Summer research overview 2019 - Bowdoin College · Champasa, K.; Longwell, S.A.; Stemmler, E.A.; Dube, D.H. Mol. Cell. Proteom., 2013, 12, 2568-2586 P PP PP PP PP GT flippase 1 2

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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/ugspInternships 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

CHEMISTRY:

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 [email protected] [email protected]

Corey Colwill, Assistant [email protected]

Institutional Fellowships

Stemmler Laboratory

Applications of analytical chemistry to address questions in chemistry and biology

N3

N3 HN

N3

Ph2PO

PPh2

OCH3

O

O

detection reagent or drug

2

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 SH H

Identify ActiveNeuropeptides

Project 1: What mechanisms underlie differences in modulatory capacity for closely related crab species?

Libinia emarginataPugettia 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 emarginataPugettia 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

HPLCFractionation

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 LaboratoryDepartment of Chemistry & Biochemistry, Bowdoin College

N3

N3 HN

N3

Ph2PO

PPh2

OCH3

O

O

detection reagent or drug

N3

N3 HN

N3

Ph2PO

PPh2

OCH3

O

O

3

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

flippaseGT1 GT2 GT3-GTn

OGTperiplasm

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 ([email protected])

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 ([email protected])

The Takematsu Research Group ([email protected])

Sean

Gabby Eva Gabby

solventsorganic to ionic liquids

cyano addition

SeanNH3

+

OH

CN

Eva

Isomerization

Schiff base chemistry

Summer 2019

Research in the Dzubak Group: [email protected]

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: [email protected]

Transition Metals in Organic Chemistry

Why Transition Metals?

VarietyOxidation states availableNumber of ligandsGeometry- d orbitals increase possibilitiesLigand binding

Periodic PropertiesIf 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 techniquesThe Gorske Lab: Synthesis of biomimetic

molecules for chemical biology and catalysis

protein-protein interactions• cellular signaling• Alzheimer’s disease• cancer

common techniqueschemical synthesis – solution and solid phaseNMR spectroscopy and X-ray crystallographic analysisHPLC purification and mass spectrometryProtein 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 CF3Me3Si

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

HN O

Cl

FF

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

organic compounds interactwith

surfaces relevant to soils, sediments, synthetic matrices.

31VASUDEVAN LAB: [email protected] 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

-

DiclofenacAnti-inflammatory

TrimethoprimAnti-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 KCEprobe,KCEXS f KSC CBprobe,KSC CB

XS

NegativeCharge

PositiveCharge

PolarNeutral

SurficialFe and Al

Non-polardomain

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

Pyridine4-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(KdXS)

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 4AMAt LLBean in a tent, at 4am

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