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I need help with my chemistry lab Molecular Scavenger Hunt.

Instructions are in the document attached.

Spring 2021
Chem 410A lab 11: Molecular Scavenger Hunt
Chem 410A Lab 11: Molecular Scavenger Hunt
This is the last lab of the chem 410A lab series, and is for extra credit, consisting of 5 points. You
will partake in a molecular scavenger hunt, which may be useful to you when you need to find
molecular properties, reaction mechanisms, or similar structures in research or industry. Due to
the prevalence of students with biochemical leanings, I have included a search for fluorescent
proteins in an open source fluorescent protein database (fpbase.org). You will also be using
Scifinder, a database which is accessible through the American Chemical Society (ACS), but is
also supplied by SDSU; as well as NIST, the national institute of standards and technology.
Part 1: Fluorescent proteins
Navigate to the website fpbase.com in a web browser, and search for one of the following
fluorescent proteins, which will be assigned to you mcherry2, tdTomato, mTagBFP2, or Citrine2.
After searching for one of these, you will record important information from both a
photophysical and structural perspective, namely the peak excitation wavelength, the peak
emission wavelength (both of these are in nanometers), the quantum yield (the ratio of the
number photons out to photons in), the extinction coefficient (in M-1cm-1), the brightness,
and the amino acid sequence. Record this information along with the name of your
fluorescent protein.
Spectral overlap is one factor involved in FRET, (Forster Resonance Energy Transfer), a process
by which a donor molecule is excited, emits in the spectral region of the absorption spectrum of
the second molecule, and is emitted by the second molecule. This is important because the
distances and relative orientations of two molecules can be obtained via FRET, providing a
useful probe of biomolecules. Click on the explore tab, then spectra, plotting CyPet and YPet
proteins. Take and save a screenshot of the spectrum.
Part 2: Scifinder
Scifinder provides literature references for compounds along with data extracted. Register for
Scifinder at SciFinder Scholar | SDSU Library. Then log into Scifinder and search for “tricyclic cytidine”.
View the references containing “tricyclic cytidine” as entered, as opposed to the concept of tricyclic
cytidine. On the references tab on the left under “Analyze” click “more” and then “export”, saving the
resulting excel file and sending it to hpearce@sdsu.edu via email. Go back to the explore tab and click
on the structure search. From here, create the tricyclic Cytidine nucleoside, as shown below
Spring 2021
Chem 410A lab 11: Molecular Scavenger Hunt
and run a similarity search. Now search and get references, looking for H-Pyrimido[5,4-b][1,4]benzoxazin2(3H)-one. Include screenshots of the proton and carbon 13 NMR spectra. Now click “Get reaction” with the
nucleoside selected as the product. This will provide a list of reaction steps. Provide the DOI to the article which
provides these steps (located on the right hand side under “source”). The DOI (Digital Object Indicator)
provides a permanent URL to the associated paper.
Part 3: NIST webbook
The NIST (National Institute of Standards and Technology) webbook provides electronic, vibrational, and
thermodynamic molecular data in a regulated database. Navigate to NIST Chemistry WebBook and search for
methanol. Take screenshots of the absorbance and emission peaks on the IR spectra and record the
frequencies corresponding to the strong IR peaks in the gas phase as well as the vibrational motions
which correspond to such peaks.

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