Scanning Tunneling Microscopy and Atomic Force Microscopy in Organic Chemistry

When Kekulé awoke from dreams of snakes biting their own tails, he didn't have the benefit of a scanning tunneling microscope (STM) image to confirm that his vision of benzene as a cyclic molecule was accurate. References to STM in the chemical literature increase steadily, although the technique was perhaps oversold in its early days of the 1980s, with such promises as DNA sequencing and tailored bi-molecular chemical reactions (literally, two molecules). Publications alternate between attempting to explain the process by which images of traditional insulators are obtained and simply presenting the end images themselves as stunning views of atoms and molecules. While imaging mechanisms are still being debated, these instruments' ability to “see” single molecules has been established, albeit at the fringes of our expectations. For example, whereas STM studies at present might not be able to answer the question of why adsorption of CO doubles the density of platinum atoms on the surface of a single crystal of the metal, the images go far in illustrating that this is a process which platinum undergoes. As with any emerging analytical tool, these scanning, very localized microscopic methods are undergoing the growing pains of irreproducible results and mis-marketed artifacts. Nonetheless, we assemble here, primarily for the uninitiated, a collection of careful and credible studies to mark the progress of scanning tunneling microscopy and atomic force microscopy into chemistry, and to encourage a healthy blend of idealism and skepticism toward future work.     

Chemical cleavage reactions of DNA on solid support: application in mutation detection

Background  

The conventional solution-phase Chemical Cleavage of Mismatch (CCM) method is time-consuming, as the protocol requires purification of DNA after each reaction step. This paper describes a new version of CCM to overcome this problem by immobilizing DNA on silica solid supports.     

Interfacial glass transition profiles in ultrathin, spin cast polymer films

Interfacial glass transition temperature (T(g)) profiles in spin cast, ultrathin films of polystyrene and derivatives were investigated using shear-modulated scanning force microscopy. The transitions were measured as a function of film thickness (delta), molecular weight, and crosslinking density. The T(g)(delta) profiles were nonmonotonic and exhibited two regimes: (a) a sublayer extending about 10 nm from the substrate, with T(g) values lowered up to approximately 10 degrees C below the bulk value, and (b) an intermediate regime extending over 200 nm beyond the sublayer, with T(g) values exceeding the bulk value by up to 10 degrees C. Increasing the molecular weight was found to shift the T(g)(delta) profiles further from the substrate interface, on the order of 10 nm/kDa. Crosslinking the precast films elevated the absolute T(g) values, but had no effect on the spatial length scale of the T(g)(delta) profiles. These results are explained in the context of film preparation history and its influence on molecular mobility. Specifically, the observed rheological anisotropy is interpreted based on the combined effects of shear-induced structuring and thermally activated interdiffusion.     

Solubility and diffusivity of water and of salts in an aromatic polyamide film

The solubility and the diffusivity for water and NaCl in a fully aromatic polyamide (PA) film have been determined. From these the “intrinsic permeability characteristics” of this polymer have been calculated and its suitability for desalination by reverse osmosis is compared with that of the commonly used cellulose acetate (CA). It has been found that, although the solubility of NaCl in the PA film is higher than that in a CA film, PA membranes will reject salt better than CA membranes having identical structure and morphology. This is because the diffusivity of NaCl through the PA film is substantially lower, and the permeability of water through it (as well as the solubility and the diffusivity of water in it) are higher than the comparable values for CA films.     

The effect of nonlinearity on unstable zones of Mathieu equation

Mathieu equation is a well-known ordinary differential equation in which the excitation term appears as the non-constant coefficient. The mathematical modelling of many dynamic systems leads to Mathieu equation. The determination of the locus of unstable zone is important for the control of dynamic systems. In this paper, the stable and unstable regions of Mathieu equation are determined for three cases of linear and nonlinear equations using the homotopy perturbation method. The effect of nonlinearity is examined in the unstable zone. The results show that the transition curves of linear Mathieu equation depend on the frequency of the excitation term. However, for nonlinear equations, the curves depend also on initial conditions. In addition, increasing the amplitude of response leads to an increase in the unstable zone.     

Live Imaging of Glucose Homeostasis in Nuclei of COS-7 Cells

Measuring subcellular glucose levels deep in tissues can provide new insights into compartmentalization and specialization of glucose metabolism among different cells. As shown previously, a FRET-based glucose-sensor consisting of two GFP-variants and the Escherichia coli periplasmic glucose/galactose binding protein was successfully expressed in the cytosol of COS7-cells and used to determine cytosolic glucose levels. Recording cytosolic fluorescence intensities in cells located in deeper layers of tissues is often difficult due to loss of signal intensity caused by effects of other cell layers on excitation and emission light. These interfering effects may be reduced by restricting fluorophores to occupy only a fraction of the assayed tissue volume. This can be accomplished by confining fluorophores to a sub-compartment of each cell in the tissue, such as the nucleus. The glucose-sensor was targeted to nuclei of COS7-cells. To determine, whether nuclear glucose levels can be used to track cytosolic changes, nuclear glucose concentrations were quantified as the cells were challenged with external glucose over a range of 0.5 to 10 mM and compared to cytosolic levels. Internal glucose concentrations in both compartments were similar, corresponding to approximately 50% of the external concentration. Taken together, these results indicate that nuclear glucose levels can be used to determine cytosolic levels indirectly, permitting more reliable quantification of fluorescence intensities and providing a tool for measurements not only in cell cultures but also in tissues.     

Reductive Charge Transfer through an RNA Aptamer

The transfer of charges through double helical DNA is a very well investigated bioelectric phenomenon. RNA, on the contrary, has been less studied in this regard. The few available data report on charge transfer through RNA duplex structures mainly composed of homonucleotide sequences. In the light of the RNA world scenarios, it is an interesting question, if charge transfer can be coupled with RNA function. Functional RNAs however, contain versatile structural motifs. Therefore, electron transport also through non-Watson–Crick base-paired regions might be required. We here demonstrate distance-dependent reductive charge transfer through RNA duplexes and through the non-Watson–Crick base-paired region of an RNA aptamer.     

A variational framework for the inverse Henderson problem of statistical mechanics

Tensor network states (TNS) are a powerful approach for the study of strongly correlated quantum matter. The curse of dimensionality is addressed by parametrizing the many-body state in terms of a network of partially contracted tensors. These tensors form a substantially reduced set of effective degrees of freedom. In practical algorithms, functionals like energy expectation values or overlaps are optimized over certain sets of TNS. Concerning algorithmic stability, it is important whether the considered sets are closed because, otherwise, the algorithms may approach a boundary point that is outside the TNS set and tensor elements diverge. We discuss the closedness and geometries of TNS sets, and we propose regularizations for optimization problems on non-closed TNS sets. We show that sets of matrix product states (MPS) with open boundary conditions, tree tensor network states, and the multiscale entanglement renormalization ansatz are always closed, whereas sets of translation-invariant MPS with periodic boundary conditions (PBC), heterogeneous MPS with PBC, and projected entangled pair states are generally not closed. The latter is done using explicit examples like the W state, states that we call two-domain states, and fine-grained versions thereof.