[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

J. Appl. Cryst.の発刊に際して

Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Synthetic molecular motors and mechanical machines.

The widespread use of molecular machines in biology has long suggested that great rewards could come from bridging the gap between synthetic molecular systems and the machines of the macroscopic world. In the last two decades, it has proved possible to design synthetic molecular systems with architectures where triggered large amplitude positional changes of submolecular components occur. Perhaps the best way to appreciate the technological potential of controlled molecular-level motion is to recognize that nanomotors and molecular-level machines lie at the heart of every significant biological process. Over billions of years of evolution, nature has not repeatedly chosen this solution for performing complex tasks without good reason. When mankind learns how to build artificial structures that can control and exploit molecular level motion and interface their effects directly with other molecular-level substructures and the outside world, it will potentially impact on every aspect of functional molecule and materials design. An improved understanding of physics and biology will surely follow.

The first steps on the long path to the invention of artificial molecular machines were arguably taken in 1827 when the Scottish botanist Robert Brown observed the haphazard motion of tiny particles under his microscope.1,2 The explanation for Brownian motion, that it is caused by bombardment of the particles by molecules as a consequence of the kinetic theory of matter, was later provided by Einstein, followed by experimental verification by Perrin.3,4 The random thermal motion of molecules and its implications for the laws of thermodynamics in turn inspired Gedankenexperiments (“thought experiments”) that explored the interplay (and apparent paradoxes) of Brownian motion and the Second Law of Thermodynamics. Richard Feynman’s famous 1959 lecture “There’s plenty of room at the bottom” outlined some of the promise that manmade molecular machines might hold.5,6 However, Feynman’s talk came at a time before chemists had the necessary synthetic and analytical tools to make molecular machines. While interest among synthetic chemists began to grow in the 1970s and 1980s, progress accelerated in the 1990s, particularly with the invention of methods to make mechanically interlocked molecular systems (catenanes and rotaxanes) and control and switch the relative positions of their components.7−24

Here, we review triggered large-amplitude motions in molecular structures and the changes in properties these can produce. We concentrate on conformational and configurational changes in wholly covalently bonded molecules and on catenanes and rotaxanes in which switching is brought about by various stimuli (light, electrochemistry, pH, heat, solvent polarity, cation or anion binding, allosteric effects, temperature, reversible covalent bond formation, etc.). Finally, we discuss the latest generations of sophisticated synthetic molecular machine systems in which the controlled motion of subcomponents is used to perform complex tasks, paving the way to applications and the realization of a new era of “molecular nanotechnology”.

1.1. The Language Used To Describe Molecular Machines
Terminology needs to be properly and appropriately defined and these meanings used consistently to effectively convey scientific concepts. Nowhere is the need for accurate scientific language more apparent than in the field of molecular machines. Much of the terminology used to describe molecular-level machines has its origins in observations made by biologists and physicists, and their findings and descriptions have often been misinterpreted and misunderstood by chemists. In 2007 we formalized definitions of some common terms used in the field (e.g., “machine”, “switch”, “motor”, “ratchet”, etc.) so that chemists could use them in a manner consistent with the meanings understood by biologists and physicists who study molecular-level machines.14

The word “machine” implies a mechanical movement that accomplishes a useful task. This Review concentrates on systems where a stimulus triggers the controlled, relatively large amplitude (or directional) motion of one molecular or submolecular component relative to another that can potentially result in a net task being performed. Molecular machines can be further categorized into various classes such as “motors” and “switches” whose behavior differs significantly.14 For example, in a rotaxane-based “switch”, the change in position of a macrocycle on the thread of the rotaxane influences the system only as a function of state. Returning the components of a molecular switch to their original position undoes any work done, and so a switch cannot be used repetitively and progressively to do work. A “motor”, on the other hand, influences a system as a function of trajectory, meaning that when the components of a molecular motor return to their original positions, for example, after a 360° directional rotation, any work that has been done is not undone unless the motor is subsequently rotated by 360° in the reverse direction. This difference in behavior is significant; no “switch-based” molecular machine can be used to progressively perform work in the way that biological motors can, such as those from the kinesin, myosin, and dynein superfamilies, unless the switch is part of a larger ratchet mechanism.14

Artificial Molecular Machines

The Lectin-Carbohydrate interaction was investigated by combining the Quartz Crystal Microbalance-QCM technique with signal amplifying biomimetic nanoparticle-NP platforms. A library of glyconanoparticles was prepared and the avidity of these NPs for immobilised lectin layers was then evaluated by a QCM setup. Large responses were observed as a result of surface recognition by nanoparticles displaying the appropriate molecular functionality. Large affinity enhancements were also in evidence due to the biomimetic nature of the glyconanoparticle assemblies' carbohydrate presentation demonstrating evidence of the cluster glycoside effect.

Multivalent Biomimetic Glyconanoparticle Platforms as QCM Amplifiers for Lectin-carbohydrate Interactions

Shatruk and Alabugin propose an alternative structural model for the observed electron density that we have attributed to the photochemical formation of 1,3-dimethylcyclobutadiene in a protective solid crystalline matrix. The main criticism from Shatruk and Alabugin concerns the modeling of the disorder in the calixarene cavity and in particular the neglect of a residual electron density close to the O1 atom. We published (Chem. Eur. J. 2011, 17, 10021) our opinion concerning this "ignored peak" in the Supporting Information of the paper. The current response to the Correspondence demonstrates that Shatruk and Alabugin have over-modeled our data by assigning a small electron density peak, which is hardly more than the density corresponding to a hydrogen atom, to an under-occupied oxygen site, using inappropriate refinement contraints.

A constrained disorder refinement: "Reinvestigation of "Single-crystal X-ray structure of 1,3-dimethylcyclobutadiene" by M. Shatruk and I. V. Alabugin".

Back Cover: Self‐Assembled Columnar Triazole Quartets: An Example of Synergistic Hydrogen‐Bonding/Anion–π Interactions (Angew. Chem. Int. Ed. 35/2019)

Back Cover: Imidazole-Quartet Water and Proton Dipolar Channels (Angew. Chem. Int. Ed. 48/2011)

In the title compound, [Na2(N3)2(C21H34N2O6)2]·2CHCl3, the sodium cation is hepta­coordinated by five O atoms of the crown ether unit of the 1-hexyl-3-(2,3,5,6,8,9,11,12-octa­hydro-1,4,7,10,13-benzopenta­oxacyclo­penta­decin-15-yl)urea (L) ligand, the O atom of the urea group of the second, symmetry-related L ligand, and one N atom of the azide anion. The experimentally determined distance 2.472 (2) A between the terminal azide N atom and the sodium cation is substanti­ally longer than that predicted from density functional theory (DFT) calculations (2.263 A). The crown ethers complexing the sodium cation are related by an inversion centre and form dimers. The urea groups of the two L ligands are connected in a head-to-tail fashion by classical N—H⋯N hydrogen-bonding inter­actions and form a ribbon-like structure parallel to the b axis. Parallel ribbons are weakly linked through C—H⋯N, C—H⋯O and C—H⋯π inter­actions.

https://journals.iucr.org/e/issues/2012/05/00/rk2333/rk2333.pdf

Mihail Barboiu

Papers

Multivalent Biomimetic Glyconanoparticle Platforms as QCM Amplifiers for Lectin-carbohydrate Interactions

A constrained disorder refinement: "Reinvestigation of "Single-crystal X-ray structure of 1,3-dimethylcyclobutadiene" by M. Shatruk and I. V. Alabugin".

Back Cover: Self‐Assembled Columnar Triazole Quartets: An Example of Synergistic Hydrogen‐Bonding/Anion–π Interactions (Angew. Chem. Int. Ed. 35/2019)

Back Cover: Imidazole-Quartet Water and Proton Dipolar Channels (Angew. Chem. Int. Ed. 48/2011)

Bis[μ-1-hexyl-3-(2,3,5,6,8,9,11,12-octahydro-1,4,7,10,13-benzopentaoxacyclopentadecin-15-yl)urea]bis(azidosodium) chloroform disolvate

Mihail Barboiu

Papers

Multivalent Biomimetic Glyconanoparticle Platforms as QCM Amplifiers for Lectin-carbohydrate Interactions

A constrained disorder refinement: "Reinvestigation of "Single-crystal X-ray structure of 1,3-dimethylcyclobutadiene" by M. Shatruk and I. V. Alabugin".

Back Cover: Self‐Assembled Columnar Triazole Quartets: An Example of Synergistic Hydrogen‐Bonding/Anion–π Interactions (Angew. Chem. Int. Ed. 35/2019)

Back Cover: Imidazole-Quartet Water and Proton Dipolar Channels (Angew. Chem. Int. Ed. 48/2011)

Bis[μ-1-hexyl-3-(2,3,5,6,8,9,11,12-octa­hydro-1,4,7,10,13-benzopenta­oxacyclo­penta­decin-15-yl)urea]bis­(azido­sodium) chloro­form disolvate

Bis[μ-1-hexyl-3-(2,3,5,6,8,9,11,12-octahydro-1,4,7,10,13-benzopentaoxacyclopentadecin-15-yl)urea]bis(azidosodium) chloroform disolvate