Single Molecular Systems Research Articles

A Scanning Tunneling Microscopy Study of the Photoisomerization of Diazocine.

Azobenzenes are fascinating molecular machines that can reversibly transform between two isomeric forms by an external stimulus. Diazocine, a type of bridged azobenzene, has been shown to possess enhanced photoexcitation properties. Due to the distortion caused by the ethyl bridge in the E-isomer, the Z-form becomes the thermodynamically stable configuration. Despite a comprehensive understanding of its photophysical properties, there is still much to learn about the behavior of diazocine on a metal surface. Here we show the operando photoswitching of diazocine molecules deposited directly on a Au(111) surface using scanning tunneling microscopy. Molecules were shown to aggregate into disordered islands with edge sites being susceptible to photon-induced movement. A few molecules were shown to undergo directional movement under UV irradiation with the motion reversed under blue light exposure. These findings contribute new insight into the activity of single and ensemble molecular systems toward purposefully guided motion.

Walking with the Atoms in a Chemical Bond: A Perspective Using Quantum Phase Transition.

Phase transitions happen at critical values of the controlling parameters, such as the critical temperature in classical phase transitions, and system critical parameters in the quantum case. However, true criticality happens only at the thermodynamic limit, when the number of particles goes to infinity with constant density. To perform the calculations for the critical parameters, a finite-size scaling approach was developed to extrapolate information from a finite system to the thermodynamic limit. With the advancement in the experimental and theoretical work in the field of ultra-cold systems, particularly trapping and controlling single atomic and molecular systems, one can ask: do finite systems exhibit quantum phase transition? To address this question, finite-size scaling for finite systems was developed to calculate the quantum critical parameters. The recent observation of a quantum phase transition in a single trapped 171 Yb+ ion indicates the possibility of quantum phase transitions in finite systems. This perspective focuses on examining chemical processes at ultra-cold temperatures, as quantum phase transitions-particularly the formation and dissociation of chemical bonds-are the basic processes for understanding the whole of chemistry.

Development of Thixotropic Molecular Oleogels Comprising Alkylanilide Gelators by Using a Mixing Strategy.

Molecular oleogels have the potential to be used as materials in healthcare applications. However, their design and synthesis are complex, thus requiring simple and effective methods for their preparation. This paper reports on alkylanilides that are low molecular-weight organogelators, which when appropriately mixed with different alkyl chain lengths could result in the formation of mixed molecular gels that exhibit excellent gel-forming ability and mechanical properties. In addition, the single and mixed molecular organogel systems were found to be applicable as single and mixed molecular oleogel systems capable of gelling oils such as olive oil and squalane. This has been found to be true, especially in molecular oleogel systems consisting of squalane, which is used as solvents in healthcare. The mixed squalene-molecular oleogel systems showed an increase in the critical (minimum) gelation concentration from 1.0 to 0.1 wt.% in the single system and an improvement in the thixotropic behavior recovery time. The thixotropic behavior of the molecular oleogels in the mixed system was quantitatively evaluated through dynamic viscoelasticity measurements; however, it was not observed for the single-system molecular oleogels. Scanning electron microscopy of the xerogels suggested that this behavior is related to the qualitative improvement of the network owing to the refinement of the mesh structure. These mixed molecular oleogels, composed of alkylanilides displaying such thixotropic behavior, could be used as candidates for ointment-base materials in the healthcare field.

Full‐Color Luminescence from Single‐Component Hydrocarbon Crystal: RGB Emission by Altering Molecular Packing Under Pressure

AbstractFull‐color emission from solid single‐component organic materials is highly desired to realize inexpensive and non‐toxic organic electronics. However, as the three primary colors, red, green, and blue (RGB), have significantly different energies, observation of RGB luminescence from a single‐component molecule is extremely challenging. In this study, a coronene nanorod single‐component single‐crystal is prepared, which exhibits blue fluorescence at ambient conditions and realizes full‐color emission, for the first time, by altering the molecular packing through high‐pressure compression. A valuable insight into the relationships between structure and optical properties of coronene at high pressures is obtained by combining various spectroscopic studies. During compression, it is found that the tuneable piezochromic luminescence of coronene is strictly related to the molecular packing and crystallographic symmetry. This study not only provides insight into the structure‐optical property relationships of hydrocarbon but also promotes the development of single molecular systems with different molecular packing that exhibit RGB emissions even at ambient conditions even with a single excitation wavelength.

Tuneable tetrel bonds between tin and heavy pnictogens.

The first example of a binary cocrystal, comprised of SnPh3Cl and PPh3, whose components are organized via short and directional tetrel bonds (TtB) between tin and phosphorus, is described. DFT elucidates, for the first time, the factors influencing the strength of TtBs involving heavy pnictogens. A CSD survey reveals that such TtBs are also present and determinative in single component molecular systems, highlighting their significant potential as tuneable structure-directing elements.

Advances in detection and regulation of surface-supported molecular quantum states

Single molecular systems are typical quantum confinement systems, which have rich electronic states, photon states and spin states due to their discrete energy levels, localized orbitals and diverse chemical structures. The states determined by quantum mechanics in these molecular systems make it possible to serve as great physical entities for future quantum information technology. The detection and manipulation of quantum states on a single molecule scale are beneficial to the bottom-up construction of quantum devices. Owing to the highly limited spatial localization of single molecular systems, it is difficult to accurately address and manipulate them with conventional macroscopic characterization methods. Scanning tunneling microscope (STM) is such a powerful tool that it can achieve high-resolution real-space imaging as well as spectroscopic investigation, with the ability to <i>in-situ</i> manipulating the individual atoms or molecules. It can also work jointly with various near-field or external field characterization techniques, making it a most important technique for precisely detecting and manipulating quantum properties at a single molecule level. In this paper, we review recent research progress of quantum states of surface-supported single molecules and relevant structures based on scanning tunneling microscopy. We start from the methods for the synthesis of molecular structures with desired quantum states, and then we review the recent advances in the local spin states for single molecular systems and the optical properties of single molecules serving as a single-photon source. An emerging family of molecular nanographene systems showing intriguing topological properties and magnetic properties is also reviewed. In the last part, we summarize the research progress made recently and prospect the future development of the quantum states at a single molecular level.

Effect of protonation on the photophysical properties of 4-substituted and 4,7-disubstituted quinazoline push-pull chromophores

White-light emission from single molecular systems has attracted a great deal of attention due to their advantages over multicomponent emitters. Azaheterocyclic push-pull derivatives have been demonstrated to be white emitters by combining neutral and protonated forms in the appropriate ratio, although limited cases of white-light emission have been reported from quinazoline derivatives. Herein, we describe a series of push-pull 4-substituted and 4,7-disubstituted quinazolines that show white photoluminescence both in solution and in the solid state. All of the materials were prepared by straightforward Suzuki–Miyaura cross-coupling reactions and the compounds exhibited remarkable emission solvatochromism. In some cases the presence of acid prompted the appearance of emission bands of complementary colors. Thus, multicolor photoluminescence, including white light, could be finely tuned by the controlled protonation of the electron-deficient quinazoline ring.

Entropy Production beyond the Thermodynamic Limit from Single-Molecule Stretching Simulations.

Single-molecular systems are a test bed to analyze to what extent thermodynamics applies when the size of the system is drastically reduced. Isometric and isotensional single-molecule stretching experiments and their theoretical interpretations have shown the lack of a thermodynamic limit at those scales and the nonequivalence between their corresponding statistical ensembles. This disparity between thermodynamic results obtained in both experimental protocols can also be observed in entropy production, as previous theoretical results have shown. In this work, we present results from molecular dynamics simulations of stretching of a typical polymer, polyethylene-oxide, where this framework is applied to obtain friction coefficients associated with stretching at the two different statistical ensembles for two different system sizes, from which the entropy production follows. In the smallest system, they are different up to a factor of 2, and for the bigger system, the difference is smaller, as predicted. In this way, we provide numerical evidence that a thermodynamic description is still meaningful for the case of single-molecule stretching.

MCDCalc: Markov Chain Molecular Descriptors Calculator for Medicinal Chemistry.

Cheminformatics models are able to predict different outputs (activity, property, chemical reactivity) in single molecules or complex molecular systems (catalyzed organic synthesis, metabolic reactions, nanoparticles, etc.). Cheminformatics models are able to predict different outputs (activity, property, chemical reactivity) in single molecules or complex molecular systems (catalyzed organic synthesis, metabolic reactions, nanoparticles, etc.). Cheminformatics prediction of complex catalytic enantioselective reactions is a major goal in organic synthesis research and chemical industry. Markov Chain Molecular Descriptors (MCDs) have been largely used to solve Cheminformatics problems. There are different types of Markov chain descriptors such as Markov-Shannon entropies (Shk), Markov Means (Mk), Markov Moments (πk), etc. However, there are other possible MCDs that have not been used before. In addition, the calculation of MCDs is done very often using specific software not always available for general users and there is not an R library public available for the calculation of MCDs. This fact, limits the availability of MCMDbased Cheminformatics procedures. We studied the enantiomeric excess ee(%)[Rcat] for 324 α-amidoalkylation reactions. These reactions have a complex mechanism depending on various factors. The model includes MCDs of the substrate, solvent, chiral catalyst, product along with values of time of reaction, temperature, load of catalyst, etc. We tested several Machine Learning regression algorithms. The Random Forest regression model has R2 > 0.90 in training and test. Secondly, the biological activity of 5644 compounds against colorectal cancer was studied. We developed very interesting model able to predict with Specificity and Sensitivity 70-82% the cases of preclinical assays in both training and validation series. The work shows the potential of the new tool for computational studies in organic and medicinal chemistry.

DFT Investigations of the Magnetic Properties of Actinide Complexes

Over the past 25 years, magnetic actinide complexes have been the object of considerable attention, not only at the experimental level, but also at the theoretical one. Such systems are of great interest, owing to the well-known larger spin–orbit coupling for actinide ions, and could exhibit slow relaxation of the magnetization, arising from a large anisotropy barrier, and magnetic hysteresis of purely molecular origin below a given blocking temperature. Furthermore, more diffuse 5f orbitals than lanthanide 4f ones (more covalency) could lead to stronger magnetic super-exchange. On the other hand, the extraordinary experimental challenges of actinide complexes chemistry, because of their rarity and toxicity, afford computational chemistry a particularly valuable role. However, for such a purpose, the use of a multiconfigurational post-Hartree-Fock approach is required, but such an approach is computationally demanding for polymetallic systems—notably for actinide ones—and usually simplified models are considered instead of the actual systems. Thus, Density Functional Theory (DFT) appears as an alternative tool to compute magnetic exchange coupling and to explore the electronic structure and magnetic properties of actinide-containing molecules, especially when the considered systems are very large. In this paper, relevant achievements regarding DFT investigations of the magnetic properties of actinide complexes are surveyed, with particular emphasis on some representative examples that illustrate the subject, including actinides in Single Molecular Magnets (SMMs) and systems featuring metal-metal super-exchange coupling interactions. Examples are drawn from studies that are either entirely computational or are combined experimental/computational investigations in which the latter play a significant role.

Effect of end group of amorphous perfluoro-polymer electrets on electron trapping

Charge trap in amorphous perfluoro-polymer electret is studied, focusing on electron trap site and trap energy. Low-energy inverse photoelectron spectroscopy is adopted to measure solid-state electron affinity (EA) of cyclic transparent optical polymer (CYTOP). EA of CYTOP CTL-S is discovered by compensating the unwanted charge-up effect. Negatively-charged electret materials (polyethylene, ethylene-tetra-fluoro-ethylene, poly-tetra-fluoro-ethylene, and CYTOP) are analyzed by quantum mechanical calculation. Density functional theory with long-range correction is adopted to analyze orbital energies of single molecular systems. Intramolecular distribution of trapped electron and EA are investigated. Calculated electron affinities of CYTOP polymers with different end group are qualitatively in accordance with trapped charge stability measured with thermal stimulated discharge, signifying that electron affinities obtained with the present simulation can be used as an index of amorphous polymer electret.

Growth of II-VI/III-V heterovalent quantum structures

Lattice-matched heterovalent II-VI/III-V semiconductor structures, such as quantum wells and double heterostructures consisting of ZnSe/GaAs and ZnTe/GaSb, are grown using single and dual-chamber molecular beam epitaxy systems by utilizing migration-enhanced epitaxy and a substrate temperature ramp method. Specific elemental overpressures are utilized after each epilayer growth to control the surface termination and to prevent defective III-VI compounds from forming at the heterovalent interfaces. Characterization using x-ray diffraction and transmission electron microscopy confirms sharp interfaces and coherent bonding between the heterovalent materials. Photoluminescence measurements show optical transitions from the heterovalent double heterostructures and quantum wells, as well as evidence for midgap defect states in the III-V layers. The III-V layers have a very low density of structural defects, but some stacking faults are observed in the II-VI layers.

Understanding the non-covalent interaction mediated modulations on the electronic structure of quasi-zero-dimensional graphene nanoflakes.

In recent years, magnetic or electric field induced modulations on the electronic environment of single molecular systems are common practice. In this particular study, we have instigated the possibility of controlling the electronic and spin-dependent properties of hydrogen-terminated graphene fragments, so-called graphene nanoflakes (GNF), using weak non-covalent interactions as the external stimuli. The topological frustration in the graphene fragment appreciated the compelling electronic behavior of the system. This leads to some unorthodox spin-distribution in the system and it is possible to synchronize this electronic perturbation switching through a non-covalent interaction. These findings institute a new avenue for sculpting such donor-acceptor composites as self-regulated spintronic devices in next generation electronics.

Effects of Tailored Dispersity on the Self-Assembly of Dimethylsiloxane–Methyl Methacrylate Block Co-Oligomers

The effect of dispersity on block polymer self-assembly was studied in the monodisperse limit using a combination of synthetic chemistry, matrix-assisted laser desorption ionization spectroscopy, and small-angle X-ray scattering. Oligo(methyl methacrylate) (oligoMMA) and oligo(dimethylsiloxane) (oligoDMS) homopolymers were synthesized by conventional polymerization techniques and purified to generate an array of discrete, semidiscrete, and disperse building blocks. Coupling reactions afforded oligo(DMS-MMA) block polymers with precisely tailored molar mass distributions spanning single molecular systems (Đ = 1.0) to low-dispersity mixtures (Đ ≈ 1.05). Discrete materials exhibit a pronounced decrease in domain spacing and sharper scattering reflections relative to disperse analogues. The order-disorder transition temperature (TODT) also decreases with increasing dispersity, suggesting stabilization of the disordered phase, presumably due to the strengthening of composition fluctuations at the low molar masses investigated.

Molecular photoelectron interference effects by intense circularly polarized attosecond x-ray pulses

We present photoelectron interference effects in molecular photoionization by intense circularly polarized attosecond X-ray laser pulses. Simulations are performed on single electron molecular systems, H\(_{2}^{+}\), HeH2+, and H\(_{3}^{2+}\), by numerically solving the corresponding three-dimensional time dependent Schrodinger equations. Photoelectron spectra show that both momentum ring and stripe patterns are obtained, arising respectively from the interference of the direct ionized and scattered electron wave packets. Multi-center electron interference models in molecular ultrafast photoionization are used to describe the ionized electron dynamics. The interference patterns are shown to be dependent on molecular orbital symmetry, thus offering tools for attosecond imaging molecular structure at different molecular geometries.

Efficient White‐Light Generation from Ionically Self‐Assembled Triply‐Fluorescent Organic Nanoparticles

Low cost, simple, and environmentally friendly strategies for white-light generation which do not require rare-earth phosphors or other toxic or elementally scare species remain an essentially unmet challenge. Progress in the area of all-organic approaches is highly sought, single molecular systems remaining a particular challenge. Taking inspiration from the designer nature of ionic-liquid chemistry, we now introduce a new strategy toward white-light emission based on the facile generation of nanoparticles comprising three different fluorophores assembled in a well-defined stoichiometry purely through electrostatic interactions. The building blocks consist of the fluorophores aminopyrene, fluorescein, and rhodamine 6G which represent blue, green, and red-emitting species, respectively. Spherical nanoparticles 16(±5) nm in size were prepared which display bright white-light emission with high fluorescence quantum efficiency (26 %) and color coordinate at (0.29, 0.38) which lie in close proximity to pure white light (0.33, 0.33). It is noteworthy that this same fluorophore mixture in free solution yields only blue emission. Density functional theory calculations reveal H-bond and ground-state proton transfer mediated absolute non-parallel orientation of the constituent units which result in frustrated energy transfer, giving rise to emission from the individual centers and concomitant white-light emission.

Defocused Emission Patterns from Chiral Fluorophores: Application to Chiral Axis Orientation Determination

Experimental defocused fluorescence emission patterns from single chiral molecular systems are compared to semiclassical simulations as a means for a priori determination of chiral axis orientation in single-molecule systems. Using a coupled-oscillator model as a radiation source, we show that the basic features of defocused emission patterns from chiral fluorophores can be recovered and suggests the feasibility of chiral axis orientation determination (within some limits) in single-molecule systems.

The experimental determination of the conductance of single molecules

The measurement of the electrical properties of molecules, down to the single molecule level, has become an experimental reality in recent years. A number of methods are now available for experimentally achieving this feat. The common aim of these methods is to entrap a single or small numbers of molecules between a pair of metallic contacts. This topical review focuses on describing and comparing experimental methods for entrapping and measuring the electrical properties of single molecules in metallic contact gaps. After describing the methods, reasons are tendered for apparent discrepancies in the literature between measured single molecule conductance values, with a focus on the most widely studied alkanedithiol system. Illustrative examples are then presented of the determination of the electrical properties of a range of single molecular systems, in order to highlight the progress which has been made in recent years.

New Single Molecular Detection System from Three-Dimensional Tracking of Single Nanocrystals using Scanning Electron Microscope

Recent technological progress in dynamical observations of individual functional single protein molecules in living cell has been achieved with several single molecular techniques and systems. In order to improve monitoring precisions and stability of the signal intensity from single molecular units under physiological conditions, we have proposed that single molecular techniques using shorten wavelength, for example, X-rays, electrons, neutron, and other accelerated ion probes. In this work, we demonstrate three-dimensional tracking of single nanocrystals using Scanning Electron Microscope. We called Diffracted Electron Tracking (DET).Diffracted X-Ray tracking (DXT) [1] has been developed for obtaining the information about the dynamics of single molecules. This method can observe the rotating motion of an individual nanocrystal, which is linked to specific sites in single protein molecules, using a time-resolved Laue diffraction technique. This method needs a very strong X-ray source, such as the SPring-8, so we began to develop a compact instrument for monitoring the rotation of the single protein molecules, using the electron beam instead of the X-ray.Instead of the Laue diffraction using white X-ray, the Electron Back-Scattered Diffraction Pattern (EBSP) is adopted to monitor the crystal orientation of the nano-crystals linked to the single protein molecules. For this purpose, it is necessary to realize (1) wet cell with very thin sealing film, (2) EBSP system with high sensitivity, (3) damage-less electron irradiation technique and (4) perfect gold nano-crystals.[1] H. Shimizu, M. Iwamoto, F. Inoue, T. Konno, Y.C. Sasaki, S. Oiki: Cell 132, 67-78 (2008).[2] T.Sagawa, T.Azuma, Y. C. Sasaki, Biochem. Biophy. Res. Commun. 335, 770-775 (2007).

Semi Empirical Approach to the Charge Transport Characteristics of Molecular Junctions

The idea of using molecules and molecular structures as functional electronic device, promises to substantially decrease the size and improve the performance of electronic devices. In this paper, nonequilibrium Green's function formalism (NEGF) combined with extended Huckel theory (EHT), a semiempirical approach is used to study the electron transport phenomenon in single molecular junction systems. Benzene diamine molecule is studied to investigate the bonding of amine group to gold electrodes and the electron transport across the junction. The results are compared with that of benzene dithiol molecule with thiol end groups. Furthermore, the influence of charging and torsion angle on the transport characteristics is emphasized.