Automated and Efficient Generation of General Molecular Aggregate Structures

Modeling intermolecular interactions of complex non-covalent structures is important in many areas of chemistry. To facilitate the generation of reasonable dimer, oligomer, and general aggregate geometries, we introduce an automated computational interaction site screening (aISS) workflow. This easy-to-use tool combines a genetic algorithm employing the intermolecular force-field xTB-IFF for initial search steps with the general force-field GFN-FF and the semi-empirical GFN2-xTB method for geometry optimizations. Compared with the alternative CREST program, aISS yields similar results but with computer time savings of 1–3 orders of magnitude. This allows for the treatment of systems with thousands of atoms composed of elements up to radon, e.g., metal-organic complexes, or even polyhedra and zeolite cut-outs which were not accessible before. Moreover, aISS can identify reactive sites and provides options like site-directed (user-guided) screening.     

A Bidentate Antimony Pnictogen Bonding Host System

A bidentate pnictogen bonding host-system based on 1,8-diethynylanthracene was synthesized by a selective tin-antimony exchange reaction and investigated regarding its ability to act as a Lewis acidic host component for the complexation of Lewis basic or anionic guests. In this work, the novel C≡C−Sb(C₂F₅)₂ unit was established to study the potential of antimony(III) sites as representatives for the scarcely explored pnictogen bonding donors. The capability of this partly fluorinated host system was investigated towards halide anions (Cl⁻, Br⁻, I⁻), dimethyl chalcogenides Me₂Y (Y=O, S, Se, Te), and nitrogen heterocycles (pyridine, pyrimidine). Insights into the adduct formation behavior as well as the bonding situation of such E⋅⋅⋅Sb−C^F moieties were obtained in solution by means of NMR spectroscopy, in the solid state by X-ray diffraction, by elemental analyses, and by computational methods (DFT, QTAIM, IQA), respectively.     

Macrocycle-Based Crystalline Supramolecular Assemblies Built with Intermolecular Charge-Transfer Interactions

Synthetic macrocycles have served as principal tools for supramolecular chemistry, have greatly extended the scope of organic charge transfer (CT) complexes, and have proved to be of great practical value in the solid state during the past few years. In this Minireview, we summarize the research progress on the macrocycle-based crystalline supramolecular assemblies primarily driven by intermolecular CT interactions (a.k.a. macrocycle-based crystalline CT assemblies, MCCAs for short), which are classified by their donor–acceptor (D-A) constituent elements, including simplex macrocyclic hosts, heterogeneous macrocyclic hosts, and host–guest D-A pairs. Particular attention will be focused on their diverse functions and applications, as well as the underlying CT mechanisms from the perspective of crystal engineering. Finally, the remaining challenges and prospects are outlined.     

Empirical Model of Solvophobic Interactions in Organic Solvents

An empirical model was developed to predict organic solvophobic effects using N-phenylimide molecular balances functionalized with non-polar alkyl groups. Solution studies and X-ray crystallography confirmed intramolecular alkyl-alkyl interactions in their folded conformers. The structural modularity of the balances allowed systematic variation of alkyl group lengths. Control balances were instrumental in isolating weak organic solvophobic effects by eliminating framework solvent-solute effects. A ¹⁹F NMR label enabled analysis across 46 deuterated and non-deuterated solvent systems. Linear correlations were observed between organic solvophobic effects and solvent cohesive energy density (ced) as well as changes in solvent-accessible surface areas (SASA). Using these empirical relationships, a model was constructed to predict organic solvophobic interaction energy per unit area for any organic solvent with known ced values. The predicted interaction energies aligned with recent organic solvophobic measurements and literature values for the hydrophobic effect on non-polar surfaces confirmed the model‘s accuracy and utility.     

多巴胺盐酸盐与二甲亚砜的相互作用研究

使用核磁共振技术、密度泛函理论(DFT)和分子中原子(AIM)理论,研究了多巴胺盐酸盐(DH)与二甲亚砜(DMSO)的相互作用。结果表明,DH中酚羟基和氨基正离子上的氢原子、苯环上位于酚羟基和侧链之间碳上的氢原子,甚至侧链上与苯环直接相连的亚甲基上的氢原子都可与DMSO中的氧原子形成分子间氢键。     

Engineering Flexible Metal-Phenolic Networks with Guest Responsiveness via Intermolecular Interactions

Flexible metal-organic materials are of growing interest owing to their ability to undergo reversible structural transformations under external stimuli. Here, we report flexible metal-phenolic networks (MPNs) featuring stimuli-responsive behavior to diverse solute guests. The competitive coordination of metal ions to phenolic ligands of multiple coordination sites and solute guests (e.g., glucose) primarily determines the responsive behavior of the MPNs, as revealed experimentally and computationally. Glucose molecules can be embedded into the dynamic MPNs upon mixing, leading to the reconfiguration of the metal-organic networks and thus changes in their physicochemical properties for targeting applications. This study expands the library of stimuli-responsive flexible metal-organic materials and the understanding of intermolecular interactions between metal-organic materials and solute guests, which is essential for the rational design of responsive materials for various applications.     

Cover Picture: Supramolecular Self-Assembly as a Tool To Preserve the Electronic Purity of Perylene Diimide Chromophores (Angew. Chem. Int. Ed. 12/2023)

Organic semiconductors are promising for efficient, printable optoelectronics. However, strong excited-state quenching due to uncontrolled aggregation limits their use in devices. We report on the self-assembly of a supramolecular pseudo-cube formed from six perylene diimides (PDIs). The rigid, shape-persistent cage sets the distance and orientation of the PDIs and suppresses intramolecular rotations and vibrations, leading to non-aggregated, monomer-like properties in solution and the solid state, in contrast to the fast fluorescence quenching in the free ligand. The stabilized excited state and electronic purity in the cage enables the observation of delayed fluorescence due to a bright excited multimer, acting as excited-state reservoir in a rare case of benign inter-chromophore interactions in the cage. We show that self-assembly provides a powerful tool for retaining and controlling the electronic properties of chromophores, and to bring molecular electronics devices within reach.     

An Organic Molecular Nanobarrel that Hosts and Solubilizes C60

Organic cages have gained increasing attention in recent years as molecular hosts and porous materials. Among these, barrel-shaped cages or molecular nanobarrels are promising systems to encapsulate large hosts as they possess windows of the same size as their internal cavity. However, these systems have received little attention and remain practically unexplored despite their potential. Herein, we report the design and synthesis of a new trigonal prismatic organic nanobarrel with two large triangular windows with a diameter of 12.7 Å optimal for the encapsulation of C₆₀. Remarkably, this organic nanobarrel shows a high affinity for C₆₀ in solvents in which C₆₀ is virtually insoluble, providing stable solutions of C₆₀.     

Epoxidation of Olefins Catalyzed by Sulfate-based Supramolecular Ion Pairs

The development of inexpensive and effective catalysts for the epoxidation of olefins to epoxides, which are key commodities for the chemical industry, is a continuing challenge. In this context, we present a supramolecular solution with the development of new host-guest assemblies of sulfate ions and amidoammonium receptor cations that, for the first time, are shown to act as catalysts for olefin epoxidation by hydrogen peroxide under biphasic conditions. Analysis of the reaction mechanism shows that the reactive and oxidizing peroxymonosulfate is formed in the organic phase. Furthermore, a variety of readily available precursors may be used to form the supramolecular ion pairs (SIPs), which is enabling a large-scale synthesis of the catalysts while maintaining catalytic control and effectiveness.     

Integrating Computation,Experiment, and Machine Learning in the Design of Peptide-Based Supramolecular Materials and Systems

Interest in peptide-based supramolecular materials has grown extensively since the 1980s and the application of computational methods has paralleled this. These methods contribute to the understanding of experimental observations based on interactions and inform the design of new supramolecular systems. They are also used to virtually screen and navigate these very large design spaces. Increasingly, the use of artificial intelligence is employed to screen far more candidates than traditional methods. Based on a brief history of computational and experimentally integrated investigations of peptide structures, we explore recent impactful examples of computationally driven investigation into peptide self-assembly, focusing on recent advances in methodology development. It is clear that the integration between experiment and computation to understand and design new systems is becoming near seamless in this growing field.     

Molecular machines operated by light

The bottom-up construction and operation of machines and motors of molecular size is a topic of great interest in nanoscience, and a fascinating challenge of nanotechnology. Researchers in this field are stimulated and inspired by the outstanding progress of molecular biology that has begun to reveal the secrets of the natural nanomachines which constitute the material base of life. Like their macroscopic counterparts, nanoscale machines need energy to operate. Most molecular motors of the biological world are fueled by chemical reactions, but research in the last fifteen years has demonstrated that light energy can be used to power nanomachines by exploiting photochemical processes in appropriately designed artificial systems. As a matter of fact, light excitation exhibits several advantages with regard to the operation of the machine, and can also be used to monitor its state through spectroscopic methods. In this review we will illustrate the design principles at the basis of photochemically driven molecular machines, and we will describe a few examples based on rotaxane-type structures investigated in our laboratories.      

α/β类蛋白折叠中π-π相互作用的特异性

以α/β类蛋白的2种典型折叠类型为研究对象,对205个低相似度蛋白样本中的π-π相互作用进行统计分析.计算结果表明,(α/β)8-barrel折叠中π-π相互作用的分布密度高于经典Rossmann折叠,且在关键的局部区域的差异更加显著;芳香族氨基酸在(α/β)8-barrel结构中更容易形成π-π相互作用;色氨酸对应的3种π-π相互作用组合在(α/β)8-barrel折叠中出现的几率显著高于经典Rossmann折叠;(α/β)8-barrel折叠中π-π相互作用形成复杂π网络的能力强于经典Rossmann折叠.上述结果表明,π-π相互作用在α/β类蛋白的不同折叠类型中存在特异性,其在稳定(α/β)8-barrel结构中的作用强于经典Rossmann折叠.     

Rational Design of the β-Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing**

Detection of anions in complex aqueous media is a fundamental challenge with practical utility that can be addressed by supramolecular chemistry. Biomolecular hosts such as proteins can be used and adapted as an alternative to synthetic hosts. Here, we report how the mutagenesis of the β-bulge residues (D137 and W138) in mNeonGreen, a bright, monomeric fluorescent protein, unlocks and tunes the anion preference at physiological pH for sulfate, resulting in the turn-off sensor SulfOFF-1. This unprecedented sensing arises from an enhancement in the kinetics of binding, largely driven by position 138. In line with these data, molecular dynamics (MD) simulations capture how the coordinated entry and gating of sulfate into the β-barrel is eliminated upon mutagenesis to facilitate binding and fluorescence quenching.     

Self-assembling Dimeric and Trimeric Aggregates Based on Solvophobic and Charge-pairing Interactions

Self-assembly processes based on shape complementarity and noncovalent binding interactions are widely recognized as a fundamental principle in nature. Besides charge pairing and hydrogen bonding, hydrophobic interactions play a crucial role in water. Here we report the self-assembly of structurally simple monomers to yield defined dimeric and trimeric aggregates in highly polar media, based on ionic and solvophobic interactions. NMR, mass spectrometry and curve fitting were used to characterize these supramolecular assemblies in water–methanol solutions.     

Engineered Metallacycle-Based Supramolecular Photosensitizers for Effective Photodynamic Therapy

Although metallacycle-based supramolecular photosensitizers (PSs) have attracted increasing attention in biomedicine, their clinical translation is still hindered by their inherent dark toxicity. Herein, we report what to our knowledge is the first example of a molecular engineering approach to building blocks of metallacycles for constructing a series of supramolecular PSs ( RuA–RuD ), with the aim of simultaneously reducing dark toxicity and enhancing phototoxicity, and consequently obtaining high phototoxicity indexes (PI). Detailed in vitro investigations demonstrate that RuA–RuD display high cancer cellular uptake and remarkable antitumor activity even under hypoxic conditions. Notably, RuD exhibited no dark toxicity and displayed the highest PI value (≈406). Theoretical calculations verified that RuD has the largest steric hindrance and the lowest singlet-triplet energy gap (ΔE_ST, 0.61 eV). Further in vivo studies confirmed that RuD allows safe and effective phototherapy against A549 tumors.     

Frontispiece: Controlled Self-assembly of Gold(I) Complexes by Multiple Kinetic Aggregation States with Nonlinear Optical and Waveguide Properties

Introduction of multiple kinetic aggregation states (Aggs) into the self-assembly pathway could bring complexity and flexibility to the self-assemblies, which is difficult to realize due to the delicate equilibria established among different Aggs bonded by weak noncovalent interactions. Here, we describe a series of chiral and achiral d¹⁰ Au^I bis(N-heterocyclic carbene, NHC) complexes, and the achiral complex could undergo self-assembly with multiple kinetic Aggs. Generation of multiple kinetic Aggs was realized by applying chiral or achiral seeds exhibiting large differences in elongation temperatures for their respective cooperative self-assembly processes. We further showed that the chiral Au^I self-assemblies having non-centrosymmetric packing forms exhibit nonlinear optical response of second harmonic generation (SHG), while the SHG signal is absent in the achiral analogue. The crystalline achiral Au^I self-assemblies could function as optical waveguides with strong emission polarization.     

A Fourfold Gold(I)−Aryl Macrocycle with Hyperbolic Geometry and its Reductive Elimination to a Carbon Nanoring Host

An ethylene glycol-decorated [6]cyclo-meta-phenylene (CMP) macrocycle was synthesized and utilized as a subunit to construct a fourfold Au^I₂−aryl metallacycle with an overall square arrangement. The corners consist of rigid dinuclear gold(I) complexes previously known to form only triangular metallacycles. The interplay between the conformational flexibility of the [6]CMP macrocycle and the rigid dinuclear gold(I) moieties enable the square geometry, as revealed by single-crystal X-ray diffraction. The formation of the gold complex shows size-selectivity compared to an alternative route using platinum(II) corner motifs. Upon reductive elimination, an all-organic ether-decorated carbon nanoring was obtained. Investigation as a host for the complexation of large guest molecules with a suitable convex π-surfaces was accomplished using isothermal NMR binding titrations. Association constants for [6]cycloparaphenylene ([6]CPP), [7]CPP, C₆₀, and C₇₀ were determined.     

Synthesis of Supramolecular A8Bn Miktoarm Star Copolymers by Host-Guest Complexation

We report a new synthetic method to construct supramolecular A₈B_n (n=1, 2, 4) miktoarm star copolymers by host-guest complexation between a resorcinarene-based coordination capsule possessing eight polystyrene chains and 4,4-diacetoxybiphenyl guest molecules that retain one, two or four polymethyl acrylate chains. The formation of the supramolecular A₈B_n (n=1, 2, 4) miktoarm star copolymers was confirmed by dynamic light scattering (DLS), size-exclusion chromatography (SEC), and diffusion-ordered NMR spectroscopy (DOSY). Differential scanning calorimetry (DSC) measurements revealed that the miktoarm copolymers were phase-separated in the bulk. The micro-Brownian motion of the A₈B₄ structure was markedly enhanced in the bulk due to a weak segregation interaction between the immiscible arms.     

Carbohydrate Recognition through Noncovalent Interactions: A Challenge for Biomimetic and Supramolecular Chemistry

Carbohydrates are not always as “sticky” as one might expect . Even in organic solvents they are difficult targets for the supramolecular chemist, due to their complex, three-dimensional structures. In their natural environment (water) they are especially elusive, presenting challenges which will occupy synthetic and theoretical chemists for some time to come. The complex of an octaamide supramolecular receptor with β-D -glucopyranose, which binds through apolar and polar contacts, is shown.     

DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution

DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype–phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow “translation” into the synthetic product it is linked to. In this Review, we cover technologies that enable the “translation” of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.