Structure and Function of Molecular Assembly. A Personal Reminiscence

Abstract

In this account is described an outline of research the author has conducted over the last 35 years. Depending on the type of molecular assemblies dealt with, the whole work is divided into four parts, i.e., small hostguest systems in organic media, infinite solid systems, huge but finite nano systems in aqueous media, and manipulated biological systems. The essence of the hostguest systems (Section 2) is molecular recognition based on convergent multiple interactions involving OH£O hydrogen bonds, where sugar binding and detailed thermodynamic analysis of multipoint recognition may be taken as highlights. A couple of new fields arise from the hostguest chemistry by paradigm shift. One is in the direction of multiple interactions, from convergent to divergent. Section 3 thus concerns molecular alignment control in crystals using orthogonal aromatic triad and diad building blocks. Catalysis by microporous metallo-organic frameworks as organic zeolites is also described. The other shift in paradigm is in the media, from organic to aqueous, and also in the significance of sugar binding, from sugars as a guest to sugars as a probe. Section 4 is devoted to the highly adhesive (hydrogen bonding) nature of glycocluster compounds and their micelle-like aggregates, focusing on the formation of glycoviruses and glycoviral gene delivery. With DNA and RNA manipulation techniques in hand, we became interested in in-cell gene sensing and transcription monitoring. The latest activity in this area is shown in Section 5. The entire work is design-based. The author, who is soon retiring from Kyoto University, now has mixed feelings about this apparently natural approach, as briefly referred to in the Closing Remark (Section 6).

A Chiral Bis‐Naphthylated Tetrandrine Dibromide: Synthesis, Self‐Assembly into an Organic Framework Based On Nanosized Spherical Cages, and Inclusion Studies

“…Purely organic structures assembled by non‐covalent interactions are also known. They have the advantage of being soluble in most common solvents and in some cases they show an assembly‐disassembly behaviour, making them useful for a wide range of applications . Crystalline organic supramolecular assemblies can be classified in two groups: POFs, being porous infinite networks of organic molecules interconnected through non‐covalent interactions, forming a solid‐state material; and POCs, which are materials with discrete pores and cavities assembled by organic tectons only.…”

“…They have the advantage of being soluble in most common solvents and in some cases they show an assembly-disassembly behaviour, making them useful for a wide range of applications. [6][7][8][9][10][11][12][13] Crystalline organic supramolecular assemblies can be classified in two groups: POFs, being porous infinite networks of organic molecules interconnected through non-covalent interactions, forming a solid-state material; and POCs, which are materials with discrete pores and cavities assembled by organic tectons only. 3 In this regard, Davis' group has reported a series of POFs consisting in chiral steroidal ureas assembled through hydrogen bonds with unit cell volumes in the range of 8,053-8,636 Å 3 .…”

“…Quaternization of the two nitrogens in S,S-(+)-tetrandrine with 2-(bromomethyl)naphthalene gave a single chiral stereoisomer in good yields, the S C ,S C , R N ,R N -derivative DNT (see Figure 1). DNT was isolated as tetrahydrate and fully characterized by elemental analysis, NMR ( 1 H, 13 C) spectroscopy and mass spectrometry (Figures S1-S3, Supporting Information). Colourless rectangularshaped molecular crystals of DNT (Figure 2, left) were obtained first by slow evaporation of a solution in methanol at room temperature (DNT-MeOH).…”

Dynamics of Water Molecules in a 3-Fold Interpenetrated Hydrogen-Bonded Organic Framework Based on Tetrakis(4-pyridyl)methane

“…A hydrogen bond is one of the strong interactions to establish a higher order structure in organic crystals. − In the past, organic porous materials called organic zeolites or hydrogen-bonded organic frameworks (HOFs) have been studied intensively, especially by Aoyama and co-workers. − They researched the construction of two-dimensional hydrogen-bonded networks and their zeolitic properties. Other types of porous materials such as organic–inorganic hybrid materials named metal organic frameworks (MOFs) have considerable attractiveness because they show interesting properties by combining various types of host frameworks and guest molecules. − Among the various host–guest materials, flexibility in host frameworks, which can change their structure during the absorption and desorption processes of guest molecules, is an important issue in developing responsive materials. − One of the requirements for this special property is a softness of the host framework, and a hydrogen-bonded linkage in HOF is considered to satisfy this requirement.…”

Spatially Directional Resorcin[4]arene Cavitand Glycoconjugates for Organic Catalysis

“…[5][6][7][8] The synthesis and biological applicationso fr esorcin[4]arene glycoconjugates werea lmost exclusively reported by the laboratory of Prof. Aoyama in Japan. [9] However, no reporto ft hese amphiphilic compounds as host-guest systems and/ori nchemical catalysis exists and is known.…”