Kinetic and Thermodynamic Approaches for the Efficient Formation of Mechanical Bonds

Among the growing collection of molecular systems under consideration for nanoscale device applications, mechanically interlocked compounds derived from electrochemically switchable bistable [2]rotaxanes and [2]catenanes show great promise. These systems demonstrate dynamic, relative movements between their components, such as shuttling and circumrotation, enabling them to serve as stimuli-responsive switches operated via reversible, electrochemical oxidation−reduction rather than through the addition of chemical reagents. Investigations into these systems have been intense for a number of years, yet limitations associated with their synthesis have hindered incorporation of their mechanical bonds into more complex architectures and functional materials. We have recently addressed this challenge by developing new template-directed synthetic protocols, operating under both kinetic and thermodynamic control, for the preparation of bistable rotaxanes and catenanes. These methodologies are compatible with the molecular recognition between the π-electron-accepting cyclobis(paraquat-p-phenylene) (CBPQT4+) host and complementary π-electron-donating guests. The procedures that operate under kinetic control rely on mild chemical transformations to attach bulky stoppering groups or perform macrocyclizations without disrupting the host−guest binding of the rotaxane or catenane precursors. Alternatively, the protocols that operate under thermodynamic control utilize a reversible ring-opening reaction of the CBPQT4+ ring, providing a pathway for two cyclic starting materials to thread one another to form more thermodynamically stable catenaned products. These complementary pathways generate bistable rotaxanes and catenanes in high yields, simplify mechanical bond formation in these systems, and eliminate the requirement that the mechanical bonds be introduced into the molecular structure in the final step of the synthesis. These new methods have already been put into practice to prepare previously unavailable rotaxane architectures and novel complex materials. Furthermore, the potential for utilizing mechanically interlocked architectures as device components capable of information storage, the delivery of therapeutic agents, or other desirable functions has increased significantly as a result of the development of these improved synthetic protocols

Efficient Templated Synthesis of Donor−Acceptor Rotaxanes Using Click Chemistry

The mild reaction conditions, remarkable functional group compatibility, and complete regioselectivity of the Cu-catalyzed Huisgen 1,3-dipolar cycloaddition (“click chemistry”) between organic azides and terminal alkynes have led to a threading-followed-by-stoppering approach to the synthesis of donor−acceptor rotaxanes incorporating cyclobis(paraquat-p-phenylene) (CBPQT^(4+)) as the π-accepting ring component. Rotaxane formation is initiated by reacting azide-functionalized pseudorotaxanes containing π-donating 1,5-dioxynaphthalene (DNP) recognition units with appropriate alkyne-functionalized stoppers. The high yields obtained in this efficient, kinetically controlled post-assembly covalent modification, as well as the excellent convergence of the synthetic protocol, are demonstrated by the preparation of [2]-, [3]-, and [4]rotaxanes containing multiple DNP/CBPQT^(4+) donor−acceptor recognition motifs

Structural and Co-conformational Effects of Alkyne-Derived Subunits in Charged Donor−Acceptor [2]Catenanes

Four donor−acceptor [2]catenanes with cyclobis(paraquat-p-phenylene) (CBPQT^(4+)) as the π-electron-accepting cyclophane and 1,5-dioxynaphthalene (DNP)-containing macrocyclic polyethers as π-electron donor rings have been synthesized under mild conditions, employing Cu^+-catalyzed Huisgen 1,3-dipolar cycloaddition and Cu^(2+)-mediated Eglinton coupling in the final steps of their syntheses. Oligoether chains carrying terminal alkynes or azides were used as the key structural features in template-directed cyclizations of [2]pseudorotaxanes to give the [2]catenanes. Both reactions proceed well with precursors of appropriate oligoether chain lengths but fail when there are only three oxygen atoms in the oligoether chains between the DNP units and the reactive functional groups. The solid-state structures of the donor−acceptor [2]catenanes confirm their mechanically interlocked nature, stabilized by [π···π], [C−H···π], and [C−H···Ο] interactions, and point to secondary noncovalent contacts between 1,3-butadiyne and 1,2,3-triazole subunits and one of the bipyridinum units of the CBPQT^(4+) ring. These contacts are characterized by the roughly parallel orientation of the inner bipyridinium ring system and the 1,2,3-triazole and 1,3-butadiyne units, as well as by the short [π···π] distances of 3.50 and 3.60 Å, respectively. Variable-temperature ^1H NMR spectroscopy has been used to identify and quantify the barriers to the conformationally and co-conformationally dynamic processes. The former include the rotations of the phenylene and the bipyridinium ring systems around their substituent axes, whereas the latter are confined to the circumrotation of the CBPQT^(4+) ring around the DNP binding site. The barriers for the three processes were found to be successively 14.4, 14.5−17.5, and 13.1−15.8 kcal mol^(-1). Within the limitations of the small dataset investigated, emergent trends in the barrier heights can be recognized:  the values decrease with the increasing size of the π-electron-donating macrocycle and tend to be lower in the sterically less encumbered series of [2]catenanes containing the 1,3-butadiyne moiety

How to print a crystal structure model in 3D

We present a simple procedure for the conversion of Crystallographic Information Files (CIFs) into Virtual Reality Modelling Language (VRML2,.wrl) files, which can be used as input files for three-dimensional (3D) printing. This procedure permits facile production of customized full-colour 3D models of X-ray crystal structures of segments of extended structures, including metal-organic frameworks (MOFs) as well as small molecules. The method uses freely available software that runs under Microsoft Windows, MacOSX and Linux operating systems. © the Partner Organisations 2014

Synthesis and Columnar Organization of Partially Fluorinated Dehydrobenz[18]annulenes

Two diamond-shaped and partially fluorinated dehydrobenz[18]annulene macrocycles have been synthesized through a one-pot synthesis relying on fourfold Sonogashira coupling. Single crystal structures of the prepared macrocycles show continuous columnar stacks of these molecules that are mediated by the fluoroarene–alkyne, arene–alkyne, fluoroarene–fluoroarene, and alkyne–alkyne [π···π] interactions instead of the expected fluoroarene–arene [π···π] interaction

Rigidity-stability relationship in interlocked model complexes containing phenylene-ethynylene-based disubstituted naphthalene and benzene

Structural rigidity has been found to be advantageous for molecules if they are to find applications in functioning molecular devices. In the search for an understanding of the relationship between the rigidity and complex stability in mechanically interlocked compounds, the binding abilities of two π-electron-rich model compounds (2 and 4), where rigidity is introduced in the form of phenylacetylene units, toward the π-electron deficient tetracationic cyclophane, cyclobis(paraquat-p-phenylene) (CBPQT4+), were investigated. 1,4-Bis(2-(2-methoxyethoxy)ethoxy)-2,5-bis(2-phenylethynyl)benzene 2 and 1,5-bis(2-(2-methoxyethoxy)ethoxy)-2,6-bis(2-phenylethynyl)naphthalene 4 were synthesized, respectively, from the appropriate precursor dibromides 1 and 3 of benzene and naphthalene carrying two methoxyethoxyethoxy side chains. The rigid nature of the compounds 2 and 4 is reflected in the reduced stabilities of their 1:1 complexes with CBPQT4+. Binding constants for both 2 (100 M−1) and 4 (140 M−1) toward CBPQT4+ were obtained by isothermal titration microcalorimetry (ITC) in MeCN at 25 °C. Compounds 1−4 were characterized in the solid state by X-ray crystallography. The stabilization within and beyond these molecules is achieved by a combination of intra- and intermolecular [C−H···O], [C−H···π], and [π−π] stacking interactions. The diethyleneglycol chains present in compounds 1−4 are folded as a consequence of both intra- and intermolecular hydrogen bonds. The preorganized structures in both precursors 1 and 3 are repeated in both model compounds 2 and 4. In the structures of compounds 2 and 4, the geometry of the rigid backbone is differentthe two terminal phenyl groups are twisted with respect to the central benzenoid ring in compound 2 and roughly perpendicular to the plane central naphthalene core in compound 4. To understand the significantly decreased stabilities of these complexes toward rigid guest molecules, relative to more flexible systems, we performed density functional theory (DFT) calculations using the newly developed M06-suite of density functionals. We conclude that the reduced binding abilities are a consequence of electronic and not steric factors, originating from the extended delocalization of the aromatic system.None of the abov