Summer research overview 2019 - Bowdoin College · Champasa, K.; Longwell, S.A.; Stemmler, E.A.;...
Transcript of Summer research overview 2019 - Bowdoin College · Champasa, K.; Longwell, S.A.; Stemmler, E.A.;...
1
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.
4
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
5
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
6
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
32
33
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
34
Process of Interest: Sorption
Project 1: Evaluation of salicylic acid and similar compounds as probes for anionic pharmaceutical sorption to soils
35
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
7
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
38
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
39