Artificial molecular-level machines

The concept of "machine" can be extended to the molecular level by designing supramolecular species capable of performing mechanical-like movements as a consequence of an appropriate energy supply. Molecular-level machines operate via electronic and nuclear rearrangements, for example, through some kind of chemical reaction. Like macroscopic machines, they are characterized by: (i) the kind of energy input supplied to make them work, (ii) the kind of movement performed by their components, (iii) the way in which their operation can be controlled and monitored, (iv) the possibility to repeat the operation at will and establish a cyclic process, (v) the time scale needed to complete a cycle of operation, and (vi) the function performed. A crucial issue is that concerning energy supply. Artificial machines powered by chemical energy ("fuels") produce waste products whose accumulation compromises the operation of the machine unless they are removed from the system. Photochemical and electrochemical energy inputs, however, can be used to make a machine work without formation of waste products. Examples of chemically, electrochemically, and photochemically powered machines investigated in our laboratory are reviewed, and future directions for the construction of novel machines are illustrated. The two most interesting kinds of applications of molecular-level machines are related to the mechanical aspect, which can be exploited, for example, for molecular-level transportation purposes, and the logic aspect, which can be exploited for information processing at the molecular level and, in the long run, for the construction of molecular level (chemical) computers.     

Light operated molecular machines

In future, artificial molecular machines could enable the construction of intelligent materials or perform functions inside our body. We describe the role of light for the operation of molecular machines, and show the level of sophistication reached in their development by illustrating a few significant examples reported since the millennium.     

Synthetic molecular motors and mechanical machines

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.     

From chemical topology to molecular machines

The chemistry of molecules displaying novel topologies has experienced an explosive development in the course of the last 25 years. The fast growth of this field originates to a large extent from the new templated synthetic methods which allow one to prepare these compounds at a real macroscopic level. Our group, in particular, has proposed a particularly efficient copper(I)-based template synthesis of a large variety of catenanes and rotaxanes at an early stage, participating in the revival of molecular topology. One of the highlights of the field has been the synthesis of the trefoil knot, a particularly challenging target. This object is not only an aesthetically attractive molecule but it also displays interesting properties in relation to coordination chemistry and chirality. A highly promising extension of molecular topology is that of molecular machines. By combining the specific properties of catenanes and rotaxanes, i.e., marked flexibility and propensity to undergo large amplitude motions, and coordination chemistry, it has been possible to elaborate and study a large variety of molecular machines. A recent example is that of an adjustable receptor, based on a [3]rotaxane attached to two mobile porphyrinic plates. This compound and related molecules will lead to “molecular presses” and, eventually, to molecular machines usable in solution to catalyse reactions or change the conformation of given substrates.     

Artificial polymerases and molecular chaperones

Cyclodextrins (CDs) were found to initiate polymerization of lactone to give polyesters with a CD ring at the end of the polymer chain in high yields only by mixing and heating with monomer without cocatalysts or solvents. CD‐tethered polyester propagates with the formation of poly‐pseudorotaxane, which is necessary to initiate further polymerization. CDs threaded onto the polymer chain are also essential for maintaining the propagating state of the polyester. By polymerizing with CD, switching the activity of the polymerization by photoisomerization was demonstrated. This polymerization system showed specific substrate recognition, releasing the products from the active site. By using the above polymerization system, β‐CD nanospheres which initiates the oligomerization of lactone were constructed. It was found that the formation of poly‐pseudorotaxane on the nanosphere enabled further polymerization activity for lactone. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 4469–4481, 2009     

Molecular assemblers: molecular machines performing chemical synthesis

Molecular assemblers were proposed by K. Eric Drexler in 1986, based on the ideas of R. Feynman. In his (quite lurid) book “Engines of Creation: The Coming Era of Nanotechnology” and follow-up publications Drexler proposes molecular machines capable of positioning reactive molecules with atomic precision and to build larger, more sophisticated structures via mechanosynthesis. These imaginative visions started a hot controversy. The debate culminated in a cover story of Chemical & Engineering News in 2003 (ref. 1) with the key question: “Are molecular assemblers – devices capable of positioning atoms and molecules for precisely defined reactions – possible?” with Drexler as the proponent and Nobelist Richard E. Smalley being the opponent. Smalley raised two major objections: the “fat fingers” and the “sticky fingers” problem. To grab and guide each individual atom the assembler must have many nano-fingers. Smalley argued that there is just not enough room in the nanometer-sized reaction region to accommodate all the fingers of all the manipulators necessary to have complete control of the chemistry. The sticky finger issue arises from the problem that …“the atoms of the manipulator hands will adhere to the atom that is being moved. So it will often be impossible to release the building block in precisely the right spot.” Smalley concludes that the fat and the sticky finger problems are fundamental and cannot be avoided. While some of the statements of E. Drexler are bold and probably not very realistic, his ideas are inspiring and might be a good starting point to assess on how far laboratory chemistry has advanced towards real “molecular assemblers” within the last two decades.

Molecular assemblers were proposed by K. Eric Drexler in 1986, based on the ideas of R. Feynman.     

Microscopic reversibility and reciprocal relations for Brownian molecular machines

Chemists have made great progress in synthesizing molecules that emulate in part the remarkable properties of biological molecular motors, most especially the ability to use chemical energy to drive directed motion and do mechanical work. Here the mechanism of a molecular motor is treated as a renewal process in which the motor molecule fluctuates away from, and then returns to some arbitrary initial configurational state. During this excursion, some number of fuel molecules will have been catalytically converted to product, and the motor will have undergone some number of mechanical cycles in which work is done on the environment. The dependences of the number of catalytic and mechanical processes per renewal obey reciprocal relations for arbitrarily strong load force and chemical driving force. These relations characterize the behavior of the system far from thermodynamic equilibrium in the same way that the Onsager reciprocal relations characterize the system close to thermodynamic equilibrium.     

Chiral ferrocenes as novel rotary modules for molecular machines

Ferrocene, a double-decker organometallic compound that generates angular motion, can be used as a unique rotary module for molecular machines. By interlocking a ferrocene-based rotary module with a photochromic unit, we have developed novel molecular machines that operate via power-conversion mechanisms. This design strategy, which mimics real machines in our daily life, allows for remote control of molecular events.     

Simulations of optically switchable molecular machines for particle transport

A promising application for design and deployment of molecular machines is nanoscale transport, driven by artificial cilia. In this contribution, we present several further steps toward this goal, beyond our first‐generation artificial cilium (Raeker et al., J. Phys. Chem. A 2012, 116, 11241). Promising new azobenzene‐derivatives were tested for use as cilium motors. Using a QM/MM partitioning in on‐the‐fly photodynamics, excited‐state surface‐hopping trajectories were calculated for each isomerization direction and each motor version. The methods used were reparametrized semiempirical quantum chemistry together with floating‐occupation configuration interaction as the QM part and the OPLSAA‐L forcefield as MM part. In addition, we simulated actual particle transport by a single cilium attached to a model surface, with varying attachment strengths and modes, and with transport targets ranging from single atoms to multi‐molecule arrangements. Our results provide valuable design guidelines for cilia‐driven nanoscale transport and emphasize the need to carefully select the whole setup (not just the cilium itself, but also its surface attachment and the dynamic cilium‐target interaction) to achieve true transport. © 2018 Wiley Periodicals, Inc.     

Observing a molecular knife at work

Sum frequency generation (SFG) vibrational spectroscopy has been employed to study the molecular interactions between a single substrate supported lipid bilayer and an amphiphilic antibiotic compound 1, with a design based on the common structural motif of natural antimicrobial peptides. The interfacial sensitivity of SFG allows real-time in situ monitoring of ordering changes in both leaflets of the bilayer and orientation of 1 simultaneously. A critical concentration of about 0.8 microg/mL of 1 is found, above which the inner leaflet of the bilayer is significantly perturbed. This concentration corresponds well to the minimum inhibition concentration of 1 that is obtained from bacterial experiments. Orientation of 1 in the bilayer is shown to be perpendicular to the bilayer surface, in agreement with simulation results. SFG can be developed into a very informative technique for studying the cell membrane and the interactions of membrane-active molecules.     

碘化银为什么可用于人工降雨

在科学技术水平很低的年代里,人类为了抵御旱灾,只能以一种敬畏的眼光来注视各种云的变化,期望它们带来雨水。原始人尝试过跳求雨之舞,我国农民也曾去过龙王庙,祷求龙王招云致雨……当然这些都不会有什么成效。     

Artificial intelligence systems for molecular spectral analysis

A brief survey is given of the most recent publications on development of artificial-intelligence systems for molecular spectral analysis. A new approach to solution of the problems of qualitative molecular spectral analysis is based on an applied logical calculus developed by the authors for fuzzy predicates. It is suggested that spectral-structural knowledge should be specified in the language of fuzzy predicates, and mechanical theorem-proving procedures used for solving qualitative problems of spectral analysis, the initial information being considered as a set of axioms. System-oriented matters are given consideration. The formalism suggested is a basis for the development of an artificial-intelligence dialogue system capable of solving various problems in molecular spectral analysis while maintaining a dialogue with a research worker using a professionally-restricted natural language.     

A generic basis for some simple light-operated mechanical molecular machines

A novel type of mechanical switch is described in which light-induced translation of a macrocycle in a [2]rotaxane quenches anthracene fluorescence. Features of the system include the remarkable 200:1 difference in fluorescence intensity between the two positional states of the molecule ( approximately 85:1 between one isomer and the photostationary state). In principle the same concept could be used for mechanically switching virtually any property that can be influenced by functional group proximity effects.     

Correlated motion and mechanical gearing in amphidynamic crystalline molecular machines

In this review we highlight the recent efforts towards the development of molecular gears with an emphasis on building molecular gears in the solid state and the role that molecular gearing and correlated motions may play in the function of crystalline molecular machines. We discuss current molecular and crystal engineering strategies, challenges associated with engineering correlated motion in crystals, and outline experimental and theoretical tools to explore gearing dynamics while highlighting key advances made to date.

Here we highlight recent efforts towards the development of molecular gears in the solid state and the role that molecular gearing and correlated motions may play in the function of crystalline molecular machines.     

Development of photoresponsive supramolecular machines inspired by biological molecular systems

In the growing research area on molecular machinery, light is one of the attractive and useful stimuli source to operate synthetic molecular machines, since light allows selective operation of photoresponsive moieties without additives. We have proposed a new approach to design of photoresponsive molecular machines by interlocking mechanical motions between photoresponsive and movable units through covalent and non-covalent bonds. This approach is inspired by biological molecular machines consisting of multiple protein subunits, and potentially useful for construction of giant mechanical systems. In this review, we will introduce our concepts of the molecular design with several successful examples as well as their applications for controlling chemical events, and also glance at a semi-biological molecular machine controllable by light, which reveals a potential of biological systems for development of elaborate molecular devices.     

Effective surface motion on a reactive cylinder of particles that perform intermittent bulk diffusion

In many biological and small scale technological applications particles may transiently bind to a cylindrical surface. In between two binding events the particles diffuse in the bulk, thus producing an effective translation on the cylindrical surface. We here derive the effective motion on the surface allowing for additional diffusion on the cylindrical surface itself. We find explicit solutions for the number of adsorbed particles at one given instant, the effective surface displacement, as well as the surface propagator. In particular sub- and superdiffusive regimes are found, as well as an effective stalling of diffusion visible as a plateau in the mean squared displacement. We also investigate the corresponding first passage problem.     

Artificial molecular-level machines. Dethreading-rethreading of a pseudorotaxane powered exclusively by light energy

The reversible light-driven dethreading-rethreading of a pseudorotaxane is obtained in solution by exploiting the (E)-(Z) photoisomerisation of azobenzene, and monitored through fluorescence signals.