Allosteric effects: an on-off switch

Dibenzoarsacrowns: an experimental and computational study on the coordination behaviors

Dibenzoarsacrowns have been synthesized as a novel class of heteroatom-fused crown ethers. The dibenzoarsacrowns can size-selectively capture alkali metal cations, and the arsenic atoms chemoselectively coordinated to gold(i) chloride (AuCl) due to the soft Lewis acid-base interaction. It is notable that the AuCl complex of 21-dibenzoarsacrown-7 further encapsulated Na⁺ with the enhanced association constant from bare 21-dibenzoarsacrown-7. The positive allosteric effect was studied computationally.

Tetra-porphyrin molecular tweezers: two binding sites linked via a polycyclic scaffold and rotating phenyl diimide core

The synthesis of a tetra-porphyrin molecular tweezer with two binding sites is described. The bis-porphyrin binding sites are aligned by a polycyclic scaffold and linked via a freely rotating phenyl diimide core. Synthesis was achieved using a divergent approach employing a novel coupling method for linking two polycyclic units to construct the core, with a copper(ii)-mediated phenyl boronic acid coupling found to extend to our polycyclic imide derivative. We expect this chemistry to be a powerful tool in accessing functional polycyclic supramolecular architectures in applications where north/south reactivity and/or directional interactions between modules are important. Porphyrin receptor functionalisation was undertaken last, by a four-fold ACE coupling reaction on the tetra-epoxide derivative of the core.

An unprecedented porphyrin-pillar[5]arene hybrid ditopic receptor

A porphyrin-pillar[5]arene hybrid host compound with a ditopic receptor nature was synthesized for the first time, which combines a neutral 1,4-bis(imidazol-1-yl)butane guest by means of its two active centers to form a stable supramolecular complex.

Density functional theory study of a molecular allosteric switch for 2,2'-bipyridyl-3,3'-15-crown-5

A classical model of "molecular machine," which acts as an ON-OFF switch for 2,2'-bipyridyl-3,3'-15-crown-5 (L), has been theoretically studied. It is highly important to understand the mechanism of this switch. The alkali-metal cations (Na(+) and K(+) ) and W(CO)(4) fragment are introduced to coordinate with the different active sites of L, respectively. The density functional theory (DFT) method is used for understanding the stereochemical structural natures and thermodynamic properties of all the target molecules at B3LYP/6-31G(d) and SDD (Stuttgart-Dresden) level, together with the corresponding effective core potential (ECP) for tungsten (W). The fully optimized geometries have been performed with real frequencies, which indicate the minima states. The nucleophilicity of L has been investigated by the Fukui functions. The natural bond orbital analysis is used to study the intermolecular charge-transfer interactions and explore the origin of the internal forces of the molecular switch. In addition, the binding energies, enthalpies, Gibbs free energies, and the cation exchange energies have been studied for L, W(CO)(4) L, and their corresponding complexes. The properties of the complexes displayed by in presence or absence of the W(CO)(4) fragment are also analyzed. The calculated results of allosterism displayed by L are in a good agreement with the experimental results.

[External stimulus-responsive conformational alterations of aromatic amides]

Three-dimensional structure of a molecule and its alteration is an important issue, and it is essential problem for controlling the function of a molecule such as a molecular switch or device. In most cases, molecular switches have relatively high activation energy for interconversion between alternative structures, however in some biological systems, conformational preference plays an important role in regulation of bioactivity. We have interested in conformational alteration of aromatic amides, which have interesting features about conformation. Most of secondary aromatic amides such as benzanilide tend to prefer trans conformation, whereas N-methylation makes its conformation cis-favored. Recently we found several aromatic amides altered the preferred conformation depending on the external stimuli. Thus, N-phenyl-N-quinonyl type of amides changed their preferred conformation according to redox state of quinonyl moiety. N-Methyl pyridylamides showed conformational alteration according to solvent acceptor ability or addition of acid. N-Methylated pyridylamide oligomer also showed unique conformational folding and unfolding. These properties of the aromatic amides can be applied to stimuli-responsive molecular switches and functional molecules.

Photochemically stable fluorescent heteroditopic ligands for zinc ion

Photochemically stable fluorescent heteroditopic ligands (9 and 10) for zinc ion were prepared and studied. Two independent metal coordination-driven photophysical processes, chelation-enhanced fluorescence (CHEF) and internal (or intramolecular) charge transfer (ICT), were designed into our heteroditopic ligand framework. This strategy successfully relates three coordination states of a ligand, non-, mono-, and dicoordinated, to three fluorescence states, fluorescence OFF, ON at one wavelength, and ON at another wavelength. This ligand platform has provided chemical foundation for applications such as the quantification of zinc concentration over broad ranges (Zhang, L.; Clark, R. J.; Zhu, L. Chem.-Eur. J. 2008, 14, 2894-2903) and molecular logic functions (Zhang, L.; Whitfield, W. A.; Zhu, L. Chem. Commun. 2008, 1880-1882). The binding stoichiometries of dipicolylamino and 2,2'-bipyridyl, the two binding sites featured in heteroditopic ligands 7-10, were studied in acetonitrile using both Job's method of continuous variation and isothermal titration calorimetry (ITC). The fluorescence enhancement of 7-10 upon the formation of monozinc complexes (defined as the fluorescence quantum yield ratio of monozinc complex and free ligand) is qualitatively related to the highest occupied molecular orbital (HOMO) energy levels of their fluorophores. This is consistent with our hypothesis on the thermodynamics of the coordination-driven photophysical processes embodied in the designed heteroditopic system, which was supported by cyclic voltammetry studies. In conclusion, compounds 9 and 10 not only possess better photochemical stability but also display a higher degree of fluorescence turn-on upon formation of monozinc complexes than their vinyl counterparts 7 and 8.

Contortions of encapsulated alkyl groups

Rotors are recalled as early molecular devices that transmit information through changes in conformation. Specific cases involve bipyridyls and biphenyls in which the biaryl bond acts as a fulcrum to relay applied stresses from one site to another. New types of molecular stress encountered by encapsulated molecules are identified--including bending, straightening, squeezing, grinding and compression. For flexible molecules in reversibly formed capsules a fluid model of recognition is proposed that is neither lock-and-key nor induced fit. Instead, the guest assumes the shape that best fills the available space, even if contortions to higher energy conformations are required. For encapsulated alkanes, a delicate balance of attraction and repulsion exists when the size of a guest molecule approaches the space available to it. The complexes are analyzed by both NMR and computational methods and detailed maps of the host-guest interfaces in solution are provided. The reversible transition of an encapsulated alkane between a compressed, coiled conformation and a relaxed, extended one is described. The system is a spring-loaded molecular device under the control of acids and bases that offers an alternative to the rotors of current molecular machinery.

Photochemical ion receptor based on a structurally distorted ruthenium(II) complex having a crown-ether moiety at the 3,3'-positions on the 2,2'-bipyridine ligand

Ru(bpy)2(CE-bpy)2+ was prepared where bpy and CE-bpy were 2,2'-bipyridine and bpy having a crown-ether moiety at the 3,3'-positions, respectively. Although Ru(bpy)2(CE-bpy)2+ showed only very weak emission in acetonitrile, recognition of Na+, Li+, or K+ by the crown-ether moiety in CE-bpy resulted in increases in both the emission intensity and the lifetime of the complex, demonstrating that it acted as a photoreceptor. The results were discussed in terms of a steric hindrance between the 3,3'-substituents on CE-bpy and structural changes in both CE-bpy and the complex upon ion recognition, as studied by variable-temperature 1H-NMR and steady-state/dynamic emission spectroscopy of the complex.

Regiocontrolled one-step synthesis of 3,3'-disubstituted 2,2'-bipyridine ligands by cobalt(I)-catalyzed cyclotrimerization

A one-step, regioselective synthesis of annelated symmetric and asymmetric 3,3'-disubstituted 2,2'-bipyridines by cobalt(I)-catalyzed [2+2+2] cycloadditions between 5-hexynenitrile and 1,3-diynes is described. In the symmetric case, the total regioselectivity of the first cycloaddition is ensured electronically by the conjugation of the triple bonds, and for aminomethylated diynes that of the second is ensured by the cobalt coordinating to the aminomethyl rather than to the hexynenitrile nitrogen. In the asymmetric case, the first cycloaddition took place chemoselectively, which in the case of bis(trimethylsilyl)-1,3,5-hexatriyne (viewed as a 1,3-diyne) is explained by semiempirical calculation of LUMO coefficients. The copper(I) complex of 6b, constituting the first reported complex of the form ML2 (L is a symmetric 3,3'-disubstituted 2,2'-bipyridine), has been prepared. It had UV/Vis and NMR spectra reflecting the 3-substituent-induced mutual torsion of the bipyridine rings in the cis conformation, as was confirmed by x-ray diffractometric determination. The bipyridine 6c forms the dinuclear complex [Cu2(6c)2(CH3CN)2]2+ in the solid state.

Artificial Molecular Machines

The miniaturization of components used in the construction of working devices is being pursued currently by the large-downward (top-down) fabrication. This approach, however, which obliges solid-state physicists and electronic engineers to manipulate progressively smaller and smaller pieces of matter, has its intrinsic limitations. An alternative approach is a small-upward (bottom-up) one, starting from the smallest compositions of matter that have distinct shapes and unique properties-namely molecules. In the context of this particular challenge, chemists have been extending the concept of a macroscopic machine to the molecular level. A molecular-level machine can be defined as an assembly of a distinct number of molecular components that are designed to perform machinelike movements (output) as a result of an appropriate external stimulation (input). In common with their macroscopic counterparts, a molecular machine is characterized by 1) the kind of energy input supplied to make it work, 2) the nature of the movements of its component parts, 3) the way in which its operation can be monitored and controlled, 4) the ability to make it repeat its operation in a cyclic fashion, 5) the timescale needed to complete a full cycle of movements, and 6) the purpose of its operation. Undoubtedly, the best energy inputs to make molecular machines work are photons or electrons. Indeed, with appropriately chosen photochemically and electrochemically driven reactions, it is possible to design and synthesize molecular machines that do work. Moreover, the dramatic increase in our fundamental understanding of self-assembly and self-organizational processes in chemical synthesis has aided and abetted the construction of artificial molecular machines through the development of new methods of noncovalent synthesis and the emergence of supramolecular assistance to covalent synthesis as a uniquely powerful synthetic tool. The aim of this review is to present a unified view of the field of molecular machines by focusing on past achievements, present limitations, and future perspectives. After analyzing a few important examples of natural molecular machines, the most significant developments in the field of artificial molecular machines are highlighted. The systems reviewed include 1) chemical rotors, 2) photochemically and electrochemically induced molecular (conformational) rearrangements, and 3) chemically, photochemically, and electrochemically controllable (co-conformational) motions in interlocked molecules (catenanes and rotaxanes), as well as in coordination and supramolecular complexes, including pseudorotaxanes. Artificial molecular machines based on biomolecules and interfacing artificial molecular machines with surfaces and solid supports are amongst some of the cutting-edge topics featured in this review. The extension of the concept of a machine to the molecular level is of interest not only for the sake of basic research, but also for the growth of nanoscience and the subsequent development of nanotechnology.

Allosteric behavior of artificial compounds

The artificial allosteric molecules were prepared by connecting two independent metal porphyrin molecules by covalent bond. These molecules as fragments behave very similarly to the monomeric metal porphyrins except adsorption dissociation characteristics. In this paper we would like to discuss mostly on interesting and useful cooperativity or cooperative binding dissociation of small molecules like CO, O2, or base to both of porphyrin metals. The original structure of the dimeric porphyrin, especially when they are very strongly cooperative, usually needs chemical strain between two porphyrin rings and this strain is released by the first binding of small molecule which causes coordinating change of the metal porphyrin.