spatially dependent mobility. We also allow for the presence of boundaries and external potentials. Such systems lead to the study of nonlocal interaction equations on subsets ? of ? ^d endowed with a Riemannian metric g. We obtain conditions, relating the interaction potential and the geometry, which imply existence, uniqueness and stability of solutions. We study the equations in the setting of gradient flows in the space of probability measures on ? endowed with Riemannian 2-Wasserstein metric.     

Synthesis of Soluble,Alkyne‐Substituted Trideca‐ and Hexadeca‐Starphenes

Two literature‐known TIPS‐ethynyl‐dibromoacenes were prepared and employed to synthesize cyclotrimers by using Yamamoto coupling conditions. Two large, well‐soluble starphenes were isolated in good yields. Crystallographic characterization verifies the triangular shape and shows significant differences in crystal packing.     

Mukaiyama–Michael Reactions with trans‐2,5‐Diarylpyrrolidine Catalysts: Enantioselectivity Arises from Attractive Noncovalent Interactions,Not from Steric Hindrance

The scope of the enantioselective Mukaiyama–Michael reactions catalyzed by trans‐2,5‐diphenylpyrrolidine has been expanded to include both α‐ and β‐substituted enals. However, the rationalization of the observed enantioselectivity is far from obvious since the catalyst is not very sterically hindered. DFT calculations were carried out to rationalize the observed stereoselectivities. Transition states of the C?C bond formation between iminium intermediates and silyloxyfurans were located and their relative energies were used to estimate the stereoselectivity data. We find excellent agreement between the predicted and observed stereoselectivities. The analysis of intermolecular forces reveals that the enantioselectivity is mostly due to stabilizing noncovalent interactions between the reacting partners, not due to steric hindrance. The role of attractive noncovalent interactions in enantioselective catalysis may be underappreciated.     

Self-Sorting Supramolecular Polymerization: Helical and Lamellar Aggregates of Tetra-Bay-Acyloxy Perylene Bisimide

A new perylene bisimide (PBI), with a fluorescence quantum yield up to unity, self-assembles into two polymorphic supramolecular polymers. This PBI bears four solubilizing acyloxy substituents at the bay positions and is unsubstituted at the imide position, thereby allowing hydrogen-bond-directed self-assembly in nonpolar solvents. The formation of the polymorphs is controlled by the cooling rate of hot monomer solutions. They show distinctive absorption profiles and morphologies and can be isolated in different polymorphic liquid-crystalline states. The interchromophoric arrangement causing the spectral features was elucidated, revealing the formation of columnar and lamellar phases, which are formed by either homo- or heterochiral self-assembly, respectively, of the atropoenantiomeric PBIs. Kinetic studies reveal a narcissistic self-sorting process upon fast cooling, and that the transformation into the heterochiral (racemic) sheetlike self-assemblies proceeds by dissociation via the monomeric state.     

G-Protein-Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State

G-protein-coupled receptors (GPCRs) are the largest family of human membrane proteins and serve as primary targets of approximately one-third of currently marketed drugs. In particular, adenosine A₁ receptor (A₁AR) is an important therapeutic target for treating cardiac ischemia–reperfusion injuries, neuropathic pain, and renal diseases. As a prototypical GPCR, the A₁AR is located within a phospholipid membrane bilayer and transmits cellular signals by changing between different conformational states. It is important to elucidate the lipid–protein interactions in order to understand the functional mechanism of GPCRs. Here, all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method were performed on both the inactive (antagonist bound) and active (agonist and G-protein bound) A₁AR, which was embedded in a 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) lipid bilayer. In the GaMD simulations, the membrane lipids played a key role in stabilizing different conformational states of the A₁AR. Our simulations further identified important regions of the receptor that interacted distinctly with the lipids in highly correlated manner. Activation of the A₁AR led to differential dynamics in the upper and lower leaflets of the lipid bilayer. In summary, GaMD enhanced simulations have revealed strongly coupled dynamics of the GPCR and lipids that depend on the receptor activation state. © 2019 Wiley Periodicals, Inc.     

Bio-inspired short peptide self-assembly: From particles to functional materials

Natural systems are typically featured with tremendous molecular complexity and construct exquisite architectures and functional materials through precise spatial and temporal control. Supramolecular self-assembly from peptides and proteins is believed to be the key player. Thus, knowledge of the fundamental mechanisms driving peptides into vast functional hierarchical structures will certainly help the rational control of self-assembly process, leading to more precise structural organization and functional optimization. In this review, we briefly summarize the recent progress of this burgeoning field mainly from two directions: peptide-based self-assembly and co-assembly with other functional molecules, each part is further divided into two subparts and representative examples are given for each subpart according to their development timeline. At the end of each part, brief summaries of the closely related applications are outlined. For the closing remarks, we conclude with our own understanding of the area and perspectives are given based on recent developments. Overall, this review could be suitable for both new readers to gain a comprehensive overview of the area and experienced readers to get a summary of the development in short peptide self-assembly from particles to functional materials.     

The Density Functional Theory Account of Interplaying Long-Range Exchange and Dispersion Effects in Supramolecular Assemblies of Aromatic Hydrocarbons with Spin

Aromatic hydrocarbons with fused benzene rings and regular triangular shapes, called n-triangulenes according to the number of rings on one edge, form groundstates with n-1 unpaired spins because of topological reasons. Here, we focus on methodological aspects emerging from the density functional theory (DFT) treatments of dimer models of the n = 2 triangulene (called also phenalenyl), observing that it poses interesting new problems to the issue of long-range corrections. Namely, the interaction comprises simultaneous spincoupling and van der Waals effects, i.e., a technical conjuncture not considered explicitly in the benchmarks calibrating long-range corrections for the DFT account of supramolecular systems. The academic side of considering dimer models for calculations and related analysis is well mirrored in experimental aspects, and synthetic literature revealed many compounds consisting of stacked phenalenyl cores, with intriguing properties, assignable to their long-range spin coupling. Thus, one may speculate that a thorough study assessing the performance of state-of-the-art DFT procedures has relevance for potential applications in spintronics based on organic compounds.     

Spectroscopic and quantum-chemical study of molecular interactions of iso-quinolinium ylids in polar solutions

Abstract

Three iso-quinolinium ylids are studied by visible electron absorption spectroscopy from the point of view of their interactions with solvent molecules. The quantum mechanical calculations with Spartan 14 Program and solvatochromism of the intramolecular charge transfer visible absorption band of the studied molecules emphasized the prevalence of universal orientation-induction interactions in aprotic solvents and additionally the presence of hydrogen bond between the ylid molecules and the hydroxyl groups of the solvent molecules. The contribution of each type of interactions in the studied solutions is finally established by a multilinear regression applied to solvatochromic data.     

Uncertainty quantification for dynamics of geometrically nonlinear structures coupled with internal acoustic fluids in presence of sloshing and capillarity

In this paper, we propose an uncertainty quantification analysis, which is the continuation of a recent work performed in a deterministic framework. The fluid–structure system under consideration is the one experimentally studied in the sixties by Abramson, Kana, and Lindholm from the Southwest Research Institute under NASA contract. This coupled system is constituted of a linear acoustic liquid contained in an elastic tank that undergoes finite dynamical displacements, inducing geometrical nonlinear effects in the structure. The liquid has a free surface on which sloshing and capillarity effects are taken into account. The problem is expressed in terms of the acoustic pressure field in the fluid, of the displacement field of the elastic structure, and of the normal elevation field of the free surface. The nonlinear reduced-order model constructed in the recent work evoked above is reused for implementing the nonparametric probabilistic approach of uncertainties. The objective of this paper is to present a sensitivity analysis of this coupled fluid–structure system with respect to uncertainties and to use a classical statistical inverse problem for carrying out the experimental identification of the hyperparameter of the stochastic model. The analysis show a significant sensitivity of the displacement of the structure, of the acoustic pressure in the liquid, and of the free-surface elevation to uncertainties in both linear and geometrically nonlinear simulations.     

Energy transport in boundary driven quantum spin systems: One-way street phenomenon in models with long range interactions

We address the investigation of non trivial properties of the energy current in boundary driven XXZ quantum spin models. In specific, we focus on the occurrence of the one-way street phenomenon in asymmetrical chains, a phenomenon stronger than rectification, which establishes the existence of a unique way for the energy current in the absence of external magnetic field, that is, the magnitude and direction of the energy flow does not change as we invert the baths at the boundaries. For general target polarizations at the boundaries, we show that such a phenomenon holds in the presence of long range interactions, ingredient which increases the flow and the rectification in chains of classical oscillators, and so, of interest in the study of manipulation and control of the energy flow.