November Research Round-Up

Congratulations to our amazing research teams here in the Department of Chemistry for their publications this month!

Bowman Group:

Chen, Q., & Bowman, J. M. (2018). Quantum approaches to vibrational dynamics and spectroscopy: is ease of interpretation sacrificed as rigor increases?Physical Chemistry Chemical Physics.

Yang, B., Zhang, P., Chen, Q., Stancil, P., Bowman, J. M., Naduvalath, B., & Forrey, R. C. (2018). Inelastic Vibrational Dynamics of CS in Collision with H2 Using a Full-dimensional Potential Energy SurfacePhysical Chemistry Chemical Physics.

Dunham Group:

Hong, S., Sunita, S., Maehigashi, T., Hoffer, E. D., Dunkle, J. A., & Dunham, C. M. (2018). Mechanism of tRNA-mediated+ 1 ribosomal frameshiftingProceedings of the National Academy of Sciences115(44), 11226-11231.

Rivera, S., Young, P. G., Hoffer, E. D., Vansuch, G. E., Metzler, C. L., Dunham, C. M., & Weinert, E. E. (2018). Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled SensorsInorganic chemistry.

Hoffer, E. D., Maehigashi, T., Fredrick, K., & Dunham, C. M. (2018). Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscodingNucleic Acids Research.

Hill Group:

Sullivan, K. P., Wieliczko, M., Kim, M., Yin, Q., Collins-Wildman, D. L., Mehta, A. K., … & Hill, C. L. (2018). Speciation and Dynamics in the [Co4V2W18O68] 10-/Co (II) aq/CoOx Catalytic Water Oxidation SystemACS Catalysis.

Kaledin, A. L., Troya, D., Karwacki, C. J., Balboa, A., Gordon, W. O., Morris, J. R., … & Musaev, D. G. (2018). Key Mechanistic Details of Paraoxon Decomposition by Polyoxometalates: Critical Role of Para-Nitro SubstitutionChemical Physics.

Lian Group:

Clark, M. L., Ge, A., Videla, P. E., Rudshteyn, B., Miller, C. J., Song, J., … & Kubiak, C. P. (2018). CO2 Reduction Catalysts on Gold Electrode Surfaces Influenced by Large Electric FieldsJournal of the American Chemical Society.

Lutz Group:

Williams, E., Jung, S. M., Coffman, J. L., & Lutz, S. (2018). Pore engineering for enhanced mass transport in encapsulin nano-compartmentsACS synthetic biology.

Musaev Group:

Kaledin, A. L., Troya, D., Karwacki, C. J., Balboa, A., Gordon, W. O., Morris, J. R., … & Musaev, D. G. (2018). Key Mechanistic Details of Paraoxon Decomposition by Polyoxometalates: Critical Role of Para-Nitro Substitution. Chemical Physics.

Salaita Group:

Hong, J., Ge, C., Jothikumar, P., Yuan, Z., Liu, B., Bai, K., … & Palin, A. (2018). A TCR mechanotransduction signaling loop induces negative selection in the thymusNature Immunology, 1.

Weinert Group

Rivera, S., Young, P. G., Hoffer, E. D., Vansuch, G. E., Metzler, C. L., Dunham, C. M., & Weinert, E. E. (2018). Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled SensorsInorganic chemistry.

Fontaine, B. M., Duggal, Y., & Weinert, E. E. (2018). Exploring the Links Between Nucleotide Signaling and Quorum Sensing Pathways in Regulating Bacterial VirulenceACS infectious diseases.

Wuest Group:

Kontos, R. C., Schallenhammer, S. A., Bentley, B. S., Morrison, K. R., Feliciano, J. A., Tasca, J. A., … & Minbiole, K. P. (2018). An Investigation Into Rigidity‐Activity Relationships in bisQAC Amphiphilic AntisepticsChemMedChem.

Shapiro, J. A., Varga, J. J., Parsonage, D., Walton, W., Redinbo, M. R., Ross, L. J., … & Goldberg, J. B. (2018). Identification of Specific and Non‐specific Inhibitors of Bacillus anthracis Type III Pantothenate Kinase (PanK)ChemMedChem.

Kilgore, M. B., Morrison, K. R., Wuest, W. M., & Chandler, J. D. (2018). Influence of pH on the reactions of heme peroxidase-derived oxidants with R19SFree Radical Biology and Medicine128, S101-S102.

October Research Round-Up

Congratulations to our amazing research teams here in the Department of Chemistry for their publications this month!

Bowman Group:

Nandi, A., Qu, C., & Bowman, J. M. (2018). Diffusion Monte Carlo Calculations of Zero‐Point Energies of Methanol and Deuterated Methanol. Journal of computational chemistry.

Davies Group:

Davies, H. M., Itami, K., & Stoltz, B. M. (2018). New directions in natural product synthesisChemical Society Reviews.

Evangelista Group:

Huang, Y., Xu, Z., Jin, S., Li, C., Warncke, K., Evangelista, F. A., … & Egap, E. (2018). Conjugated Oligomers with Stable Radical Substituents: Synthesis, Single Crystal Structures, Electronic Structure and Excited State DynamicsChemistry of Materials.

Heaven Group

Torbin, A., Pershin, A., Zagidullin, M., Heaven, M., Mebel, A., & Azyazov, V. (2018). Ozone recovery in the presence of CO and N2O. In MATEC Web of Conferences(Vol. 209, p. 00016). EDP Sciences.

Tolstov, G. I., Zagidullin, M. V., Khvatov, N. A., Medvedkov, I. A., Mebel, A. M., Heaven, M. C., & Azyazov, V. N. (2018). Measurements of rate constants of O2 (b) quenching by CH4, NO, N2O at temperatures 300-800 K. In MATEC Web of Conferences(Vol. 209, p. 00006). EDP Sciences.

Heaven, M. C. (2018, October). Optically pumped rare gas lasers (Conference Presentation). In High-Power Lasers: Technology and Systems, Platforms, and Effects II(Vol. 10798, p. 1079806). International Society for Optics and Photonics.

Heemstra Group

Wilson, C. J., Bommarius, A. S., Champion, J. A., Chernoff, Y. O., Lynn, D. G., Paravastu, A. K., … & Heemstra, J. M. (2018). Biomolecular Assemblies: Moving from Observation to Predictive DesignChemical reviews.

Morris, F. D., Peterson, E. M., Heemstra, J. M., & Harris, J. M. (2018). Single-Molecule Kinetic Investigation of Cocaine-Dependent Split-Aptamer AssemblyAnalytical chemistry.

Hill Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2018). A bulk adjusted linear combination of atomic orbitals (BA‐LCAO) approach for nanoparticlesJournal of computational chemistry.

Ke Group

Wang, P., & Ke, Y. (2018). Attack on the Cell Membrane: The Pointy Ends of DNA Nanostructures Lead the Way.

Wang, D., Song, J., Wang, P., Pan, V., Zhang, Y., Cui, D., & Ke, Y. (2018). Design and operation of reconfigurable two-dimensional DNA molecular arraysNature protocols, 1.

Kindt Group

Patel, L. A., & Kindt, J. T. (2018). Simulations of NaCl Aggregation from Solution: Solvent Determines Topography of Free Energy LandscapeJournal of computational chemistry.

Guo, Z., & Kindt, J. T. (2018). Partitioning of Size-mismatched Impurities to Grain Boundaries in 2-d Solid Hard Sphere MonolayersLangmuir.

Lian Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2018). A bulk adjusted linear combination of atomic orbitals (BA‐LCAO) approach for nanoparticlesJournal of computational chemistry.

Huang, Y., Xu, Z., Jin, S., Li, C., Warncke, K., Evangelista, F. A., … & Egap, E. (2018). Conjugated Oligomers with Stable Radical Substituents: Synthesis, Single Crystal Structures, Electronic Structure and Excited State DynamicsChemistry of Materials.

Lynn Group

Wilson, C. J., Bommarius, A. S., Champion, J. A., Chernoff, Y. O., Lynn, D. G., Paravastu, A. K., … & Heemstra, J. M. (2018). Biomolecular Assemblies: Moving from Observation to Predictive DesignChemical reviews.

Musaev Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2018). A bulk adjusted linear combination of atomic orbitals (BA‐LCAO) approach for nanoparticles. Journal of computational chemistry.

Haines, B. E., Nelson, B. M., Grandner, J. M., Kim, J., Houk, K. N., Movassaghi, M., & Musaev, D. G. (2018). Mechanism of Permanganate-Promoted Dihydroxylation of Complex Diketopiperazines: Critical Roles of Counter-cation and Ion-PairingJournal of the American Chemical Society.

Wuest Group

Ernouf, G., Wilt, I., Zahim, S., & Wuest, W. M. (2018). Epoxy isonitriles, a unique class of antibiotics–Synthesis of their metabolites and biological investigationsChemBioChem.

 

Frank McDonald Authors New Textbook

Frank McDonald
Frank McDonald. Photo by Jessica Lily Photography.

Prof. Frank McDonald has announced the publication of the first volume of his graduate-level textbook,  “Finding the Right Partner”, now available in e-book form at Amazon.com.  This volume focuses on selectivity in carbon-heteroatom bond-forming reactions; a second volume on carbon-carbon bond-forming reactions is under development and hopefully will be published within the next couple of years. 

[Finding the Right Partner on Amazon]

Weinert Group in Nature Communications

Clip from the image RsbR haem pocket model and haem spectra." This image, and the article referenced, are licensed under a Creative Commons Attribution 4.0 International License.
Clip from the image RsbR haem pocket model and haem spectra.” This image, and the article referenced, are licensed under a Creative Commons Attribution 4.0 International License.

The Weinert Group has research featured in the June issue of Nature Communications. The paper, “An O2-sensing stressosome from a Gram-negative bacterium,” is co-authored by Xin Jia, Jian-bo Wang, Shannon Rivera, Duc Duong, and Emily E. Weinert.

Abstract:

Bacteria have evolved numerous pathways to sense and respond to changing environmental conditions, including, within Gram-positive bacteria, the stressosome complex that regulates transcription of general stress response genes. However, the signalling molecules recognized by Gram-positive stressosomes have yet to be identified, hindering our understanding of the signal transduction mechanism within the complex. Furthermore, an analogous pathway has yet to be described in Gram-negative bacteria. Here we characterize a putative stressosome from the Gram-negative bacterium Vibrio brasiliensis. The sensor protein RsbR binds haem and exhibits ligand-dependent control of the stressosome complex activity. Oxygen binding to the haem decreases activity, while ferrous RsbR results in increased activity, suggesting that the V. brasiliensis stressosome may be activated when the bacterium enters anaerobic growth conditions. The findings provide a model system for investigating ligand-dependent signalling within stressosome complexes, as well as insights into potential pathways controlled by oxygen-dependent signalling within Vibrio species.

[Full Article]

Joel Bowman Published in Chemical Reviews

"Drof [sic] of Water" is a CC BY-SA 2.0 image by Tim Geers on Flickr
“Drof [sic] of Water” is a CC BY-SA 2.0 image by Tim Geers on Flickr
Joel Bowman has a paper in Chemical Reviews. The paper, “Energetics and Predissociation Dynamics of Small Water, HCl, and Mixed HCl–Water Clusters” is a collaboration between the Bowman Group and scientists at the University of Southern California, part of a project to undertake fundamental physical chemical studies of hydration.

[Full Article] (subscriber access)