Simple thermodynamics for unravelling sophisticated self-assembly processes

During the past 15 years, coordination chemistry has rapidly developed toward multicomponent assemblies involving several ligands and metal ions, which are connected via intra- or intermolecular processes. The fascinating structural aspect of these complexation reactions has been early recognized for the design of sophisticated (supra)molecular architectures with novel topologies and functions, while the concomitant energetic part only recently emerged as a potential tools for controlling and programming self-assemblies. In this Perspective, we focus on the modelling of the free energy changes accompanying self-assembly processes. Starting with the original protein-ligand model borrowed from biology, which describes complicated multicomponent assemblies, we present (i) its adaptation to coordination chemistry and (ii) its significance for addressing cooperativity as an extra energy cost resulting from intercomponent interactions. An additional entropic concept arising from the separation of intra- and intermolecular complexation processes is then discussed, together with its explicit consideration for modeling multicomponent complexation reactions. Finally, both aspects (i.e. cooperativity and intra-/intermolecular connections) are combined in the extended site binding model, which is able to dissect free energy changes occurring in sophisticated metal-ligand assemblies with a minimum set of microscopic parameters. Applications to experimental complexation reactions of increasing complexity are systematically discussed, and illustrate the potential and limitations of each model.     

A simple thermodynamic model for quantitatively addressing cooperativity in multicomponent self-assembly processes--Part 2: Extension to multimetallic helicates possessing different binding sites

The extended site-binding model, which explicitly separates intramolecular interactions (i.e., intermetallic and interligand) from the successive binding of metal ions to polytopic receptors, is used for unravelling the self-assembly of trimetallic double-stranded Cu(I) and triple-stranded Eu(III) helicates. A thorough analysis of the available stability constants systematically shows that negatively cooperative processes operate, in strong contrast with previous reports invoking either statistical behaviours or positive cooperativity. Our results also highlight the need for combining successive generations of complexes with common binding units, but with increasing metallic nuclearities, for rationalizing and programming multicomponent supramolecular assemblies.     

Supramolecular metal-polypyridyl and Ru(II) porphyrin complexes: photophysical, electron paramagnetic resonance, and electrochemical studies

A series of mixed-metal supramolecular porphyrin arrays in which the geometry of the central metal-polypyridyl moiety defines the spatial arrangement of two or more Ru(II)-porphyrin units through axial coordination have been prepared by employing self-assembly based protocols, and their photophysical and electrochemical properties have been studied. The electrochemical properties of the constituent parts of these arrays depend only on their own chemical environment, regardless of the nuclearity and the overall charge of the compound; in this way species with predetermined redox patterns can be obtained via the synthetic control of the self-assembly process. Interestingly, several of these arrays are luminescent both at room and at low temperatures, and in many cases core-to-periphery or periphery-to-core intramolecular energy transfer processes take place according to the nature of the central metal template.     

Modeling negative cooperativity in streptavidin adsorption onto biotinylated microtubules

The nanoscale architecture of binding sites can result in complex binding kinetics. Here, the adsorption of streptavidin and neutravidin to biotinylated microtubules is found to exhibit negative cooperativity due to electrostatic interactions and steric hindrance. This behavior is modeled by a newly developed kinetic analogue of the Fowler-Guggenheim adsorption model. The complex adsorption kinetics of streptavidin to biotinylated structures needs to be considered when these intermolecular bonds are employed in self-assembly and nanobiotechnology.     

Chirality organization of ferrocenes bearing podand dipeptide chains: synthesis and structural characterization

A variety of ferrocenes bearing podand dipeptide chains have been synthesized to form an ordered structure in both solid and solution states and have been investigated by 1H NMR, FT-IR, CD, and X-ray crystallographic analyses. Conformational enantiomerization through chirality organization was achieved by the intramolecular hydrogen bondings between the podand dipeptide chains. The single-crystal X-ray structure determination of the ferrocene 2 bearing the podand dipeptide chains (-D-Ala-D-Pro-OEt) revealed two C2-symmetric intramolecular hydrogen bondings between CO (Ala) and NH (another Ala) of each podand dipeptide chain to induce the chirality-organized structure. The molecular structures of the ferrocene 1 composed of the podand L-dipeptide chains (-L-Ala-L-Pro-OEt) and 2 are in a good mirror image relationship, indicating that they are conformational enantiomers. An opposite helically ordered molecular arrangement was formed in the crystal packing of 2 as compared with 1. The ferrocene 2 exhibited induced circular dichroism (CD), which appeared at the absorbance of the ferrocene moiety. The mirror image of the CD signals between 1 and 2 was observed, suggesting that the chirality-organized structure via intramolecular hydrogen bondings is present even in solution. The ferrocene 4 bearing the podand dipeptide chains (-Gly-L-Leu-OEt) also showed an ordered structure in the crystal based on two intramolecular hydrogen bondings between CO (Gly) and NH (another Gly) of each podand dipeptide chain, together with intermolecular hydrogen bondings between CO adjacent to the ferrocene unit and NH (neighboring Leu) to create the highly organized self-assembly. A different self-assembly was observed in the crystal of the ferrocene 5 composed of the podand dipeptide chains (-Gly-L-Phe-OEt), wherein each molecule is bonded to two neighboring molecules through two pairs of symmetrical intermolecular hydrogen bonds to form a 14-membered intermolecularly hydrogen-bonded ring. These ordered structures based on the intramolecular hydrogen bondings in the solution state are also confirmed by 1H NMR and FT-IR.     

The intermolecular potential in NO-N2 and (NO-N2)+ systems: implications for the neutralization of ionic molecular aggregates

The characterization of the non covalent interaction potential, responsible for the intermolecular bond in NO-N(2) and (NO-N(2))(+) molecular aggregates, has been achieved by coupling the predictions of a semiempirical method with the results of a scattering experiment and ab initio calculations. The potential wells for the most stable configurations of the neutral and ionic state, having approximatively a T shape in both cases, fall in the same intermolecular distance range. In addition, in the ionic state, the charge is completely localized on the NO partner. Important implications on the dynamics of the neutralization process, occurring as a vertical transition from ionic to neutral state, are obtained by exploiting the analytical formulation of the interaction and calculating energy spacings and relevant Franck-Condon factors for both intramolecular and intermolecular vibration modes.     

Analytical terahertz spectroscopy.

Recent progress in analytical terahertz (THz) spectroscopy is reviewed with illustrative examples showing that it is an effective method for detecting and identifying intermolecular interactions in chemical compounds, such as hydrogen bonds. The unique and characteristic properties of THz waves, their significance to both science and industry, and the bases of one of the successful fields of analytical THz spectroscopy, namely THz time-domain spectroscopy and THz imaging for chemical analysis, are described. Preliminary quantitative studies are presented to show the potential of THz spectroscopy for the detection and identification of intermolecular hydrogen bonds in unknown mixture samples. The selective detection of intramolecular hydrogen bonds and the detection of intramolecular interactions in ice are also introduced. Some brief remarks are provided on future developments, the main issues, and the prospects for analytical THz spectroscopy.     

Covalently Linked Bis(Amido-Corroles): Inter- and Intramolecular Hydrogen-Bond-Driven Supramolecular Assembly

Four bis-corroles linked by diamide bridges were synthesized through peptide-type coupling of a trans-A₂B-corrole acid with aliphatic and aromatic diamines. In the solid state, the hydrogen-bond pattern in these bis-corroles is strongly affected by the type of solvent used in the crystallization process. Although intramolecular hydrogen bonds play a decisive role, they are supported by intermolecular hydrogen bonds and weak N−H⋅⋅⋅π interactions between molecules of toluene and the corrole cores. In an analogy to mono(amido-corroles), both in crystalline state and in solutions, the aliphatic or aromatic bridge is located directly above the corrole ring. When either ethylenediamine or 2,3-diaminonaphthalene are used as linkers, incorporation of polar solvents into the crystalline lattice causes a roughly parallel orientation of the corrole rings. At the same time, both NHCO⋅⋅⋅NH corrole hydrogen bonds are intramolecular. In contrast, solvation in toluene causes a distortion with one of the hydrogen bonds being intermolecular. Interestingly, intramolecular hydrogen bonds are always formed between the –NHCO– functionality located further from the benzene ring present at the position 10-meso. In solution, the hydrogen-bonds pattern of the bis(amido-corroles) is strongly affected by the type of the solvent. Compared with toluene (strongly high-field shifted signals), DMSO and pyridine disrupt self-assembly, whereas hexafluoroisopropanol strengthens intramolecular hydrogen bonds.     

Comparison of inter- and intramolecular cyclodextrin complexes

Abstract

We present the first comparative steady-state and time-resolved fluorescence studies of inter- and intramolecular cyclodextrin complexes. Specifically, we report equilibrium and kinetic results for dansyl-glycine complexed with β-cyclodextrin (intermolecular) and the dansyl-glycine-β-cyclodextrin adduct (intramolecular). The fluorescence intensity decay profile for the intermolecular system is best described by a discrete triple exponential decay law. This is consistent with stepwise 1:1 and 2:1 (β-cyclodextrin:guest) inclusion complexation. Equilibrium constants are in line with previous results on similar species. In contrast, we found that the intramolecular case was described by a doubly exponential decay law—consistent with a single intramolecular inclusion complex. Displacement experiments, with borneol, confirm the simplicity of the intramolecular complex. In all cases, continuous distribution models failed to fit the experimental data.     

Stereoselective On-Surface Cyclodehydrofluorization of a Tetraphenylporphyrin and Homochiral Self-Assembly

The thermally induced cyclodehydrofluorization of iron tetrakis(pentafluorophenyl)porphyrin proceeded highly stereoselectively to give a prochiral product on a gold surface in an ultrahigh vacuum, whereas dehydrocyclization of the respective iron tetrakisphenylporphyrin did not show such selectivity. Stereoselectivity was predominantly observed for closely packed layers, which is an indication of intermolecular cooperativity and steric constraints induced by adjacent species. Density functional theory identified intermolecular packing constraints as the origin of such selectivity during the reaction. Scanning tunneling microscopy revealed the formation of an enantiomerically pure two-dimensional self-assembly as a conglomerate of mirror domains. On-surface two-dimensional topochemistry, as reported herein, may open new routes for stereoselective synthesis.     

Edge-to-face CH/pi aromatic interaction and molecular self-recognition in epi-cinchona-based bifunctional thiourea organocatalysis

The impact of cooperativity between intermolecular interactions is demonstrated by the molecular self-recognition properties of highly enantioselective epi-cinchona bifunctional thiourea organocatalysts. Low-temperature NMR experiments in inert solvents have revealed two sets of nonequivalent resonances in equal population for thiourea-modified members of the epi-quinine and epi-quinidine families. In solution, the predominance of an asymmetric (C1) dimeric self-assembly with noteworthy structural motifs became evident: simultaneous intra- and intermolecular thiourea hydrogen bonding and a CH/pi interaction were observed. Both the stereochemical and the diverse conformational features of the system favor the observed quinoline T-shaped aromatic pi-pi stacking interaction. The structure findings are supported by quantitative proton-proton distance data that were available from NOE buildup curves. The 3D structure of the dimeric assembly has been modeled in agreement with the H-H distance restraints. Owing to the geometrical preference associated with the dimerization process, the self-assembled bifunctional system is interpreted as a charge-transfer complex with the potential for catalyst self-activation.     

Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems

In several previous studies, we performed sensitivity analysis to gauge the relative importance of different atomic partial charges in determining protein-ligand binding. In this work, we gain further insights by decomposing these results into three contributions: desolvation, intramolecular interactions, and intermolecular interactions, again based on a Poisson continuum electrostatics model. Three protein kinase-inhibitor systems have been analyzed: CDK2-deschloroflavopiridol, PKA-PKI, and LCK-PP2. Although our results point out the importance of specific intermolecular interactions to the binding affinity, they also reveal the remarkable contributions from the solvent-mediated intramolecular interactions in some cases. Thus, it is necessary to look beyond analyzing protein-ligand interactions to understand protein-ligand recognition or to gain insights into designing ligands and proteins. In analyzing the contributions of the three components to the overall binding free energy, the PKA-PKI system with a much larger ligand was found to behave differently from the other two systems with smaller ligands. In the former case, the intermolecular interactions are very favorable, and together with the favorable solvent-mediated intramolecular interactions, they overcome the large desolvation penalties to give a favorable electrostatics contribution to the overall binding affinity. On the other hand, the other two systems with smaller ligands only present modest intermolecular interactions and they are not or are only barely sufficient to overcome the desolvation penalty even with the aid of the favorable intramolecular contributions. As a result, the binding affinity of these two systems do not or only barely benefit from electrostatics contributions.     

Symmetry numbers and statistical factors in self-assembly and multivalency

Evaluation of statistical factors in self-assembly processes is not a firmly settled question. As a contribution to solve this problem, a critical re-examination of the symmetry number method and generalization of the direct count method are presented. The two approaches, producing the same results, mutually reinforce their role with respect to other discordant methods whose results cannot be independently checked. The direct count method moreover serves as a rationale for the apparently odd results the symmetry number method sometimes provides. The two methods thus turn out to be complementary to each other. Discussion of some exemplary cases points to the importance and subtlety of the role played by the geometrical features of assemblies involving intramolecular bonds.     

Asymmetric inter- and intramolecular cyclopropanation of alkenes catalyzed by chiral ruthenium porphyrins. Synthesis and crystal structure of a chiral metalloporphyrin carbene complex.

Extensive investigations of asymmetric intermolecular cyclopropanation of terminal alkenes with diazoacetates catalyzed by ruthenium porphyrin [Ru(P*)(CO)(EtOH)] (1, H2P = 5,10,15,20-tetrakis[(1S,4R,5R,8S)-1,2,3,4,5,6,7,8-octahydro-1,4:5,8-dimethanoanthracene-9-yl]porphyrin) and the application of catalyst 1 to asymmetric intramolecular cyclopropanation of allylic or homoallylic diazoacetates are described. The intermolecular cyclopropanation of styrene and its derivatives with ethyl diazoacetate afforded the corresponding cyclopropyl esters in up to 98% ee with high trans/cis ratios of up to 36 and extremely high catalyst turnovers of up to 1.1 x 10(4). Examination of the effects of temperature, diazoacetate, solvent, and substituent in the intermolecular cyclopropanation reveals that (i) both enantioselectivity and trans selectivity increase with decreasing temperature, (ii) sterically encumbered diazoacetates N2CHCO2R, such as R = Bu(t), and donor solvents, such as diethyl ether and tetrahydrofuran, are beneficial to the trans selectivity, and (iii) electron-donating para substituents on styrene accelerate the cyclopropanations, with the log(k(X)/k(H)) vs sigma(+) plot for para-substituted styrenes p-X-C6H4CH=CH2 (X = MeO, Me, Cl, CF3) exhibiting good linearity with a small negative rho(+) value of -0.44 +/- 0.09. In the case of intramolecular cyclopropanation, complex 1 promoted the decomposition of a series of allylic diazoacetates to form the cyclopropyl lactones in up to 85% ee, contributing the first efficient metalloporphyrin catalyst for an asymmetric intramolecular cyclopropanation. Both the inter- and intramolecular cyclopropanations were proposed to proceed via a reactive chiral ruthenium carbene intermediate. The enantioselectivities in these processes were rationalized on the basis of the X-ray crystal structures of closely related stable chiral carbene complexes [Ru(P*)(CPh2)] (2) and [Ru(P*)(C(Ph)CO2CH2CH=CH2)] (3) obtained from reactions of complex 1 with N2CPh2 and N2C(Ph)CO2CH2CH=CH2, respectively.     

Preorganizing linear (self-complementary) quadruple hydrogen-bonding arrays using intramolecular hydrogen bonding as the sole force

[structures: see text] In this article we describe a rational approach for prefixing multiple cooperative binding sites in an ideal spatial arrangement on a structurally rigid backbone, constrained exclusively by intramolecular hydrogen bonding. The idea is exemplified by the ability of the self-assembling constructs 1a-e and 2a,b to form hydrogen-bonded dimers, whose structural preorganization has been solely effected by intramolecular hydrogen bonding. The readily accessible amidinourea backbone has been used as a common platform for the construction of a variety of such self-assembling systems. ESI mass spectrometry and single-crystal X-ray diffraction studies have been particularly effective in investigating the self-assembling propensities of these systems. Remarkably, most the H-bonded dimers reported herein undergo an unusual mode of self-assembly, using intermolecular four-membered ring hydrogen-bonded interaction, affording extended supramolecular networks.     

Nickel-catalyzed reductive coupling of alkynes and epoxides

Nickel-catalyzed, intramolecular and intermolecular reductive coupling of alkynes and epoxides affords synthetically useful homoallylic alcohols of defined alkene geometry. Very high regioselectivity is generally observed, and cyclizations proceed with complete selectivity for endo epoxide opening. This catalytic reaction represents the first use of a non-pi-based electrophile in a growing class of nickel-catalyzed, multicomponent coupling reactions, and is the first catalytic method of reductive coupling of alkynes and epoxides that is effective for both intermolecular and intramolecular cases, and mechanistically distinct from these, possibly involving a nickella(II)oxetane.     

从超分子聚合物到超分子有机框架:组装溶液相超分子结构的周期性

单体分子在溶液相自发形成周期性的网络结构,是超分子化学和分子自组装研究领域的重大挑战.多头基分子在溶液相通过分子间非共价键作用可以形成超分子聚合物.提高多头基(三头基和四头基)分子骨架的刚性,可以提高结合位点的结构预组织,进而增强分子间相互作用的协同性和多价性特征,提高自组装结构的有序性或周期性.本文综述了多头基分子自组装形成超分子聚合物的一些重要进展,介绍了二维超分子有机框架(一类新的溶液相周期性自组装网络结构研究的最新进展.     

Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions,Chemical Properties,and Ligand/Protein Fluorine NMR Screening

It is known that strong hydrogen‐bonding interactions play an important role in many chemical and biological systems. However, weak or very weak hydrogen bonds, which are often difficult to detect and characterize, may also be relevant in many recognition and reaction processes. Fluorine serving as a hydrogen‐bond acceptor has been the subject of many controversial discussions and there are different opinions about it. It now appears that there is compelling experimental evidence for the involvement of fluorine in weak intramolecular or intermolecular hydrogen bonds. Using established NMR methods, we have previously characterized and measured the strengths of intermolecular hydrogen‐bond complexes involving the fluorine moieties CH₂F, CHF₂, and CF₃, and have compared them with the well‐known hydrogen‐bond complex formed between acetophenone and the strong hydrogen‐bond donor p‐fluorophenol. We now report evidence for the formation of hydrogen bonds involving fluorine with significantly weaker donors, namely 5‐fluoroindole and water. A simple NMR method is proposed for the simultaneous measurement of the strengths of hydrogen bonds between an acceptor and a donor or water. Important implications of these results for enzymatic/chemical reactions involving fluorine, for chemical and physical properties, and for ligand/protein ¹⁹F NMR screening are analyzed through experiments and theoretical simulations.