The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.

The hydrogen bond in the solid state.

A geometrical analysis has been performed on π–π stacking in metal complexes with aromatic nitrogen-containing ligands based on a Cambridge Structural Database search and on X-ray data of examples in the recent literature. It is evident that a face-to-face π–π alignment where most of the ring-plane area overlaps is a rare phenomenon. The usual π interaction is an offset or slipped stacking, i.e. the rings are parallel displaced. The ring normal and the vector between the ring centroids form an angle of about 20° up to centroid–centroid distances of 3.8 A. Such a parallel-displaced structure also has a contribution from π–σ attraction, the more so with increasing offset. Only a limited number of structures with a near to perfect facial alignment exists. The term π–π stacking is occasionally used even when there is no substantial overlap of the π-ring planes. There is a number of metal–ligand complexes where only the edges of the rings interact in what would be better described a C–H⋯π attraction.

A critical account on π–π stacking in metal complexes with aromatic nitrogen-containing ligands

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.

Artificial Molecular Machines.

The nature and characteristics of the CH/π interaction are discussed by comparison with other weak molecular forces such as the CH/O and OH/π interaction. The CH/π interaction is a kind of hydrogen bond operating between a soft acid CH and a soft base π-system (double and triple bonds, C6 and C5 aromatic rings, heteroaromatics, convex surfaces of fullerenes and nanotubes). The consequences of CH/π hydrogen bonds in supramolecular chemistry are reviewed on grounds of recent crystallographic findings and database analyses. The topics include intramolecular interactions, crystal packing (organic and organometallic compounds), host/guest complexes (cavity-type inclusion compounds of cyclodextrins and synthetic macrocyclic hosts such as calixarenes, catenanes, rotaxanes and pseudorotaxanes), lattice-inclusion type clathrates (including liquid crystals, porphyrin derivatives, cyclopentadienyl compounds and C60 fullerenes), enantioselective clathrate formation, catalytic enantioface discriminating reactions and solid-state photoreaction. The implications of the CH/π concept for crystal engineering and drug design are evident.

CH/π hydrogen bonds in crystals

Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.

Binding Mechanisms in Supramolecular Complexes

This treatise is an update to a preceding highlight (CH/π hydrogen bonds in crystals) published in this journal 5 years ago (M. Nishio, CrystEngComm, 2004, 6, 130–156). After the introductory part (sections 1 and 2), we survey recent results (mostly since 2004) relevant to the CH/π hydrogen bond: crystal conformation, packing and host/guest chemistry (section 3). Section 4 summarizes the results obtained by crystallographic database (CSD and PDB) analyses. In section 5, several topics in related fields (selectivity in organic reactions, surface chemistry, structural biology, drug design and high-level ab initio calculations of protein/substrate complexes and natural organic compounds) are introduced, and in the final part we comment on the prospects of this emerging field of chemistry.

CH/π hydrogen bonds in organic and organometallic chemistry

The CH/π interaction is a weak molecular force occurring between CH groups and π-groups. A study was carried out by use of the Cambridge Structural Database in order to obtain insights into the nature of the CH/π interaction and to examine its role in the crystal packing. The proportion of organic molecules bearing at least one CH/π interaction in their crystal structures has been found considerable. The CH hydrogen atoms tend to point toward the center of the aromatic ring. A number of short CH/π distances have been shown in the crystal structures of organic compounds. Moreover, the mean CH/π distance decreases as the acidity of the CH group increases. These results suggest that the CH/π interaction is not simply due to the dispersion force but involves other types of interactions, which are orientation-dependent and effective at wider ranges. It was suggested that the CH/π interaction constitutes one of the important factors in controlling the crystal packing of molecules.

CH/π Interaction in the Crystal Structure of Organic Compounds. A Database Study

interaction in the conformation of organic compounds. A database study

A statistical study was carried out to investigate the role of the CH/π interaction in the crystal structure of transition metal compounds. Thus, short CH/π distances were surveyed in crystal structures deposited in the Cambridge Structural Database. Among organometallic entries bearing C6 or C5 aromatic rings, a substantial part of the structures has been found to have intermolecular CH/π contacts shorter than the van der Waals distance. Further, in many structures short intramolecular CH/π contacts have been found. Interligand and intraligand CH/π interactions were also surveyed in coordination compounds bearing the typical ligands 1,10-phenanthroline, 2,2′-bipyridine, and 2,2′:6′,2′′-terpyridine, as well as triphenylphosphane complexes of ruthenium, rhenium, and rhodium. The results were discussed in the context of the CH/π interaction in controlling the crystal packing and the molecular structure of transition metal compounds. The compact structure with CH/π interactions is a general aspect in coordination and organometallic chemistry. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)

CH/π Interactions Implicated in the Crystal Structure of Transition Metal Compounds − A Database Study

Crystal structures in the Cambridge Structural Database (CSD) were examined to investigate the role of the CH⋯π interaction in the crystal packing and the structure of clathrates. More than 77% of organic crystals have been found to bear CH⋯π interatomic distances shorter than 3.05 A. Database subsets were edited by monitoring the entire CSD with the structure of included solvents (CHCl3, CH2Cl2, MeNO2, MeCN, MeOH, Me2CO, DMSO, DMF, 1,4-dioxane, benzene, toluene and p-xylene). A great many of the examined compounds have been shown to bear short CH⋯π distances among themselves and between supramolecular components. A variety of different solvents (protic, dipolar aprotic as well as non-polar) has been found to be included by CH⋯π interactions. The crystal structures were retrieved and examined in detail for clathrates of 1,1,6,6-tetraphenylhexa-2,4-diyne-1,6-diol and
1,1′-binaphthyl-2,2′-dicarboxylic acid in complexation with their specific guests. The results are discussed in the context of the CH⋯π interaction in controlling the specific structure of supramolecular aggregates.

Sei Tsuboyama

Papers

CH/π hydrogen bonds in organic and organometallic chemistry

CH/π Interaction in the Crystal Structure of Organic Compounds. A Database Study

interaction in the conformation of organic compounds. A database study

CH/π Interactions Implicated in the Crystal Structure of Transition Metal Compounds − A Database Study

The CH⋯π interaction as an important factor in the crystal packing and in determining the structure of clathrates