Atomic control of water interaction with biocompatible surfaces: the case of SiC(001)

The interaction of water with Si- and C- terminated beta-SiC(001) surfaces was investigated by means of ab initio molecular dynamics simulations. Irrespective of coverage, varied from 1/4 to 1 monolayer, we found that water dissociates on the Si-terminated surface, substantially modifying the clean surface reconstruction, while the C-terminated surface is nonreactive and hydrophobic. Based on our results, we propose that STM images and photoemission experiments may detect specific changes induced by water on both the structural and electronic properties of SiC(001) surfaces.     

A computationally efficient finite element model with perfectly matched layers applied to scattering from axially symmetric objects

A frequency-domain finite-element (FE) technique for computing the radiation and scattering from axially symmetric fluid-loaded structures subject to a nonsymmetric forcing field is presented. The Berenger perfectly matched layer (PML), applied directly at the fluid-structure interface, makes it possible to emulate the Sommerfeld radiation condition using FE meshes of minimal size. For those cases where the acoustic field is computed over a band of frequencies, the meshing process is simplified by the use of a wavelength-dependent rescaling of the PML coordinates. Quantitative geometry discretization guidelines are obtained from a priori estimates of small-scale structural wavelengths, which dominate the acoustic field at low to mid frequencies. One particularly useful feature of the PML is that it can be applied across the interface between different fluids. This makes it possible to use the present tool to solve problems where the radiating or scattering objects are located inside a layered fluid medium. The proposed technique is verified by comparison with analytical solutions and with validated numerical models. The solutions presented show close agreement for a set of test problems ranging from scattering to underwater propagation.     

Diastereoselective fragmentation of chiral alpha-aminophosphonic acids/metal ion aggregates

Diastereomeric clusters of general formula [MAB(2)](+) and [MA(2)B](+) (M = Li(I), Na(I), Ag(I), Ni(II)-H, or Cu(II)-H; A = (R)-(-)- and (S)-(+)-(1-aminopropyl)phosphonic acid; B = (1R)-(-)- and (1S)-(+)-(1-aminohexyl)phosphonic acid) have been readily generated in the electrospray ionization (ESI) source of a triple-quadrupole mass spectrometer and their collision-induced dissociation (CID) investigated. CID of diastereomeric complexes, e.g. [MA(S)(B(S))(2)](+) and [MA(R)(B(S))(2)](+), leads to fragmentation patterns characterized by R(homo) = [MA(S)B(S)](+)/[M(B(S))(2)](+) and R(hetero) = [MA(R)B(S)](+)/[M(B(S))(2)](+) abundance ratios, which depend upon the relative stability of the diastereomeric [MA(S)B(S)](+) and [MA(R)B(S)](+) complexes in the gas phase. The chiral resolution factor R(chiral) = R(homo)/R(hetero) is found to depend not only on the nature of the M ion but also on that of the fragmenting species, whether [MAB(2)](+) or [MA(2)B](+). The origin of this behavior is discussed.     

Retention effects of oxidized polyphenols during analytical extraction of phenolic compounds of virgin olive oil

The hydrophilic extract of virgin olive oil contains several phenolic compounds such as simple phenols, lignans, and secoiridoids that have been widely studied in recent years. Interest in the hydrophilic extract has also been extended to the fraction of oxidized phenols that form during storage as a consequence of oxidative stress. The present investigation compares the two most commonly used extraction methods, namely liquid-liquid extraction and SPE, on fresh virgin olive oil and that kept at different temperatures in the presence of oxygen to promote the formation of oxidative products. The selective retention of these natural and oxidized phenolic compounds in relation to the extraction method was assessed. Quantification of eight identified phenolic molecules and 11 unknown peaks was performed by HPLC-DAD/MSD.     

The role of the atomic charges on the ligands and platinum(II) in affecting the cis and trans influences in [PtXL(PPh3)2]+ complexes (X = NO3, Cl, Br, I; L = 4-substituted pyridines, amines, PPh3). A 31P NMR and DFT investigation

One bond Pt-P coupling constants (1)J(PtP) of a series of cationic complexes [PtXL(PPh(3))(2)](+) (X = NO(3), Cl, Br, I; L = 4-Z-pyridines, Z = electron withdrawing or releasing groups, 4a-k; or X = Cl, L = NH(3), PhCH(2)NH(2) and (i)PrNH(2), 5a-c) have been used to establish the trans and cis influence sequences of X and pyridines. The crystal structure of compound 4f(BF(4)) with Z = (t)Bu has been resolved. In the pyridine complexes 4a-d (Z = H, variable X), both the trans and cis influence series of the anionic ligands X decrease along the same sequence I > Br > Cl > NO(3), as previously found for [PtX(PPh(3))(3)](+) (X = NO(3), Cl, Br, I, 3a-d), however in 4a-d the cis influence turns out to be more important than the trans. On the contrary, in [PtCl(4-Z-py)(PPh(3))(2)](+) (4b,e-k) the sequence of the trans influence of the 4-Z-pyridines is opposite to that of the cis, the latter being Z = CN > CHO > Br > PhCO > H > Me > (t)Bu > NH(2), i.e. the most basic pyridine gives rise to the lowest cis influence. This correlation was found to hold also for complexes 5a-c (L = amines). All the observed trends have been fully reproduced by B3LYP/def2-SVP DFT calculations, by looking at the relevant optimized bond lengths of selected complexes of type 3, 4 and 5. Subsequent evaluation of the atomic charges, by resorting to two independent methods, i.e., the Natural Bond Order analysis of the wavefunction and the Bader's Quantum Theory of Atoms in Molecules, allowed for rationalization of the origin of the cis and trans influences. The negative charge on the nitrogen atoms of free pyridines becomes more negative upon protonation and even more so when coordinated to the [PtCl(PPh(3))(2)](+) moiety. The least negatively charged nitrogen atom of coordinated pyridines is that of 4-CN-py (the highest cis influencing pyridine derivative), which gives rise to the lowest positive charge on Pt, confirming the relationship between the lowering of the charge on the metal ion and a high cis influence. The trans influence can be described in terms of competition between the charges on the two trans donor atoms. In contrast with the behaviour of pyridines, the positive charge on the phosphorous atom of free PPh(3) increases upon coordination to Pt(II), moreover the PPh(3) ligands acquire a substantial positive charge, thus efficiently delocalising the charge of the cationic complex.     

Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance.     

Sensitizing effect of bio-based chemicals from urban wastes on the photodegradation of azo-dyes

To promote bio-based products for the industry, six bio-organic substances (cHALi) isolated from yard trimmings (green) and food (humid) urban residues aged under aerobic digestion for 0–60 days were investigated for their potential to perform as sensitizers for azo-dyes photodegradation. Ethylorange (EO) was used as probe molecule at 5 mg L^?1 starting concentration and irradiated in a closed Pyrex^® cell with a Xenon (1500 W) lamp and a cut-off filter for wavelengths below 340 nm or in a cylindrical photochemical reactor equipped with a 125 W medium pressure Hg lamp. The cHALi/EO ratio in the starting EO solution varied in the 0–200 (w/w) range. The % dye abatement was found a function of the irradiation time, of the type of cHALi substance and of the cHALi/EO ratio. The best results were achieved with cHALi isolated after 7 days biomass aerobic digestion. Total dye abatement was achieved within relatively short few hours. A progressive dye mineralization was observed under the same experimental conditions. On the contrary no significant degradation was evident for the cHALi substances within the same irradiation time. Several hydroxylated azo compounds were identified as likely responsible of residual color after total EO abatement. The results, coupled to the previously reported good performance of the same cHALi substances as auxiliaries for textile dyeing, augur well for the development of both efficient and environmentally friendly textile dyeing processes.     

Chiral Fibers Formation Upon Assembly of Tetraphenylalanine Peptide Conjugated to a PNA Dimer

Self-assembly of biomolecules such as peptides, nucleic acids or their analogues affords supramolecular objects, exhibiting structures and physical properties dependent on the amino-acid or nucleobase composition. Conjugation of the peptide diphenylalanine (FF) to peptide nucleic acids triggers formation of self-assembled structures, mainly stabilized by interactions between FF. In this work we report formation of homogeneous chiral fibers upon self-assembly of the hybrid composed of the tetraphenylalanine peptide (4F) conjugated to the PNA dimer adenine-thymine (at). In this case nucleobases seem to play a key role in determining the morphology and chirality of the fibers. When the PNA “at” is replaced by guanine-cytosine dimer “gc”, disordered structures are observed. Spectroscopic characterization of the self-assembled hybrids, along with AFM and SEM studies is reported. Finally, a structural model consistent with the experimental evidence has also been obtained, showing how the building blocks of 4Fat arrange to give helical fibers.