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Permanent link for this collectionhttps://hdl.handle.net/2022/25762
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Item 5-G MD Simulations(Wiley VCH, 2022) Lewis, Jared C.; Roux, Benoit; Li, Ying; Upp, DavidSee https://doi.org/10.1002/anie.202107982 An excerpt from the experimental of that manuscript is provided here: To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D. MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 3/2 100 3/2 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size. Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24Item Automated, Multistep Continuous-Flow Synthesis of 2,6-Dideoxy and 3-Amino-2,3,6-trideoxy Monosaccharide Building Blocks(2021) Subbarao, Yalamanchili; Nguyen, Tu-Anh; Zsikla, Alexander; Stamper, Gavin; DeYong, Ashley; Florek, John; Vasquez, Olivea; Pohl, Nicola; Bennett, ClayAn automated continuous flow system capable of producing protected deoxy-sugar donors from commercial material is described. Four 2,6-dideoxy and two 3-amino-2,3,6-trideoxy sugars with orthogonal protecting groups were synthesized in 11-32% overall yields in 74-131.5 minutes of total reaction time. Several of the reactions were able to be concatenated into a continuous process, avoiding the need for chromatographic purification of intermediates. The modular nature of the experimental setup allowed for reaction streams to be split into different lines for the parallel synthesis of multiple donors. Further, the continuous flow processes were fully automated and described through the design of an open-source Python-controlled automation platform.Item Hydrocarbon Oxidation by a Multiply Bonded Iron(III) Oxo Complex(2021) Valdez, Juan; Beagan, Daniel; Yang, Hao; Telser, Joshua; Hoffman, Brian; Pink, Maren; Carta, Veronica; Smith, JeremyItem Item Structural and spectroscopic characterization of an Fe(VI) bis(imido) complex(2020) Martinez, Jorge; Lutz, Sean; Yang, Hao; Xie, Jiaze; Telser, Joshua; Hoffman, Brian; Carta, Veronica; Pink, Maren; Losovyj, Yaroslav; Smith, Jeremy