Vibrational Analysis of Phosphorothioate DNA: II. The POS Group in the Model Compound Dimethyl Phosphorothioate [(CH3O)2(POS)]-

Abstract

The results of Raman and Infrared (IR) spectroscopic investigations on the vibrational modes of dimethyl phosphorothioate (DMPS) anion, [(CH₃O)₂(POS)]^?, are reported. Ab initio calculations of the vibrational modes, the IR and Raman spectra and the interatomic force constants of DMPS were performed. A normal mode calculation was performed and the results were used to calculate the potential energy distribution for the vibrational modes. This analysis shows that in DMPS the P-S stretching mode has a frequency of about 630 cm^?1 and an angle bending mode involving the sulfur atom has a frequency of about 440 cm^?1. The proposed vibrational mode assignments will serve as marker bands in the conformational studies of phosphorothioate oligonucleotides which play a central role in the novel antisense therapeutic paradigm.     

Interatomic Potentials in Conducting Polymer Systems

Abstract

Although the crystal structures of some ion-doped lattices of polyacetylene and polyparaphenylene have been investigated by diffraction methods there remain ambiguities both in the overall structures and in the precise locations of the dopant ions. We have used bonding and non-bonding interatomic potentials developed from empirical and quantum chemical data in a CASCADE atomistic lattice simulation method which permits full optimization of the lattic geometry. These calculations lead to stable structures which are consistent with diffraction data, and suggest the tendency of these lattices towards polymorphism.     

Structure-properties relations in graphene derivatives and metamaterials obtained by atomic-scale modeling

ABSTRACT

Recent findings of atomic-scale modelling studies are reviewed on graphene derivatives and metamaterials fabricated through chemical functionalization and/or defect engineering of graphene sheets. Results of molecular-statics and molecular-dynamics simulations according to a reliable bond-order potential, as well as first-principles density functional theory calculations are reviewed that have established useful structure-properties relations in two-dimensional materials, such as graphene nanomeshes (GNMs), electron-irradiated graphene, and interlayer-bonded twisted bilayer graphene. Quantitative relationships are established for the elastic moduli, mechanical properties, and thermal conductivity of GNMs as a function of the nanomesh porosity and the mechanical response of GNMs to uniaxial tensile straining is explored over the range of nanomesh porosities. The dependence of structural, mechanical, and thermal transport properties of electron-irradiated graphene sheets on the density of irradiation-induced defects is reviewed, highlighting an amorphization transition accompanied by a brittle-to-ductile transition and a transition in thermal transport mechanism beyond a critical defect concentration. The tunability of the electronic band structure, mechanical properties, and structural response to mechanical loading of graphene-diamond nanocomposite superstructures consisting of nanodiamond superlattices in interlayer-bonded twisted bilayer graphene also is demonstrated by precise control of the density and distribution of covalent interlayer C–C bonds.     

Non-bonded interatomic potential functions and crystal structure. Correction of the functions for use with macromolecules and application to polypeptide helixes

On the basis of a set of nonbonded interatomic potential functions derived earlier from heats of sublimation and experimental crystal structures, we derive a second, less repulsive, set which is to be used in the absence of the expansion caused by thermal motion and in particular in macromolecular systems where thermal motion is much reduced compared with crystals of small molecules. Working with a pair of octane molecules, we calculate the intermolecular potential (U) in the presence of thermal motion from potentials U° (in the absence of thermal motion), by letting a system of pairs of molecules assume a Boltzmann distribution over the intermolecular distance, in the presence of a force of varied magnitude applied to obtain different equilibrium distances. The potential U° is adjusted until the calculated and the empirical potentials U agree. Finally, best interatomic Lennard-Jones potentials which reproduce the function U° are calculated. The resulting functions are tested by calculating the crystal structure of benzene and comparing it with experimental data at low temperature, by energy minimization of the crystal structure of polyethylene and of the β-structure of poly-L -alanine, and by comparing the energy of the α-helix and the β-structure of poly-L -alanine. In all cases, the corrected functions give more satisfactory results than the uncorrected set.     

High Performance Thermoelectric Materials: Progress and Their Applications

Thermoelectric (TE) materials have the capability of converting heat into electricity, which can improve fuel efficiency, as well as providing robust alternative energy supply in multiple applications by collecting wasted heat, and therefore, assisting in finding new energy solutions. In order to construct high performance TE devices, superior TE materials have to be targeted via various strategies. The development of high performance TE devices can broaden the market of TE application and eventually boost the enthusiasm of TE material research. This review focuses on major novel strategies to achieve high‐performance TE materials and their applications. Manipulating the carrier concentration and band structures of materials are effective in optimizing the electrical transport properties, while nanostructure engineering and defect engineering can greatly reduce the thermal conductivity approaching the amorphous limit. Currently, TE devices are utilized to generate power in remote missions, solar–thermal systems, implantable or/wearable devices, the automotive industry, and many other fields; they are also serving as temperature sensors and controllers or even gas sensors. The future tendency is to synergistically optimize and integrate all the effective factors to further improve the TE performance, so that highly efficient TE materials and devices can be more beneficial to daily lives.     

Analytical and numerical calculations of interatomic forces and stresses

Atomistic simulation methods such as molecular dynamics require an efficient calculation of interatomic forces and stresses from pre–defined interatomic potentials. Both analytical and numerical approaches can be used to do this. Analytical approach directly calculates forces and stresses using analytical formulae, and can therefore yield accurate results. However, the force and stress expressions may become extremely complicated as the complexity level of the potential increases, resulting in a prolonged development cycle to implement new potentials. Numerical approach uses finite difference method to evaluate forces and stresses through simple calculation of energies at selected perturbations of crystal configurations. The method can be quickly implemented and tested for any potentials. However, it may result in significant numerical errors. We have compared analytical and numerical calculations of interatomic forces and stresses in molecular dynamics, and identified the conditions where numerical method can be successfully used without significant errors.     

Ab initio calculations on the thermodynamic properties of azaborospiropentanes

Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties of azaborospiropentanes. Properties reported in this study include optimized structural parameters, vibrational frequencies, enthalpies of formation, specific enthalpies of combustion, proton affinities, and hydride affinities. Our results indicate that azatriborospiropentane gives off most energy when combusted, as evidenced by its specific enthalpy of combustion of about −52 kJ per gram. Figure Optimized geometry for R-azatriborospiropentane (10) Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Hydration of Nucleic Acid Bases Studied Using Novel Atom-Atom Potential Functions

Abstract

New simple atom-atom potential functions for simulating behavior of nucleic acids and their fragments in aqueous solutions are suggested. These functions contain terms which are inversely proportional to the first (electrostatics), sixth (or tenth for the atoms, forming hydrogen bonds) and twelfth (repulsion of all the atoms) powers of interatomic distance. For the refinement of the potential function parameters calculations of ice lattice energy, potential energy and configuration of small clusters consisting of water and nucleic acid base molecules as well as Monte Carlo simulation of liquid water were performed. Calculations using new potential functions give rise to more linear hydrogen bonds between water and base molecules than using other potentials. Sites of preferential hydration of five nucleic bases—uracil, thymine, cytosine, guanine and adenine as well as of 6,6,9-trimethyladenine were found. In the most energetically favourable sites water molecule interacts with two adjacent hydrophilic centres of the base. Studies of interaction of the bases with several water molecules showed that water-water interaction play an important role in the arrangement of the nearest to the base water molecules. Hydrophilic centres are connected by “bridges” formed by hydrogen bonded water molecules. The results obtained are consistent with crystallographic and mass-spectrometric data.     

The Effect of a Crystalline Environment on Calculated Electron Densities

Abstract

Central to the calculation of useful interatomic potentials is a reliable determination of the electron densities of interacting ions. When the ions are embedded in a crystalline environment, it is reasonable to expect the effect of the crystal to be important in such calculations.

For certain ions (for example Mg²⁺ ions in MgO) the crystal has little effect on ion electron densities. Conversely, ions such as O^2? can only exist as a result of the stabilizing influence of lattice potentials; consequently, they are significantly modified by different lattice environments.

This paper will discuss the relevance of lattice effects to ions in MgO, in particular, Mg²⁺, Mg⁺, O^2? and F^?. Of these examples, the defect ions Mg⁺ and F^? are used to demonstrate how, in certain circumstances, the usual assumption that cations are not affected by lattice potentials but that anions are greatly influenced is not applicable. This work also emphasises the role of embedding electron-electron interactions in addition to the Madelung potential.     

Stillinger-Weber Type Potentials in Monte Carlo Simulation of Amorphous Silicon

The growth of amorphous silicon on a substrate of a two-layer slab of crystalline silicon with various surface indices is simulated with Stillinger-Weber type interatomic potentials. The growth is realized by means of a continuum Monte Carlo method and the radial distribution functions are evaluated for various cases.     

Molecular Dynamics Studies of Electrolyte Solution/Metal Interfaces

Abstract

The results of Molecular Dynamics simulations of pure water near a Pt(100) and a mercury surface as well as an aqueous LiI solution in contact with the Pt(100) surface are reported. The flexible BJH water model is employed in the simulations and the metal-water, ion-water and platinum-ion potentials are derived from molecular orbital calculations. It is shown that the structural and dynamical properties of water and the ions in the adsorbed water layer are significantly different from those in the bulk region.     

New Nanometric Solid Dispersions of Glibenclamide in Neusilin<Superscript>®</Superscript> UFL2

To improve the poor water solubility and dissolution rate of the oral hypoglycemic drug glibenclamide, it was molecularly dispersed in Neusilin^® UFL2, an amorphous synthetic form of magnesium aluminometasilicate, at different proportions; the physicochemical and biopharmaceutical properties, as well as the stability of the four different batches recovered were characterised, and it was determined that complete dispersion of glibenclamide in the amorphous polymer was obtained at the drug to Neusilin ratio of 1 to 2.5. Completely amorphous dispersion was proven by Thermal Analysis and X-Ray Powder Diffractometry. Very small particles were obtained, ranging from approximately 200 to 400 nm. The amorphous batches were physically and chemically stable for the entire duration of experiments. The physicochemical properties of the four batches were compared to those of the starting materials and physical mixtures of Neusilin^® UFL2 and glibenclamide, the latter showing the typical behaviour of simple mixes, i.e., the additivity of properties of single components. The dissolution studies of the four solid dispersions revealed a very high dissolution rate of the completely amorphous batches (Batches 3 and 4), behaviour that was ascribed to their high Intrinsic dissolution rate due to the amorphous characteristics of the solid dispersions, to their very small particle size, and to the presence of polysorbate 80 that improved solid wettability. The technique under investigation thus proved effective for recovering stable amorphous dispersions of very small particle sizes.     

Methane in Water: An Ab Initio Study

Abstract

In preceding publications we discussed some properties of pure water in condensed phases using an ab initio approach. Here this study is used as a basis of comparison for analysing the behaviour of water as a solvent in the presence of an apolar molecule. Our analysis is focused on the process of organization of the hydrogen bonding network around the solute. For this purpose we perform some ab initio calculations for a system of 32 water molecules and one methane molecule at 300 K; in particular, the average molecular dipole moment of water is determined and the result is compared with that of pure water. Next the attention is switched to the methane molecule; related properties such as excluded volume and sphericity of its shape are illustrated and discussed. A comparison with results obtained using classical approaches suggests that some classical models of water can be considered to be still valid when they are used to analyse the water-methane system.     

Rational design of thiolated polyenes as trifunctional Raman reporter molecules in surface‐enhanced Raman scattering nanotags for cytokine detection in a lateral flow assay

The characteristic vibrational spectroscopic fingerprint of Raman reporter molecules adsorbed on noble metal nanoparticles is employed for the identification of target proteins by the corresponding surface‐enhanced Raman scattering (SERS) nanotag‐labeled antibodies. Here, we present the modular synthesis of thiolated polyenes with two to five C═C double bonds introduced via stepwise Wittig reactions. The experimental characterization of their electronic and vibrational properties is complemented by density functional theory calculations. Highly SERS‐active nanotags are generated by using the thiolated polyenes as Raman reporter molecules in Au/Au core/satellite supraparticles with multiple hot spots. The cytokines IL‐1β and IFN‐γ are detected in a duplex SERS‐based lateral flow assay on a nitrocellulose test strip by Raman microscopy. The thiolated polyenes are suitable for use in immuno‐SERS applications such as point‐of‐care testing as well as cellular and tissue imaging.     

A Molecular Dynamics Simulation of an Aqueous Beryllium Chloride Solution

Abstract

A Molecular Dynamics simulation of a 1.1 molal aqueous BeCl₂ solution was performed with the flexible BJH model for water and a newly developed three-body potential for Be²⁺ -H₂O interactions derived from ab-initio calculations. The properties of the potential are discussed and radial distribution functions, angular distributions and dynamic properties of the solution like vibrational modes and hindered rotations are analyzed.     

RhoGTPase signalling at epithelial tight junctions: Bridging the GAP between polarity and cancer

The establishment and maintenance of epithelial polarity must be correctly controlled for normal development and homeostasis. Tight junctions (TJ) in vertebrates define apical and basolateral membrane domains in polarized epithelia via bi-directional, complex signalling pathways between TJ themselves and the cytoskeleton they are associated with. RhoGTPases are central to these processes and evidence suggests that their regulation is coordinated by interactions between GEFs and GAPs with junctional, cytoplasmic adapter proteins. In this InFocus review we determine that the expression, localization or stability of a variety of these adaptor proteins is altered in various cancers, potentially representing an important mechanistic link between loss of polarity and cancer. We focus here, on two well characterized RhoGTPases Cdc42 and RhoA who's GEFs and GAPs are predominantly localized to TJ via cytoplasmic adaptor proteins.     

Superconductivity in Bismuth. A New Look at an Old Problem

To investigate the relationship between atomic topology, vibrational and electronic properties and superconductivity of bismuth, a 216-atom amorphous structure (a-Bi216) was computer-generated using our undermelt-quench approach. Its pair distribution function compares well with experiment. The calculated electronic and vibrational densities of states (eDOS and vDOS, respectively) show that the amorphous eDOS is about 4 times the crystalline at the Fermi energy, whereas for the vDOS the energy range of the amorphous is roughly the same as the crystalline but the shapes are quite different. A simple BCS estimate of the possible crystalline superconducting transition temperature gives an upper limit of 1.3 mK. The e-ph coupling is more preponderant in a-Bi than in crystalline bismuth (x-Bi) as indicated by the λ obtained via McMillan’s formula, λ^c = 0.24 and experiment λ^a = 2.46. Therefore with respect to x-Bi, superconductivity in a-Bi is enhanced by the higher values of λ and of eDOS at the Fermi energy.     

Modelling of hydrated Ca-rich zeolites

The successful modelling of the structure of two hydrated calcium-rich natural zeolites is described, showing how modelling can reproduce their complex structure, in excellent agreement with experiment. Furthermore, we demonstrate how such methods are able to determine the preferred Al ordering in the mineral Goosecreekite. The dehydration behaviour of Goosecreekite is also predicted. The interatomic potentials for water, evaluated here, are found to be robust and transferable to zeolitic materials.     

Rho GAPs and GEFs: Controling switches in endothelial cell adhesion

Within blood vessels, endothelial cell–cell and cell–matrix adhesions are crucial to preserve barrier function, and these adhesions are tightly controlled during vascular development, angiogenesis, and transendothelial migration of inflammatory cells. Endothelial cellular signaling that occurs via the family of Rho GTPases coordinates these cell adhesion structures through cytoskeletal remodelling. In turn, Rho GTPases are regulated by GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs). To understand how endothelial cells initiate changes in the activity of Rho GTPases, and thereby regulate cell adhesion, we will discuss the role of Rho GAPs and GEFs in vascular biology. Many potentially important Rho regulators have not been studied in detail in endothelial cells. We therefore will first overview which GAPs and GEFs are highly expressed in endothelium, based on comparative gene expression analysis of human endothelial cells compared with other tissue cell types. Subsequently, we discuss the relevance of Rho GAPs and GEFs for endothelial cell adhesion in vascular homeostasis and disease.     

Structural Transformations of Ice at High Pressures Via Molecular Dynamics Simulations

Abstract

A simple classical model is used for the study of the structural transformations of ice under high pressures, such as ice VIII to VII and X, via classical molecular dynamics (MD) simulation. In the present MD simulation, pair potentials of a simple form between pair of atoms and a thee-body potential representing the H-O-H angle dependence, originally developed by Kawamura et al., were used. Starting with a stable ice VIII at low pressure and low temperature, we have carried out two different MD runs, one with increasing pressure keeping the temperature constant (simulation I) and the other with increasing temperature under constant pressure (simulation II). From these MD simulations we have obtained the structural transformations from ice VIII to VII for both simulations; the former was finally transformed into ice X for the simulation I. The present results are compatible with recent experiments on high pressure ices.