As we begin to work on research-based assignments and to deal with nature s complexity, it is

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As we begin to work on research-based assignments and to deal with nature s complexity, it is worthwhile to reflect on a quote from Melville s Moby Dick: As for me, I am tormented with an everlasting

1 As we begin to work on research-based assignments and to deal with nature s complexity, it is worthwhile to reflect on a quote from Melville s Moby Dick: As for me, I am tormented with an everlasting itch for things remote. I love to sail forbidden seas, and land on barbarous coasts. Assignment A04: Characterization of Analytical Markers in Opiate Samples This assignment is based on the following recently published research article (the Source): Unambiguous Characterization of Analytical Markers in Complex, Seized Opiate Samples Using an Enhanced Ion Mobility Trace Detector-Mass Spectrometer. P. Liuni, V. Romanov, M.-J. Binette, H. Zaknoun, M. Tam, P. Pilon, J. Hendrikse, and D. J. Wilson. Anal. Chem. 2014, 86, (dx.doi.org/ /ac502676d). The article is linked to the assignment section of the course web site (direct link and links to local PDF files of article and SI). 1

The goals of assignment A04 include (i) to review some principles of Ion Mobility Spectroscopy (IMS)-based trace compound detectors (TCD) and of an enhanced hybrid TCD-IMS/mass spectrometer

2 The goals of assignment A04 include (i) to review some principles of Ion Mobility Spectroscopy (IMS)-based trace compound detectors (TCD) and of an enhanced hybrid TCD-IMS/mass spectrometer (TCD-IMS/MS) and to create Scheme 1 to depict the components of the hybrid TCD-IMS/MS instrument, (ii) to learn about the positive ion mode IMS-MS characterization of seized opium sample Opium A (Figures 2 & 3 in Source) and to create Scheme 2 to show the structures of the main markers, (iii) to learn about the negative ion mode IMS-MS characterization of seized opium sample Opium A (Figures 5 and 6 in source) and to create Scheme 3 to show the structures of the main markers, (iv) to create your Figure 1 by simulation of part (a) of Figure 3 of the Source, (v) to create your Figure 2 by simulation of part (a) of Figure 6 of the Source, and (vi) to write some text to summarize the principle of the TCD method and the analytical chemistry observed. The simulations in (iv) and (v) are at the core of A04, they require the generation and manipulation of large arrays of data, and you need to be well organized from the start. Use the examples and samples posted on the assignments section of the course web site for guidance, and (try to) enjoy the challenge. Assignments A04 in previous semesters involved the 2

3 simulation of spectra, that is, the x-axis provided a measure of light frequency or wavelength. Here we will simulate mobility spectra, that is, the x-axis shows drift times in milliseconds. Read the Source and try to understand what the paper is about; this will take some time. Review the basics of gas chromatography (GC), mass spectrometry (MS), and ion mobility spectroscopy (IMS). A webinar on How Ion Mobility Coupled with High-Resolution Mass Spec Enables Analysis of Complex Samples is available online ( p0oaf1s3krs). Here are some thoughts to guide your studies. (i) Create Scheme 1 to Describe the Hybrid TCD-IMS/MS Instrument. Your Scheme 1 should be a highly abstracted version of Figure 1(b) of the Source. The scheme should show the sampling region, the reaction region, the drift region and the mass spectrometer. Pay attention to the relative dimensions of the sampling, reaction, and drift regions. Understand the purpose of each component. Understand the timescales of the thermal desorption process, of the gas phase ionization, of the journey of ions traversing the drift-cell, and of the ion detection in the MS unit. Use color to enhance the message. Pay attention to alignment and spacing. Import the scheme into a Word file and add a Scheme legend. The text that will accompany your Scheme 1 (the first paragraph of the text, see below) should include the definition of the reduced mobility of a species. Nicotinamide was injected with the drift gas and used as the internal standard. Briefly describe how K 0 was calculated for nicotinamide and how the K 0 values of the other compounds are determined. (ii) Create Scheme 2 to Show the Structures of the Ions Detected by Positive Ion Mode IMS-MS. In Figure 3 of the Source, the four IMS peaks in positive ion mode with reduced mobility values K 0 of (m/z = 414), (m/z = 340), (m/z = 312), and cm 2 V 1 s 1 (m/z = 220) were found to correspond to noscapine, papaverine, thebaine, and a fragment of noscapine, respectively. Your Scheme 2 should show the structures of the detected ions with the m/z values given in parentheses, i.e., if the molecular mass of the neutral species differs from 3

4 the observed m/z value then you need to suggest a structure of the observed ion. Use ChemDraw and pay attention to stereochemistry, alignment and spacing. Use color to enhance the message. Import the scheme into a Word file and add a Scheme legend. (iii) Create Scheme 3 to Show the Structures of the Ions Detected by Negative Ion Mode IMS-MS. In Figure 6 of the Source, the broad IMS peak in negative ion mode with reduced mobility value K 0 = 1.18 cm 2 V 1 s 1 results by overlap of three distinct ions with m/z values of 284, 291, and 311. Your Scheme 2 should show seven structures as follows. Show the structures with names and their molecular mass of four neutral acids: poppy acid (a.k.a. meconic acid), comenic acid, pyroglutamic acid, and threonic acid. And show the structures of the three detected ions with the m/z values given above. Use ChemDraw and pay attention to stereochemistry, alignment and spacing. Use color to enhance the message. Import the scheme into a Word file and add a Scheme legend. (iv) Create Figure 1 by Simulation of Figure 3a of the Source. Your Figure 1 should be a complete re-creation of part (a) of Figure 3 of the Source in every way (same sizes, same labels, same tick marks, same colors, shaded areas, same everything) using the program EXCEL. Obviously, there is no need to simulate the experimental noise in the experimental spectra. You can omit the inset LEGEND. The ion mobility curve N(t) can be approximated as the sum of a number of Gaussian functions N i (t) which are determined by the positions of their maxima t max,i and their ion counts N max,i which determine the ion mobility spectrum; N(t) = Σ N i (t). At least nine Gaussians are needed for the simulation of the curve (i = 9). Start with reasonable initial guesses for t max,i and N max,i and adjust the parameters to obtain a good fit. You may choose a fitting procedure of any sophistication; i.e., from visual inspection to mathematical regression. Refer to the posted examples to get an idea about the organization of your excel sheet to generate Figure 1. 4

5 Generation of Mobility Spectrum N(t): For each Gaussian N i (t) list the parameters for t max,i, height h i (N max,i ) and width σ i on top of the sheet, i.e., in the posted example in rows 3, 4 and 5, respectively. List discrete values of drift time t in column B, i.e., 0-30 s in steps of 0.5 s (or better) starting in row 8 in the example. Then compute the values of the Gaussian function and place the values in a column to the right of the wavenumbers (i.e., column D in the example); this default Gaussian is normed such that its integral equals unity. Once you have the Gaussian values computed, determine the maximum value n i of your Gaussian (i.e., D50 in the example). You can now compute the value of the height-normed and intensity-weighted Gaussian and place it in a new column (i.e., Column E in the example) by dividing the value of the default Gaussian by the maximum values of the Gaussian (height normation) and multiplication by h i (intensityweighted). Proceed in the same fashion for the other Gaussians N i (t). Finally, compute the N(t) values in a new column and plot the mobility spectrum as an unmarked XY scatter plot. Do not plot the individual Gaussians N i (t); only plot the spectrum N(t). Import the plot as Figure 1 into your Word file and add a Figure legend. Report the parameters used for the Gaussians of the ion mobility spectrum in the legend to this Figure 1, that is, list the values (t max,i [s], N max,i ), σ i [s]) for all i Gaussians. (v) Create Figure 2 by Simulation of Figure 6a of the Source. Your Figure 2 should be a complete re-creation of part (a) of Figure 6 of the Source in every way (same sizes, same labels, same tick marks, same colors, shaded areas, same everything) using the program EXCEL. Generate and integrate your Figure 2 in complete analogy to your work on your Figure 1. At least twelve Gaussians are needed for the simulation of the curve (i = 12). (vi) Write Text with Proper Bridges to Schemes 1-3 and Figures 1 and 2. Write a brief and concise description of the context (try to stay within 2-3 pages of text, double-spaced, Times New Roman, 12 pt, 1 inch margins, your names in the header, page numbers centered in the footer) at the beginning of a Word file. Cite the schemes and the figures in your text using appropriate bridges at the most suitable places. Schemes 1-3 and Figures 1 & 2 follow the text, 5

6 each with its own legend and on separate pages. Cite references in the text where needed and have them appear as numbered footnotes. Your text should include five paragraphs. Begin with a brief introduction of overall purpose of the study, that is, the detection of opioids in seized sample A using IMS/MS. In the next paragraph and using Scheme 1, briefly explain the principles of IMS/MS detection. In the third paragraph and using Figure 1 and Scheme 2, explain the outcome of the positive ion mode detection of sample A. In the fourth paragraph and using Figure 2 and Scheme 3, explain the outcome of the negative ion mode detection of sample A. Finally, in the fifth paragraph conclude whether the outcome of the instrumental analysis of sample A suggests that the carrier of sample A should be free to go or warrants his/her arrest. Feel free to dig into the literature and cite some literature to clarify the chemistry reported in the Source. Software, Formatting, Etc: The assignment must be completed with MS WORD, MS EXCEL, and ChemDraw. Create one WORD file with the name A04_ your_last_names.docx and one EXCEL file with the name A04_ your_last_names.xlsx. Organize the XL file as clearly as you can so that it will be easily accessible (as in understandable ) to the peer reviewers! Label your sheets. Perhaps show the graph in a separate sheet (you can Move Chart to a new sheet). Deadlines: Instructor and/or GTA will provide feedback and an opportunity to update before the peer review starts. Here is how it works: Submit drafts of both electronic files on Tuesday, 02/27/18 by midnight. Instructor will review submissions and comment in class on Wednesday, 02/28/18. Submit updates of both electronic files on Thursday, 03/01/18 by midnight. Bring one hardcopy (stapled) of the Word file only to class on Friday, 03/02/18. Peer reviewers will receive the associated EXCEL file via once peer review assignments will have been made. 6

7 Importing Graphs from Excel: (cf. A02 about importing ChemDraw schemes.) There are many ways to import an Excel Graph into a WORD file. One way to import a graph from Excel into Word involves the following steps: select the graph in Excel, copy the graph to the clipboard (click Copy in the Edit menu, or type Command-C), go to the Word file, and paste the clipboard (click Paste in the Home menu, or type Command-V). This import method inserts the graph as a Microsoft Excel Chart Object and such an object can be edited after it was inserted in the Word file. Double-clicking the chart in the Word file will open a Excel window where you can edit the graph and the respective XLSX file. For other ways to import a graph from Excel into Word use Paste Special. Click the small triangle under Paste in the Home menu to see the Paste Options and then select Paste Special. A menu comes up and you can chose among various formats including Microsoft Excel Chart Object, Bitmap, several Picture formats (Enhanced Metafile, GIF, PNG, JPEG), and Microsoft Office Graphic Object. Embedding a Microsoft Excel Chart Object can be advantageous and it is straightforward if the WORD file and the associated CDX files are in the same file system. However, in collaborations that involve several people working on several computer systems, there are advantages to using alternatives. As a general rule, we want to paste schemes and graphs as Picture (Enhanced Metafile). Even if the assignment only requests the submission of embedded figures, keep the associated XLSX files because you might be asked for their submission during review. 7

As we begin to work on research-based assignments and to deal with nature s complexity, it is

Assignment A04: Electrochemical [Mn(CO) 3 (DIPIMP)] + -Catalyzed CO 2 Reduction As we begin to work on research-based assignments and to deal with nature s complexity, it is worthwhile to reflect on a