Supramolecular Assembly: A Comparative Structural Study of the Incorporation of Bis(2-guanidinobenzimidazolo)nickel(II) into Supramolecular Arrays

The structural effects of incorporating a non-planar neutral metal complex, bis(2-guanidinobenzimidazolo)nickel(II), into three supramolecular arrays are described. The complex has a donor-acceptor-donor (DAD) hydrogen bonding motif on each ligand and this motif is used to link it to bis(biureto)nickelate(II) ions, or to 1,8-naphthalimide or phthalimide molecules, all of which incorporate a complementary acceptor-donor-acceptor (ADA) hydrogen bonding motif. The geometry about the metal ion as well as the nature of the network of hydrogen bonds formed have significant influences on the supramolecular structure adopted. An interesting combination of intramolecular hydrogen bonding and close ~ -stacking interactions also occur in each species.     

Selective product amplification of thymine photodimer by recognition-directed supramolecular assistance

Two symmetric ditopic supramolecular templates (1 and 2) each presenting two hydrogen bonding recognition subunits were synthesized. Each such subunit comprises the same donor and acceptor pattern, capable of binding a substrate molecule with complementary hydrogen bonding groups to form a supramolecular complex. Substrate molecules, such as thymine or uracil derivatives, yield 2 : 1 complexes with the acceptors involving two hydrogen bonds to each subunit with ideal orientation for subsequent [2 + 2] dimerization upon photoirradiation. Selective syn photoproduct formation and concomitant suppression of the trans isomer are favored by orientation of the two guest nucleobases within the template cleft. Complementary donor and acceptor hydrogen bonding induced positioning of the two substrates and steric hindrance within the template clefts are responsible for the selective product formation.     

A systematic study of ligand intermolecular interactions in crystals of copper(II) complexes of bidentate guanidino derivatives

The synthesis and X-ray structures of four neutral copper(II) complexes and one cationic complex incorporating bidentate alkyl N-(4-oxo-5,5-diphenyl-4,5-dihydro-1H-imidazol-2-yl)imidocarbamate ligands are reported. The neutral complexes, which possess potential doublet (DA) hydrogen bonding motifs, form supramolecular structures based on synthons involving hydrogen bonding or phenyl embraces. The formation of sheets within the crystal through combination of these synthons, and the occurrence of guest molecules trapped in cavities between the sheets, are described. The cationic complex forms an extended hydrogen-bonded structure that incorporates nitrate ions. The structures of the five complexes are compared with others reported previously for complexes of related ligands.     

Self-assembly driven by an aromatic primary amide motif

Primary amides are unique supramolecular synthons possessing two hydrogen donors and two hydrogen acceptors. By interacting in a complementary fashion, primary amides reliably generate two-dimensional hydrogen bonded networks that differ from conventional hydrogen bonded structures such as carboxylic acid dimers or one-dimensional secondary amide chains. This feature permits the design of sophisticated supramolecular assemblies based on primary amides (especially aromatic amides). Several interesting crystal structures have been constructed utilizing primary amides, although such structures have been applied only in the field of crystal engineering because the networks strongly favor crystallization. Expansion of the applications of primary amides to liquid crystals and self-assembly in solution requires an appropriate balance between primary amide-based hydrogen bonding and other noncovalent interactions. This perspective article reviews the key hydrogen bonding properties of primary amides determined from crystal structure studies, and a variety of supramolecular assemblies involving primary amides are discussed. A new strategy for overcoming crystallinity and solubility issues is proposed, involving introduction of a trifluoromethyl group at the ortho position of the aromatic primary amide. Such substitutions produce highly processable primary amides, while maintaining the two-dimensional hydrogen bonded network. Examples of self-assembly using 2-trifluoromethylbenzamide demonstrate its usefulness in self-assembly.     

From Distinct Metallopeptoids to Self-Assembled Supramolecular Architectures

The construction of synthetic protein mimics is a central goal in chemistry. A known approach for achieving this goal is the self-assembly of synthetic biomimetic sequences into supramolecular structures. Obtaining different 3D structures via a simple sequence modification, however, is still challenging. Herein we present the design and synthesis of biomimetic architectures, via the self-assembly of distinct copper-peptoid duplexes. We demonstrate that changing only one non-coordinating side-chain within the peptoids—sequence-specific N-substituted glycine oligomers—leads to different supramolecular structures. Four peptoid trimers incorporating 2,2’-bipyridine and pyridine ligands, and a non-coordinating but rather a structure-directed bulky group were synthesized, and their solutions were treated with Cu²⁺ in a 1:1 ratio. Single-crystal X-ray analysis of the products revealed the self-assembly of each peptoid into a metallopeptoid duplex, followed by the self-assembly of multiple duplexes and their packing into a three-dimensional supramolecular architecture via hydrogen bonding and π–π interactions. Tuning the non-coordinating side-chain enables to regulate both the final structure being either a tightly packed helical rod or a nano-channel, and the pore width of the nano-channels. Importantly, all the metallopeptoids structures are stable in aqueous solution as verified by cryo-TEM measurements and supported by UV/Vis and EPR spectroscopies and by ESI-MS analysis. Thus, we could also demonstrate the selective recognition abilities of the nano-channels towards glycerol.     

Conformer-independent ureidoimidazole motifs--tools to probe conformational and tautomeric effects on the molecular recognition of triply hydrogen-bonded heterodimers

Linear arrays of hydrogen bonds are useful for the reversible assembly of “stimuli‐responsive” supramolecular materials. There is thus an ongoing requirement for easy‐to‐synthesise motifs that are capable of presenting hydrogen‐bonding functionality in a predictable manner, such that high‐affinity and high‐fidelity recognition occurs. The design of linear arrays is made challenging as a consequence of their ability to adopt multiple conformational and tautomeric configurations; with each additional hydrogen‐bonding heteroatom added to an array, the available tautomeric and conformational space increases and it can be difficult to anticipate where unproductive conformers/tautomers will arise. This paper describes a detailed study on the complementary ureidoimidazole donor–donor–acceptor (DDA) array ( 1 ) and amidoisocytosine donor–acceptor–acceptor (DAA) array ( 2 ). A specific feature of 1 is that two degenerate, intramolecular hydrogen‐bonded conformations are postulated, both of which present a DDA array that is complementary to appropriate DAA partners. 1D and 2D ¹H NMR spectroscopy, isothermal titration calorimetry, and ab initio structure calculations confirm 1 interacts with 2 (K_a≈33000 M ^?1 in CDCl₃) in a conformer‐independent fashion driven by enthalpy. Comparison of the binding behaviour of 1 with hexylamidocytosine ( 4 ) and amidonaphthyridine ( 5 ) provides insight on the role that intramolecular hydrogen‐bonding plays in mediating affinity towards DAA partners.     

Directed self-assembly of inorganic redox complexes with artificial peptide scaffolds

An ongoing challenge in the construction of supramolecular systems is controlling the relative geometry of functional redox species for molecular electronics devices, including wires, switches, and gates. This review focuses on the use of artificial peptide strands to assemble inorganic complexes that are redox active. These approaches toward macromolecular assembly use varying oligoamide backbones and assembly motifs that grew from earlier reports of single oligolysine or proline chains containing pendant redox species that undergo photoinduced charge separation. Recently, peptide nucleic acid chains that form double-stranded duplexes analogous to DNA by hydrogen bonding of complementary base pairs have been modified to contain metal complexes. In these structures, hydrogen bonding and metal coordination combine to form crosslinks between the PNA strands. Finally, a family of structures is described that is based on an aminoethylglycine scaffold with pendant metal coordination sites, but without intervening nucleic acid base pairs. These structures form multimetallic complexes that are either single- or double-stranded, or that form hairpin loop structures. These motifs for using artificial peptide strands for self-assembly hold electron donors and acceptors in relative positions that provide structural connectivity and permit electron transfers between linked metal complexes. This is a new approach for creating polyfunctional redox architectures that could ultimately enable the construction of potentially large and complex molecular electronics devices.     

Effect of interfacial molecular recognition of non-surface-active species on the main characteristics of monolayers

Recent progress in studies of the main characteristics of supramolecular assemblies formed by interfacial molecular recognition between an amphiphilic monolayer and a non-surface-active species, which is dissolved in the aqueous subphase, by complementary hydrogen bonding and/or electrostatic interaction at the air-water interface is reviewed. Systems consisting of an amphiphilic melamine-type monolayer and an pyrimidine derivative dissolved in the aqueous subphase are representative model systems for molecular recognition on the basis of complementary hydrogen bonding. Most of the studies have been performed with 2,4-di(n-undecylamino)-6-amino-1,3,5-triazine (2C11H23-melamine) monolayers as host component and thymine, uracil or barbituric acid as dissolved non-surface-active pyrimidine derivatives. The combination of surface pressure studies with Brewster angle microscopy (BAM) imaging and Grazing incidence X-ray diffraction (GIXD) measurements is optimal for the characterization of the change in structure and phase behavior at the interfacial recognition process. The molecular recognition of all pyrimidine derivatives dissolved in the aqueous subphase changes drastically and in a specific way the characteristic features (pi-A isotherms, morphology of the condensed phase domains) of the 2C11H23-melamine monolayer. The small condensed phase domains of the pure 2C11H23-melamine monolayer are compact without an inner texture. The monolayers of the supramolecular 2C11H23-melamine entities with thymine or uracil form specifically well-shaped condensed phase domains with an inner alkyl chain texture essentially oriented parallel to the periphery. The completely different morphology of the 2C11H23-melamine-barbituric acid monolayers is characterized by the formation of large homogeneous areas of condensed phase that transfer at smaller areas per molecule to a homogeneous condensed monolayer. The striking differences in the main characteristics between the supramolecular entities are related to their different chemical structures: complementary hydrogen bonding of two thymine or uracil molecules by one 2C11H23-melamine molecule and a linearly extended hydrogen bonding network between 2C11H23-melamine and barbituric acid. The high values of hydrogen bonding energy obtained by quantum chemical calculations on the basis of the semi-empirical PM3 method state the high stability of the supramolecular entities. The GIXD results reveal that the formation of hydrogen-bond based superstructures between the polar head groups of the amphiphilic 2C11H23-melamine monolayer and the non-surface-active pyrimidine derivatives gives rise only to quantitative changes in the two-dimensional lattice structure of the alkyl chains. The alternative possibility to construct interfacial molecular recognition systems on the basis of acid-base interaction is demonstrated by the experimental results obtained by molecular recognition of the heptadecyl-benzamidinium chloride monolayers with dissolved non-surface-active phenylacetate ions. The formation of supramolecular assemblies causes also drastical changes of the surface features in these systems. Here, the development of a substructure in the condensed phase domains consisting of long filigree strings and the favoured formation of bilayers overgrowing the strings indicates a linearly extended amidinium-carboxylate interfacial structure of the base and acid component in alternating sequence.     

Long,Multicenter Bonding—A New Concept for Supramolecular Materials

A new concept for constructing supramolecular architectures is discussed. In addition to van der Waals and hydrogen‐bonding intermolecular interactions that primarily account for supramolecular structures for all materials lacking extended 3D network structures, directional, long, multicenter bonding that can occur for anionic, cationic, neutral, and zwitterionic radicals and can direct intermolecular recognition through π interactions and form extended network supramolecular structural motifs.     

DNA-inspired hierarchical polymer design: electrostatics and hydrogen bonding in concert

Nucleic acids and proteins, two of nature's biopolymers, assemble into complex structures to achieve desired biological functions and inspire the design of synthetic macromolecules containing a wide variety of noncovalent interactions including electrostatics and hydrogen bonding. Researchers have incorporated DNA nucleobases into a wide variety of synthetic monomers/polymers achieving stimuli-responsive materials, supramolecular assemblies, and well-controlled macromolecules. Recently, scientists utilized both electrostatics and complementary hydrogen bonding to orthogonally functionalize a polymer backbone through supramolecular assembly. Diverse macromolecules with noncovalent interactions will create materials with properties necessary for biomedical applications.     

The novel hydrogen bonding motifs and supramolecular patterns in 2,4-diaminopyrimidine-nitrobenzoate complexes

The crystal structures of the hydrogen-bonded, 1:1 molecular complexes of nitro (ortho, meta and para) benzoic acids with two 2,4-diaminopyrimidine derivatives (trimethoprim and pyrimethamine) have been investigated in detail (1-5). In all the crystal structures except pyrimethamine o-nitrobenzoate (3), the carboxylate group of the respective anions interacts with the protonated trimethoprim or pyrimethamine moiety in a linear fashion through a pair of N-H?O hydrogen bonds to form a cyclic hydrogen-bonded motif. This cyclic hydrogen-bonded motif is self-organized in different ways to get the novel types of hydrogen bonding motifs and supramolecular patterns. In the crystal structure of pyrimethamine o-nitrobenzoate (3), the chelating type of hydrogen bonding motif is self-organized to get a helical supramolecular pattern. In the crystal structures of both pyrimethamine m-nitrobezoate (4) and pyrimethamine p-nitrobenzoate (5), a novel type of an alternate arrangement of DADA (D represents donor and A represents acceptor) and DDAA arrays is present, resulting in the formation of hydrogen-bonded ladders.     

Second‐Generation Supramolecular Dendrimer with a Defined Structure due to Orthogonal Binding

A second‐generation supramolecular dendrimer has been prepared by orthogonal multiple hydrogen bonding. In the first (inner) recognition domain, the interaction of one bis‐isocyanuric acid ( 25 ) with two branching units ( 21 ) that carry complementary Hamilton receptors has been exploited. In the second (outer) generation, the two ADDA (A=hydrogen‐bond acceptor, D=donor) receptors of each branching unit ( 21 ) have bound complementary DAAD units ( 4 ). The problem of limited solubility of the building blocks has been overcome by the introduction of branched ethylhexyl residues and by the use of flexible alkylene or oligo(ethylene glycol) linking chains. The orthogonal binding of the two hydrogen‐bonding pairs was elucidated by chemical induced shift NMR titrations, which proved that the two pairs, isocyanuric acid with the Hamilton receptor and ADDA with DAAD, bind preferentially. The formation of the supramolecular self‐assembled 1:2:4 dendrimer with a molecular weight of 5065 g mol^?1 was investigated by diffusion NMR spectroscopy.     

Supramolecular Paradigm for Capture and Co-Precipitation of Gold(III) Coordination Complexes

A new supramolecular paradigm is presented for reliable capture and co-precipitation of haloauric acids (HAuX₄) from organic solvents or water. Two classes of acyclic organic compounds act as complementary receptors (tectons) by forming two sets of directional non-covalent interactions, (a) hydrogen bonding between amide (or amidinium) NH residues and the electronegative X ligands on the AuX₄⁻, and (b) electrostatic stacking of the electron deficient Au center against the face of an aromatic surface. X-ray diffraction analysis of four co-crystal structures reveals the additional common feature of proton bridged carbonyls as a new and predictable supramolecular design element that creates one-dimensional polymers linked by very short hydrogen bonds (CO⋅⋅⋅OC distance <2.5 Å). Two other co-crystal structures show that the amidinium-π⋅⋅⋅XAu interaction will reliably engage AuX₄⁻ with high directionality. These acyclic compounds are very attractive as co-precipitation agents within new “green” gold recovery processes. They also have high potential as tectons for controlled self-assembly or co-crystal engineering of haloaurate composites. More generally, the supramolecular paradigm will facilitate the design of next-generation receptors or tectons with high affinity for precious metal square planar coordination complexes for use in advanced materials, nanotechnology, or medicine.     

Mesomorphic phases obtained through molecular recognition of complementary adenine and thymine nucleobases functionalized with long aliphatic chains

Complementary adenine and thymine nucleobases were functionalized with long aliphatic chains. The materials exhibited a mesomorphic character which was attributed to the formation of supramolecular architectures. Molecular recognition through hydrogen bonding of the complementary ends of the molecules was the driving force for their formation. It was also found that these structures are affected by the crystallization medium.     

Intramolecular hydrogen bonding in calixarenes

The construction of a molecular cavity for recognition and catalysis requires either covalent synthesis or intermolecular self-assembly of complementary units. Intramolecular hydrogen bonding is another tool to control the cavity-forming process. When properly positioned within the same molecular structure, hydrogen bonding sites are responsible for the formation, preorganization, and binding ability of the host. The most typical examples from the supramolecular chemistry of calixarenes, the key cavity-containing building blocks, and derived from them receptor molecules are discussed.     

A supramolecular multi-block copolymer with a high propensity for alternation

Alternating, multi-block supramolecular copolymers were created using quadruple hydrogen bonding as the noncovalent binding force. One block consisted of two guanosine butyl urea (UG) units attached at the ends of a triethylene glycol linker or a PEG chain (MW = 2 kD). The other block contained a 2,7-diamido-1,8-naphthyridine (DAN) unit at each end of a short alkane diester linker or a 100 kD poly(butyl methacrylate) macromolecule. The UG unit presents an ADDA hydrogen bonding array that is complementary to the DAAD array of DAN, and these form a very strong complex (Kassoc approximately 5 x 107 M-1), whereas UG and DAN weakly self-associate. These recognition properties allowed a multi-block supramolecular polymer to form which exhibits a high propensity for alternation. The self-assembled polymeric structure was shown to be reversibly formed and it was characterized by a combination of dynamic light scattering (DLS), 1H NMR, size exclusion chromatography (SEC), and viscometry.     

Syntheses and structures of isomeric diaminotriazinyl-substituted 2,2'-bipyridines and 1,10-phenanthrolines

Isomeric 2,2'-bipyridines 4a-6a and 1,10-phenanthrolines 7a-9a with two diaminotriazinyl (DAT) substituents were synthesized to explore their dual ability to direct association by the chelation of metals and the characteristic hydrogen bonding of DAT groups. Crystals of compounds 4a-6a and 7a-9a were grown under diverse conditions, and their structures were solved by X-ray crystallography. Analysis revealed multiple shared features analogous to those observed in the structures of simpler DAT-substituted pyridines 1-3. For example, the bipyridines and phenanthrolines favor flattened conformations except in the cases of compounds 8a and 9a, where the patterns of substitution prevent the DAT groups from lying in the plane of the phenanthroline core. As expected, the DAT groups form approximately coplanar hydrogen bonds according to standard motifs I-III, which play a key role in directing molecular organization. However, the structures of simple pyridines 1-3, which favor efficiently packed chains and sheets, differ predictably from those of bipyridines 4a-6a and phenanthrolines 7a-9a in two ways: (1) The larger number of DAT groups in compounds 4a-9a typically leads to complex three-dimensional networks held together by a larger number of hydrogen bonds per molecule, and (2) the need to respect multiple directional interactions prevents compounds 4a-9a from forming closely packed structures, and significant quantities of guests are included. Together, these observations confirm the effectiveness of incorporating special groups such as DAT within more complex molecular structures to control association according to reliable patterns. Bipyridines 4a-6a and phenanthrolines 7a-9a promise to be particularly rich sources of new supramolecular chemistry because they have well-defined molecular topologies and a dual ability to direct association by chelating metals and by engaging in multiple hydrogen bonds according to reliable patterns.     

Hydrogen-bonding-mediated anthranilamide homoduplexes. Increasing stability through preorganization and iterative arrangement of a simple amide binding site

This paper describes the assembly of two new series of self-complementary duplexes by making use of amide units, the simplest assembling units of hydrogen bonding, as binding sites. All the new monomers possess a rigidified anthranilamide skeleton, which is stabilized by intramolecular hydrogen bonding. Amide units are iteratively introduced to one side of the preorganized skeletons to facilitate the formation of intermolecular hydrogen bonding. Compounds 2 and 3 bear two and three CONH(2) units, respectively, while 4, 6, and 7 are incorporated with two, three, and four AcNH units, respectively. For comparison, compound 5, which is similar to 4 but contains one AcNH and one CF(3)CONH unit, is also prepared. X-ray diffraction analysis of 2, 4, and 5 revealed homodimeric motifs in the solid state which are stabilized by two or more intermolecular hydrogen bonds. (1)H NMR investigations in CDCl(3) indicated that all the compounds form hydrogen-bonded homoduplexes. Duplexes 3.3, 6.6, and 7.7 are highly stable in CDCl(3), with a lower K(assoc) limit of 2.3 x 10(5) M(-1). The K(assoc) values of the three duplexes in more polar CDCl(3)/CD(3)CN (9:1, v/v) were determined with the (1)H NMR dilution method. The result opens the way for the development of new polymeric duplexes of well-ordered structures.     

Heteromolecular grids of free-base and zinc-tetra(4-pyridyl)porphyrins with benzenetetracarboxylic acid

This study describes the formation of hetero-molecular networks involving the 1,2,4,5-benzenetetracarboxylic acid (BTCA) and either the free-base or zinc-metallated tetra(4-pyridyl)porphyrin (TPyP or Zn–TPyP, respectively), taking advantage of the complementary tetradentate H-atom donor and H-atom acceptor capacity of the component species. The reaction of BTCA with TPyP yields flat square-grid-type hydrogen bonded arrays, wherein every BTCA moiety interacts with four different porphyrin units and each one of the latter links laterally to four different tetraacid molecules. Replacement of TPyP by Zn–TPyP adds axial coordination capacity to the porphyrin unit and changes the intermolecular interaction pattern. In this case, the supramolecular self-assembly involves trans-axial coordination of BTCA to Zn–TPyP, into a 2:1 complex of the two species, as well as extended hydrogen bonding in four lateral directions between the (BTCA)₂(Zn–TPyP) units thus formed. The hydrogen-bond networking takes place between the four N(pyridyl)-sites of the porphyrin scaffold and the axial tetracid ligands of four neighboring complexes. In the two crystals, the open hydrogen bonded molecular networks stack in an offset manner, incorporating molecules of the 1,1,2,2-tetrachloroethane solvent within channel zones that penetrate through the layered structure. Application of the TPyP scaffold in the formation of hydrogen-bonded (rather than coordination-driven) assemblies has not been explored prior to our work on this subject.     

Mesomorphic phases obtained through molecular recognition of complementary adenine and thymine nucleobases functionalized with long aliphatic chains

Abstract

Complementary adenine and thymine nucleobases were functionalized with long aliphatic chains. The materials exhibited a mesomorphic character which was attributed to the formation of supramolecular architectures. Molecular recognition through hydrogen bonding of the complementary ends of the molecules was the driving force for their formation. It was also found that these structures are affected by the crystallization medium.