Modeling chemoadaptive behavior: X-ray structure of the trimethylamine oxide-urea (1∶4) complex

The structure of a trimethylamine oxide (TMAO)-urea 14 complex was investigated by x-ray crystallographic methods. C₃H₉NO, 4CH₄N₂O, M_r=315.33, monoclinic P2₁/n, a=11.004(2), b=9.8259, c=15.419(2),=106.88(4), V=1595.4(2) å₃, Z=4, D_x=1.313(1) g cm^–3, monochromatized Cu (=1.5418 å),=8.94 cm^–1, F(OOO)=680, temperature = 110K, final R=0.067, for 1786 unique observed reflections. Based on these studies and comparison with related compounds a model of the interaction of urea and TMAO with proteins, especially enzymes, is proposed. This is important in the physiology of many organisms, especially elasmobranchs. The counteracting effect of TMAO on urea perturbation of protein structure and function is interpreted in terms of water structure as a balance between the structure breaking effect of urea and the structure-stabilizing effect of TMAO.     

Dynamically modified silica — the use of bare silica in reversed-phase high-performance liquid chromatography

A new approach to reversed-phase high-performance liquid chromatography has been developed and investigated in some detail. Bare silica is used as the column packing material with an aqueous eluent containing a buffer, an organic solvent as the modifier and a long-chain quaternary ammonium ion. The eluent exhibits a high affinity to the silica surface at pH values above 5, thus, dynamically, forming a nonpolar stationary phase.     

Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

Rotational CARS N2 thermometry: validation experiments for the influence of nitrogen spectral line broadening by hydrogen

Rotational coherent anti‐Stokes Raman spectroscopy (CARS) in fuel‐rich hydrocarbon flames, with a large content of hydrogen in the product gases (∼20%), has in previous work shown that evaluated temperatures are raised several tens of Kelvin by taking newly derived N₂ H₂ Raman line widths into account. To validate these results, in this work calibrated temperature measurements at around 300, 500 and 700 K were performed in a cell with binary gas mixtures of nitrogen and hydrogen. The temperature evaluation was made with respect to Raman line widths either from self‐broadened nitrogen only, N₂ N₂ [energy‐corrected‐sudden (ECS)], or by also taking nitrogen broadened by hydrogen, N₂ H₂ [Robert–Bonamy (RB)], Raman line widths into account. With increased amount of hydrogen in the cell at constant temperature, the evaluated CARS temperatures were clearly lowered with the use of Raman line widths from self‐broadened nitrogen only, and the case with inclusion of N₂ H₂ Raman line widths was more successful. The difference in evaluated temperatures between the two different sets increases approximately linearly, reaching 20 K (at T ∼ 300 K), 43 K (at T = 500 K) and 61 K (at T = 700 K) at the highest hydrogen concentration (90%). The results from this work further emphasize the importance of using adequate Raman line widths for accurate rotational CARS thermometry. Copyright © 2010 John Wiley & Sons, Ltd.     

A new "spectroscopic" potential energy surface for formaldehyde in its ground electronic state

We report a new "spectroscopic" potential energy surface (PES) of formaldehyde (H(2)(12)C(16)O) in its ground electronic state, obtained by refining an ab initio PES in a least-squares fitting to the experimental spectroscopic data for formaldehyde currently available in the literature. The ab initio PES was computed using the CCSD(T)/aug-cc-pVQZ method at 30 840 geometries that cover the energy range up to 44 000 cm(-1) above equilibrium. Ro-vibrational energies of formaldehyde were determined variationally for this ab initio PES by means of the program TROVE [Theoretical ROtation-Vibration Energies; S. N. Yurchenko, W. Thiel, and P. Jensen, J. Mol. Spectrosc. 245, 126 (2007)]. The parameter values in the analytical representation of the PES were optimized in fittings to 319 ro-vibrational energies with J = 0, 1, 2, and 5. The initial parameter values in the fittings were those of the ab initio PES, the ro-vibrational eigenfunctions obtained from this PES served as a basis set during the fitting process, and constraints were imposed to ensure that the refined PES does not deviate unphysically from the ab initio one in regions of configuration space not sampled by the experimental data. The resulting refined PES, referred to as H(2)CO-2011, reproduces the available experimental J ≤ 5 data with a root-mean-square error of 0.04 cm(-1).     

Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase

The catalytic mechanism of molybdenum containing CO dehydrogenase has been studied using hybrid DFT methods with quite large chemical models. The recent high-resolution X-ray structure, showing the surprising presence of copper linked to molybdenum, was used as a starting point. A pathway was initially found with a low barrier for C-O bond formation and CO2 release. However, this pathway did not include the formation of any S-CO2 species, which had been suggested by experiments with an n-butylisocyanide inhibitor. When these SCO2 structures were studied they were found to lead to deep minima, making CO2 release much more difficult. A large effort was spent, including investigations of other spin states, varying the number of protons and electrons, adding water, etc., until a plausible pathway for S-C bond cleavage was found. In this pathway a water molecule is inserted in between molybdenum and the SCO2 group. Full catalytic cycles, including electron and proton transfers, are constructed both with and without S-C bond formation. When these pathways are extended to two full catalytic cycles it can be understood why the formation of the S-C bond actually makes catalysis faster, even though the individual step of CO2 release becomes much more difficult. These results agree well with experimental findings.     

Functionalized foldamers: synthesis and characterization of a glycosylated beta-peptide 314-helix conveying the TN-antigen

Herein we describe the design, synthesis, and solution structure of a novel type of conjugate composed of a naturally occurring bio-active ligand bound to an artificial peptidomimetic backbone; in this first report on such functionalized foldamers we utilized a beta-peptide as backbone and a GalNAc carbohydrate residue as ligand.     

Synthesis of imidazoles as novel emivirine and S‐DABO analogues

5‐Alkyl‐4‐benzyl‐1,3‐dihydroimidazol‐2‐ones ( 3a‐d ) and 5‐alkyl‐4‐benzyl‐1,3‐dihydroimidazole‐2‐thiones (7a‐d) were prepared via Dakin West reaction on DL‐phenylalanine with the appropriate aliphatic acid anhydrides followed by hydrolysis and reaction with potassium cyanate or potassium thiocyanate. Compounds 3a‐d were alkylated with ethoxymethyl chloride to give the alkylated imidazoles 5a‐d which were considered analogues of Emivirine with deletion of carbonyl group at the 4‐position. Alkylation of 7a‐d afforded the corresponding S‐alkylated derivatives 8a‐p which in a similar way were considered analogues of S‐DABO. However all the imidazole derivatives were devoid of activity against HIV.     

The Degree of Disorder in Hardwood Kraft Pulps Studied by Means of LODP

The amount of disordered material in two types of hardwood kraft pulps was estimated by determining the weight loss at the point where the levelling-off degree of polymerisation (LODP) was reached. The pulps used were commercial pulps viz (1)one conventional birch kraft and (2)one mixed hardwood (MHW) kraft pulp that had been prehydrolysed prior to cooking. The results indicated that the hemicellulose xylan is closely associated with the cellulose in commercial birch pulps. It is therefore only possible to use LODP as a measure of the crystallite length of hardwood cellulose in highly purified pulps, such as prehydrolysed kraft pulp. A model explaining the LODP-results is proposed.