Liquid interfacial nanoarchitectonics: Molecular machines,organic semiconductors,nanocarbons, stem cells,and others

The concept of nanoarchitectonics has been proposed as an extensional development of nanotechnology through fusions with material science and the other fields. In nanoarchitectonics, nano-units of atoms, molecules, and nanomaterials are architected into construction of functional material systems. In order to assemble intended structures or hierarchical structures from nano-units, it is more useful to confine nano-units at the interface. In addition, nanoarchitectonics is expected to output functions by harmonizing many units in dynamic environments. However, the liquid interfaces still have lots of unexplored matters in nanoscale because supports by advanced apparatus and techniques in nanotechnology are not always available. Specifically, this review paper summarizes examples of research on molecular manipulation, molecular arrangement and assembly, materials synthesis, and life manipulation at the liquid interface. These examples demonstrate that the liquid interface enables the control of dynamic functions of various size regions, from molecular-level phenomena such as the control of molecular machines to techniques of living creature size such as the control of stem cell differentiation. Liquid interfaces are very useful environments for controlling dynamic functions for a wide range of targets and would have tremendous potential in terms of functional exploration. The great potential of nanoarchitectonics at the liquid interface and the challenges to be solved in the future are also discussed.     

The evolution of molecular dynamics from picoseconds to years

The dielectric relaxation of dipolar solutes in vitreous and viscous decalin is composed of at least two loss peaks. There is an universal γ process appearing at THz frequencies and equivalent to the Poley absorption in liquids, and a low frequency process sometimes resolved into α and β components. The complete spectrum covers twelve frequency decades or more.     

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.     

Nanoarchitectonics in combat against bacterial infection using molecular,interfacial, and material tools

Nanoarchitectonics, as a post-nanotechnology concept, is the methodology for constructing functional materials from nano-units, which bridges the gap between nanotechnology and materials science. The research accomplishes advocating nanoarchitectonics has increased dramatically as overviewed in the initial part of this review. Then, as socially impactful subjects, we exemplify nanoarchitectonics research for bacterial infections according to classifications featured with molecular tools, interfaces, and hierarchically structured materials. In particular, this review article discusses namely three kinds of antibacterial strategies: (i) new antimicrobial agents and therapeutic modalities based on nanoarchitectonics present high bactericidal efficacy against methicillin-resistant Staphylococcus aureus; (ii) antimicrobial nanoarchitectonics structures are integrated into the surface of medical devices to detach or kill approaching bacteria; (iii) the nanoarchitectonics hydrogels act as antimicrobial reservoirs to produce sustained-release antimicrobial agents for long-lasting bacterial killing.     

Aqua ions-graphene interfacial and confinement behavior: insights from isobaric-isothermal molecular dynamics

We carry out a systematic microstructural characterization of the solid-fluid interface (SFI) of water and simple metal chloride aqueous solutions in contact with a free-standing plate or with two such plates separated by an interplate distance 0 ≤ h (?) ≤ 30 at ambient conditions via isothermal-isobaric molecular dynamics. With this characterization, we target the interrogation of the system in search for answers to fundamental questions regarding the structure of the "external" and "internal" (confined) SFIs, the effect of the differential hydration behavior among species, and its link to species expulsion from confinement. For water at ambient conditions, we found that the structure of the "external" SFIs is independent of the interplate distance h in the range 0 ≤ h (?) ≤ 30, that is, the absence of wall-mediated correlation effects between "external" and "internal" SFIs, and that for h < 9 ? the slit-pores dewet. Moreover, we observed a selective expulsion of ions caused by the differential hydration between the anion and the cations with a consequent charging of the slit-pore. All these observations were interpreted in terms of the axial profiles for precisely defined order parameters, including tetrahedral configuration, hydrogen bonding, and species coordination numbers.     

Aptamers: molecular tools for analytical applications

Aptamers are artificial nucleic acid ligands, specifically generated against certain targets, such as amino acids, drugs, proteins or other molecules. In nature they exist as a nucleic acid based genetic regulatory element called a riboswitch. For generation of artificial ligands, they are isolated from combinatorial libraries of synthetic nucleic acid by exponential enrichment, via an in vitro iterative process of adsorption, recovery and reamplification known as systematic evolution of ligands by exponential enrichment (SELEX). Thanks to their unique characteristics and chemical structure, aptamers offer themselves as ideal candidates for use in analytical devices and techniques. Recent progress in the aptamer selection and incorporation of aptamers into molecular beacon structures will ensure the application of aptamers for functional and quantitative proteomics and high-throughput screening for drug discovery, as well as in various analytical applications. The properties of aptamers as well as recent developments in improved, time-efficient methods for their selection and stabilization are outlined. The use of these powerful molecular tools for analysis and the advantages they offer over existing affinity biocomponents are discussed. Finally the evolving use of aptamers in specific analytical applications such as chromatography, ELISA-type assays, biosensors and affinity PCR as well as current avenues of research and future perspectives conclude this review.     

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.     

The art of building small: from molecular switches to molecular motors

Molecular switches and motors are essential components of artificial molecular machines. In this perspective, we discuss progress in our design, synthesis, and functioning of photochemical and electrochemical switches and chemical and light-driven molecular motors. Special emphasis is given to the control of a range of functions and properties, including luminescence, self-assembly, motion, color, conductance, transport, and chirality. We will also discuss our efforts to control mechanical movement at the molecular level, a feature that is at the heart of molecular motors and machines. The anchoring of molecular motors on surfaces and molecular motors at work are discussed.     

Polymer-nanoparticle interfacial behavior revisited: a molecular dynamics study

By tuning the polymer-filler interaction, filler size and filler loading, we use a coarse-grained model-based molecular dynamics simulation to study the polymer-filler interfacial structural (the orientations at the bond, segment and chain length scales, chain size and conformation), dynamic and stress-strain properties. Simulated results indicate that the interfacial region is composed of partial segments of different polymer chains, which is consistent with the experimental results presented by Chen et al. (Macromolecules, 2010, 43, 1076). Moreover, it is found that the interfacial region is within one single chain size (R(g)) range, irrespective of the polymer-filler interaction and the filler size, beyond which the bulk behavior appears. In the interfacial region, the orientation and dynamic behaviors are induced by the interfacial enthalpy, while the size and conformation of polymer chains near the filler are controlled by the configurational entropy. In the case of strong polymer-filler interaction (equivalent to the hydrogen bond), the innerest adsorbed polymer segments still undergo adsorption-desorption process, the transport of chain mass center in the interfacial region exhibits away from the glassy behavior, and no plastic-like yielding point appears in the stress-strain curve, which indicates that although the mobility of interfacial polymer chains is restricted, there exist no "polymer glassy layers" surrounding the filler. In addition, it is evidenced that the filler particle prefers selectively adsorbing the long polymer chains for attractive polymer-filler interaction, validating the experimental explanation of the change of the bound rubber (BR). In short, this work provides important information for further experimental and simulation studies of polymer-nanoparticle interfacial behavior.     

Calculation of the crystal-melt interfacial free energy of succinonitrile from molecular simulation

The crystal-metal interfacial free energy for a six-site model of succinonitrile [N triple bond C-(CH(2))(2)-C triple bond N] has been calculated using molecular-dynamics simulation from the power spectrum of capillary fluctuations in interface position. The orientationally averaged magnitude of the interfacial free energy is determined to be (7.0+/-0.4)x10(-3) J m(-2). This value is in agreement (within the error bars) with the experimental value [(7.9+/-0.8)x10(-3) J m(-2)] of Marasli et al. [J. Cryst. Growth 247, 613 (2003)], but is about 20% lower than the earlier experimental value [(8.9+/-0.5)x10(-3) J m(-2)] obtained by Schaefer et al. [Philos. Mag. 32, 725 (1975)]. In agreement with the experiment, the calculated anisotropy of the interfacial free energy of this body-centered-cubic material is small. In addition, the Turnbull coefficient from our simulation is also in agreement with the experiment. This work demonstrates that the capillary fluctuation method of Hoyt et al. [Phys. Rev. Lett. 86, 5530 (2001)] can be successfully applied to determine the crystal-melt interfacial free energy of molecular materials.     

Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations

We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents promiscuous activity as a diesterase. The analysis of our simulations, carried out by means of molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, shows that the reaction takes place through a D(N)A(N) or dissociative mechanism, the same mechanism employed by AP in the hydrolysis of monoesters. The promiscuous activity observed in this superfamily can be then explained on the basis of a conserved reaction mechanism. According to our simulations the specialization in the hydrolysis of phosphomonoesters or phosphodiesters, developed in different members of the superfamily, is a consequence of the interactions established between the protein and the oxygen atoms of the phosphate group and, in particular, with the oxygen atom that bears the additional alkyl group when the substrate is a diester. A water molecule, belonging to the coordination shell of the Mg(2+) ion, and residue Lys328 seem to play decisive roles stabilizing a phosphomonoester substrate, but the latter contributes to increase the energy barrier for the hydrolysis of phosphodiesters. Then, mutations affecting the nature or positioning of Lys328 lead to an increased diesterase activity in AP. Finally, the capacity of this enzymatic family to catalyze the reaction of phosphoesters having different leaving groups, or substrate promiscuity, is explained by the ability of the enzyme to stabilize different charge distributions in the leaving group using different interactions involving either one of the zinc centers or residues placed on the outer side of the catalytic site.     

Chiral molecular assemblies from a novel achiral amphiphilic 2-(heptadecyl) naphtha[2,3]imidazole through interfacial coordination

A novel amphiphilic compound 2-(heptadecyl) naphtha[2,3]imidazole (NpImC17) was synthesized, and its coordination with AgNO(3) in situ in the monolayer at the air/water interface and ex situ in the Langmuir-Blodgett (LB) film on solid substrate has been investigated. It has been found that interfacial coordination between NpImC17 and Ag(I) ion occurred both in the monolayer and in the LB film. It is interesting to note that the Ag(I)-coordinated ultrathin film became chiral although the ligand itself is achiral. It was suggested that the chirality of the Ag(I)-coordinated LB film was developed due to the formation of a helical coordination polymer through the interfacial coordination. To the best of our knowledge, this is the first report on the formation of chiral monolayer and LB films from an achiral molecule through interfacial coordination.     

The molecular level modification of surfaces: from self-assembled monolayers to complex molecular assemblies

The modification of surfaces with self-assembled monolayers (SAMs) containing multiple different molecules, or containing molecules with multiple different functional components, or both, has become increasingly popular over the last two decades. This explosion of interest is primarily related to the ability to control the modification of interfaces with something approaching molecular level control and to the ability to characterise the molecular constructs by which the surface is modified. Over this time the level of sophistication of molecular constructs, and the level of knowledge related to how to fabricate molecular constructs on surfaces have advanced enormously. This critical review aims to guide researchers interested in modifying surfaces with a high degree of control to the use of organic layers. Highlighted are some of the issues to consider when working with SAMs, as well as some of the lessons learnt (169 references).     

Proteasome inhibitors: from research tools to drug candidates

The 26S proteasome is a 2.4 MDa multifunctional ATP-dependent proteolytic complex, which degrades the majority of cellular polypeptides by an unusual enzyme mechanism. Several groups of proteasome inhibitors have been developed and are now widely used as research tools to study the role of the ubiquitin-proteasome pathway in various cellular processes, and two inhibitors are now in clinical trials for treatment of multiple cancers and stroke.     

Aerogel nanoarchitectonics based on cellulose nanocrystals and nanofibers from eucalyptus pulp: preparation and comparative study

Cellulose - Nanocellulose-based materials have attracted significant attention because of their attractive advantages. Particularly, aerogel, a porous nanocellulose material, have been used in...     

Lectins: tools for the molecular understanding of the glycocode

Recent progress in glycobiology has revealed that cell surface oligosaccharides play an essential role in recognition events. More precisely, these saccharides may be complexed by lectins, carbohydrate-binding proteins other than enzymes and antibodies, able to recognise sugars in a highly specific manner. The ubiquity of lectin-carbohydrate interactions opens enormous potential for their exploitation in medicine. Therefore, extraordinary effort is made into the identification of new lectins as well as into the achievement of a deep understanding of their functions and of the precise mechanism of their association with specific ligands. In this review, a summary of the main features of lectins, particularly those found in legumes, will be presented with a focus on the mechanism of carbohydrate-binding. An overview of lectin-carbohydrate interactions will also be given, together with an insight into their energetics. In addition, therapeutic applications of lectins will be discussed.     

The role of nonsurface-active species at interfacial molecular recognition by melamine-type monolayers

The main characteristics of Langmuir monolayers are radically changed by molecular recognition of hydrogen bond nonsurface-active species. The change in the thermodynamic, phase, and structural features by molecular recognition of dissolved uracil or barbituric acid by 2,4-di(n-undecylamino)-6-amino-1,3,5-triazine (2C11H23-melamine) monolayers is characterized by combination of surface pressure studies with Brewster angle microscopy (BAM) imaging and Grazing incidence X-ray diffraction (GIXD) measurements. Phase behavior of the 2C11H23-melamine monolayer and morphology of the condensed phase domains are changed drastically, but in a specific way, by molecular recognition of uracil or barbituric acid. The main characteristics of the interfacial system can be essentially affected by the kinetics of the recognition process. Pure 2C11H23-melamine monolayers show only small compact, but nontextured domains. The monolayers of 2C11H23-melamine-uracil assemblies develop well-shaped circular condensed-phase domains having an inner texture with alkyl chains essentially oriented parallel to the periphery and having a striking tendency to two-dimensional (2D) Ostwald ripening. The 2C11H23-melamine-barbituric acid monolayers form large homogeneous areas of condensed phase that transfer at smaller areas per molecule to a homogeneous condensed monolayer. BAM imaging of corresponding assemblies with ((CH3(CH2)11O(CH2)3)2-melamine having modified alkyl chains demonstrates the specific effect of the monolayer component. GIXD results reveal that molecular recognition of pyrimidine derivatives gives rise only to quantitative changes in the two-dimensional lattice structure. The striking differences in the main characteristics between the supramolecular species are related to their different chemical structures. Quantum chemical calculations using the semiempirical PM3 method provide information about the different nature of the hydrogen-bonding-based supramolecular structures.     

Inorganic nanotubes formation through the synergic evolution of dynamic templates and metallophosphates: from vesicles to nanotubes

A novel synergic evolution of dynamic assembly, from vesicles to nanotubes, between the metallophosphates and organic amines, is disclosed, by which the multicomponent metallophosphate (Cu(2)(OH)PO(4)) nanotubes are synthesized for the first time.