Elastic constants of uniaxial nematic liquid crystals of non-cylindrically symmetric molecules

We study in detail the influence of deviations from the molecular cylindrical symmetry on the fundamental elastic properties of uniaxial nematic liquid crystals. Results for the elastic constants are obtained for a range of molecular length-width ratio, temperature, density and molecular parameters. We compare calculated values with the experimental data of 8 OCB. It is observed that the effect of non-cylindrical molecular symmetry on the values of elastic constants of uniaxial of a nematic phase is small.     

Molecular path for ligand search

A ligand is a small molecule bind to several residues of a receptor.We adapt the concept of molecular path for effective ligand search with its contacting residues.Additionally,we allow wild type definitions on atoms and bonds of molecular paths for fuzzy algorithms on structural match.We choose hydrogen bond interactions to characterize the binding mode of a ligand by several proper molecular paths and use them to query the deposited ligands in PDBe that interact with their residues in the same way. Expression of molecular path and format of database entries are described with examples.Our molecular path provides a new approach to explore the ligand-receptor interactions and to provide structural framework reference on new ligand design.     

Kernel approach to molecular similarity based on iterative graph similarity

Similarity measures for molecules are of basic importance in chemical, biological, and pharmaceutical applications. We introduce a molecular similarity measure defined directly on the annotated molecular graph, based on iterative graph similarity and optimal assignments. We give an iterative algorithm for the computation of the proposed molecular similarity measure, prove its convergence and the uniqueness of the solution, and provide an upper bound on the required number of iterations necessary to achieve a desired precision. Empirical evidence for the positive semidefiniteness of certain parametrizations of our function is presented. We evaluated our molecular similarity measure by using it as a kernel in support vector machine classification and regression applied to several pharmaceutical and toxicological data sets, with encouraging results.     

Theoretical study of molecular conduction: I. Effective Green's function based on perturbation theory

There have been many experimental and theoretical studies on molecular conduction, as it is a fundamental parameter in the study of molecular‐scale electronics. We have investigated the features of molecular conduction using a Green's function method, which has often been used to solve problems in quantum transport and is also effective in elucidating electron transport in molecules. We have obtained the novel effective Green's functions, including the first‐order energy corrections, by accommodating the self‐energy of the electrodes as perturbation terms. Although these approximate Green's functions only provide information on the first‐order energy corrections, they can involve the elementary properties of molecular conduction. We propose a scheme for the analysis of the relations between molecular orbitals and their roles in molecular conduction and present analytical calculations for normal and cyclic polyenes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Self-assembly of extended polycyclic aromatic hydrocarbons on Cu111

We present a low-temperature scanning tunneling microscopy study on the self-assembly of extended polycyclic aromatic hydrocarbons with different symmetries on the Cu111 surface. All molecules show a commensurate monolayer structure, with significant structural differences with respect to the unit cell of the molecular lattice and the orientational ordering. We find that the molecular lattice and the molecular orientation are largely dominated by molecule-substrate interactions, whereas molecule-molecule interactions determine the molecular packing density via steric repulsion. Moreover, we show that the structure of the monolayer is transferred to the second layer via molecule-molecule interaction.     

Fabrication of Two-dimensional Monolayer and One-dimensional Wire of Zn-tetra-[3,5-di-t-butylphenyl]-porphyrin on Cu(100) Surface

1 INTRODUCTION Metalloporphyrins and their derivatives having been intensively studied play an important role in biological processes, such as oxygen transport and photosynthesis. They can act as catalysts[1] and un- dergo reversible redox reactions in which the site of electron transfer may be localized on the porphyrin ring or the central metal ion. Both reactions are important in natural processes[2]. Recently, it hasbecome known that structural distortion from planar geometry is fairl…     

Molecular-scale structure in fluid-gel patterned bilayers: stability of interfaces and transmembrane distribution

Variations in two-dimensional membrane structures on the molecular length scale are considered to have an effect on the mechanisms by which living cell membranes maintain their functionality. We created a molecular model of a patterned bilayer to asses the static and dynamic variations of membrane lateral and transbilayer distribution in two-component lipid bilayers on the molecular level. We study DSPC (distearoylphosphatidylcholine) nanometer domains in a fluid DLPC (dilauroylphosphatidylcholine) background. The system exhibits coexisting fluid and gel phases and is studied on a microsecond time scale. We characterize three different kinds of patterns: symmetric domains, asymmetric domains, and symmetric-asymmetric domains. Preferred bilayer configurations on the nanoscale are those that minimize the hydrophobic mismatch. We find nanoscale patterns to be dynamic structures with mainly lateral and rotational diffusion affecting their stability on the microsecond time scale.     

Surface anchoring of rodlike molecules on corrugated substrates

We studied the mechanism of surface anchoring of rodlike molecules on substrates with the surfaces corrugated at molecular scale by molecular-dynamics simulation. We constructed a model for substrates that can have anisotoropic topographical patterns such as corrugation. The structural and thermodynamic properties of rodlike molecules on the corrugated surfaces, including the elastic and anchoring properties, were calculated and the influence of the surface structure on the anchoring was discussed. We found that the rodlike molecules are aligned along the grooves of the corrugated surfaces guided by the anisotropic molecular interaction between the molecules and the corrugated surface. The strength of anchoring was found to be increased when the period of corrugation is decreased at molecular level.     

Why can we not sequence thousands of DNA bases on a polyacrylamide gel?

Pulsed fields have been remarkably useful at extending the range of DNA molecular sizes that can be separated on agarose gels by controlling the field-induced molecular orientation that often limits the resolution of large molecules. Unfortunately, the same approach seems to be much less effective for DNA sequencing on polyacrylamide gels. We present an experimental and theoretical (modelling) study of DNA sequencing which shows that molecular orientation is indeed not the main limiting factor for sequencing devices that use moderate field intensities and polyacrylamide as a separating matrix. We examine the interplay between electric field intensity, molecular size and resolution, and we suggest different approaches to increase the resolution limit of standard and automated sequencing gels. The theoretical limits of high-field electrophoretic sequencing are also discussed. We conclude that new ideas will be needed to go beyond one kilobase.     

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.     

Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions: Understanding the Molecular Mechanisms

We study the molecular mechanisms of alkali halide ion interactions with the single‐wall carbon nanotube surface in water by means of fully atomistic molecular dynamics simulations. We focus on the basic physical‐chemical principles of ion–nanotube interactions in aqueous solutions and discuss them in light of recent experimental findings on selective ion effects on carbon nanotubes.     

Metrology for molecular electronics

Building reliable molecular electronic devices requires the ability to accurately and reproducibly measure the electronic response of the system under study. Here we review our work with three distinct molecular electronic test structures which show excellent agreement for measurements on molecular wires and molecular switch molecules. We also discuss how inelastic electron tunneling spectroscopy enables chemical characterization of molecular electronic elements in actual device geometries.     

Path integral methods for rotating molecules in superfluids

We present a path integral Monte Carlo (PIMC) methodology for quantum simulation of molecular rotations in superfluid environments such as helium and para-hydrogen that combines the sampling of rotational degrees of freedom for a molecular impurity with multilevel Metropolis sampling of Bose permutation exchanges for the solvating species. We show how the present methodology can be applied to the evaluation of imaginary time rotational correlation functions of the molecular impurity, from which the effective rotational constants can be extracted. The combined rotation/permutation sampling approach allows for the first time explicit assessment of the effect of Bose permutations on molecular rotation dynamics, and the converse, i.e., the effect of molecular rotations on permutation exchanges and local superfluidity. We present detailed studies showing that the effect of Bose permutations in the solvating environment is more significant for the dynamics of heavy than light molecules in helium, and that Bose permutation exchanges are slightly enhanced locally by molecular rotation. Finally, the examples studied here reveal a size dependence of rotational excitations for molecules possessing a strongly anisotropic interaction with helium in 4HeN clusters between N approximately 20 and N approximately 10(3).     

The synthesis of functionalized nanoscale molecular rods of defined length

We report a synthetic approach to spiro-ladder oligomers of defined length and structure that form water-soluble molecular rods. We describe the synthesis of a chiral molecular building block 1 and its assembly on solid support to form flexible chains that were then rigidified by the parallel formation of several diketopiperazine rings. Two molecular rods approximately 15 and 25 A in length were synthesized containing three and five monomers, respectively. The molecular rods were easily functionalized on both ends and were shown to have high water solubility, making them compatible with biological buffers. These molecules may find use as scaffolds for the display of ligands in chemical-biology applications and as spacers and construction materials for nanoscience applications.     

Effect of strain on the thermal conductivity of solids

We present a systematic study of the effect of strain (equivalent to uniform pressure) on the thermal conductivity of an insulating solid. Following a theoretical analysis that uncovers the dependence of the thermal conductivity on temperature and strain, we present classical molecular dynamics calculations of the thermal conductivity. We find that the molecular dynamics results closely match the theoretical result.     

First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bioinorganic systems

We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metalorganic systems. Our results show that accurate density-functional theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.     

Langmuir-Blodgett film of hydrophobin protein from Pleurotus ostreatus at the air-water interface

We present results concerning the formation of Langmuir-Blodgett (LB) films of a class I hydrophobin from Pleurotus ostreatus at the air-water interface, and their structure as Langmuir-Blodgett (LB) films when deposited on silicon substrates. LB films of the hydrophobin were investigated by atomic force microscopy (AFM). We observed that the compressed film at the air-water interface exhibits a molecular depletion even at low surface pressure. In order to estimate the surface molecular concentration, we fit the experimental isotherm with Volmer's equation describing the equation of state for molecular monolayers. We found that about (1)/ 10 of the molecules contribute to the surface film formation. When transferred on silicon substrates, compact and uniform monomolecular layers about 2.5 nm thick, comparable to a typical molecular size, were observed. The monolayers coexist with protein aggregates, under the typical rodlet form with a uniform thickness of about 5.0 nm. The observed rodlets appear to be a hydrophilic bilayer and can then be responsible for the surface molecular depletion.