meso-Dichloropyrimidinyl substituted expanded porphyrins

Condensation of 4,6-dichloro-2-phenylpyrimidine-5-carbaldehyde with pyrrole enables the synthesis of a number of expanded porphyrins of which the [26]hexaphyrin was easily isolated and successfully converted into the decasubstituted doubly N-fused hexaphyrin variant.     

Matrix-isolation FT-IR spectroscopic study and theoretical DFT(B3LYP)/6-31++G** calculations of the vibrational and conformational properties of tyrosine

The complicated conformational isomerism of tyrosine is studied by experimental matrix-isolation FT-IR spectroscopy combined with theoretical DFT(B3LYP)/6-31++G** calculations. Not less than 18 possible conformations of tyrosine have been considered theoretically. The results revealed that the most and the less stable forms of neutral tyrosine have the same conformation of the main part of amino acid (conformation II) but they differ in orientation of the phenyl ring. The calculated values of the relative energies suggest that all conformations would be detectable in the experimental spectrum. However, it appeared that it is not possible to distinguish in the experimental spectrum between the bands due to the forms with the same conformation of the main part of amino acid but a different orientation of the phenol ring.     

Solvent effects on IR and VCD spectra of natural products: an experimental and theoretical VCD study of pulegone

The VCD spectra of pulegone, dissolved in CDCl3, CD2Cl2 and CS2 have been recorded in the frequency range from 1000 to 3000 cm(-1). The assignment of the absolute configuration was performed by comparing the experimental data with theoretical spectra computed at the B3LYP/6-311+G(d,p) level. Analysis of the agreement in several spectral regions revealed significant shortcomings when comparing with vacuum calculations. It is shown that the agreement improves when the solvent effects are taken into account by a continuum model. For the measurements in CDCl3 and CD2Cl2 further improvement was found when considering explicitly 1 : 1 complexes between a pulegone and a CDCl3 or CD2Cl2 solvent molecule in vacuo, while the best agreement was obtained when embedding these in a continuum model. The presence of the chiral solute was found to induce a VCD active C-D stretch band which could be modeled also at ab initio level.     

Low-frequency mode activity of heme: femtosecond coherence spectroscopy of iron porphine halides and nitrophorin

The low-frequency mode activity of metalloporphyrins has been studied for iron porphine-halides (Fe(P)(X), X = Cl, Br) and nitrophorin 4 (NP4) using femtosecond coherence spectroscopy (FCS) in combination with polarized resonance Raman spectroscopy and density functional theory (DFT). It is confirmed that the mode symmetry selection rules for FCS are the same as for Raman scattering and that both Franck-Condon and Jahn-Teller mode activities are observed for Fe(P)(X) under Soret resonance conditions. The DFT-calculated low-frequency (20-400 cm (-1)) modes, and their frequency shifts upon halide substitution, are in good agreement with experimental Raman and coherence data, so that mode assignments can be made. The doming mode is located at approximately 80 cm (-1) for Fe(P)(Cl) and at approximately 60 cm (-1) for Fe(P)(Br). NP4 is also studied with coherence techniques, and the NO-bound species of ferric and ferrous NP4 display a mode at approximately 30-40 cm (-1) that is associated with transient heme doming motion following NO photolysis. The coherence spectra of three ferric derivatives of NP4 with different degrees of heme ruffling distortion are also investigated. We find a mode at approximately 60 cm (-1) whose relative intensity in the coherence spectra depends quadratically on the magnitude of the ruffling distortion. To quantitatively account for this correlation, a new "distortion-induced" Raman enhancement mechanism is presented. This mechanism is unique to low-frequency "soft modes" of the molecular framework that can be distorted by environmental forces. These results demonstrate the potential of FCS as a sensitive probe of dynamic and functionally important nonplanar heme vibrational excitations that are induced by the protein environmental forces or by the chemical reactions in the aqueous phase.     

The Edge-Based Face Element Method for 3D-Stream Function and Flux Calculations in Porous Media Flow

We present a velocity-oriented discrete analog of the partial differential equations governing porous media flow: the edge-based face element method. Conventional finite element techniques calculate pressures in the nodes of the grid. However, such methods do not satisfy the requirement of flux continuity at the faces. In contrast, the edge-based method calculates vector potentials along the edges, leading to continuity of fluxes. The method is algebraically equivalent with the popular block-centered finite difference method and with the mixed-hybrid finite element method, but is algorithmically different and has the same robustness as the more conventional node-based velocity-oriented method. The numerical examples are computed analytically and may, therefore, be considered as an 'heuristic proof' of the theory and its practical applicability for reservoir engineering and geohydrology.     

How accurately do mechanophores report on bond scission in soft polymer materials?

Mechanophores are molecules that are incorporated into a host material and react to the local mechanical condition—the state of stress or strain—of that host material. Among their many purposes is that of a reporter: Mechanophores whose optical activity changes in response to mechanical cues can reveal bulk material processes that are ordinarily hidden, such as fatigue and fracture. Moreover, they may do so well before a material is fully fractured. To extract quantitative information from the optical signals from embedded mechanophores it is important that the mechanophores, which are generally a minority component of the material, report proportionally and unambiguously on the mechanical condition of the bulk. This is particularly important for early reporting of damage and wear, for which the optical signal from the mechanophore should accurately reflect bulk bond scission. In this article, we develop and analyze a general theory for the quality of optical mechanoreporting by mechanophores in soft materials, based on the Bell-Evans theory of bond breaking. We find, that at the typical low fractions in which mechanophores are incorporated the overall change in strength is limited, but that the proportionality of the reporting can be off by significant amounts, particularly at short times after loading but, for non-scissile bonds, at long times as well.     

Rotating States in Driven Clock- and XY-Models

We consider 3D active plane rotators, where the interaction between the spins is of XY-type and where each spin is driven to rotate. For the clock-model, when the spins take N≫1 possible values, we conjecture that there are two low-temperature regimes. At very low temperatures and for small enough drift the phase diagram is a small perturbation of the equilibrium case. At larger temperatures the massless modes appear and the spins start to rotate synchronously for arbitrary small drift. For the driven XY-model we prove that there is essentially a unique translation-invariant and stationary distribution despite the fact that the dynamics is not ergodic.     

Hyphenated techniques in anticancer drug monitoring. I. Capillary gas chromatography-mass spectrometry

Muramic acid (Mur) is present in the cell wall of Eubacteria and serves as a chemical marker for the trace detection of bacteria and bacterial cell wall debris in complex matrices. There have been numerous studies using a variety of derivatives of Mur, particularly in combination with gas chromatography-tandem mass spectrometry (GC-MS-MS) where the detection limit has been steadily lowered. A stable, halogenated derivative, the pentafluorobenzyl oxime (PFBO) acetate of Mur, has been developed by others and successfully used for GC with electron-capture detection. The current report is the first use of this derivative for GC-MS-MS analysis of Mur, or indeed any other carbohydrate, using negative ion chemical ionization (NICI) with GC-MS-MS. Mur was readily detected in settled surface dust (166 ng/mg), as well as dust collected from indoor air (1.4-5.9 ng/mg). Analyses of Mur as a PFBO acetate by GC-NICI-MS-MS or as alditol acetates by electron impact GC-electron impact ionization MS-MS serve as complementary approaches for trace detection in complex matrices.