Variational Phase Field Modeling of Fracture Caused by Fluid Transport in Poroelastic Solids

The numerical modeling of failure mechanisms due to fracture based on sharp crack discontinuities is extremely demanding and suffers in situations with complex crack topologies. This drawback can be overcome by recently developed diffusive crack modeling concepts, which are based on the introduction of a crack phase field. Such an approach is conceptually in line with gradient-extended continuum damage models which include internal length scales. In this paper, we extend our recently outlined mechanical framework [1–3] towards the phase field modeling of fracture in the coupled problem of fluid transport in deforming porous media. Here, extremely complex crack patterns may occur due to drying or hydraulic induced fracture, the so called fracking. We develop new variational potentials for Biot-type fluid transport in porous media at finite deformations coupled with phase field fracture. It is shown, that this complex coupled multi-field problem is related to an intrinsic mixed variational principle for the evolution problem. This principle determines the rates of deformation, fracture phase field and fluid content along with the fluid potential. We develop a robust computational implementation of the coupled problem based on the potentials mentioned above and demonstrate its performance by the numerical simulation of complex fracture patterns. (© 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Processes To Separate Enantiomers

The provision of pure enantiomers is of increasing importance not only for the pharmaceutical industry but also for agrochemistry and biotechnology. In general, there are two rival approaches to provide pure enantiomers. The “chiral” approach is based on developing an asymmetric synthesis of just one of the enantiomers, while the “racemic” approach is based on separating mixtures of the two enantiomers. In the last few years remarkable progress has been achieved in the latter area. This Review focuses in particular on enantioselective crystallization processes and preparative chromatography, including hybrid processes and the incorporation of racemization steps. Several examples from our research are used for illustration purposes.     

Relating surface-enhanced Raman scattering signals of cells to gold nanoparticle aggregation as determined by LA-ICP-MS micromapping

The cellular response to nanoparticle exposure is essential in various contexts, especially in nanotoxicity and nanomedicine. Here, 14-nm gold nanoparticles in 3T3 fibroblast cells are investigated in a series of pulse-chase experiments with a 30-min incubation pulse and chase times ranging from 15 min to 48 h. The gold nanoparticles and their aggregates are quantified inside the cellular ultrastructure by laser ablation inductively coupled plasma mass spectrometry micromapping and evaluated regarding the surface-enhanced Raman scattering (SERS) signals. In this way, both information about their localization at the micrometre scale and their molecular nanoenvironment, respectively, is obtained and can be related. Thus, the nanoparticle pathway from endocytotic uptake, intracellular processing, to cell division can be followed. It is shown that the ability of the intracellular nanoparticles and their accumulations and aggregates to support high SERS signals is neither directly related to nanoparticle amount nor to high local nanoparticle densities. The SERS data indicate that aggregate geometry and interparticle distances in the cell must change in the course of endosomal maturation and play a critical role for a specific gold nanoparticle type in order to act as efficient SERS nanoprobe. This finding is supported by TEM images, showing only a minor portion of aggregates that present small interparticle spacing. The SERS spectra obtained after different chase times show a changing composition and/or structure of the biomolecule corona of the gold nanoparticles as a consequence of endosomal processing.     

Chromophore/DNA interactions: femto- to nanosecond spectroscopy, NMR structure, and electron transfer theory

The mechanism of photoinduced hole injection into DNA has been studied using an integrated approach that combines NMR structural analysis, time-resolved spectroscopy, and quantum-chemical calculations. A covalently linked acridinium derivative, the protonated 9-amino-6-chloro-2-methoxyacridine (X+), is replacing a thymine and separated from either guanine (G) or the easier to oxidize 7-deazaguanine (Z) by one adenine.thymine (A.T) base pair. The key features of this donor/acceptor system are the following: (i) In more than 95% of the duplexes, X+ is located in a central, coplanar position between the neighboring A.T base pairs with its long axis in parallel showing minimal twist and tilt angles (<15 degrees). The complementary adenine base is turned out into the extrahelical space. In a minority of less than 5%, X+ is found to be still attached to the duplex. X+ is most probably associated with one of the phosphates, since it is neither intercalated between more remote base pairs nor bound to sugars or grooves. This minority characterized by an excited state lifetime >10 ns gives rise to a small background signal in time-resolved measurements and contributes predominantly to steady-state fluorescence spectra. (ii) Although the intercalation mode of X+ is well defined, the NMR structure reveals that there are two conformations of X+ with respect to the arrangement of its methoxy substituent. In one conformation, the methoxy group is in the plane of the chromophore, while, in the other extraplanar conformation, the methoxy group forms an angle of 70 degrees with the acridinium ring. The fluorescence decay of 5'-ZAX and 5'-GAX tracts can be fitted to a biexponential function with similar amplitudes, reflecting the oxidation dynamics of G and Z, with the slower rate being determined by larger thermal activation energy. The attribution of biexponential electron transfer (ET) dynamics to the bimodal orientation of the methoxy group at the acridinium is supported by quantum-chemical calculations. These predict a larger free energy change for hole transfer in the nonplanar conformation as compared to the planar one, whereas the difference in the electronic couplings is negligible. (iii) Kinetic studies of the directionality of the 1(X+)* induced hole injection reveal similarly fast decay components in both directions of the duplex, that is, in 5'-ZAX and 5'-XAZ, with the amplitude of the fast component being significantly reduced in 5'-XAZ. The NMR structure shows that local structural deviations from B-DNA are much more pronounced in the 3'-5' direction than in the 5'-3' direction. According to quantum-chemical calculations, the directionality of charge injection is not a universal feature of the DNA duplex but depends critically on the rotation angle of the aromatic plane of the acridinium within the pi stack. The arrangement of X+ in 5'-ZAX and 5'-XAZ corresponds to a conformation with weak directionality of the electronic couplings. The increased disorder in the 3'-5'direction favors slow hole transfer components at the expense of the fast ones. (iv) A comparison of the hole transfer in 5'-GAX and 5'-ZAG shows that classical Marcus theory can explain the ratio of the charge shift rates of more than 2 orders of magnitude on the basis of a free energy difference between G and Z of 0.3 eV. Both NMR structures and quantum-chemical calculations justify the appreciable neglect of differences of electronic couplings as well as in the reorganization energy in 5'-GAX and 5'-ZAG. Despite the attractive concept for the behavior of floppy DNA oligonucleotides, in this acridinium/DNA system, there is no evidence for conformational gating, that is, for fluctuations in the electronic couplings that permit the ET to occur.     

Intestinal permeability of cyclic peptides: common key backbone motifs identified

Insufficient oral bioavailability is considered as a key limitation for the widespread development of peptides as therapeutics. While the oral bioavailability of small organic compounds is often estimated from simple rules, similar rules do not apply to peptides, and even the high oral bioavailability that is described for a small number of peptides is not well understood. Here we present two highly Caco-2 permeable template structures based on a library of 54 cyclo(-D-Ala-Ala(5)-) peptides with different N-methylation patterns. The first (all-trans) template structure possesses two β-turns of type II along Ala(6)-D-Ala(1) and Ala(3)-Ala(4) and is only found for one peptide with two N-methyl groups at D-Ala(1) and Ala(6) [(NMe(1,6)]. The second (single-cis) template possesses a characteristic cis peptide bond preceding Ala(5), which results in type VI β-turn geometry along Ala(4)-Ala(5). Although the second template structure is found in seven peptides carrying N-methyl groups on Ala(5), high Caco-2 permeability is only found for a subgroup of two of them [NMe(1,5) and NMe(1,2,4,5)], suggesting that N-methylation of D-Ala(1) is a prerequisite for high permeability of the second template structure. The structural similarity of the second template structure with the orally bioavailable somatostatin analog cyclo(-Pro-Phe-NMe-D-Trp-NMe-Lys-Thr-NMe-Phe-), and the striking resemblance with both β-turns of the orally bioavailable peptide cyclosporine A, suggests that the introduction of bioactive sequences on the highly Caco-2 permeable templates may result in potent orally bioavailable drug candidates.     

Two‐Dimensional Infrared Spectroscopy Reveals the Structure of an Evans Auxiliary Derivative and Its SnCl4 Lewis Acid Complex

Determining the structure of reactive intermediates is the key to understanding reaction mechanisms. To access these structures, a method combining structural sensitivity and high time resolution is required. Here ultrafast polarization‐dependent two‐dimensional infrared (P2D‐IR) spectroscopy is shown to be an excellent complement to commonly used methods such as one‐dimensional IR and multidimensional NMR spectroscopy for investigating intermediates. P2D‐IR spectroscopy allows structure determination by measuring the angles between vibrational transition dipole moments. The high time resolution makes P2D‐IR spectroscopy an attractive method for structure determination in the presence of fast exchange and for short‐lived intermediates. The ubiquity of vibrations in molecules ensures broad applicability of the method, particularly in cases in which NMR spectroscopy is challenging due to a low density of active nuclei. Here we illustrate the strengths of P2D‐IR by determining the conformation of a Diels–Alder dienophile that carries the Evans auxiliary and its conformational change induced by the complexation with the Lewis acid SnCl₄, which is a catalyst for stereoselective Diels–Alder reactions. We show that P2D‐IR in combination with DFT computations can discriminate between the various conformers of the free dienophile N‐crotonyloxazolidinone that have been debated before, proving antiperiplanar orientation of the carbonyl groups and s‐cis conformation of the crotonyl moiety. P2D‐IR unequivocally identifies the coordination and conformation in the catalyst–substrate complex with SnCl₄, even in the presence of exchange that is fast on the NMR time scale. It resolves a chelate with the carbonyl orientation flipped to synperiplanar and s‐cis crotonyl configuration as the main species. This work sets the stage for future studies of other catalyst–substrate complexes and intermediates using a combination of P2D‐IR spectroscopy and DFT computations.     

Mass transport characteristics of alkyl amines in a water/n-decane system

Rhenium (Re) nanoparticles have been synthesized by pulsed-laser decomposition of ammonium perrhenate (NH(4)ReO(4)) or dirhenium decacarbonyl (Re(2)(CO)(10)) in the presence of 3-mercaptopropionic acid (MPA) as capping agent, in both aqueous and organic media. Preliminary studies showed that the MPA-capped Re nanoparticles are capable of catalyzing the isomerization of 10-undecen-1-ol to internal alkenols via long chain migration of the C=C double bond at ca. 200°C. A one-pot synthesis of graphite-coated Re nanoparticles has also been achieved by pulsed-laser decomposition of Re(2)(CO)(10), due to photo-induced catalytic graphitization of the phenyl groups of PPh(3) on the surface of rhenium nanoparticles.     

A new synthesis for thermolabile low-valent palladium complexes by electron transfer reactions from nickel(0) to palladium(II) compounds

The nickel(0) complex [Ni(bpy)(cod)] (bpy: 2,2′-bipyridine, cod: cycloocta-1,5-diene) was used as a mild reducing reagent for the synthesis of the extremely reactive low-valent palladium complexes [Pd₂X₂(cod)₂] (1: X = Cl, 2: X = Br), Pd(cod)₂ (3) and Pd(norbornene)₃ (4). The X-ray analysis of 1 showed that the two [Pd(cod)(Cl)] moieties are only connected by a short Pd(I)-Pd(I) bond (bond length: 2.5379(4) Å) with the chloride ions as monodentate ligands. The X-ray structure of 3 which is also known to be an extremely reactive compound could be determined by X-ray diffraction. As expected, the Pd(0) centre is surrounded by the two cod ligands to form a PdC₄ tetrahedron with typical Pd-C bond lengths. The crystal structure of 3 shows it to be very similar to the closely related complexes M(cod)₂ (M: Ni, Pt). The X-ray structure of 4 displays that the Pd(0) centre is in a trigonal planar environment of the three olefin groups. According to ¹H NMR measurements the complexes have the same structure in solution as found in the solid state.     

Electron emission from photo-excited testosterone in water–ethanol solution

Testosterone (TES; 4-androstene-17β-ol-3-on) is found for the first time to eject electrons from its singlet excited state in water–ethanol solvent mixture. This ability was very recently also observed for 17β-estradiol (17βE2) and progesterone (PRG)/1/. With increasing TES-concentration, the yield of solvated electrons (${\text{e}}_{\text{s}}^{-}$) is decreasing, because of “associate” formation. At higher absorbed UV-doses (λ = 254 nm) the ${\text{e}}_{\text{s}}^{-}$ yield is passing a sharp maximum by formation of TES–ethanol adducts, which are able likewise to emit electrons when excited. At prolonged irradiation the resulting photolytic products of TES–ethanol adducts are also able to emit electrons.The capability of the hormones: 17βE2, PRG and TES to eject electrons and the resulting metabolites, some of which can induce cancer, is discussed.