1 Project 1: What mechanisms underlie differences in Identification - - PDF document

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Off-campus undergraduate summer research opportunities in chemistry, biochemistry, materials science. etc.

• Programs at other universities:

NSF-REU programs: http://www.nsf.gov/crssprgm/reu/reu_search.cfm

• Programs at governmental institutions:

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)

Summer Research Opportunities at Bowdoin

• Chemistry Department (James Stacy Coles/Littlefield

Fellowships

http://www.bowdoin.edu/chemistry/research/index.shtml

• Institutional (Faculty sponsor required)

https://www.bowdoin.edu/student-fellowships/ https://www.bowdoin.edu/student-fellowships/summer-fellowships/index.html Key Dates

• February 10, 2020 (noon)* Phase One Deadline
• February 24, 2020 (noon)* Phase Two Deadline
• March 11, 2020 First round of awards are released
• March 27, 2020 Deadline for students from the first round of awards to

accept/decline fellowship awards

• April 8, 2020 All applicants not selected in the first round of awards will be

notified of their final award status

• April 10, 2020 Deadline for students who were notified of a fellowship

award on April 9 to accept/decline offer *Late applications will not be accepted; students should plan accordingly

CHEMI STRY: James Stacy Coles Summer Research Fellowships $425/ week for 8 to 10 weeks of full time research; housing subsidy; funding for research supplies. Littlefield $425/ week for 8 to 10 weeks of full time research; housing subsidy; funding for research supplies.

Contacts for more information

Chemistry Department Dharni Vasudevan dvasudev@bowdoin.edu Emily Murphy emurphy@bowdoin.edu Corey Colwill, Assistant Director ccolwill@bowdoin.edu Institutional Fellowships Stemmler Laboratory

Applications of analytical chemistry to address questions in chemistry and biology

N3 N3 HN N3 Ph2P O PPh2 OCH3 O O

detection reagent

• r drug

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Electrophysiology Mass Spectrometry Identification of Signaling Molecules in Crustaceans Genetics/Transcriptomics With Patsy Dickinson (Bowdoin) and Andy Christie (University of Hawai’i at Manoa)

S S H H

Identify Active Neuropeptides Project 1: What mechanisms underlie differences in modulatory capacity for closely related crab species? Libinia emarginata Pugettia producta Eats only kelp Highly diverse diet Not responsive to many neuropeptide modulators Responsive to neuropeptide modulators Goal: Use mass spectrometry to compare the identities and concentrations of neuropeptides Project 2: What are the identities of antimicrobial peptides (AMPs) present in lobster circulatory fluid? Libinia emarginata Pugettia producta Goal: Use mass spectrometry and transcriptomics to identify crustin-family AMPs from the lobster, H. americanus Hoa-D1 Putative Crustins

Vu, et al. 2018. Molecular Immunology 101:320-343

Projects 1 and 2 will use methods to extract and analyze small and large peptides coupled with the predictive power of transcriptomics

Gross and Fine Dissection Tissue Extraction HPLC Fractionation

Column

Fractions analyzed by mass spectrometry Sequences from transcriptome

Project 3: What products are produced by photodegradation of pharmaceuticals with and without a photocatalyst? Goal: To use chromatography and mass spectrometry to monitor kinetics and identify photoproducts

Pollutant CO2 + H2O (Ideal) Photoproducts

No catalyst With catalyst Assess Kinetics Identify photoproducts

Chemical tools to discover and target sugar- coated proteins on disease-causing bacteria

Dube Laboratory Department of Chemistry & Biochemistry, Bowdoin College

N3 N3 HN N3 Ph2P O PPh2 OCH3 O O

detection reagent

• r drug

N3 N3 HN N3 Ph2P O PPh2 OCH3 O O

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Helicobacter pylori synthesizes a suite of sugar-coated proteins that are linked to its pathogenesis

• 125 candidate sugar-coated proteins

cover the cell surface

• 20% have known links to disease
• contain distinctive sugar building blocks

Champasa, K.; Longwell, S.A.; Stemmler, E.A.; Dube, D.H. Mol. Cell. Proteom., 2013, 12, 2568-2586 P PP PP PP PP flippase GT1 GT2 GT3-GTn OGT periplasm cytosol inner membrane

Discovering how bacterial glycoproteins are assembled Targeting glycans that are unique to pathogens

Chemical tools to discover and target bacterial sugars

inhibitor normal altered

X

X

The Takematsu Research Group (ktakemat@bowdoin.edu)

From wiki

We use spectroscopic and computational tools to understand the fundamental process of charge transfer. How do you convert light into the controlled movement of charges?

PDB: 1FBB

Aequorea victoria jellyfish “green fluorescent protein”

Our group is currently using photoacids to investigate the parameters that drive excited state proton transfer.

pKa= 9.5 pKa*= 2.8

Emits light!

2-naphthol

The Takematsu Research Group (ktakemat@bowdoin.edu) The Takematsu Research Group (ktakemat@bowdoin.edu)

Sean Gabby Eva Gabby solvents

• rganic to ionic liquids

cyano addition Sean

NH3

+

OH CN

Eva Isomerization

Schiff base chemistry

Summer 2019

Research in the Dzubak Group: adzubak@bowdoin.edu

Nanoporous metal-organic frameworks (MOFs)

metal ions or clusters held together by organic functional groups

Energy applications and technology with broad social implications:

CO2 capture, H2 and methane storage, water purification, etc.

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How do you model the capture or adsorption of molecules in MOF? A computational approach!

Design of cooperative heterogeneous interactions: capturing CO2 Multiscale modeling from angstroms to nanometers Advancing tools in electronic structure theory

Research in the Dzubak Group: adzubak@bowdoin.edu

Transition Metals in Organic Chemistry Why Transition Metals?

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

Reaction 1 Cone Angle

 Predict more favorable ratios with smaller 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

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Organic Syntheses Identification techniques Identification techniques

The Gorske Lab: Synthesis of biomimetic molecules for chemical biology and catalysis

protein-protein interactions

• cellular signaling
• Alzheimer’s disease
• cancer

common techniques

chemical synthesis – solution and solid phase NMR spectroscopy and X-ray crystallographic analysis HPLC purification and mass spectrometry Protein binding assays n* interactions C–H interactions

Synthesis of protein mimics for investigating the roles of cellular signaling in disease.

The Gorske Lab: Synthesis of biomimetic molecules for chemical biology and catalysis

Developing enzyme mimics for trifluoromethylation

R O CF3 Me3Si R O R = H, Me Me3Si-CF3

Catalysts (B*)

Br N N HO N N OH Br Me4N F

R = Me: 70-94% ee

O N

New structures?

• N. Shibata et al. Tetrahedron: Asymmetry 2008, 19, 2633.

O H N O Cl F F F

Efavirenz

The Gorske Lab: Synthesis of biomimetic molecules for chemical biology and catalysis

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Environmental Chemistry Research Exploring and understanding the mechanisms by which

• rganic compounds interact

with surfaces relevant to soils, sediments, synthetic matrices.

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VASUDEVAN LAB: dvasudev@bowdoin.edu or Druk 258

So why do we care ?

Theoretical Context:

• Surface chemistry in aqueous systems
• Soil/Sediment Chemistry

Environmental Context:

• Contaminant fate and transport  human and

ecosystem exposure

• Soil/Sediment and Groundwater cleanup –

remediation

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Chemicals of Interest: Pharmaceuticals

• Risk to ecosystems
• Antibiotic resistance

O NH+ NH2

+HN

H2N O O

• Diclofenac

Anti-inflammatory Trimethoprim Anti-biotic

SORPTION or RETENTION of organic compounds onto soils and particulates is key to contaminant fate

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Process of Interest: Sorption

Project 1: Evaluation of salicylic acid and similar compounds as probes for anionic pharmaceutical sorption to soils

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salicylic acid

Continuation of research by’, Alandra Lopez 16’, Leah Alper 17’ and Eric Guiang 18’

Kd KTypeI f KCE

probe, KCE XS f KSCCB probe, KSCCB XS

Negative Charge Positive Charge Polar Neutral Surficial Fe and Al Non-polar domain

Benzylamine (BA) Salicylic Acid (SA) ciprofloxacin

CE SC+CB

Probes Sorbate of Interest Continuation of research by Reaha Goyetche ’14, John Medina ‘18, Katie Carter 16’, Alandra Lopez 16’, Leah Alper 17’

Project 1: Evaluation of salicylic acid and similar compounds as probes for anionic pharmaceutical sorption to soils

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Project 2: Building structure-cation exchange relationships for heterocyclic amine sorption to montmorillonite

Pyridine 4-Picoline 3-Picoline 2-Picoline 3,4-Lutdine

Continuation of research Basyl Stuyvesant ’13 and James Sullivan ’16 and Danielle Freeman 17’

Log(Kd 3-picoline) = Log(Kd pyridine) + Log(Kd

XS)

Examples of Experimental Work relevant to Projects 1 and 2 1. Design and conduct of sorption experiments.

• 2. Analysis of concentration via HPLC-DAD, ICP-OES,

GC-MS (sometimes) and development of analytical methods

• 3. FT-IR spectroscopy of compounds sorbed onto

mineral surfaces

• 4. Simple statistical Analyses and Computational

Chemistry

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Summer here and beyond is really fun…. Although…Lab coats are optional, outside of the lab ; ) Sunrise At LLBean at 4AM At LLBean in a tent, at 4am

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