Blantonsanders1431

The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.The prevalence of intrinsically disordered proteins (IDPs) and protein regions in structural biology has prompted the recent development of molecular dynamics (MD) force fields for the more realistic representations of such systems. Using experimental nuclear magnetic resonance backbone scalar 3J-coupling constants of the intrinsically disordered proteins α-synuclein and amyloid-β in their native aqueous environment as a metric, we compare the performance of four recent MD force fields, namely, AMBER ff14SB, CHARMM C36m, AMBER ff99SB-disp, and AMBER ff99SBnmr2, by partitioning the polypeptides into an overlapping series of heptapeptides for which a cumulative total of 276 μs MD simulations were performed. The results show substantial differences between the different force fields at the individual residue level. Except for ff99SBnmr2, the force fields systematically underestimate the scalar 3J(HN,Hα)-couplings due to an underrepresentation of β-conformations and an overrepresentation of either α- or PPII conformations. The study demonstrates that the incorporation of coil library information in modern MD force fields, as shown here for ff99SBnmr2, provides substantially improved performance and more realistic sampling of the local backbone dihedral angles of IDPs as reflected by the good accuracy of the computed scalar 3J(HN,Hα)-couplings with less than 0.5 Hz error. Such force fields will enable a better understanding of how structural dynamics and thermodynamics influence the IDP function. Although the methodology based on heptapeptides used here does not allow the assessment of potential intramolecular long-range interactions, its computational affordability permits well-converged simulations that can be easily parallelized. This should make the quantitative validation of intrinsic disorder observed in MD simulations of polypeptides with experimental scalar J-couplings widely applicable.A key step in gas-phase polycyclic aromatic hydrocarbon (PAH) formation involves the addition of acetylene (or other alkyne) to σ-type aromatic radicals, with successive additions yielding more complex PAHs. A similar process can happen for N-containing aromatics. In cold diffuse environments, such as the interstellar medium, rates of radical addition may be enhanced when the σ-type radical is charged. This paper investigates the gas-phase ion-molecule reactions of acetylene with nine aromatic distonic σ-type radical cations derived from pyridinium (Pyr), anilinium (Anl), and benzonitrilium (Bzn) ions. Three isomers are studied in each case (radical sites at the ortho, meta, and para positions). Using a room temperature ion trap, second-order rate coefficients, product branching ratios, and reaction efficiencies are measured. The rate coefficients increase from para to ortho positions. Selleckchem TP-0903 The second-order rate coefficients can be sorted into three groups low, between 1 and 3 × 10-12 cm3 molecule-1 s-1 (3Anl and 4Anl); intermediate, between 5 and 15 × 10-12 cm3 molecule-1 s-1 (2Bzn, 3Bzn, and 4Bzn); and high, between 8 and 31 × 10-11 cm3 molecule-1 s-1 (2Anl, 2Pyr, 3Pyr, and 4Pyr); and 2Anl is the only radical cation with a rate coefficient distinctly different from its isomers. Quantum chemical calculations, using M06-2X-D3(0)/6-31++G(2df,p) geometries and DSD-PBEP86-NL/aug-cc-pVQZ energies, are deployed to rationalize reactivity trends based on the stability of prereactive complexes. The G3X-K method guides the assignment of product ions following adduct formation. The rate coefficient trend can be rationalized by a simple model based on the prereactive complex forward barrier height.Oxidation of ammonium to nitrite rather than nitrate, i.e., nitritation, is critical for autotrophic nitrogen removal. This study demonstrates a robust nitritation process in treating low-strength wastewater, obtained from a mixture of real mainstream sewage with sidestream anaerobic digestion liquor. This is achieved through cultivating acid-tolerant ammonia-oxidizing bacteria (AOB) in a laboratory nitrifying bioreactor at pH 4.5-5.0. It was shown that nitrite accumulation with a high NO2-/(NO2- + NO3-) ratio of 95 ± 5% was stably maintained for more than 300 days, and the obtained volumetric NH4+ removal rate (i.e., 188 ± 14 mg N L-1 d-1) was practically useful. 16S rRNA gene sequencing analyses indicated the dominance of new AOB, "Candidatus Nitrosoglobus," in the nitrifying guild (i.e., 1.90 ± 0.08% in the total community), with the disappearance of typical activated sludge nitrifying microorganisms, including Nitrosomonas, Nitrospira, and Nitrobacter. This is the first identification of Ca. Nitrosoglobus as key ammonia oxidizers in a wastewater treatment system. It was found that Ca. Nitrosoglobus can tolerate low pH ( less then 5.0), and free nitrous acid (FNA) at levels that inhibit AOB and nitrite-oxidizing bacteria (NOB) commonly found in wastewater treatment processes. The in situ inhibition of NOB leads to accumulation of nitrite (NO2-), which along with protons (H+) also produced in ammonium oxidation generates and sustains FNA at 3.0 ± 1.4 mg HNO2-N L-1. As such, robust PN was achieved under acidic conditions, with a complete absence of NOB. Compared to previous nitritation systems, this acidic nitritation process is featured by a higher nitric oxide (NO) but a lower nitrous oxide (N2O) emission level, with the emission factors estimated at 1.57 ± 0.08 and 0.57 ± 0.03%, respectively, of influent ammonium nitrogen load.We show the synthesis and characterization of four heterobimetallic compounds derived from s-indacene of general formula [(CO)3Mn-s-Ic-MCp*]q with M = Fe, Co, Ni, and Ru; q = 0, 1+. The complexes reported here were characterized by 1H and 13C NMR, elemental analysis and FT-IR. Additionally, the X-ray crystal structure of [(CO)3Mn-s-Ic-FeCp*] (1) and Mössbauer spectra are reported. The heterobimetallic compounds exhibit higher quasireversible redox potentials compared with ferrocene and catocene under the same reaction conditions. The complexes were tested as catalysts on the thermal decomposition of ammonium perchlorate examined by a differential scanning calorimetry technique to study their catalytic behavior. Compound (1) causes a decrease of ammonium perchlorate's decomposition temperature to 315 °C, consequently increasing the heat release by 138 J·g-1. Conversely, [(CO)3Mn-s-Ic'-CoCp*] (2) presents a higher heat release (2462 J·g-1), comparable to catocene.