Single Guest Molecules Research Articles

Imaging of Single Molecular Behaviors Under Bifurcated Three-Centered Hydrogen Bonding.

The mechanism for interaction and bonding of single guest molecules with active sites fundamentally determines the sorption and subsequent catalytic processes occurring in host zeolitic frameworks. However, no real-space studies on these significant issues have been reported thus far, since atomically visualizing guest molecules and recognizing single Al T-sites in zeolites remain challenging. Here, we atomically resolved single thiophene probes interacting with acid T-sites in the ZSM-5 framework to study the bonding behaviors between them. The synergy of bifurcated three-centered hydrogen bonds and van der Waals interactions can "freeze" the near-horizontal thiophene and make it stable enough to be imaged. By combining the imaging results with simulations, direct atomic observations enabled us to precisely locate the single Al T-sites in individual straight channels. Then, we statistically found that the thiophene bonding probability of the T11 site is 15 times higher than that of the T6 site. For different acid T-sites, the variation in the interaction synergy changes the inner angle of the host-guest O-H···S hydrogen bond, thereby affecting the stability of the near-horizontal thiophene and leading to considerable bonding inhomogeneities.

Imaging of Single Molecular Behaviors Under Bifurcated Three‐Centered Hydrogen Bonding

AbstractThe mechanism for interaction and bonding of single guest molecules with active sites fundamentally determines the sorption and subsequent catalytic processes occurring in host zeolitic frameworks. However, no real‐space studies on these significant issues have been reported thus far, since atomically visualizing guest molecules and recognizing single Al T‐sites in zeolites remain challenging. Here, we atomically resolved single thiophene probes interacting with acid T‐sites in the ZSM‐5 framework to study the bonding behaviors between them. The synergy of bifurcated three‐centered hydrogen bonds and van der Waals interactions can “freeze” the near‐horizontal thiophene and make it stable enough to be imaged. By combining the imaging results with simulations, direct atomic observations enabled us to precisely locate the single Al T‐sites in individual straight channels. Then, we statistically found that the thiophene bonding probability of the T11 site is 15 times higher than that of the T6 site. For different acid T‐sites, the variation in the interaction synergy changes the inner angle of the host–guest O−H⋅⋅⋅S hydrogen bond, thereby affecting the stability of the near‐horizontal thiophene and leading to considerable bonding inhomogeneities.

Spatial distribution of single guest molecules along thickness of thin films of poly(2-hydroxyethyl acrylate).

We have investigated three-dimensional distribution and diffusion behaviors of single guest dyes in 1-µm thick films of poly(2-hydroxyethyl acrylate) (PHEA) by using astigmatism imaging method. Perylene diimide derivative (BP-PDI) in the PHEA films localized along the Z-axis at ca. Z = 600-700nm distant from the interface (Z = 0) between PHEA and glass substrate. This Z-localization was not observed in different polymer films of poly(methyl methacrylate) (PMMA), poly(methyl acrylate) (PMA), and polystyrene (PSt). Because the glass transition temperature of the PHEA is lower than the room temperature, BP-PDI in the PHEA films exhibited Brownian motion, normal diffusion on the XY plane and confined motion along the Z-direction. For elucidating the mechanism of the peculiar localization of the guest dyes along film thickness in the PHEA films, we measured diffusion behaviors of different dyes, R6G and Atto 488, in 1-µm thick PHEA films, obtaining result that the Z-distributions of the dyes were overall similar to that of BP-PDI. The result indicates that the Z-localization of the guest dyes should be ascribed not to the interaction between glass surface and guest dye but mainly to the Z-dependent property of the PHEA film. Indeed, the lateral diffusion coefficients of the guest dyes depended on their Z-positions.

Rotation in an Enantiospecific Self-Assembled Array of Molecular Raffle Wheels.

Tailored nano‐spaces can control enantioselective adsorption and molecular motion. We report on the spontaneous assembly of a dynamic system—a rigid kagome network with each pore occupied by a guest molecule—employing solely 2,6‐bis(1H‐pyrazol‐1‐yl)pyridine‐4‐carboxylic acid on Ag(111). The network cavity snugly hosts the chemically modified guest, bestows enantiomorphic adsorption and allows selective rotational motions. Temperature‐dependent scanning tunnelling microscopy studies revealed distinct anchoring orientations of the guest unit switching with a 0.95 eV thermal barrier. H‐bonding between the guest and the host transiently stabilises the rotating guest, as the flapper on a raffle wheel. Density functional theory investigations unravel the detailed molecular pirouette of the guest and how the energy landscape is determined by H‐bond formation and breakage. The origin of the guest's enantiodirected, dynamic anchoring lies in the specific interplay of the kagome network and the silver surface.

On the synergy of matrix-isolation infrared spectroscopy and vibrational configuration interaction computations

The key feature of matrix-isolation infrared (MI-IR) spectroscopy is the isolation of single guest molecules in a host system at cryogenic conditions. The matrix mostly hinders rotation of the guest molecule, providing access to pure vibrational features. Vibrational self-consistent field (VSCF) and configuration interaction computations (VCI) on ab initio multimode potential energy surfaces (PES) give rise to anharmonic vibrational spectra. In a single-sourced combination of these experimental and computational approaches, we have established an iterative spectroscopic characterization procedure. The present article reviews the scope of this procedure by highlighting the strengths and limitations based on the examples of water, carbon dioxide, methane, methanol, and fluoroethane. An assessment of setups for the construction of the multimode PES on the example of methanol demonstrates that CCSD(T)-F12 level of theory is preferable to compute (a) accurate vibrational frequencies and (b) equilibrium or vibrationally averaged structural parameters. Our procedure has allowed us to uniquely assign unknown or disputed bands and enabled us to clarify problematic spectral regions that are crowded with combination bands and overtones. Besides spectroscopic assignment, the excellent agreement between theory and experiment paves the way to tackle questions of rather fundamental nature as to whether or not matrix effects are systematic, and it shows the limits of conventional notations used by spectroscopists.

Structural and vibrational properties of agrellite

Agrellite, NaCa2Si4O10F, is a tubular silicate mineral which crystal structure is characterized by extended [Si8O20]8– tubes and has a two-dimensional channel system. The mineral is a representative of a complex silicate family which contains some structural voids but cannot be considered as microporous because of small channel widths. However, the channel system of such minerals is able to host single guest atoms, molecules or radicals which can affect their physical properties. Presently, the exact mechanism of such hosting is undetermined. However, such information could be quite useful for materials’ application as zeolites as well as for a better understanding of their formation mechanisms. In this work we couple X-ray diffraction, infrared (IR) spectroscopy and ab initio calculations to identify structural features in agrellite from Malyy Murun massif (Russia) caused by incorporation of either H2O or OH− into the channel system. We construct structural models of water-containing NaCa2Si4O10F and identified H2O positions. The derivation of H2O sites is based on simulation of IR-spectra. Infrared spectroscopy in combination with the ab initio calculation has proven to be an effective tool for the identification of the structural positions of hydroxyl anions (OH−) and neutral water groups (H2O) in minerals.

Hydrate thermal dissociation behavior and dissociation enthalpies in methane-carbon dioxide swapping process

The swapping of methane with carbon dioxide in hydrate has been proposed as a potential strategy for geologic sequestration of carbon dioxide and production of methane from natural hydrate deposits. However, this strategy requires a better understanding of the thermodynamic characteristics of CH4 and CO2 hydrate as well as (CH4+CO2) or (CH4+CO2+N2) mixed hydrates (since (CO2+N2) gas mixture is often used as the swapping gas), along with the thermal physics property changes during gas exchange. In this study, a high pressure micro-differential scanning calorimetry (HP μ-DSC) was performed on synthesized gas hydrates to investigate the dissociation behavior of various hydrates. The hydrate dissociation enthalpies were determined by both μ-DSC measurement and Clapeyron equation. For the single guest molecule hydrate system, the average dissociation enthalpies of CH4 hydrate and CO2 hydrate measured by integrating the endothermic peak area are 55.01kJ·mol−1 and 58.96kJ·mol−1, respectively, which are very close to the values calculated by Clapeyron equation. However, in the multicomponent guest hydrates system, the μ-DSC measured dissociation enthalpies of the (CH4+CO2) binary hydrates and (CH4+CO2+N2) ternary hydrates are a little higher than that of Clapeyron equation, it was found that their dissociation enthalpies are located between the limiting values of pure CH4 hydrate and CO2 hydrate, increasing with the mole fraction of CO2 in hydrate phase. By monitoring the heat flow changes with the μ-DSC apparatus, it was observed that there was no noticeable dissociation or reformation process of hydrate occurring in the CH4−CO2/(CO2+N2) swapping, which indicates that most CH4 hydrate forms (CH4+CO2) or (CH4+CO2+N2) mixed hydrates directly instead of dissociating into liquid water or ice first. The dissociation equilibrium data obtained from the endothermic thermograms of the mixed hydrates after CO2 and (CO2+N2) swapping demonstrates that about 66% and 85% of CH4 in hydrate phase are replaced, respectively.

Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions

The self-organizational properties of DNA have been used to realize synthetic hosts for protein encapsulation. However, current strategies of DNA–protein conjugation still limit true emulation of natural host–guest systems, whose formation relies on non-covalent bonds between geometrically matching interfaces. Here we report one of the largest DNA–protein complexes of semisynthetic origin held in place exclusively by spatially defined supramolecular interactions. Our approach is based on the decoration of the inner surface of a DNA origami hollow structure with multiple ligands converging to their corresponding binding sites on the protein surface with programmable symmetry and range-of-action. Our results demonstrate specific host–guest recognition in a 1:1 stoichiometry and selectivity for the guest whose size guarantees sufficient molecular diffusion preserving short intermolecular distances. DNA nanocontainers can be thus rationally designed to trap single guest molecules in their native form, mimicking natural strategies of molecular recognition and anticipating a new method of protein caging.

Significance of Jobs Plot in Cyclodextrin Complexation

Jobs plot or continuous variation method is used to estimate the stoichiometry in cyclodextrin complexation. Cyclodextrin complexation is well known as widely acceptable technique for improving the poor physicchemical properties of BCS class II and class IV drugs. The stoichiometry of the inclusion complex is given by the number of guest and host molecules present in the supramolecular complex/inclusion system. The most common stoichiometry is 1: 1, implying the inclusion of a single guest molecule. Now-a-days jobs plot is replaced by phase-solubility study. Jobs plot deals with spectral methods mainly for molecular modelling study of drugs and bioactives.

Fluorescence Behavior of Single Guest Molecules in Nonpolar Oil Droplets Covered with Stabilizing Surfactants

By using confocal and wide-field microscopic techniques we have investigated fluorescence behaviors of a single perylenediimide derivative, N,N′-dipropyl-1,6,7,12-tetrakis(4-tert-butylphenoxy)-3,4,9,10-perylenetetracarboxydiimide (BP-PDI), in ca. 200–300 nm sized droplets of n-octane covered with surfactant molecules. The guest dye did not show distinguishable blinking in the droplets prepared with a nonionic surfactant, Triton X-100, while frequent blinking was observed in the droplets with a cationic surfactant, trimethylstearylammonium chloride (STAC). The survival time of the guest dye before the permanent photodegradation was much longer in the droplets with Triton X-100 than those with STAC. On the basis of the analysis with a model assuming the transition from the S1 state to the dark state (DS) and the permanent photodegradation during the dark state, it was deduced that the probability of the transition from the S1 state to the DS in the droplet with STAC, 7.2 × 10–6, was significantly larger than that with Triton X-100, 1.1 × 10–6. On the other hand, the probability of the photodegradation during the dark state was comparable between these two systems. These results indicate that the probability of transition from the S1 state to the DS essentially dominates the survival time of the guest dyes. Fluorescence polarization measurements also revealed that guest dyes frequently stay in the vicinity of polar interface in the droplets prepared with STAC.

Formation kinetics & phase stability of double hydrates of C4H8O and CO2/CH4: A comparison with pure systems

Gas hydrate based technology plays a key role in capturing carbon dioxide (CO2) or methane (CH4) gas molecules from its source locations. The parameters like hydrate phase stability, formation kinetics and gas uptake capacity (hydrate yield) are measured for carbon dioxide (CO2) and methane (CH4) at different initial gas pressures. The behaviour is also compared with double hydrates, prepared using 6 mol% of tetrahydrofuran (C4H8O -THF) aqueous solution. Measured thermodynamic phase boundary points for the hydrates with single guest molecules (CO2 or CH4) concur with the literature data. However, the phase stability of double hydrates with THF + CO2/CH4 appeared to be controlled by the stability of THF hydrates. Hydrate formation kinetics is faster in double hydrates than corresponding pure hydrates. Further, the yields in double hydrates with CH4 guest molecule show increasing trends with the gas pressure, whereas, it remains unchanged in double hydrates with CO2 guest molecule beyond some gas pressure. This is attributed to the occupancy of vacant cages by the gas molecules.

Fluorescence detection of single guest molecules in ultrasmall droplets of nonpolar solvent

We have investigated emissive behaviours of individual perylenebisimide derivatives, N,N'-dipropyl-1,6,7,12-tetrakis(4-tert-butylphenoxy)-3,4,9,10-perylenetetra-carboxydiimide (BP-PDI), in single ultrasmall droplets of n-octane at room temperature by using confocal and wide-field microscopic techniques. Single BP-PDIs in the small droplets show no distinguishable blinking in the time courses of fluorescence intensity. This is attributed to small probabilities of the formation of the long-lived ionized state leading to the off-state of the fluorescence. Temporal change in the degree of polarization of fluorescence and wide-field fluorescence images indicated short-time adsorption of the fluorescent molecules at the interfaces between n-octane and watery environments. Fluorescence correlation spectroscopy revealed that the adsorption/desorption processes took place at least in two different time scales, probably due to the difference in the adsorption geometry and/or in the interaction, such as van der Waals interaction and hydrogen bonding, between the dye and the interface.

Super-Poissonian statistics of on-off jumps in blinking fluorescence of single molecules

Blinking fluorescence of a single guest molecule embedded in a polymer matrix and excited by cw laser light is considered. Such fluorescence exhibits quantum jumps from bright on-intervals to dark off-intervals, i.e., so-called on-->off jumps. A system with one type of on-intervals and with two types of off-intervals is studied. A distribution function w(N)(T) for the number N of on-->off jumps in a time interval T is derived. The distribution function is expressed via a threefold integral of three Poissonian functions, each of which relates to the corresponding exponential process in the quantum dynamics of a fluorescent impurity center. Numerical calculations of the distribution function w(N)(T) for four time intervals T of various durations are carried out. The distribution function w(N)(T) is broader as compared with the Poissonian one and has two maxima, one of which relates to observed time intervals without on-->off jumps.

Computing the Heat of Adsorption using Molecular Simulations: The Effect of Strong Coulombic Interactions.

Molecular simulations are an important tool for the study of adsorption of hydrocarbons in nanoporous materials such as zeolites. The heat of adsorption is an important thermodynamic quantity that can be measured both in experiments and molecular simulations, and therefore it is often used to investigate the quality of a force field for a certain guest-host (g - h) system. In molecular simulations, the heat of adsorption in zeolites is often computed using either of the following methods: (1) using the Clausius-Clapeyron equation, which requires the partial derivative of the pressure with respect to temperature at constant loading, (2) using the energy difference between the host with and without a single guest molecule present, and (3) from energy/particle fluctuations in the grand-canonical ensemble. To calculate the heat of adsorption from experiments (besides direct calorimetry), only the first method is usually applicable. Although the computation of the heat of adsorption is straightforward for all-silica zeolites, severe difficulties arise when applying the conventional methods to systems with nonframework cations present. The reason for this is that these nonframework cations have very strong Coulombic interactions with the zeolite. We will present an alternative method based on biased interactions of guest molecules that suffers less from these difficulties. This method requires only a single simulation of the host structure. In addition, we will review some of the other important issues concerning the handling of these strong Coulombic interactions in simulating the adsorption of guest molecules. It turns out that the recently proposed Wolf method ( J. Chem. Phys. 1999, 110 , 8254 ) performs poorly for zeolites as a large cutoff radius is needed for convergence.

Giant molecular spoked wheels in giant voids: two-dimensional molecular self-assembly goes big

We present here the formation of giant pores in surface-confined molecular networks of a triangular-shaped dehydrobenzo-[12]annulene derivative: the diameter of the pores reaches over 7 nm and the giant pores are used as templates to accommodate a giant molecular spoked wheel, which allows us to observe rotational and adsorption-desorption dynamics of single guest molecules.

On the thermodynamic stability of hydrogen clathrate hydrates

The cage occupancy of hydrogen clathrate hydrate has been examined by grand canonical Monte Carlo (GCMC) simulations for wide ranges of temperature and pressure. The simulations are carried out with a fixed number of water molecules and a fixed chemical potential of the guest species so that hydrogen molecules can be created or annihilated in the clathrate. Two types of the GCMC simulations are performed; in one the volume of the clathrate is fixed and in the other it is allowed to adjust itself under a preset pressure so as to take account of compression by a hydrostatic pressure and expansion due to multiple cage occupancy. It is found that the smaller cage in structure II is practically incapable of accommodating more than a single guest molecule even at pressures as high as 500 MPa, which agrees with the recent experimental investigations. The larger cage is found to encapsulate at most 4 hydrogen molecules, but its occupancy is dependent significantly on the pressure of hydrogen.

Nano-dimensions for the pyrogallol[4]arene cavity

The cup-like cavity of pyrogallol[4]arenes has been deepened by the addition of four hydrogen bonded bipyridine molecules to the upper-rim of the calixarene, enabling the extended cup-like molecules to stack inside one another and consequently trap and completely enshroud a single guest molecule within the 250 angstroms3 cavitand formed between two of these stacked "nano-cups".

Reversible Enantiofacial Differentiation of a Single Heterocyclic Substrate by Supramolecular Receptors

Telling top and bottom apart: Supramolecular receptors can discriminate between the “top” and “bottom” sides of a single guest molecule, such as caffeine (see picture). This reversible enantiofacial differentiation results in the preferential formation of the α or β complexes.

The inorganic chemistry of guest-mediated zeolite crystallization: a comparison of the use of boron and aluminum as lattice-substituting components in the presence of a single guest molecule during zeolite synthesis

A comparison of two zeolite systems was made with trivalent element substitution for the use of N-benzyl-DABCO as the structure-directing agent (SDA). Boron and aluminum were used at the same initial concentrations. One reason for the study was awareness that a higher number of new zeolite structures are being found when researching borosilicate reaction mixtures. The borosilicate system studied produces SSZ-42 (IFR) while the aluminosilicate system yields beta zeolite (BEA). We focused on comparisons of the kinetics and found that the borosilicate system crystallized more rapidly, kept most of the boron in solution before incorporation into the crystal, and added mass even at the point where all solids were crystalline. In contrast, the aluminosilicate gel remained almost entirely in the solid phase through a long induction period and the mass of solids was relatively constant. The kinetics were followed by using a variety of techniques including powder XRD, pH changes, elemental analyses, partitioning in centrifugation and effects of dilution. The reaction systems were followed via NMR techniques. The transformation to crystalline could be seen by NMR for both the aluminosilicate and borosilicate reactions. Proton NMR changes were followed for both sets of solids. In addition, a profile for removal of boron from solution and towards the growing SSZ-42 was quantified by NMR. An unusual tetrahedral doublet for 11B was found in the SSZ-42 product. No such doublet was observed for tetrahedral aluminum in the case of beta zeolite formation.

Polymethylated [4.1.1] Octanes Leading to Zeolite SSZ-50

In this communication, we report on the discovery of novel zeolite compositions, SSZ-50. The zeolite has the RTH topology but can be made over a large silica-to-alumina range including no aluminum at all. The surprising capability to produce a broad compositional range comes from the use of a single organo-cation guest molecule in the zeolite synthesis. The molecule is a specific derivative from within a family of 2-aza [4.1.1] bicyclo octanes that were prepared employing a sequence of organic synthesis steps from a starting ketone. Other cage-based zeolites like SSZ-35,-36,-39 and MTN arose from the use of the other derivatives in this series. We also comment on the tendency of a variety of polymethylated organo-cations to produce RTH, the closely related ITE, or the intergrowth structure, SSZ-36.