Nanostructuring of Self‐Assembled Porphyrin Networks at a Solid/Liquid Interface: Local Manipulation under Global Control

Molecules of (5,10,15,20‐tetraundecylporphyrinato)‐copper(II) [(TUP)Cu] can self‐assemble into four different polymorphs at the interface between highly oriented pyrolytic graphite and 1‐octanoic acid. Scanning tunneling microscopy (STM) reveals that it is possible to combine the global control over monolayer structure, provided by the composition and concentration of the supernatant solution, with local control, from nanomanipulation by the STM tip. In the initially formed monolayer, with a polymorph composition governed by the concentration of (TUP)Cu in the supernatant solution, the exchange of molecules physisorbed at the solid/liquid interface with those in the liquid is very limited. By using a nanoshaving procedure at the tip, defects are created in the monolayer, and these serve as local manipulation sites to create domains of higher or lower molecular density, and to incorporate a second molecular species, (TUP)Co into the monolayer of (TUP)Cu.     

Two-dimensional supramolecular nanopatterns formed by the coadsorption of guanine and uracil at the liquid/solid interface

A novel supramolecular nanostructure formed by the coadsorption of the complementary nucleobases guanine (G) and uracil (U) at the liquid (1-octanol solvent)/solid (graphite) interface is revealed by scanning tunneling microscopy (STM). The GU supramolecular structure is distinctly different from the structures observed by STM when the individual nucleobases (NB) are adsorbed on graphite in the control experiments. Using a systematic methodology and ab initio density functional theory (DFT), an atomistic structural model is proposed for the supramolecular coadsorbed GU structure, which consists of a periodic repetition of cyclic units based on the strongest GU base pairing.     

Expression of Chirality by Achiral Coadsorbed Molecules in Chiral Monolayers Observed by STM

The supramolecular packing mode of physisorbed monolayers built up by chiral isophthalic acid derivatives and coadsorbed achiral solvent molecules was imaged at the liquid/graphite interface with scanning tunneling microscopy (STM). The picture on the right shows the submolecularly resolved STM image of an enantiomorphous domain composed of the R enantiomer of the isophthalic acid derivative studied and 1-heptanol molecules; the latter express the chirality of the monolayer. Upon adsorption a racemic mixture is separated into enantiomorphous domains.     

Enforcing periodic secondary structures in hybrid peptides: a novel hybrid foldamer containing periodic gamma-turn motifs

This note describes the design, synthesis, and conformational studies of a novel hybrid foldamer that adopts a definite compact, three-dimensional structure determined by a combined effect of the special conformational properties of the foldamer constituents. The striking feature of this de novo designed foldamer is its ability to display periodic gamma-turn conformations stabilized by intramolecular hydrogen bonds. Conformational investigations by single-crystal X-ray studies, solution-state NMR, and ab initio MO theory at the HF/6-31G* level strongly support the prevalence of gamma-turn motifs in both the di- and tetrapeptide foldamers, which are presumably stabilized by bifurcated hydrogen bonds in the solid and solution states. The strategy disclosed herein for the construction of hybrid foldamers with periodic gamma-turn motifs has the potential to significantly augment the conformational space available for foldamer design with diverse backbone structures and conformations.     

Manipulating double-decker molecules at the liquid-solid interface

We have used a scanning tunneling microscope (STM) to manipulate heteroleptic phthalocyaninato, naphthalocyaninato, and porphyrinato double-decker (DD) molecules at the liquid-solid interface between 1-phenyloctane solvent and graphite. We employed nanografting of phthalocyanines with eight octyl chains to place these molecules into a matrix of heteroleptic DD molecules; the overlayer structure is epitaxial on graphite. We have also used nanografting to place DD molecules in matrices of single-layer phthalocyanines with octyl chains. Rectangular scans with a STM at low bias voltage resulted in the removal of the adsorbed DD molecular layer and substituted the DD molecules with bilayer-stacked phthalocyanines from phenyloctane solution. Single heteroleptic DD molecules with lutetium sandwiched between naphthalocyanine and octaethylporphyrin were decomposed with voltage pulses from the probe tip; the top octaethylporphyrin ligand was removed, and the bottom naphthalocyanine ligand remained on the surface. A domain of decomposed molecules was formed within the DD molecular domain, and the boundary of the decomposed molecular domain self-cured to become rectangular. We demonstrated a molecular "sliding block puzzle" with cascades of DD molecules on the graphite surface.     

Sampling unfolding intermediates in calmodulin by single-molecule spectroscopy

We used single-pair fluorescence resonance energy transfer (spFRET) measurements to characterize denatured and partially denatured states of the multidomain calcium signaling protein calmodulin (CaM) in both its apo and Ca(2+)-bound forms. The results demonstrate the existence of an unfolding intermediate. A CaM mutant (CaM-T34C-T110C) was doubly labeled with fluorescent probes AlexaFlour 488 and Texas Red at opposing globular domains. Single-molecule distributions of the distance between fluorophores were obtained by spFRET at varying levels of the denaturant urea. Multiple conformational states of CaM were observed, and the amplitude of each conformation was dependent on urea concentration, with the amplitude of an extended conformation increasing upon denaturation. The distributions at intermediate urea concentrations could not be adequately described as a combination of native and denatured conformations, showing that CaM does not denature via a two-state process and demonstrating that at least one intermediate is present. The intermediate conformations formed upon addition of urea were different for Ca(2+)-CaM and apoCaM. An increase in the amplitude of a compact conformation in CaM was observed for apoCaM but not for Ca(2+)-CAM upon the addition of urea. The changes in the single-molecule distributions of CaM upon denaturation can be described by either a range of intermediate structures or by the presence of a single unfolding intermediate that grows in amplitude upon denaturation. A model for stepwise unfolding of CaM is suggested in which the domains of CaM unfold sequentially.     

Hierarchical two-dimensional molecular assembly through dynamic combination of conformational states at the liquid/solid interface

Self-sorting of multiple building blocks for correctly positioning molecules through orthogonal recognition is a promising strategy for construction of a hierarchical self-assembled molecular network (SAMN) on a surface. Herein we report that a trigonal molecule, dehydrobenzo[12]annulene (DBA) derivative having three tetradecyloxy chains and three hydroxy groups in an alternating manner, forms hierarchical triangular clusters of different sizes ranging from 2.4 to 16.4 nm, consisting of 3 to 78 molecules, respectively, at the liquid/graphite interface. The key is the dynamic combination of three different conformational states, which is solvent and concentration dependent. The present knowledge extends design strategies for production of sophisticated hierarchical SAMNs using a single component at the liquid/solid interface.

Self-sorting of multiple building blocks for correctly positioning molecules through orthogonal recognition is a promising strategy for construction of a hierarchical self-assembled molecular network (SAMN) on a surface.     

STM studies on adsorbed liquid crystal on HOPG

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Solvent effects on two-dimensional molecular self-assemblies investigated by using scanning tunneling microscopy

Self-assembly structures investigated by using scanning tunneling microscopy (STM) at liquid/solid interface have been a topic of broad interest in surface science, molecular materials, molecular electronics. The delicate balance among the adsorbate–solvent, adsorbate–adsorbate, solvent–solvent interactions would give rise to the coadsorption or competitive deposition of solvent with adsorbate. The solvents at the interface enable dynamic absorption and desorption of the adsorbates leading to the controlled assembly of the molecular architectures. The solvent-induced polymorphism, coadsorption effect, as well as solvent effects on chirality and electronic structures are discussed in this report in view of the polarity, solubility and viscosity of the solvent, the hydrogen bonding formation between solute and solvent, and the solvophobic and solvophilic effects. The systematic studies on the solvent effects would shed light on better control of assembly structures for design of new molecular materials and molecular electronics.     

Comparative study of the thermodynamics and kinetics of the ion transfer across the liquid/liquid interface by means of three-phase electrodes

A comparative study of the behavior of different sorts of three-phase electrodes applied for assessing the thermodynamics and kinetics of the ion transfer across the liquid/liquid (L/L) interface is presented. Two types of three-phase electrodes are compared, that is, a paraffin-impregnated graphite electrode at the surface of which a macroscopic droplet of an organic solvent is attached and an edge pyrolytic graphite electrode partly covered with a very thin film of the organic solvent. The organic solvent contains either decamethylferrocene or lutetium bis(tetra-tert-butylphthalocyaninato) as a redox probe. The role of the redox probe, the type of the electrode material, the mass transfer regime, and the effect of the uncompensated resistance are discussed. The overall electrochemical process at both three-phase electrodes proceeds as a coupled electron-ion transfer reaction. The ion transfer across the L/L interface, driven by the electrode reaction of the redox compound at the electrode/organic solvent interface, is independent of the type of redox probe. The ion transfer proceeds without involving any chemical coupling between the transferring ion and the redox probe. Both types of three-phase electrodes provide consistent results when applied for measuring the energy of the ion transfer. Under conditions of square-wave voltammetry, the coupled electron-ion transfer at the three-phase electrode is a quasireversible process, exhibiting the property known as "quasireversible maximum". The overall electron-ion transfer process at the three-phase electrode is controlled by the rate of the ion transfer. It is demonstrated for the first time that the three-phase electrode in combination with the quasireversible maximum is a new tool for assessing the kinetics of the ion transfer across the L/L interface.     

温控分子动力学研究微管蛋白活性肽链的折叠机制

运用温控和常温分子动力学方法, 研究了微管蛋白活性部位Pep1-28肽链的折叠机制, 总模拟时间为380.0 ns. 对于温控分子动力学, 逐渐降温可以清晰显示Pep1-28肽链的折叠途径, 发生明显折叠的温度约为550 K, 其折叠和去折叠可逆机制为U(>1200 K)←→I1(1200-1000 K)←→I2(800 K)←→I3(600 K)←→I4(450 K)←→F1(400 K)←→F2(300 K), 其中U为去折叠态构象, I1、I2、I3和I4是折叠过程中的四个重要的中间态构象, F1和F2是两个结构相近的折叠态构象. 对于常温(300 K)分子动力学, 其构象转变和折叠过程相当迅速, 很难观察到有效、稳定的中间态构象. 尤其引人注意的是, 其折叠态结构陷入了能量局域极小点, 与温控(300 K)的有较大差异, 两者能量差高达297.53 kJ·mol-1. 可见, 温控分子动力学方法不仅清晰地显示多肽和蛋白质折叠过程的重要中间态构象, 为折叠和去折叠机制提供直接、可靠的依据, 而且还有助于跨越较高的构象能垒, 促使多肽和蛋白质折叠以形成全局能量最低的稳定结构.     

Dynamics in physisorbed monolayers of 5-alkoxy-isophthalic acid derivatives at the liquid/solid interface investigated by scanning tunneling microscopy

Monolayers of isophthalic acid derivatives at the liquid/solid interface have been studied with scanning tunneling microscopy (STM). We have investigated the dynamics related to the phenomenon of solvent co-deposition, which was previously observed by our research group when using octan-1-ol or undecan-1-ol as solvents for 5-alkoxy-isophthalic acid derivatives. This solvent co-deposition has now been visualized in real-time (two frames per second) for the first time. Dynamics of individual molecules were investigated in mixtures of semi-fluorinated molecules with video-STM. The specific contrast arising from fluorine atoms in STM images allows us to use this functionality as a probe to analyze the data obtained for the mixtures under investigation. Upon imaging the same region of a monolayer for a period of time we observed that non-fluorinated molecules progressively substitute the fluorinated molecules. These findings illustrate the metastable equilibrium that exists at the liquid/solid interface, between the physisorbed molecules and the supernatant solution.     

液晶CPBOB吸附的STM研究

利用STM对吸附在导电基底上的液晶进行研究，能提供近原子分辨的液晶分子图象，这一创新不仅拓宽了STM的研究领域，也使STM成为研究液晶吸附的重要手段之一．根据液晶相变特征不同，样品的制备方法大致分四种情况：直接法，加热法，气相沉积法和溶剂法．无论采用以上哪种方法，     

Influence of functional groups on the self-assembly of liquid crystals

Functional groups in the molecule play an important role in the molecular o rganization process.To reveal the influence of functional groups on the self-assembly at interface,herein,the self-assembly structures of three liquid crystal molecules,which only differ in the functional groups,are explicitly characterized by using scanning tunneling microscopy(STM).The high-resolution STM images demonstrate the difference between the supramolecular assembly structures of three liquid crystal molecules,which attribute to the hydrogen bonding interaction and π-π stacking interaction between different functional groups.The density functional theory(DFT) results also confirm the influence of these functional groups on the self-assemblies.The effort on the self-assembly of liquid crystal molecules at interface could enhance the understanding of the supramolecular assembly mechanism and benefit the further application of liquid crystals.     

Concentration induced the interfacial self‐assembly polymorphism of 4, 4′‐dihexadecyloxy‐benzophenon by scanning tunneling microscopy

The concentration effect on a two‐dimensional (2D) self‐assembly of 4, 4′‐dihexadecyloxy‐benzophenon (DHB) has been investigated by scanning tunneling microscopy. The self‐assembly of DHB at the phenyloctane/graphite interface was concentration dependent. Under low concentration, the DHB molecules were adsorbed intactly on the graphite surface. With the increasing of concentration, one of side chains connecting the conjugated moiety stretched into the liquid phase. The coexistence of two self‐assembled structures was observed in a moderate concentration. The result indicated that the van der Waals interactions between the molecules and the graphite lattice were decreasing with the increasing concentration. After the samples were placed in ambient conditions over 24 h, a different self‐assembled structure was obtained on the gas/solid interface, in which the DHB molecules were adsorbed on the surface with only one of the side chains. Both the benzophenon core and the other side chain were extended to the gas phase. The results demonstrated that concentration played an important role in forming the 2D molecular self‐assembly and provided an efficient approach for the control of the DHB molecular nanostructure. Copyright © 2013 John Wiley & Sons, Ltd.     

Molecular dynamics simulation of the structure, dynamics, and thermostability of the RNA hairpins uCACGg and cUUCGg

Classical replica-exchange molecular dynamics simulations are performed to study structure, dynamics and thermostability of the 14-mer RNA hairpins uCACGg and cUUCGg. Despite of the different sequence and closing base pair of the two systems, recent NMR studies have shown that the tetraloop CACG is strikingly similar in overall geometry and hydrogen bonding to the canonical UUCG tetraloop. On the other hand, the two systems differ significantly in their functionality and thermostability. The simulations confirm the structural similarities of the two RNA hairpins at room temperature but also reveal that the UUCG loop is more flexible than the CACG loop. Concerning the functionality, the CACG loop shows a stronger attitude to donate hydrogens than the UUCG loop, although their global solvent accessible surface is quite similar. The simulations qualitatively reproduce the experimentally found difference in melting temperatures (20 K). In the case of the uCACGg hairpin, the thermal unfolding occurs cooperatively in an all-or-none fashion, while the cUUCGg hairpin shows less cooperativity but exhibits intermediate states during the unfolding process.     

Self-organized monolayer of meso-tetradodecylporphyrin coordinated to Au(111)

The structure of molecular monolayers formed at the interface between atomically flat surfaces and a solution of free-base meso-tetradodecylporphyrins (H2Ps) was examined by scanning tunneling microscopy (STM) at the liquid/solid interface. On the surface of graphite (HOPG), H2Ps form a well-ordered monolayer characterized by an oblique unit cell. On Au(111), H2Ps form a self-organized monolayer comprised of two distinct domain types. In both types of domains, the density of the porphyrin cores is increased in comparison to the arrangement observed on HOPG. Also, high-resolution STM images reveal that, in contrast to what is observed on HOPG, physisorption on Au(111) induces a distortion of the porphyrin macrocycle out of planarity. By using X-ray photoelectron spectroscopy, we demonstrate that this is likely to be due to the coordination of the lone pairs of the iminic (-C=N-) nitrogen atoms of the porphyrin macrocycle to Au(111).     

Chain polymerization of diacetylene compound multilayer films on the topmost surface initiated by a scanning tunneling microscope tip

Chain polymerizations of diacetylene compound multilayer films on graphite substrates were examined with a scanning tunneling microscope (STM) at the liquid/solid interface of the phenyloctane solution. The first layer grew very quickly into many small domains. This was followed by the slow formation of the piled up layers into much larger domains. Chain polymerization on the topmost surface layer could be initiated by applying a pulsed voltage between the STM tip and the substrate, usually producing a long polymer of submicrometer length. In contrast, polymerizations on the underlying layer were never observed. This can be explained by a conformation model in which the polymer backbone is lifted up.     

Self-assembly of a catechol-based macrocycle at the liquid-solid interface: experiments and molecular dynamics simulations

This combined experimental (STM, XPS) and molecular dynamics simulation study highlights the complex and subtle interplay of solvent effects and surface interactions on the 2-D self-assembly pattern of a Schiff-base macrocycle containing catechol moieties at the liquid-solid interface. STM imaging reveals a hexagonal ordering of the macrocycles at the n-tetradecane/Au(111) interface, compatible with a desorption of the lateral chains of the macrocycle. Interestingly, all the triangular-shaped macrocycles are oriented in the same direction, avoiding a close-packed structure. XPS experiments indicate the presence of a strong macrocycle-surface interaction. Also, MD simulations reveal substantial solvent effects. In particular, we find that co-adsorption of solvent molecules with the macrocycles induces desorption of lateral chains, and the solvent molecules act as spacers stabilizing the open self-assembly pattern.     

Spectroscopic and microscopic investigations of organic ultrathin films: Correlation between geometrical structures and unoccupied electronic states

In this review, we summarize recent progress in experimental approaches to the investigation of the unoccupied electronic structures of organic ultrathin films, based on a combination of spectroscopic and microscopic techniques. At the molecule/substrate interface, electronic structures are greatly affected by the geometrical structures of adsorbed molecules. In addition, a delicate balance between substrate-molecule and intermolecular interactions plays an important role in the formation of complex polymorphism. In this context, we have clarified the correlation between geometric and electronic structures using a combination of two-photon photoemission (2PPE) spectroscopy, low energy electron diffraction (LEED) and scanning tunneling microscopy (STM). Organic ultrathin films of metal phthalocyanines and polycyclic aromatic hydrocarbons (naphthalene, rubrene and perylene) on graphite substrates were examined as model systems. Depending on the substrate temperature and coverage, unique morphologies, including well-ordered films, a metastable phase and a two-dimensional gas-like phase, were determined at the molecular level. The data show that variations in molecular orientation have a significant impact on the occupied/unoccupied electronic structures. In addition to static information regarding electronic states, ultrafast electron excitation and relaxation dynamics can be tracked in real time on the femtosecond scale by time-resolved 2PPE spectroscopy. The excited electron dynamics of rubrene films are discussed herein, taking into account structural information, in the presence and absence of an overlap of the wave function with the substrate. Spatial resolution at the molecular level is also obtainable via STM-based local spectroscopy and mapping, which have been utilized to elucidate the spatial extent of unoccupied orbitals in real space. Visible photon emissions from the unoccupied states of perylene monolayer films were observed using 2PPE, representing a characteristic deexcitation process from electronically excited states, depending on the surface structure. These spectroscopic and molecular level microscopic investigations provide fundamental insights into the electronic properties of organic/substrate interfaces.