Methods for extracting biochemical information from bacterial Raman spectra: focus on a group of structurally similar biomolecules--fatty acids

In this paper we explore the possibilities of Raman spectroscopy in order to deduce information on the fatty acid composition of bacterial cells. Therefore, representative strains of two bacterial taxa were each cultured in different conditions and in parallel analyzed by Raman spectroscopy and gaschromatographic FAME analysis. Raman spectra of pure fatty acids were recorded and used as reference spectra. The culturing conditions for each strain could be easily distinguished by the fatty acid information retrieved from bacterial Raman spectra. Chemometric techniques such as EMSC and PCA allowed to extract information about groups of fatty acids, that was consistent with the results from FAME analysis. Although the information retrieved from Raman spectroscopy is not as refined as that from FAME analysis, the presented methods could be useful to obtain basic information on the fatty acid present in bacteria when performing Raman spectroscopic analysis for fast whole cell profiling, which provides information for different types of cell components (fatty acids, amino acids, primary metabolites, etc.).     

Effect of the metal environment on the ferromagnetic interaction in the Co-NC-W pairs of octacyanotungstate(V)-Cobalt(II) three-dimensional networks

State of the art CASSCF and CASPT2 calculations have been performed to elucidate the nature of ferromagnetism of CoII-NC-WV pairs in the three-dimensional compound [[WV(CN)2]2[(micro-CN)4CoII(H2O)2]3.4H2O]n, which has been recently synthesized and investigated by a number of experimental techniques (Herrera, J. M.; Bleuzen, A.; Dromzée, Y.; Julve, M.; Lloret, F.; Verdaguer, M. Inorg. Chem. 2003, 42, 7052-7059). In this network, the Co ions are in the high-spin (S = 3/2) state, while the single unpaired electron on the W centers occupies the lowest orbital of the dz2 type of the 5d shell. In agreement with the suggestion made by Herrera et al., we find that the ferromagnetism is due to a certain occupation scheme of the orbitals from the parent octahedral t2g shell on CoII sites, in which the orbital accommodating the unpaired electron is orthogonal to the dz2 orbitals of the surrounding W ions. We investigate the stabilization of such an orbital configuration on the Co sites and find that it cannot be achieved in the ground state of isolated mononuclear fragments [CoII(NC)4(OH2)2]2- for any conformations of the coordinated water molecules and Co-N-C bond angles. On the other hand, it is stabilized by the interaction of the complex with neighboring W ions, which are simulated here by effective potentials. The calculated exchange coupling constants for the CoII-NC-WV binuclear fragments are in reasonable agreement with the measured Curie-Weiss constant for this compound. As additional evidence for the inferred electronic configuration on the Co sites, the ligand-field transitions, the temperature-dependent magnetic susceptibility, and the field-dependent low-temperature magnetization, simulated ab initio for the mononuclear Co fragments, are in agreement with the available data for another compound [WIV[(micro-CN)4-CoII(H2O)2]2.4H2O]n containing diamagnetic W and high-spin Co ions in an isostructural environment.     

A CASPT2 study of the electronic spectrum of hexacyanoosmate(III)

CASPT2 calculations reveal that the ligand field splitting parameter Delta(o) of [Os(CN)6]3- is much higher than previously proposed values of +/-38,000 cm(-1). In line with the expected increase down a transition-metal group, Delta(o) is found to be +/-55,000 cm(-1), excluding the possible appearance of ligand field transitions in the UV-vis spectrum. Instead, the calculations confirm that the observed spectrum arises from the three lowest symmetry-allowed ligand-to-metal charge-transfer (LMCT) excitations. Spin-orbit coupling in the ground state is found to be about 4350 cm(-1), leading to a spin-orbit coupling constant zeta of +/-2900 cm(-1). Spin-orbit coupling in the 2T(1u) LMCT states is found not to be negligible, contrary to previous belief.     

Synthesis and application of a carbamazepine-imprinted polymer for solid-phase extraction from urine and wastewater

A molecularly imprinted polymer (MIP) designed to enable the selective extraction of carbamazepine (CBZ) from effluent wastewater and urine samples has been synthesised using a non-covalent molecular imprinting approach. The MIP was evaluated chromatographically in the first instance and its affinity for CBZ also confirmed by solid-phase extraction (SPE). The optimal conditions for SPE consisted of conditioning of the cartridge using acidified water purified from a Milli-Q system, loading of the sample under basic aqueous conditions, clean-up using acetonitrile and elution with methanol. The attractive molecular recognition properties of the MIP gave rise to good CBZ recoveries (80%) when 100 mL of effluent water spiked with 1 μg L⁻¹ was percolated through the polymer. For urine samples, 2 mL samples spiked with 2.5 μg L⁻¹ CBZ were extracted with a recovery of 65%. For urine, the linear range was 0.05-24 mg L⁻¹, the limit of detection was 25 μg L⁻¹ and precision, expressed as relative standard deviation at 0.5 mg L⁻¹ (n = 3), was 3.1% and 12.6% for repeatability and reproducibility between days, respectively.     

Pair interaction potentials with explicit polarization for molecular dynamics simulations of La(3+) in bulk water

Pair interaction potentials (IPs) were defined to describe the La(3+)-OH(2) interaction for simulating the La(3+) hydration in aqueous solution. La(3+)-OH(2) IPs are taken from the literature or parametrized essentially to reproduce ab initio calculations at the second-order Moller-Plesset level of theory on La(H(2)O)(8) (3+). The IPs are compared and used with molecular dynamics (MD) including explicit polarization, periodic boundary conditions of La(H(2)O)(216) (3+) boxes, and TIP3P water model modified to include explicit polarization. As expected, explicit polarization is crucial for obtaining both correct La-O distances (r(La-O)) and La(3+) coordination number (CN). Including polarization also modifies hydration structure up to the second hydration shell and decreases the number of water exchanges between the La(3+) first and second hydration shells. r(La-O) ((1))=2.52 A and CN((1))=9.02 are obtained here for our best potential. These values are in good agreement with experimental data. The tested La-O IPs appear to essentially account for the La-O short distance repulsion. As a consequence, we propose that most of the multibody effects are correctly described by the explicit polarization contributions even in the first La(3+) hydration shell. The MD simulation results are slightly improved by adding a-typically negative 1r(6)-slightly attractive contribution to the-typically exponential-repulsive term of the La-O IP. Mean residence times are obtained from MD simulations for a water molecule in the first (1082 ps) and second (7.6 ps) hydration shells of La(3+). The corresponding water exchange is a concerted mechanism: a water molecule leaving La(H(2)O)(9) (3+) in the opposite direction to the incoming water molecule. La(H(2)O)(9) (3+) has a slightly distorded "6+3" tricapped trigonal prism D(3h) structure, and the weakest bonding is in the medium triangle, where water exchanges take place.     

Structural and mechanistic studies of bis(phenolato)amine zinc(II) catalysts for the polymerization of epsilon-caprolactone

The syntheses, characterization, epsilon-caprolactone (CL) polymerization activity, and kinetics investigation of two zinc(II) bis(phenolato)amine complexes L2Zn2 are reported (L = methylamino-N,N-bis(2-methylene-4,6-di-tert-butylphenolato) and/or methylamino-N,N-bis(2-methylene-4-adamantyl-6-tert-butylphenolato)). X-ray crystallographic and 1H NMR studies, including NOESY and PGSE experiments, provided insight into the solid and solution state structures, respectively, as well as evidence for the catalytically active species responsible for the ring-opening polymerization of CL. Additionally, solution polymerizations and kinetic experiments involving (L1)2Zn2 in the presence of benzyl alcohol (BnOH) were performed to elucidate the influence of catalyst structure, solvent, and the concentration dependence of the catalytically active species, CL, and BnOH on the rate and control of poly-epsilon-caprolactone (PCL) formation. The structural, polymerization, and kinetic data support equilibria involving both mononuclear and dinuclear forms of (L1)2Zn2 as well as a monomer-activated route to PCL.     

Conformationally restricted (+)-cacospongionolide B analogues. Influence on secretory phospholipase A2 inhibition

A new approach to (+)-cacospongionolide was developed to access conformationally restricted variants of the natural product. The flexible aliphatic region between the decalin and side chain portion of the natural product was replaced with alkenyl and alkynyl linkers to probe the influence of structural rigidity in the inhibition of secretary phospholipase A2 (sPLA2). It was found that when the aliphatic section is replaced with a Z-olefin or an alkyne, sPLA2 inhibitory activity suffered relative to the natural product; however, an E-olefin-containing analogue led to an enhanced activity. These results suggest that preferred sPLA2 binding conformation of the natural product is similar to the geometry of the E-olefin-containing analogue.     

A low-cost, disposable card for rapid polymerase chain reaction

A low-cost, disposable card for rapid polymerase chain reaction (PCR) was developed in this work. Commercially available, adhesive-coated aluminum foils and polypropylene films were laminated with structured polycarbonate films to form microreactors in a card format. Ice valves [1] were employed to seal the reaction chambers during thermal cycling and a Peltier-based thermal cycler was configured for rapid thermal cycling and ice valve actuation. Numerical modeling was conducted to optimize the design of the PCR reactor and investigate the thermal gradient in the reaction chamber in the direction of sample thickness. The PCR reactor was experimentally characterized by using thin foil thermocouples and validated by a successful amplification of 10 copy of E. coli tuf gene in 27 min.     

On the regularity of products and intersections of complete intersections

This paper proves the formulae

for arbitrary monomial complete intersections and , and provides examples showing that these inequalities do not hold for general complete intersections.

     

Some 3-manifolds and 3-orbifolds with large fundamental group

We provide two new proofs of a theorem of Cooper, Long and Reid which asserts that, apart from an explicit finite list of exceptional manifolds, any compact orientable irreducible 3-manifold with non-empty boundary has large fundamental group. The first proof is direct and topological; the second is group-theoretic. These techniques are then applied to prove a string of results about (possibly closed) 3-orbifolds, which culminate in the following theorem. If is a knot in a compact orientable 3-manifold such that the complement of admits a complete finite-volume hyperbolic structure, then the orbifold obtained by assigning a singularity of order along has large fundamental group for infinitely many positive integers . We also obtain information about this set of values of . When is the 3-sphere, this has implications for the cyclic branched covers over the knot. In this case, we may also weaken the hypothesis that the complement of is hyperbolic to the assumption that is non-trivial.