Off-campus undergraduate summer research opportunities Summer Research Opportunities at Bowdoin in chemistry, biochemistry, materials science. etc. • Chemistry Department (James Stacy Coles/Littlefield Fellowships • Programs at other universities: http://www.bowdoin.edu/chemistry/research/index.shtml NSF-REU programs: http://www.nsf.gov/crssprgm/reu/reu_search.cfm • Institutional (Faculty sponsor required) https://www.bowdoin.edu/student-fellowships/ • Programs at governmental institutions: https://www.bowdoin.edu/student-fellowships/summer-fellowships/index.html National Institutes of Health (NIH), Bethesda, MD: https://www.training.nih.gov/programs/ugsp Internships at National labs: Los Alamos, Sandia, Pacific Northwest, Argonne, Lawrence Livermore, and many others! (http://www.dep.anl.gov/p_undergrad/summer.htm for example) Key Dates • February 10, 2020 (noon)* Phase One Deadline CHEMI STRY: • February 24, 2020 (noon)* Phase Two Deadline $425/ week for 8 to 10 • March 11, 2020 First round of awards are released James Stacy Coles weeks of full time research; housing Summer Research • March 27, 2020 Deadline for students from the first round of awards to Fellowships subsidy; funding for accept/decline fellowship awards research supplies. • April 8, 2020 All applicants not selected in the first round of awards will be $425/ week for 8 to 10 notified of their final award status weeks of full time • April 10, 2020 Deadline for students who were notified of a fellowship Littlefield research; housing award on April 9 to accept/decline offer subsidy; funding for * Late applications will not be accepted; students should plan accordingly research supplies. Applications of analytical chemistry to address Contacts for more information questions in chemistry and biology Chemistry Department Dharni Vasudevan dvasudev@bowdoin.edu Emily Murphy emurphy@bowdoin.edu O Ph 2 P O N 3 HN O N 3 OCH 3 Institutional Fellowships PPh 2 detection reagent Corey Colwill, Assistant Director or drug N 3 ccolwill@bowdoin.edu Stemmler Laboratory 1
Project 1: What mechanisms underlie differences in Identification of Signaling Molecules in Crustaceans modulatory capacity for closely related crab species? Electrophysiology Genetics/Transcriptomics S H S H Pugettia producta Libinia emarginata Eats only kelp Highly diverse diet Identify Active Not responsive to Responsive to Neuropeptides many neuropeptide neuropeptide modulators modulators Mass Spectrometry Goal: Use mass spectrometry to compare the identities and With Patsy Dickinson (Bowdoin) and Andy Christie (University of Hawai’i at Manoa) concentrations of neuropeptides Projects 1 and 2 will use methods to extract and analyze Project 2: What are the identities of antimicrobial peptides small and large peptides coupled with the predictive (AMPs) present in lobster circulatory fluid? power of transcriptomics Hoa-D1 Gross and Tissue HPLC Fractions Putative Fine Extraction Pugettia producta Fractionation Libinia emarginata analyzed by Crustins Dissection mass spectrometry Column Sequences from Vu, et al. 2018. Molecular Immunology 101:320-343 transcriptome Goal: Use mass spectrometry and transcriptomics to identify crustin-family AMPs from the lobster, H. americanus Project 3: What products are produced by Chemical tools to discover and target sugar- photodegradation of pharmaceuticals with and without a coated proteins on disease-causing bacteria photocatalyst? Photoproducts Assess Kinetics Pollutant O O Ph 2 P Ph 2 P O O N 3 N 3 HN HN CO 2 + H 2 O O O No catalyst N 3 N 3 OCH 3 OCH 3 (Ideal) PPh 2 PPh 2 detection reagent Identify With catalyst or drug photoproducts N 3 N 3 Goal: To use chromatography and mass spectrometry to Dube Laboratory monitor kinetics and identify photoproducts Department of Chemistry & Biochemistry, Bowdoin College 2
Helicobacter pylori synthesizes a suite of sugar-coated Chemical tools to discover and target bacterial sugars proteins that are linked to its pathogenesis Discovering how bacterial glycoproteins are assembled - 125 candidate sugar-coated proteins cover the cell surface flippase - 20% have known links to disease cytosol GT 1 GT 2 GT 3 -GT n PP P PP PP inner - contain distinctive sugar building blocks membrane PP periplasm OGT Targeting glycans that are unique to pathogens X inhibitor X normal altered Champasa, K.; Longwell, S.A.; Stemmler, E.A.; Dube, D.H. Mol. Cell. Proteom., 2013 , 12, 2568-2586 The Takematsu Research Group (ktakemat@bowdoin.edu) The Takematsu Research Group (ktakemat@bowdoin.edu) We use spectroscopic and computational tools to pK a *= 2.8 Our group is currently using understand the fundamental photoacids to investigate the process of charge transfer. parameters that drive Emits light! excited state proton transfer. From wiki How do you convert light pK a = 9.5 into the controlled movement of charges? Aequorea victoria jellyfish 2-naphthol “green fluorescent protein” PDB: 1FBB The Takematsu Research Group (ktakemat@bowdoin.edu) Research in the Dzubak Group: adzubak@bowdoin.edu Nanoporous metal-organic frameworks (MOFs) Gabby Eva Gabby metal ions or clusters held together by organic functional groups solvents organic to ionic liquids Sean NH 3 + Sean OH cyano addition CN Schiff base chemistry Eva Energy applications and technology with broad social implications: Isomerization CO 2 capture, H 2 and methane storage, water purification, etc. Summer 2019 3
Research in the Dzubak Group: adzubak@bowdoin.edu How do you model the capture or adsorption of molecules in MOF? A computational approach! Design of cooperative heterogeneous interactions: capturing CO 2 Transition Metals in Organic Multiscale modeling from angstroms to nanometers Chemistry Advancing tools in electronic structure theory Why Transition Metals? Reaction 1 Variety Oxidation states available Number of ligands Geometry- d orbitals increase possibilities Ligand binding Periodic Properties If Co doesn’t work, maybe Rh or Ir will work Cone Angle Small Cone Angle Ligands Backbonding to carbene restricts rotation Chelate of N and Cp prevents rotation Isonitriles move bulky part farther from Co Predict more favorable ratios with smaller cone angle 4
Organic Syntheses Identification techniques The Gorske Lab: Synthesis of biomimetic Identification techniques molecules for chemical biology and catalysis Synthesis of protein mimics for investigating the roles of cellular signaling in disease. n * interactions C–H interactions protein-protein interactions • cellular signaling • Alzheimer ’ s disease common techniques • cancer chemical synthesis – solution and solid phase NMR spectroscopy and X-ray crystallographic analysis HPLC purification and mass spectrometry Protein binding assays The Gorske Lab: Synthesis of biomimetic The Gorske Lab: Synthesis of biomimetic molecules for chemical biology and catalysis molecules for chemical biology and catalysis Developing enzyme mimics for trifluoromethylation H N O O Me 3 Si O CF 3 O Efavirenz Me 3 Si-CF 3 Cl R R F Catalysts (B*) F F R = H, Me N Me 4 N F New structures? Br OH N N Br O N HO N R = Me: 70-94% ee N. Shibata et al . Tetrahedron: Asymmetry 2008 , 19 , 2633. 5
Environmental Chemistry So why do we care ? Research Theoretical Context : •Surface chemistry in aqueous systems Exploring and understanding the •Soil/Sediment Chemistry mechanisms by which organic compounds interact Environmental Context: • Contaminant fate and transport human and with ecosystem exposure surfaces relevant to soils, • Soil/Sediment and Groundwater cleanup – sediments, synthetic matrices. remediation VASUDEVAN LAB: dvasudev@bowdoin.edu or Druk 258 31 32 Chemicals of Interest: Pharmaceuticals Process of Interest: Sorption - O O • Risk to ecosystems Diclofenac O • Antibiotic resistance Anti-inflammatory H 2 N SORPTION or RETENTION of organic compounds onto soils and particulates is key to contaminant fate + HN NH + Trimethoprim Anti-biotic 33 34 NH 2 Project 1: Evaluation of salicylic acid and similar compounds Project 1: Evaluation of salicylic acid and similar compounds as probes for anionic pharmaceutical sorption to soils as probes for anionic pharmaceutical sorption to soils K d � K TypeI � f � K CE probe , K CE XS � � f � K SC�CB probe , K SC�CB XS � Probes Sorbate of Interest Salicylic Acid (SA) SC+CB Non-polar domain Surficial Negative Fe and Al Charge CE Polar Positive Neutral Charge ciprofloxacin salicylic acid Benzylamine (BA) Continuation of research by Reaha Goyetche ’14, John Continuation of research by’, Alandra Lopez 16’, Leah Alper 35 Medina ‘18, Katie Carter 16’, Alandra Lopez 16’, Leah Alper 17’ 17’ and Eric Guiang 18’ 6
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