Effects of dynamical couplings in IR spectra of the hydrogen bond in N-phenylacrylamide crystals

This article presents the investigation results of the polarized IR spectra of the hydrogen bond in N-phenylacrylamide crystals measured in the frequency range of the proton and deuteron, ν(N-H) and ν(N-D), stretching vibration bands. The basic spectral properties of the crystals were interpreted quantitatively in terms of the "strong-coupling" theory. The proposed model of the centrosymmetric dimer of hydrogen bonds facilitated the explanation of the well-developed, two-branch structure of the ν(N-H) and ν(N-D) bands as well as the isotopic dilution effects in the spectra. The vibronic mechanism of the generation of the long-wave branch of the ν(N-H) band ascribed to the excitation of the totally symmetric proton vibration was elucidated. The complex fine structure pattern of ν(N-H) and ν(N-D) bands in N-phenylacrylamide spectra in comparison with the spectra of other secondary amide crystals (e.g., N-methylacetamide and acetanilide) can be accounted for in terms of the vibronic model for the forbidden transition breaking in the dimers. On the basis of the linear dichroic and temperature effects in the polarized IR spectra of N-phenylacrylamide crystals, the H/D isotopic "self-organization" effects were revealed.     

Electronic structure of the two isomers of the anionic form of p-coumaric acid chromophore

A theoretical study of the electronic structure of the photoactive yellow protein (PYP) model chromophore, para-coumaric acid (p-CA), is presented. Electronically excited states of the phenolate and carboxylate isomers of the deprotonated p-CA are characterized by high-level ab initio methods including state-specific and multistate multireference pertrubation theory (SS-CASPT2, and MS-CASPT2), equation-of-motion coupled-cluster methods with single and double substitutions (EOM-CCSD) and with an approximate account of triple excitations (CC3). We found that the two isomers have distinctly different patterns of ionization and excitation energies. Their excitation energies differ by more than 1 eV, in contradiction to the experimental report [Rocha-Rinza et al., J. Phys. Chem. A 113, 9442 (2009)]. The calculations confirm metastable (autoionizing) character of the valence excited states of both phenolate and carboxylate isomers of p-CA(-) in the gas phase. The type of resonance is different in the two forms. In the phenolate, the excited state lies above the detachment continuum (a shape resonance), whereas in the carboxylate the excited π→π(*) state lies below the π-orbital ionization continuum, but is above the states derived from ionization from three other orbitals (Feshbach resonance). The computed oscillator strength of the bright electronic state in the phenolate is higher than in the carboxylate, in agreement with Hu?ckel's model predictions. The analysis of photofragmentation channels shows that the most probable products for the methylated derivatives of the phenolate and carboxylate forms of p-CA(-) are CH(3), CH(2)O and CH(3), CH(2)O, CO(2), respectively, thus suggesting an experimental probe that may discriminate between the two isomers.     

Structure elucidation and biosynthesis of lysine-rich cyclic peptides in Xenorhabdus nematophila

Thirteen novel PAX (peptide-antimicrobial-Xenorhabdus) peptides were identified in Xenorhabdus nematophila HGB081. Their structures including the absolute configuration were elucidated using a combination of labeling experiments, detailed MS/MS experiments, the advanced Marfey's method, and a detailed analysis of the biosynthesis gene cluster, which was identified as well.     

Odour-causing organic compounds in wastewater treatment plants: evaluation of headspace solid-phase microextraction as a concentration technique

Odorous emissions from wastewater collection systems and treatment facilities affecting quality of life have given local populations reasons to complain for decades. In order to characterise the composition of such malodorous emissions, a method based on headspace solid-phase microextraction (HS-SPME) and gas chromatography coupled to mass spectrometry (GC-MS) has been developed to determine a list of compounds belonging to different chemical families, which have been previously described as potentially responsible for odour complaints, in wastewater matrices. Some parameters affecting the chromatographic behaviour of the target compounds were studied (e.g. splitless time). Experimental conditions affecting the extraction process (temperature, time and salt content) were evaluated by applying a factorial design at two levels. Using a DVB/CAR/PDMS fibre and the optimised HS-SPME conditions, calibration curves were constructed with detection limits in the range of 0.003-0.6 μg L(-1). Recovery values higher than 70% and relative standard deviation values between 5 and 16% (n=5) were obtained for all compounds and found to be satisfactory. In wastewater samples, a decrease in the concentration of the analysed compounds through the different treatments was observed. Most of the target analytes were found in influent samples while only octanal and carvone were detected in samples from the plant effluent.     

Highly polar carbohydrates stack onto DNA duplexes via CH/π interactions

Carbohydrate-nucleic acid contacts are known to be a fundamental part of some drug-DNA recognition processes. Most of these interactions occur through the minor groove of DNA, such as in the calicheamicin or anthracycline families, or through both minor and major groove binders such as in the pluramycins. Here, we demonstrate that carbohydrate-DNA interactions are also possible through sugar capping of a DNA double helix. Highly polar mono- and disaccharides are capable of CH/π stacking onto the terminal DNA base pair of a duplex as shown by NMR spectroscopy. The energetics of the carbohydrate-DNA interactions vary depending on the stereochemistry, polarity, and contact surface of the sugar involved and also on the terminal base pair. These results reveal carbohydrate-DNA base stacking as a potential recognition motif to be used in drug design, supramolecular chemistry, or biobased nanomaterials.     

Poly(Acrylic Acid-b-Styrene) Amphiphilic Multiblock Copolymers as Building Blocks for the Assembly of Discrete Nanoparticles

In order to expand the utility of current polymeric micellar systems, we have developed amphiphilic multiblock copolymers containing alternating blocks of poly(acrylic acid) and poly(styrene). Heterotelechelic poly(tert-butyl acrylate-b-styrene) diblock copolymers containing an α-alkyne and an ω-azide were synthesized by atom transfer radical polymerization (ATRP), allowing control over the molecular weight while maintaining narrow polydispersity indices. The multiblock copolymers were constructed by copper-catalyzed azide-alkyne cycloaddition of azide-alkyne end functional diblock copolymers which were then characterized by (1)H NMR, FT-IR and SEC. The tert-butyl moieties of the poly(tert-butyl acrylate-b-styrene) multiblock copolymers were easily removed to form the poly(acrylic acid-b-styrene) multiblock copolymer ((PAA-PS)(9)), which contained up to 9 diblock repeats. The amphiphilic multiblock (PAA-PS)(9) (M(n) = 73.3 kg/mol) was self-assembled by dissolution into tetrahydrofuran and extensive dialysis against deionized water for 4 days. The critical micelle concentration (CMC) for (PAA-PS)(9) was determined by fluorescence spectroscopy using pyrene as a fluorescent probe and was found to be very low at 2 × 10(-4) mg/mL. The (PAA-PS)(9) multiblock was also analyzed by dynamic light scattering (DLS) and transmission electron microscopy (TEM). The hydrodynamic diameter of the particles was found to be 11 nm. Discrete spherical particles were observed by TEM with an average particle diameter of 14 nm. The poly(acrylic acid) periphery of the spherical particles should allow for future conjugation of biomolecules.     

Spontaneous waveguide Raman spectroscopy of self-assembled monolayers in silica micropores

Advances in nanoscience are critically dependent on the ability to control and probe chemical and physical phenomena in confined geometries. A key challenge is to identify confinement structures with high surface area to volume ratios and controlled surface boundaries that can be probed quantitatively at the molecular level. Herein we report an approach for probing molecular structures within nano- to microscale pores by the application of spontaneous Raman spectroscopy. We demonstrate the method by characterization of the structural features of picomole quantities of well-organized octadecyltrichlorosilane (OTS) monolayers self-assembled on the interior pore surfaces of high aspect ratio (1 μm diameter × 1-10 cm length), near-atomically smooth silica microstructured optical fibers (MOFs). The simple Raman backscattering collection geometry employed is well suited for a wide variety of diagnostic applications as demonstrated by tracking the combustion of the hydrocarbon chains of the OTS self-assembled monolayer (SAM) and spectral confirmation of the formation of an adsorbed monolayer of human serum albumin (HSA) protein. Using this MOF Raman approach, molecular processes in precisely defined, highly confined geometries can be probed at high pressures and temperatures, with a wide range of excitation wavelengths from the visible to the near-IR, and under other external perturbations such as electric and magnetic fields.     

Simultaneous production and purification ofBacillus subtilis α-amylase

Production of α-amylase withB. subtilis CCM 2722 in an aqueous two-phase polyethylene glycol/dextran system integrated with product purification by affinity chromatography on crosslinked starch during cultivation was studied. The medium was drawn from the bioreactor to the external settler during fermentation. After phase separation in the settler the dextran-rich bottom phase with cells was returned to the bioreactor. The PEG-rich top phase was pumped to the column with crosslinked starch and returned to the bioreactor after α-amylase adsorption. The same volumetric productivities, 0.53 U/mL/h, were reached in both batch and described process, but total productivity of the latter method was much higher owing to shortening upstream and downstream processing time. The enzyme of 98% homogenity in 95% yield was obtained after its elution from the column.     

Conformational properties of <Emphasis Type="Italic">ortho</Emphasis>-nitrobenzenesulfonamide in gas and crystalline phases. Intra- and intermolecular hydrogen bond

A combined gas-phase electron diffraction and quantum chemical (B3LYP/6-311+G**, B3LYP/cc-pvtz, MP2/cc-pvtz) study of molecular structure of 2-nitrobenzenesulfonamide (2-NBSA) was carried out. Quantum chemical calculations showed that 2-NBSA has four conformers, two of which are stabilized by intramolecular hydrogen bond. The latter (with the S–N bond in a close to orthogonal position around the phenyl ring and differing from each other by staggered or eclipsed positions of the N–H and S=O bonds in the SO₂NH₂ group) presented in a saturated vapor over 2-NBSA at T = 433 (3) K in commensurable amounts. Experimental internuclear distances (Ǻ) for the staggered conformer are (?): r _h1(C–H)_av. = 1.071(9), r _h1(C–C)_av. = 1.390(4), r _h1(C–S) = 1.789(8), r _h1(S=O)_av. = 1.427(6), r _h1(S–N) = 1.644(6), r _h1(N–O)_av. = 1.221(4), r _h1(C′–N) = 1.487(8), r _h1(N–H)_av. = 1.014. Calculations at B3LYP/cc-pvtz level were performed to determine the structure and the energies of the transition states between conformers. It was shown that the conformer structures of free molecule differ from those of a molecule stabilized by intermolecular hydrogen bonds in a crystal. Influence of a substituent X (X = –CH₃, –NO₂) on conformational features of the ortho-substituted benzenesulfonamide was established.