Supramolecular Transition Research Articles

A genetically encoded anomalous SAXS ruler to probe the dimensions of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) adopt ensembles of rapidly fluctuating heterogeneous conformations, influencing their binding capabilities and supramolecular transitions. The primary conformational descriptors for understanding IDP ensembles-the radius of gyration (RG), measured by small-angle X-ray scattering (SAXS), and the root mean square (rms) end-to-end distance (RE), probed by fluorescent resonance energy transfer (FRET)-are often reported to produce inconsistent results regarding IDP expansion as a function of denaturant concentration in the buffer. This ongoing debate surrounding the FRET-SAXS discrepancy raises questions about the overall reliability of either method for quantitatively studying IDP properties. To address this discrepancy, we introduce a genetically encoded anomalous SAXS (ASAXS) ruler, enabling simultaneous and direct measurements of RG and RE without assuming a specific structural model. This ruler utilizes a genetically encoded noncanonical amino acid with two bromine atoms, providing an anomalous X-ray scattering signal for precise distance measurements. Through this approach, we experimentally demonstrate that the ratio between RE and RG varies under different denaturing conditions, highlighting the intrinsic properties of IDPs as the primary source of the observed SAXS-FRET discrepancy rather than shortcomings in either of the two established methods. The developed genetically encoded ASAXS ruler emerges as a versatile tool for both IDPs and folded proteins, providing a unified approach for obtaining complementary and site-specific conformational information in scattering experiments, thereby contributing to a deeper understanding of protein functions.

Molecular and supramolecular recognition patterns in ternary copper(II) or zinc(II) complexes with selected rigid-planar chelators and a synthetic adenine-nucleoside

Four ternary metal-complexes with Cu(II) or Zn(II), 2,6-pyridine-dicarboxylate (pdc) or glycyl-glycinate (GG) and the synthetic nucleoside 9-(2-hydroxyethyl)adenine (9heade) have been synthesized and studied by single-crystal X-ray diffraction and other physical methods. Relevant supramolecular assemblies found in the solid state structures have been further studied using density functional theory (DFT) calculations. In addition, the energetic features of the non-covalent interactions as well as the cooperativity effects have been calculated and characterized using the non-covalent interaction plot computational tool. Compounds trans-[Cu(pdc)(9heade)(H2O)2]·3H2O (1a) and [Cu(pdc)(9heade)(H2O)]·H2O (1b), trans-[Zn(pdc)(9heade)(H2O)2] (2), share the same molecular recognition pattern consisting in the cooperation of the metal-N7(9heade) bond and an interligand (9heade)N6-H···O(pdc) interaction, regardless of the nature of the metal, the coordination environment and the water content. At a supramolecular level, these compounds exhibit pairs of complex molecules linked by H-bonds and interesting anion–π/π–π/π–anion assemblies (in 1a and 1b) or the unprecedented π-π interactions (in 2), involving the purine moieties or the exocyclic –6NH2 purine groups, respectively. Compound 3, {[Cu(GG)(9heade)(H2O)·Cu(GG)(μ2-9heade)]·8H2O}n, consists in asymmetric dinuclear complex units (Cu···Cu 7.83 Å) that connect with adjacent ones by pairs of very weak Cu-O(carboxylate) bonds (Cu···Cu 3.81 Å) building a polymeric chain. The supramolecular transition from a single molecule to dinuclear units and finally a polymeric chain is also observed in the electron paramagnetic resonance spectra and discussed from a structural point of view as well as by DFT calculations. The unprecedented N7 and μ-N7,O(ol) metal binding patterns of 9heade differs from that recently reported (μ-N1,N7) in a Cd(II) polymer.

A Tris(3-pyridyl)stannane as a Building Block for Heterobimetallic Coordination Polymers and Supramolecular Cages.

The systematic assembly of supramolecular arrangements is a persistent challenge in modern coordination chemistry, especially where further aspects of complexity are concerned, as in the case of large molecular mixed-metal arrangements. One targeted approach to such heterometallic complexes is to engineer metal-based donor ligands of the correct geometry to build 3D arrangements upon coordination to other metals. This simple idea has, however, only rarely been applied to main group metal-based ligand systems. Here, we show that the new, bench-stable tris(3-pyridyl)stannane ligand PhSn(3-Py)3 (3-Py=3-pyridyl) provides simple access to a range of heterometallic SnIV /transition metal complexes, and that the presence of weakly coordinating counter anions can be used to build discrete molecular arrangements involving anion encapsulation. This work therefore provides a building strategy in this area, which parallels that of supramolecular transition metal chemistry.

Conformation-dependent phosphorescence emission of individual mononuclear ruthenium-(ii)-bis-terpyridine complexes.

The potential of supramolecular transition metal coordination complexes to form robust, long-living, radiative charge transfer states makes this class of triplet state emitters ideal candidates for application as photosensitizes or in photonic devices. Antenna-enhanced phosphorescence experiments on single Ru2+-bis-terpyridine complexes incorporated into a thin PMMA film show that phosphorescence emission spectra can exhibit shifts depending on the local environment [J. F. Herrmann, P. S. Popp, A. Winter, U. S. Schubert and C. Höppener, ACS Photonics, 2016, 3, 1897-1906]. Here, we demonstrate that the environmentally altered spectral properties of individual dual-luminescent Ru2+-bis-terpyridine complexes in PMMA and acetonitrile can be reproduced by DFT-based vibrationally resolved Franck-Condon spectra, if the phosphorescent emission of different molecular conformations is taken into account. Furthermore, we demonstrate that the triplet emission of these complexes occurs from a metal-to-ligand charge transfer (MLCT) state.

Supramolecular "Big Bang" in a Single-Ionic Surfactant/Water System Driven by Electrostatic Repulsion: From Vesicles to Micelles.

In aqueous solution, dimethyldi-n-octylammonium chloride, [DiC8][Cl], spontaneously forms dimers at low concentrations (1-10 mM) to decrease the strength of the hydrophobic-water contact. Dimers represent ideal building blocks for the abrupt edification of vesicles at 10 mM. These vesicles are fully characterized by dynamic and static light scattering, self-diffusion nuclear magnetic resonance, and freeze-fracture transmission electron microscopy. An increase in concentration leads to electrostatic repulsion between vesicles that explode into small micelles at 30 mM. These transitions are detected by means of surface tension, conductivity, and solubility of hydrophobic solutes as well as by isothermal titration microcalorimetry. These unusual supramolecular transitions emerge from the surfactant chemical structure that combines two contradictory features: (i) the double-chain structure tending to form low planar aggregates with low water solubility and (ii) the relatively short chains giving high hydrophilicity. The well-balanced hydrophilic-hydrophobic character of [DiC8][Cl] is then believed to be at the origin of the unusual supramolecular sequence offering new opportunities for drug delivery systems.

Antenna-Enhanced Triplet-State Emission of Individual Mononuclear Ruthenium(II)-Bis-terpyridine Complexes Reveals Their Heterogeneous Photophysical Properties in the Solid State

The ability of supramolecular transition metal coordination complexes to form stabilized, long-living, radiative charge-separated states has drawn interest to employ these triplet-state emitters for the design of photonic devices. Their applicability as photosensitizers of electron transfer in molecular photonic systems is directly coupled to fundamental studies of their rich and highly versatile photochemical and photophysical properties. Here, we demonstrate that the properties of individual dual-luminescent Ru2+-bis-terpyridine complexes can be addressed with excellent sensitivity in single-complex antenna-enhanced phosphorescence investigations. This sensitivity enables studying environmentally imposed alterations of their photophysical properties, e.g., in thin film applications. In contrast to ensemble averaging investigations in solution, single-complex antenna-enhanced phosphorescence investigations corroborate the existence of Ru2+-bis-terpyridine complexes with spectrally shifted emission peaks ...

Calorimetric quantification of linked equilibria in cyclodextrin/lipid/detergent mixtures for membrane-protein reconstitution

Reconstitution from detergent micelles into lipid bilayer membranes is a prerequisite for many in vitro studies on purified membrane proteins. Complexation by cyclodextrins offers an efficient and tightly controllable way of removing detergents for membrane-protein reconstitution, since cyclodextrins sequester detergents at defined stoichiometries and with tuneable affinities. To fully exploit the potential advantages of cyclodextrin for membrane-protein reconstitution, we establish a quantitative model for predicting the supramolecular transition from mixed micelles to vesicles during cyclodextrin-mediated detergent extraction. The model is based on a set of linked equilibria among all pseudophases present in the course of the reconstitution process. Various isothermal titration-calorimetric protocols are used for quantifying a detergent’s self-association as well as its colloidal and stoichiometric interactions with lipid and cyclodextrin, respectively. The detergent’s critical micellar concentration, the phase boundaries in the lipid/detergent phase diagram, and the dissociation constant of the cyclodextrin/detergent complex thus obtained provide all thermodynamic parameters necessary for a quantitative prediction of the transition from micelles to bilayer membranes during cyclodextrin-driven reconstitution. This is exemplified and validated by stepwise complexation of the detergent lauryldimethylamine N-oxide in mixtures with the phospholipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine upon titration with 2-hydroxypropyl-β-cyclodextrin, both in the presence and in the absence of the membrane protein Mistic. The calorimetric approach presented herein quantitatively predicts the onset and completion of the reconstitution process, thus obviating cumbersome trial-and-error efforts and facilitating the rational optimisation of reconstitution protocols, and can be adapted to different cyclodextrin/lipid/detergent combinations.

Supramolecular transitions in native cellulose-I during progressive oxidation reaction leading to quasi-spherical nanoparticles of 6-carboxycellulose

Cellulose-I swells considerably in phosphoric acid, and converts to amorphous cellulose via a cellulose-II transition state. Controlled oxidation of cellulose-I to 6-carboxycellulose (6CC) using HNO3–H3PO4–NaNO2 oxidation system led to the selective production of 6CC's of varying carboxyl contents (1.7–22%) as well as various shapes and sizes (macro-sized fibrils of several micron length and/or spherical nanoparticles of 25–35nm), depending on the reaction conditions. 6CC's having less than 14% carboxyl content were largely in cellulose-II form (WAXRD values in-between cellulose I and cellulose II), whereas at 14–22% the 6CC's were largely amorphous; only trace crystallinity was observed at 19% and 22% carboxyl 6CC. Spherical nanoparticles retained a high degree of crystallinity having cellulose-I structure, whereas the macro-sized fibrils were largely converted to cellulose-II structure. Analysis by WAXRD as well as by CP-MAS 13C NMR studies gave similar conclusions. Reduced molecular weight with progressive oxidation, including presence of oligomers, was also evident from an increase in the reducing-end carbon peak at ∼92ppm. For high oxidation levels (>14%) the NMR 92–96ppm peaks disappeared on extracting with dilute alkali, due to soluble oligomers being removed.

Synthesis and physical properties of a ball-like three-dimensional π-conjugated molecule

Curved π-conjugated molecules with closed and three-dimensional (3D) structures, such as fullerenes and carbon nanotubes, have been the subject of intensive research due to their potential applications in molecular electronics. However, basic molecular skeletons of 3D molecules are limited because of the lack of a rational and selective synthetic method by organic synthesis. Here we report the synthesis of a 3D π-conjugated molecule based on the platinum-mediated assembly of four molecules of a stannylated trisubstituted benzene derivative forming a hexanuclear platinum complex with an octahedral shape, from which reductive elimination of platinum gave the target molecule. As many supramolecular transition metal-ligand complexes with 3D cages and polyhedral structures have been synthesized by self-assembly of ligands and metals, the current assembly/reductive elimination strategy could provide a variety of new 3D π-conjugated molecules with different structures and topologies, which are challenging to obtain using conventional synthetic methods.

Syntheses, structures, and photoluminescence properties of Zn(II)/Cd(II) supramolecular architectures based on 1,5-naphthalenedisulfonate and 1,10-phenanthroline ligands

Two new supramolecular transition metal compounds, [Zn(phen)2(1,5-NDS)(H2O)] and [Cd(phen)2(1,5-NDS)]n (1,5-NDS = 1,5-naphthalenedisulfonate, phen = 1,10-phenanthroline), were obtained under hydrothermal/solvothermal conditions and structurally characterized by elemental analysis, IR, PXRD, TG-DSC, and single-crystal X-ray determination. They represent the first examples of Zn(II)/Cd(II) supramolecular compounds based on the 1,5-NDS/phen system. The Zn compound exhibits a 3D supramolecular structure via hydrogen bond (O–H⋯O and C–H⋯O) and π–π interactions. The Cd compound is a 3D supramolecular framework generated by 1D coordinated chains through a hydrogen bond (C–H⋯O) and π–π interactions. In addition, photoluminescence properties for both have been discussed. [Zn(phen)2(1,5-NDS)(H2O)] shows an emission peak at 420 nm (λ ex = 342 nm), and [Cd(phen)2(1,5-NDS)] n displays a strong emission peak at 388 nm with a shoulder peak at 369 nm (λ ex = 332 nm). .

Bis-(thiosemicarbazonato) Zn(ii) complexes as building blocks for construction of supramolecular catalysts

In this paper we report the application of bis-(thiosemicarbazonato) Zn(II) complexes as building blocks in the construction of supramolecular transition metal assemblies. We investigated their coordination behaviour towards pyridylphosphine molecules and found these systems comparable to those based on Zn(porphyrin) and Zn(salphen) complexes. Additionally, catalytic experiments and an in situ high-pressure FTIR study of the supramolecular rhodium hydroformylation catalysts, assembled using the bis-(thiosemicarbazonato) Zn(II) complexes, demonstrate their applicability in supramolecular catalysis and their potential for application in other areas of supramolecular chemistry.

Crystallization of copper(II) sulfate based minerals and MOF from solution: Chemical insights into the supramolecular interactions

Crystallization of solids, molecular or non-molecular from solution is a supramolecular reaction. Nucleation of a lattice structure at supersaturation can be conceived to result from a critical nucleus, a high energy intermediate (supramolecular transition state). Conceptualization of a structure for the critical nucleus in terms of aggregation of tectons through non-covalent interactions provides chemical insights into the architecture of a solid. The retrosynthetic analysis of copper-based minerals and materials offers an elegant description for the crystal packing. It addresses the influence of the geometry, functionality and reactivity of copper tecton(s) in directing a specific supramolecular aggregation. The mechanistic approach provides guiding principles to chemists to account for the experimentally crystallized solids and a platform to practice structure-synthesis correlation. Rationalization of the same composition with different atomic arrangements (polymorphs), compositional variation leading to different pseudopolymorphs, degree of hydration (anhydrous to hydrated), water clusters, role of solvent, etc. can all be justified on molecular basis. Also, the method gives predictive components including directions to synthesize new solids. In a nutshell, the paper is an attempt to generalize the crystallization of inorganic solids from solution by recognizing supramolecular interactions between metal tectons and gain insights for designing new MOF.

β-Cyclodextrin modifications as related to enzyme stability in dehydrated systems: Supramolecular transitions and molecular interactions

The effect of β-cyclodextrin modifications (polymerization (PCD) and later carboxymethylation (CMPCD)) on their action as enzyme stabilizers was analyzed during freeze-drying and thermal treatment. Combined polymer-trehalose matrices were also employed. Due to their higher T g values, PCD and CMPCD provided better structural stability to the freeze-dried formulations than β-CD. However, only PCD was a good excipient to protect invertase both in amorphous and supercooled systems. FT-IR revealed increased protein denaturation in the presence of CMPCD, but not in the presence of PCD. Even though all polymers inhibited/delayed trehalose crystallization, only trehalose (T) combined with PCD (PCD + T) and with β-cyclodextrin (β-CD + T) offered the best stability to the enzyme. In β-CD + T system, trehalose was the main responsible for the protection. In PCD + T system, both additives contributed to improve the enzyme stability. FT-IR and DSC were useful to analyze the combined role of molecular and supramolecular interactions on enzyme stability in dehydrated model systems.

Hydrogen bonding effects on topological structures of two supramolecular transition metal coordination complexes based on organosulphonate ligands

Abstract The syntheses, X-ray crystal structures and topological analyses of two supramolecular coordination complexes, [Co(H2O)4(ps)2] 1 and [Cu(H2O)2(ps)2] 2 (ps− = pyridine-3-sulfonic anion), are reported. Although the basic coordination environments and patterns around the metal centers of 1 and 2 are similar, the overall topologies of the two complexes are very different due to the formation of distinct hydrogen bonding interactions resulting from organosulphonate ligands.

Self-assembly and supramolecular transition of poly(amidoamine) dendrons focally modified with aromatic chromophores

Three novel series of amphiphiles based on poly(amidoamine) dendrons (from G1 to G3) and having different aromatic chromophores (Cz I, Cz II, and Py) at the focal point were synthesized and studied for their self-assembly behavior in aqueous solution by using electronic microscopies (i.e., SEM and TEM), UV–vis, fluorescence, IR, and 1H NMR spectroscopy. It was found that the generation of dendrons affected significantly the self-assembly of these amphiphiles in aqueous solution and the morphological structures of the resulting assemblies depended greatly on the architecture of the focal chromophores. As a result, the first generation of dendrons assembled readily into vesicles at low concentrations. These vesicular structures subsequently fused to form a stable tubular structure. Similar tubular structures could also be directly obtained through self-assembly of these amphiphilic dendrons at high concentrations. X-ray investigations showed that the resulting tubules possessed a lamellar structure. A head-to-head packing model of amphiphilic dendrons in the assemblies was proposed.

Supramolecular Hydrogen Bond Isomerism in Organic Salts: A Transition from 0D to 1D

Based on nine single-crystal structures of a series of organic salts derived from dicyclohexylamine and n-alkyl monocarboxylic acids (CH3−(CH2)n−COOH, n = 1−17), it is shown that salts having n = 14 and 15 display 1D hydrogen-bonded networks, whereas majority of the salts having n = 1−9 show 0D networks. Structural analyses indicate that both intra- and internetwork alkyl−alkyl interactions appear to be responsible for such a supramolecular transition.

Bisphosphine based hetero-capsules for the encapsulation of transition metals

Just mixing of solutions of tetracationic diphosphine ligands and tetraanionic calix[4]arene building blocks leads to the formation of supramolecular heterocapsules that coordinate a palladium metal within the cavity of the assembly, giving rise to a new class of potential supramolecular transition metal catalysts.

Addressing metal centres in supramolecular assemblies

Supramolecular metal ion assemblies are deposited from their solutions onto highly orientated pyrolytic graphite (HOPG) substrates to be imaged by scanning tunnelling microscopy (STM). Since the structural and electronic information of STM measurements are strongly entangled, the spectroscopic interpretation and analysis of the images of such molecular assemblies has proven to be challenging. This tutorial review focuses on a general room temperature scanning tunnelling spectroscopy (STS) protocol, current induced tunnelling spectroscopy (CITS), applied to free-standing 1D and 2D arrangements of supramolecular metal ion assemblies rendering local tunnelling probabilities with submolecular resolution. The size of the investigated molecular assemblies was confirmed by comparison with X-ray crystallographic data, while the consistency of the spectroscopic investigations and of the determined positions of the metal ions within the assemblies was checked by DFT calculations. Due to the genuine level structure of coordinated metal centers, it was possible to map exclusively the position of the coordination bonds in supramolecular transition metal assemblies with submolecular spatial resolution using the CITS technique. CITS might thus constitute an important tool to achieve directed bottom-up construction and controlled manipulation of fully electronically functional, two-dimensional molecular designs.

Structural chemistry of complexes with an encapsulated metal ion. α-Dioximate, oximehydrazonate, and dihydrazonate clathrochelates

The review surveys the main trends in the structural chemistry of clathrochelates: the determination of the crystal and molecular structures of various types of new complexes, their symmetry and functionality; the supramolecular organization and phase transitions of clathrochelate crystals; the structure—spectral parameter relationships and the deduction of the molecular structures; the use of X-ray diffraction data for explanation of the kinetic and thermodynamic parameters of the synthesis and decomposition of clathrochelates.

Supramolecular transition metal catalysts in two-phase systems

The concept of covalently connecting a catalytically active transition metal center with a water-soluble receptor (host molecule) makes a new type of supramolecular catalysis possible in which the features of molecular recognition, phase transfer catalysis and transition metal catalysis are combined in a single system. The first examples of this principle make use of the commercially available β-cyclodextrin (β-CD) as the receptor and rhodium complexes of diphosphanes as the catalytically active center, these being covalently connected to one another via a spacer. In competitive hydrogenation of certain olefins unusual degrees of substrate selectivity based on the molecular recognition are observed, not possible by conventional transition metal catalysts. The two-phase (H 2O/organic) hydrogenation of nitro-aromatics also is a smooth process with these supramolecular catalysts. They also constitute an unusually active catalyst system for the selective hydroformylation of higher olefins such as 1-octene in a two-phase system.