Properties of alkali metal atoms deposited on a MgO surface: a systematic experimental and theoretical study

The adsorption of small amounts of alkali metal atoms (Li, Na, K, Rb, and Cs) on the surface of MgO powders and thin films has been studied by means of EPR spectroscopy and DFT calculations. From a comparison of the measured and computed g values and hyperfine coupling constants (hfccs), a tentative assignment of the preferred adsorption sites is proposed. All atoms bind preferentially to surface oxide anions, but the location of these anions differs as a function of the deposition temperature and alkali metal. Lithium forms relatively strong bonds with MgO and can be stabilized at low temperatures on terrace sites. Potassium interacts very weakly with MgO and is stabilized only at specific sites, such as at reverse corners where it can interact simultaneously with three surface oxygen atoms (rubidium and cesium presumably behave in the same way). Sodium forms bonds of intermediate strength and could, in principle, populate more than a single site when deposited at room temperature. In all cases, large deviations of the hfccs from the gas-phase values are observed. These reductions in the hfccs are due to polarization effects and are not connected to ionization of the alkali metal, which would lead to the formation of an adsorbed cation and a trapped electron. In this respect, hydrogen atoms behave completely differently. Under similar conditions, they form (H(+))(e(-)) pairs. The reasons for this different behavior are discussed.     

Adsorption and stability of streptavidin on cluster-assembled nanostructured TiOx films

The study of the adsorption of proteins on nanostructured surfaces is of fundamental importance to understand and control cell-surface interactions and, notably, cell adhesion and proliferation; it can also play a strategic role in the design and fabrication of nanostructured devices for postgenomic and proteomic applications. We have recently demonstrated that cluster-assembled nanostructured TiO x films produced by supersonic cluster beam deposition possess excellent biocompatibility and that these films can be functionalized with streptavidin, allowing the immobilization of biotinylated retroviral particles and the realization of living-cell microarrays for phenotype screening. Here we present a multitechnique investigation of the adsorption mechanisms of streptavidin on cluster-assembled TiO x films. We show that this nanostructured surface provides an optimal balance between adsorption efficacy and protein functionality. By using low-resolution protein arrays, we demonstrate that a layer of adsorbed streptavidin can be stably maintained on a cluster-assembled TiO x surface under cell culture conditions and that streptavidin retains its biological activity in the adsorbed layer. The adsorption mechanisms are investigated by atomic force microscopy in force spectroscopy mode and by valence-band photoemission spectroscopy, highlighting the potential role of the interaction of the exposed carboxyl groups on streptavidin with the titanium atoms of the nanostructured surface.     

Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality

The equilibrium free energy difference between two long-lived molecular species or "conformational states" of a protein (or any other molecule) can in principle be estimated by measuring the work needed to shuttle the system between them, independent of the irreversibility of the process. This is the meaning of the Jarzynski equality (JE), which we test in this paper by performing simulations that unfold a protein by pulling two atoms apart. Pulling is performed fast relative to the relaxation time of the molecule and is thus far from equilibrium. Choosing a simple protein model for which we can independently compute its equilibrium properties, we show that the free energy can be exactly and effectively estimated from nonequilibrium simulations. To do so, one must carefully and correctly determine the ensemble of states that are pulled, which is more important the farther from equilibrium one performs simulations; this highlights a potential problem in using the JE to extract the free energy from forced unfolding experiments. The results presented here also demonstrate that the free energy difference between the native and denatured states of a protein measured in solution is not always equal to the free energy profile that can be estimated from forced unfolding simulations (or experiments) using the JE.     

An investigation on the nature of the peptide at m/z 904, overexpressed in plasma of patients with colorectal cancer and familial adenomatous polyposis

In an investigation devoted to the search for plasma markers for colorectal cancer (CRC), carried out by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, a series of overexpressed peptides were identified in the plasma of patients. Among them the peptide with molecular weight 903 Da was the most abundant one, with a mean +/- (SD) relative abundance of 37 +/- 17% and a frequency over 60%. Interestingly, also in plasma samples of ten subjects affected by familial adenomatous polyposis (FAP), the peptide with molecular weight 903 was overexpressed. In this investigation, MALDI/MS/MS experiments were carried out on the ion at m/z 904 detected in the MALDI mass spectra of CRC and FAP patients. The data analysis by SwissProt.2007.01.09 indicates that this peptide is due to the sequence RPPGFSPF, found in the kininogen-1 precursor, which is an alpha-2-thiol proteinase inhibitor. In the case of subjects affected by a particular FAP syndrome, the MALDI/MS/MS spectra were quite different from those obtained from CRC and FAP patients. In fact, two sequences have been evidenced: RPPGFSPF belonging to kininogen-1 precursor, and PRKSSSSR belonging to Forkhead box protein 01A.     

UV spectra and excitation delocalization in DNA: influence of the spectral width.

The singlet excited states of the model DNA duplex (dA)10.(dT)10 are studied. Calculations are performed in the exciton theory framework. Molecular dynamics calculations provide the duplex geometry. The dipolar coupling is determined using atomic transition charges. The monomer transition energies are simulated by Gaussian functions resembling the absorption bands of nucleosides in aqueous solutions. Most of the excited states are found to be delocalized over at least two bases and result from the mixing of different monomer states. Their properties are only weakly affected by conformational changes of the double helix. On average, the highest oscillator strength is carried by the upper eigenstates. The duplex absorption spectra are shifted a few nanometers to higher energies with respect to the spectra of noninteracting monomers. The states with larger spatial extent are located close to the maximum of the absorption spectrum.     

Rheological behavior and structural interpretation of waxy crude oil gels

A waxy crude oil which gels below a threshold temperature has been investigated under static and dynamic conditions, using a combination of rheological methods, optical microscopy, and DSC. Particular attention is given in this work to the influence of the mechanical history on gel strength and to describing the time-dependent rheological behavior. The gels display a strong dependence of the yield stress and moduli on the shear history, cooling rate, and stress loading rate. Of particular interest is the partial recovery of the gel structure after application of small stress or strain (much smaller than the critical values needed for flow onset) during cooling, which can be used to reduce the ultimate strength of the crude oil gel formed below the pour point. A second focus of this study is to further develop the physical interpretation of the mechanism by which wax crystallization produces gelation. Gelation of the waxy crude oil studied is suggested to be the result of the association between wax crystals, which produces an extended network structure, and it is shown that the system displays features common to attractive colloidal gels, for one of which, fumed silica (Aerosil 200) in paraffin oil, rheological data are reported. The colloidal gel model provides a simple and economical basis for explaining the response of the gelled oil to various mechanical perturbations and constitutes a fruitful basis from which to develop technologies for controlling the gelation phenomenon, as suggested by the rheological results reported.     

Effects of nonionic,cationic, and anionic micelles on the kinetics of the complexation reaction of nickel (II) with pyridine-2-azo-p-dimethylaniline

The stopped-flow technique has been used to study the effect of cationic (CTAN), nonionic (Triton X-100), andanionic (SDS) micelles on the rate of the reaction between nickel(II) ion and the ligand pyridine-2-azo-p-dimethylaniline (PADA) at 20.0°C and ionic strength 0.03 mol dm^?3. The complex formation reaction is markedly inhibited by both CTAN and Triton X-100 micelles. The kinetic dataare found to conform to a reaction mechanism which implies only partitioning of the ligand between water and the micellar phase, the estimated bindingconstant of PADA being significantly larger in the presence of CTAN aggregates. Anionic micelles strongly speed the complexation reaction, Which occurs in the micellar phase with the same rate and the same mechanism as in water. The extent of binding of PADA to anionic micelles is similar to that found for the cationic micellar aggregates.     

Solvent effects in the reaction of 2-thiophenesulfonyl chloride with aniline

The second order rate constants k₂ and the activation parameters for the reaction of 2-thiophenesulfonyl chloride with aniline together with solution enthalpies of the reactants have been measured in methanol, ethanol, 2-propanol, acetonitrile and acetone. The reaction rates are slower in dipolar aprotic solvents than in protic ones due to a remarkable activation negative entropy. The rate constants k₂ are correlated with empirical solvent polarity parameters. The data seem in accord with a S_AN reaction mechanism.     

On a quadratic functional occurring in a bivariate scattered data interpolation problem

Sunto L’applicazione di noti metodi che utilizzano funzioni di tipo blending per la costruzione di funzioni bivariate C¹ per l’interpolazione di dati, richiede la conoscenza delle derivate parziali del primo ordine ai vertici di una triangolazione sottostante. In questo lavoro consideriamo il metodo proposto da Nielson, che consiste nel calcolare stime delle derivate parziali del primo ordine minimizzando un opportuno funzionale quadratico, caratterizzato da parametri di tensione non negativi. Scopo del lavoro è l’analisi di alcune proprietà particolari di questo funzionale per la costruzione di algoritmi efficienti e robusti per la determinazione delle stime suddette delle derivate quando si ha a che fare con insiemi di dati di grandi dimensioni. Abstract The application of widely known blending methods for constructingC ¹ bivariate functions interpolating scattered data requires the knowledge of the partial derivatives of first order at the vertices of an underlying triangulation. In this paper we consider the method proposed by Nielson that consists in computing estimates of the first order partial derivatives by minimizing an appropriate quadratic functional, characterized by nonnegative tension parameters. The aim of the paper is to analyse some peculiar properties of this functional in order to construct robust and efficient algorithms for determining the above estimates of the derivatives when we are concerned with extremely large data sets.      

Changes in the morphology of interstellar ice analogues after hydrogen atom exposure

The morphology of water ice in the interstellar medium is still an open question. Although accretion of gaseous water could not be the only possible origin of the observed icy mantles covering dust grains in cold molecular clouds, it is well known that water accreted from the gas phase on surfaces kept at 10 K forms ice films that exhibit a very high porosity. It is also known that in the dark clouds H(2) formation occurs on the icy surface of dust grains and that part of the energy (4.48 eV) released when adsorbed atoms react to form H(2) is deposited in the ice. The experimental study described in the present work focuses on how relevant changes of the ice morphology result from atomic hydrogen exposure and subsequent recombination. Using the temperature-programmed desorption (TPD) technique and a method of inversion analysis of TPD spectra, we show that there is an exponential decrease in the porosity of the amorphous water ice sample following D-atom irradiation. This decrease is inversely proportional to the thickness of the ice and has a value of ?(0) = 2 × 10(16) D-atoms cm(-2) per layer of H(2)O. We also use a model which confirms that the binding sites on the porous ice are destroyed regardless of their energy depth, and that the reduction of the porosity corresponds in fact to a reduction of the effective area. This reduction appears to be compatible with the fraction of D(2) formation energy transferred to the porous ice network. Under interstellar conditions, this effect is likely to be efficient and, together with other compaction processes, provides a good argument to believe that interstellar ice is amorphous and non-porous.