Potential of mean force between hydrophobic solutes in the Jagla model of water and implications for cold denaturation of proteins

Using the Jagla model potential we calculate the potential of mean force (PMF) between hard sphere solutes immersed in a liquid displaying water-like properties. Consistent estimates of the PMF are obtained by (a) umbrella sampling, (b) calculating the work done by the mean force acting on the hard spheres as a function of their separation, and (c) determining the position dependent chemical potential after calculating the void space in the liquid. We calculate the PMF for an isobar along which cold denaturation of a model protein has previously been reported. We find that the PMF at contact varies non-monotonically, which is consistent with the observed cold denaturation. The Henry constant also varies non-monotonically with temperature. We find, on the other hand, that a second (solvent separated) minimum of the PMF becomes deeper as temperature decreases. We calculate the solvent-solvent pair correlation functions for solvents near the solute and in the bulk, and show that, as temperature decreases, the two pair correlation functions become indistinguishable, suggesting that the perturbation of solvent structure by the solute diminishes as temperature decreases. The solvent-solute pair correlation function at contact grows as the temperature decreases. We calculate the cavity correlation function and show the development of a solvent-separated peak upon decrease of temperature. These observations together suggest that cold denaturation occurs when the solvent penetrates between hydrophobic solutes in configurations with favorable free energy. Our results thus suggest that cold denatured proteins are structured and that cold denaturation arises from strong solvent-solute interactions, rather than from entropic considerations as in heat denaturation.     

Cephalosporin-3'-diazeniumdiolates: Targeted NO-Donor Prodrugs for Dispersing Bacterial Biofilms

Just say NO to biofilms: NO-donors are used to disperse a bacterial biofilm so that co-administered antibiotics will kill the more susceptible unattached cells. The chemically stable cephalosporin-3'-diazeniumdiolate NO-donor prodrug is activated by bacterial β-lactamases and facilitates this two-step biofilm erradication.     

Simulation study of solvent shifts of vibrational overtone spectra

Buckingham's theory of the solvent shift of vibrational spectral frequencies predicts that the shift of the v = 0 → n overtone transition is n times the shift of the fundamental v = 0 → 1. We test this prediction by molecular dynamics simulations using existing intermolecular potential models for liquid N₂ and dilute N₂ in liquid Ar, at standard state conditions. We extend Buckingham's theory by including additional intramolecular potential and perturbation terms which lead to solvent-induced anharmonicity, i.e. O(n ²) terms in the solvent shift. The simulations show that Buckingham's prediction is not accurate for N₂ at standard liquid state conditions. We find that at these conditions there is a significant positive O(n ²) contribution to the solvent shifts and that for n ～ 20 the shifts change sign from red to blue. Simulation results and indirect evidence from shock wave experiments with liquid N₂ show that Buckingham's prediction is more accurate for high-pressure high-temperature conditions, where the shifts are blue and only slightly nonlinear in n.     

Diffusion approximation for signaling stochastic networks

This paper introduces an unified approach to diffusion approximations of signaling networks. This is accomplished by the characterization of a broad class of networks that can be described by a set of quantities which suffer exchanges stochastically in time. We call this class stochastic Petri nets with probabilistic transitions, since it is described as a stochastic Petri net but allows a finite set of random outcomes for each transition. This extension permits effects on the network which are commonly interpreted as “routing” in queueing systems. The class is general enough to include, for instance, G-networks with negative customers and triggers as a particular case. With this class at hand, we derive a heavy traffic approximation, where the processes that drive the transitions are given by state-dependent Poisson-type processes and where the probabilities of the random outcomes are also state-dependent. The objective of this approach is to have a diffusion approximation which can be readily applied in several practical problems. We illustrate the use of the results with some numerical experiments.     

Near-field Raman spectroscopy of biological nanomaterials by in situ laser-induced synthesis of tip-enhanced Raman spectroscopy tips

We report a new approach in tip-enhanced Raman spectroscopy (TERS) in which TERS-active tips with enhancement factors of ～10(-5)× can be rapidly (1-3 min) produced in situ by laser-induced synthesis of silver nanoparticles at the tip apex. The technique minimizes the risks of tip contamination and damage during handling and provides in situ feedback control, which allows the prediction of the tip performance. We show that TERS tips produced by this technique enable the measurement of spatially resolved TERS spectra of self-assembled peptide nanotubes with a spatial resolution of ～20 nm.     

Structure and magnetostructural correlation of ferrimagnetic meso-tetraphenylporphinatomanganese(III) dimethyl-N,N′-dicyanoquinone diiminide, [MnTPP]+[Me2DCNQI]·?

The structure [MnⅢ TPP][Me2 DCNQI] (TPP = tetraphenylporphinato; Me 2 DCNQI = 2,5-dimethyl-N,N′-dicyanoquinonediimine) has been determined from X-ray powder diffraction data. The nonsolvated structure is composed of linear (1-D) chains of alternating [MnⅢ TPP] + and μ-[Me 2 DCNQI] with intrachain Mn···Mn separations of 12.83 , and a Mn N DCNQI distance of 2.18. The dihedral angle between the mean Mn(N 4 ) TPP and [Me 2 DCNQI].- planes, and the Mn (N C) DCNQI angle are 84.18° and 143.6°, respectively. [MnⅢ TPP][Me 2 DCNQI] has a T c of 4.3 K from the 10 Hz χ"(T) data, 2-K coercivity of 5,600 Oe, and 6,300 emuOe/mol remnant magnetization that are reduced from that observed for related materials, and their inclusion extends the magnetostructural correlation between the intrachain coupling and both the dihedral angle between the mean Mn(N 4 ) TPP and [TCNE]*- (TCNE = tetracyanoethylene) planes and Mn (N C) TCNE angles. This is in accord with the intrachain coupling arising from the overlap of the MnⅢ d z 2 -like singly occupied molecular orbital (SOMO) and the z component of the [TCNE]*-π* (πz *) SOMO, which increases with decreasing dihedral angle between the mean Mn(N 4 ) TPP and [TCNE]*- planes and Mn (N C) TCNE angle.     

Study of the mesomorphic behaviour through the structure modification of azo and acetylene pyridinium and imidazolium-based ionic liquid crystals

ABSTRACT

In this work, 14 pyridinium and imidazolium-based ionic liquid crystal (ILC) with azo (N=N) and acetylene (C≡C) as linking group were synthesised in high yields and completely characterised. The structure of the molecules were planned in order to allow a complete investigation on how modifications such as presence and position of charges, linking group, number of alkoxy chains and their length affect the thermal stability and liquid crystalline behaviour. All compounds were thoroughly investigated using polarised optical microscopy (POM), differential scanning calorimetry (DSC), X-ray diffraction (XRD) measurements and thermogravimetric analysis (TGA). While the presence of charges favoured a liquid crystalline behaviour, especially SmA (and SmA₂) phase, a decrease of thermal stability was noticed. A strong dependence of the charge position and a preference for monolayer or bilayer molecular organisation was observed. On the other hand, it was demonstrated that the addition of a second alkoxy chain promoted layer distortions in some molecules, resulting in the formation of Smà and Cub phases. Also a direct comparison between the N=N and C≡C linking groups was realised, along with further comparison with literature data. The structure–properties are investigated in detail.