Varying molecular interactions by coverage in supramolecular surface chemistry

The possibility of modifying the intermolecular interactions of absorbed benzene-carboxylic acids from coordination to hydrogen bonding by changing their surface coverage is demonstrated through a combination of scanning tunnelling microscopy, X-ray photoemission spectroscopy and density functional theory calculations.     

Hydrogen-bond driven assembly of a molecular capsule facilitated by supramolecular chelation

Resorcinarene-based cavitands functionalized with acetamido groups capable of self-complementary hydrogen-bond interactions, were synthesized in order to construct supramolecular capsules. The 1,3-bifunctionalized cavitand produced a polymeric assembly, whereas the tetra-functionalized analogue yielded a discrete capsule held together via N-H···O hydrogen bonds. The ethynyl species attached to the rim of these host molecules deepen each cavitand and expands the volume of the resulting capsule.     

Calixarene/pillararene-based supramolecular selective binding and molecular assembly

This review mainly summarized the recent researches on the supramolecular selective binding and molecular assembly based on calixarene and pillararene. Several representative examples were provided to expound the progress in the area of recognition and sensing, multi-functional assembly and crosslinked multi-dimensional materials.     

NMR spectroscopy in coordination supramolecular chemistry: A unique and powerful methodology

Metal-mediated self-assembly is emerging as a very important strategy for the synthesis of supramolecular species. Still, a major challenge in coordination supramolecular chemistry continues to be the characterization of the self-assembled complexes and the investigation of their dynamic behaviour in solution. In this context, NMR spectroscopy appears as a unique and powerful methodology. This practical-oriented review describes the rich variety of NMR techniques which are applied to the investigation of different aspects of the structure and behaviour of supramolecular complexes. “Classic” 1D NMR spectra reflect characteristic chemical shifts due to metal–ligand interactions or encapsulation phenomena, as well as symmetry and chiral properties of host–guest assemblies. Mainstream ¹H, ¹³C, ¹⁹F and ³¹P spectra are eventually complemented by the use of NMR-active metal nuclides. Homo- and heteronuclear 2D correlation experiments are ubiquitous in the literature, providing through-bond and through-space connectivities. Increasingly, diffusion measurements are also gaining popularity in this field, being used to gain information about molecular size, intermolecular interactions and even association constants of supramolecular complexes. Knowledge about the thermodynamic properties and the dynamic behaviour of coordination supramolecular assemblies is essential for the development of their practical applications. The most frequently used NMR methodologies for the calculation of association constants (simple signal integration, NMR titration and diffusion measurements) and for the investigation of dynamic supramolecular equilibria (lineshape analysis, selective inversion recovery experiments and 2D EXSY spectra) are described, together with the use of variable-temperature investigations for the determination of the thermodynamic and activation parameters of self-assembly and encapsulation processes.     

Probing matrix isolated SiO molecular clusters by X-ray absorption spectroscopy

TheK absorption edge of Si in matrix isolated SiO molecular clusters was studied for various dilutionsR(Ar/SiO). The spectra from the clusters at different dilutions show a dramatic evolution in their relative intensity. Two types of spectral features from Si atoms present in the clusters could be detected in the spectra. The first is due to the Si atoms which are tetrahedrally coordinated to Si and O atoms responsible for the presence of different Si oxidation states. The Si⁺, Si³⁺ and Si⁴⁺ oxidation states in SiO clusters and in bulk were readily identified. The Si²⁺ oxidation state whose abundance in SiO clusters is predicted by structural considerations is not clearly observed. The second type of feature, whose intensity decreases with the dilution R, can be attributed to the presence of Si atoms possessing unsaturated bonds. In order to explain this the clustering of 4–6 SiO molecules is simulated to yield different tetrahedral bonding microstructures in which the well coordinated as well as under coordinated Si atoms are present. The behaviour of the spectral features resulting from these microstructures is discussed.     

Controlling the supramolecular assembly of redox-active dendrimers at molecular printboards by scanning electrochemical microscopy

Redox-active ferrocenyl (Fc)-functionalized poly(propylenimine) (PPI) dendrimers solubilized in aqueous media by complexation of the Fc end groups with beta-cyclodextrin (betaCD) were immobilized at monolayers of betaCD on glass ("molecular printboards") via multiple host-guest interactions. The directed immobilization of the third-generation dendrimer-betaCD assembly G3-PPI-(Fc)16-(betaCD)16 at the printboard was achieved by supramolecular microcontact printing. The redox activity of the patterned dendrimers was mapped by scanning electrochemical microscopy (SECM) in the positive feedback mode using [IrCl(6)](3-) as a mediator. Local oxidation of the Fc-dendrimers by the microelectrode-generated [IrCl(6)](2-) resulted in an effective removal of the Fc-dendrimers from the host surface since the oxidation of Fc to the oxidized form (Fc+) leads to a concomitant loss of affinity for betaCD. Thus, SECM provided a way not only to image the surface, but also to control the binding of the Fc-terminated dendrimers at the molecular printboard. Additionally, the electrochemical desorption process could be monitored in time as the dendrimer patterns were gradually erased upon multiple scans.     

A principle for the assembly of novel mononuclear building blocks for supramolecular chemistry

Abstract

The controlled assembly of supramolecular coordination oligomers may be achieved by the use of multinucleating ligands which contain two or more metal-binding domains. Examples of such ligands commonly consist of discrete metal-binding sites linked by appropriate spacers. We now show that a consideration of the donor properties of a ligand and the acceptor properties of a metal ion may be used to induce multinucleating behaviour in oligopyridine ligands which conventionally chelate to single metal centres. Such species are key building blocks for the assembly of a variety of supramolecular species in which the non-coordinated donor atoms may later interact with other metal centres. The crystal structure of the complex [Ru(bpy-N,N′)₂(tpy-N,N′)][PF₆]₂ ( P 1, a = 8.367(2), b = 11.821(4), c = 19.398(5)Å, α = 93.83(2), β = 92.25(2), γ = 89.62(2)°, Z = 2, d _c = 1.63 g cm^?3, 5084 unique observed reflections with I < 1.5σ(I), R = 0.0745) which contains a bidentate tpy ligand is presented.     

Diffusion NMR spectroscopy in supramolecular and combinatorial chemistry: an old parameter--new insights

Intermolecular interactions in solution play an important role in molecular recognition, which lies at the heart of supramolecular and combinatorial chemistry. Diffusion NMR spectroscopy gives information over such interactions and has become the method of choice for simultaneously measuring diffusion coefficients of multicomponent systems. The diffusion coefficient reflects the effective size and shape of a molecular species. Applications of this technique include the estimation of association constants and mapping the intermolecular interactions in multicomponent systems as well as investigating aggregation, ion pairing, encapsulation, and the size and structure of labile systems. Diffusion NMR spectroscopy can also be used to virtually separate mixtures and screen for specific ligands of different receptors, and may assist in finding lead compounds.     

Symmetry induced supramolecular assembly of a resorcinarene trimeric molecular box

A novel trimeric resorcinarene molecular box is induced during hydrothermal synthesis by use of the 3-fold symmetric tripyridyl triazine linker molecule.     

Probing molecular orientation at bulk heterojunctions by polarization-selective transient absorption spectroscopy

A bulk heterojunction in organic solar cells is where charge separation and recombination occur. Molecular orientation at the interface is one of the key factors that dictate solar cell efficiency. Although X–ray scattering-based methods can determine donor/acceptor domain orientations between an anisotropic phase and an isotropic fullerene-based phase, the rise of nonfullerene solar cells presents a new challenge in delineating local molecular directions at the interface between two anisotropic donor/acceptor domains. Here, we determine interfacial molecular orientations of three high-efficiency small molecule solar cells(ZR1:Y6, B1:BO–4 Cl, and BTR:BO–4 Cl) using polarization-selective transient absorption spectroscopy. The polarization anisotropy of charge separation dynamics indicates an angle of ～90° between ZR1 and Y6 molecules at the interface, an angle close to 0° between B1 and BO–4 Cl, and random orientations between BTR and BO–4 Cl. These observations provide complementary information to X–ray scattering measurements and highlight polarization-selective transient absorption spectroscopy as a tool to probe interfacial structure and dynamics of key photophysical steps in energy conversion.     

Six polycyclic pyrimidoazepine derivatives: syntheses,molecular structures and supramolecular assembly

A versatile synthetic method has been developed for the formation of variously substituted polycyclic pyrimidoazepine derivatives, formed by nucleophilic substitution reactions on the corresponding chloro‐substituted compounds; the reactions can be promoted either by conventional heating in basic solutions or by microwave heating in solvent‐free systems. Thus, (6RS)‐6,11‐dimethyl‐3,5,6,11‐tetrahydro‐4H‐benzo[b]pyrimido[5,4‐f]azepin‐4‐one, C₁₄H₁₅N₃O, (I), was isolated from a solution containing (6RS)‐4‐chloro‐8‐hydroxy‐6,11‐dimethyl‐6,11‐dihydro‐5H‐benzo[b]pyrimido[5,4‐f]azepine and benzene‐1,2‐diamine; (6RS)‐4‐butoxy‐6,11‐dimethyl‐6,11‐dihydro‐5H‐benzo[b]pyrimido[5,4‐f]azepin‐8‐ol, C₁₈H₂₃N₃O₂, (II), was formed by reaction of the corresponding 6‐chloro compound with butanol, and (RS)‐4‐dimethylamino‐6,11‐dimethyl‐6,11‐dihydro‐5H‐benzo[b]pyrimido[5,4‐f]azepin‐8‐ol, C₁₆H₂₀N₄O, (III), was formed by reaction of the chloro analogue with alkaline dimethylformamide. (6RS)‐N‐Benzyl‐8‐methoxy‐6,11‐dimethyl‐6,11‐dihydro‐5H‐benzo[b]pyrimido[5,4‐f]azepin‐4‐amine, C₂₂H₂₄N₄O, (IV), (6RS)‐N‐benzyl‐6‐methyl‐1,2,6,7‐tetrahydropyrimido[5′,4′:6,7]azepino[3,2,1‐hi]indol‐8‐amine, C₂₂H₂₂N₄, (V), and (7RS)‐N‐benzyl‐7‐methyl‐2,3,7,8‐tetrahydro‐1H‐pyrimido[5′,4′:6,7]azepino[3,2,1‐ij]quinolin‐9‐amine, C₂₃H₂₄N₄, (VI), were all formed by reaction of the corresponding chloro compounds with benzylamine under microwave irradiation. In each of compounds (I)–(IV) and (VI), the azepine ring adopts a conformation close to the boat form, with the C‐methyl group in a quasi‐equatorial site, whereas the corresponding ring in (V) adopts a conformation intermediate between the twist‐boat and twist‐chair forms, with the C‐methyl group in a quasi‐axial site. No two of the structures of (I)–(VI) exhibit the same range of intermolecular hydrogen bonds: different types of sheet are formed in each of (I), (II), (V) and (VI), and different types of chain in each of (III) and (IV).     

Investigation on DNA assembly to neutral red-cyclodextrin complex by molecular spectroscopy

DNA assembling to neutral red (NR) and cyclodextrins (CDs)-NR inclusion complex has been investigated by means of absorption, fluorescence and resonance light scattering (RLS). Depending on the molar ratio R of NR:DNA, the binding of NR with DNA involved in two processes at pH 7.50 and ionic strength 0.0045. The first process occurs in R>2.5, where the neutral form of NR was predominant and enhanced RLS was observed, indicating the aggregation of NR neutral form molecules on the molecular surface of DNA. The second process occurs in R<2.5, where an absorption band at 540 nm and a fluorescent excitation and emission band at 550 and 607 nm respectively provided compelling evidence that the binding of NR to DNA leaded to extensive NR protonation even at pH 7.50, and that a protonated NR (the acidic form of NR) can form DNA adducts with a binding mode different from that of the unprotonated form (the neutral form of NR). The results were also illustrated by the CDs-NR supramolecular system. The experimental data showed that CDs including beta-CD, hydroxypropyl-beta-CD (HP-beta-CD) and sulfobutylether-beta-CD (SBE-beta-CD) superior to include the neutral form of NR, in addition, the inclusion complex decomposed when it bound to DNA. Thus, the decomposed NR was also protonated to form DNA adducts with intercalative mode. In fact, CDs played a role to carry guest molecule to intercalate DNA. A related mechanism is proposed.     

Carbomethoxychlorocarbene: spectroscopy, theory, chemistry and kinetics.

Photolysis (254 nm) of methyl 8-chloro-3a,7a-methanoindan-8-carboxylate (5) in argon at 14 K produces carbomethoxychlorocarbene (6) as a persistent species. The IR and UV-vis spectra of the carbene were recorded and analyzed with the aid of density functional calculations (B3-LYP/6-31G). The IR spectrum of 6 is consistent with the carbene having a nonplanar singlet ground state, in agreement with the G3(MP2)//B3-LYP calculations of Scott and Radom (accompanying paper). Irradiation (300 nm) of 5 in solution produces indane in 97% yield. In cyclohexane, carbene 6 is trapped by insertion into a CH bond, whereas in 2,3-dimethylbutene it adds to the double bond to form a cyclopropane. Laser flash photolysis of 5 (308 nm, 17 ns, XeCl excimer) produces carbene 6 which reacts with pyridine to form an ylide (lambda(max) = 440 nm). It was possible to resolve the growth of the ylide in Freon-113 (CF(2)ClCFCl(2)) to measure the lifetime (tau = 114 ns, ambient temperature) of the carbene and the absolute rate constant of its reaction with pyridine (k(pyr) = 2 x 10(9) M(-)(1) s(-)(1)). A plot of log(1/tau) versus 1/T in CF(2)ClCFCl(2) is linear with Arrhenius parameters E(a) = 10.9 +/- 0.8 kJ/mol and A = 10(9.1)(+/-)(0.2) s(-)(1). In perfluorohexane, a less reactive solvent than Freon-113, E(a) = 23.4 +/- 1.7 kJ/mol, A = 10(10.6)(+/-)(0.) s(-)(1), and tau = 354 ns at 293 K. It is argued that the activation barrier to carbene disappearance in perfluorohexane represents the lower limit to the barrier to Wolff rearrangement of the carbene.     

Drug-dendrimer supramolecular complexation studied from molecular dynamics simulations and NMR spectroscopy

Fully atomistic molecular dynamics (MD) simulations and NMR spectroscopy were employed to get insights about the molecular details of drug-dendrimer supramolecular association phenomena, using piroxicam (PRX) and the third generation poly(amido amine) (PAMAM-G3) dendrimer as model systems. Theoretical results concerning the complex stoichiometry suggest that PRX forms drug-dendrimer complexes of the type 24:1 at pH 7.0. This result was validated with the experimental quantities obtained from aqueous solubility profiles, which led to an empiric stoichiometry of 23:1 for the PRX:PAMAM-G3 system. The predicted binding mode between PRX and PAMAM-G3 accounts for the preferred encapsulation of the drug inside dendrimer cavities, which is mainly driven by van der Waals and hydrogen bonding interactions, and to a lesser extent, for the external association of the guest through electrostatic contacts with the positively charged amino groups of PAMAM periphery. The binding mode obtained from MD simulations was confirmed with 2D-NOESY experiments, which evidence the preferred internal complexation of PRX with PAMAM-G3. The predominance of internal encapsulation over external contacts in the PRX:PAMAM-G3 system differs from the general behaviour expected for acidic anionic guests, for which external electrostatic interactions with the positively charged PAMAM surface have been postulated as the most relevant factor for drug association.     

Multivalency in supramolecular chemistry and nanofabrication

Multivalency is a powerful and versatile self-assembly pathway that confers unique thermodynamic and kinetic behavior onto supramolecular complexes. The diversity of the examples of supramolecular multivalent systems discussed in this perspective shows that the concept of multivalency is a general phenomenon, and that any supramolecular interaction can be employed in multivalent displays to attain the attractive aspects characteristic of multivalent interactions. After a general introduction reviewing the general aspects of multivalency, a number of different supramolecular multivalent complexes are discussed that highlight the different features of multivalent interactions. In contrast to the many biochemical multivalent interactions, supramolecular multivalent interactions are ideal to attain a quantitative and fundamental understanding of multivalency. Several examples in which multivalency has been utilized in supramolecular nanofabrication schemes are described in detail.     

From molecular chemistry to supramolecular chemistry to superdupermolecular chemistry. Controlling covalent bond formation through non-covalent and magnetic interactions

The reactions of carbon centered radical pairs often involve diffusion controlled combination and/or disproportionation reactions which are non-selective. A triplet geminate pair of radicals is produced by the photolysis of suitable ketones. The reactions of such geminate pairs can be controlled though the application of supramolecular concepts which emphasize non-covalent interaction to "steer" the geminate pair toward a selected pathway. In addition, "superdupermolecular" concepts, which emphasize the control of radical pair reactions through the orientation of electron spins, can be employed to further control the course of geminate pair reactions. Examples of control of a range of the selectivity of geminate radical combinations, which form strong covalent bonds, through supramolecular and superdupermolecular effects will be presented for the photolysis of ketones adsorbed in the supercages of zeolites.     

The spatial effect of near-infrared spectroscopy and its application to the study of supramolecular chemistry

An unlooked-for experimental observation that in near-infrared spectroscopy (NIR) the absorption peak of the second overtone of aniline adsorbed by 13X molecular sieve nearly disappeared led us investigate a fundamental question: the behavior of NIR when the outside space surrounding a molecule is too small to allow the molecule to vibrate freely. Through NIR of various organic compounds adsorbed by different porous inorganic materials like 13X molecular sieve, silica gel and active aluminium oxide, and NIR of supramolecular cyanuric acid-melamine, we can reasonably confirm a theoretical inference that in the micro-environment above, all intensities of NIR absorbance decrease, and the second overtone decreases more than the first overtone does. Furthermore, one distinct feature of NIR, higher sensitivity to the size of micro-environmental space as compared with mid-infrared (MIR), and its potential application to the study of supramolecular structure are outlined by our experiments.     

Halogen bonding in supramolecular chemistry

Halogen bonding is the noncovalent interaction where halogen atoms function as electrophilic species. The energetic and geometrical features of the interaction are described along with the atomic characteristics that confer molecules with the specific ability to interact through this interaction. Halogen bonding has an impact on all research fields where the control of intermolecular recognition and self-assembly processes plays a key role. Some principles are presented for crystal engineering based on halogen-bonding interactions. The potential of the interaction is also shown by applications in liquid crystals, magnetic and conducting materials, and biological systems.     

Carbon dioxide and supramolecular chemistry

Concepts and techniques of supramolecular chemistry are applied to the century-old chemistry between CO2 and amines to design novel sensing systems and nanoscale, self-assembling polymeric materials and networks.