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highlighting our recent NSF project!

To see how the GC-MS was implemented into these courses, click on one of the above buttons.
To read an overview of this project, please view the report below.

Implementing Guided-Inquiry Laboratories Utilizing Gas chromatography-Mass Spectrometry in the Chemistry/Biochemistry Majors Sequence

 Jeffrey T. F. Ashley, Cheryl A. Longfellow, and Kris L. Bhat

Abstract: A gas-chromatograph mass-spectrometer (GC-MS) was purchased for Philadelphia University’s School of Science and Health with partial support from the National Science Foundation’s Course, Curriculum, and Laboratory Improvement program (DUE 0126468). By acquiring a GC-MS and partially redesigning four courses (organic chemistry, physical chemistry, environmental chemistry, instrumental methods of analysis) to include its use, we have helped prepare our students for post-graduate experiences.  Also, through implementation of guided-inquiry laboratories in three of our courses, we have further developed and honed our students’ critical thinking, communication, and teamwork skills.


Chemistry students need experience with modern research equipment to prepare them for careers in chemistry or studies at the graduate level.  A gas-chromatograph mass-spectrometer (GC-MS) was purchased for Philadelphia University’s School of Science and Health with partial support from the National Science Foundation’s Course, Curriculum, and Laboratory Improvement program (DUE 0126468). By acquiring a GC-MS and partially redesigning four courses to include its use, we have helped prepare our students for post-graduate experiences.  Also, through implementation of guided-inquiry laboratories in three of our courses, we have further developed and honed our students’ critical thinking, communication, and teamwork skills.  

To accomplish our goal of implementing GC-MS throughout our curriculum, we devised a multi-course sequence whereby students would be incrementally exposed to analytical techniques and applications of GC-MS (Table 1).  For the guided-inquiry laboratories, we divided the students into groups and charged them with answering a specific scientific question (1).  A guided-inquiry laboratory using GC-MS to elucidate the distribution of the products of a reaction is introduced to students taking organic chemistry in the spring of the sophomore year sequence; these students include chemistry, biochemistry, and biology majors.  In the fall semester of their junior year, chemistry and biochemistry majors take physical chemistry followed by instrumental methods of analysis (IMA) in their spring semester. The physical chemistry laboratory focuses on design, implementation, and interpretation of data on a guided-inquiry project. The previously theoretical IMA GC-MS discussion is now augmented with hands-on experience.  Finally, optimally in the fall of their senior year, students who have completed IMA may take an environmental chemistry course where a half-semester, guided-inquiry project culminates with a group presentation to an organization having an environmentally-based mission.  This course sequence also prepares juniors for independent research projects utilizing GC-MS in the summer and during their senior year. 

Table 1: Course sequence highlighting the incorporation of theoretical and practical experience in GC-MS.

Implementation of GC-MS in Organic Chemistry

Use of GC/MS is widespread in organic chemistry for elucidating reaction mechanisms and determining product and/or intermediate identity. In the developed guided-inquiry laboratory project, the question posed to the students is “Will thermodynamics or kinetics control the reaction?”.  The experiment is “guided” in that the system to be studied is chosen by the instructor. The reaction of phenyl magnesium bromide with 2-methylcyclohexanone followed by acidic reagent addition is expected to yield the unsymmetrical 2-methyl-1-phenyl cyclohexanol (2). The acid-catalyzed dehydration at low temperature initially gives the kinetically favored alkene as the major product. As the temperature is increased, the trend reverses to give, as the major product, the more substituted alkene, which is thermodynamically favored. By observing the dehydration reaction over time with GC-MS, students are able to determine the relative abundances of each product using changes in the peak areas for the two products.

This laboratory project extends over a three to four week period in the spring semester and has replaced two “cookbook” laboratories.  In the first laboratory session, an overview of GC-MS is given. Once the synthesis is complete, students analyze their samples with the assistance of their laboratory instructor.  Because the products are expected to be primarily one to two-component mixtures, the GC-MS analysis is relatively straightforward. Traditionally in our organic chemistry laboratory, only the results section of a laboratory report has been required. With this experiment, students are introduced to writing a full formal research report.  The goal is to strengthen students’ scientific writing skills as well as their quantitative reasoning about their data and what its interpretation means in a kinetic and thermodynamic context.  During the second half of this semester, students are also required to develop an independent multi-step synthesis project. With previous exposure to the GC-MS, we have found that some students choose a project where the analysis lends itself to using instrument.

Implementation of GC-MS in Physical Chemistry

An important aspect of physical chemistry is the exploration of the fundamental relationships between the structures of molecular compounds and their physical properties. Modeled after a laboratory in which students separated complex mixtures using GC-MS (3), our students considered “How is molecular structure related to odor?” The students have two four-hour laboratory periods to obtain data to answer their question and the third period is used to analyze and interpret their data. In this manner, teamwork and collaboration is emphasized as in real-life research laboratory settings. Students choose from a predetermined set of compounds that have been previously identified as workable.  The students’ goal is to isolate and identify the compounds that result in the odor. The National Institute of Standards and Technology (NIST) databases, purchased with the GC-MS software, are used to facilitate this task as well as analyses of fragmentation patterns. Once the compounds have been identified, students compare these characteristics with other naturally occurring compounds with distinct odors in order to identify one or more important characteristics of the molecular structure of a “smelly” compound. 

The lab runs over a four-week period during the fall semester, and coincides with a discussion of thermodynamics, equilibrium, and kinetics in the lecture component of the course. This guided-inquiry laboratory leads the students from noting the smell of a common product to identifying the chemical(s) responsible for that smell and its molecular characteristics. Students develop their own procedures, form hypotheses, analyze samples, interpret data, and draw conclusions based on their interpretation of the data. Their final report, during the fourth week, is a group presentation to the faculty and interested students on their findings.

Implementation of GC-MS in Instrumental Methods of Analysis

The IMA course strives to leave students with an understanding of the theory and application of many currently-used analytical instruments while further honing students' analytical skills through various preparatory and instrumental methods. This course has been modified to expand the lecture material to include more theory of mass spectrometry, incorporate additional analyses of acquired spectra, and facilitate a laboratory experiment highlighting the analysis of an unknown and quantifying the sample using the internal standard method. A detailed discussion of the different components of our GC-MS is given and students are expected to identify spectra based on fragmentation patterns and the ion source used (e.g., negative chemical ionization vs. electron impact).  With this base knowledge of GC-MS, students then participate in a 3 hour hands-on laboratory that: 1) further acquaints them with GC-MS hardware and software, 2) introduces them to the concept of an internal standard as a means of quantifying organic analytes, and 3) requires them to determine which polycyclic aromatic hydrocarbon (PAH) is contained in their 'unknown' solution and at what concentration. 

Implementation of GC-MS in Environmental Chemistry

With the current dominance of environmental-based monitoring in research and development in academia, industry, and government, it is becoming essential to expose undergraduates to those analytical tools that are vital to environmental chemists. Perhaps the most powerful of these tools is the GC-MS.  Students in the guided-inquiry, collaborative environmental chemistry laboratory project consider the question “Are Philadelphia’s sediments contaminated?”.  Using the “sediment quality triad” approach (4,5), results from chemical analyses using a GC-MS are coupled with simple bench-top toxicity studies and biology population community surveys to assess the extent and significance of pollution-induced degradation.  This highly multidisciplinary approach encompasses aspects of organic, analytical, and environmental chemistry. 

Resources are made available to the students to provide the necessary information to allow students to design their own approaches to the research questions. With minimal guidance from the instructor, students decide and subsequently justify the sites they feel should be sampled in addition to what analytes (e.g., criteria pollutants such as benzo[a]pyrene) and parameters (e.g., percent carbon, chlorophyll a, grain size, etc.) should be measured. When field sampling, students are required to work collaboratively. At other times, individuals or smaller groups take on specific tasks such as assessing macrobenthic communities in collected sediment, performing sediment toxicity tests, or extracting and cleaning up samples in preparation for analysis by GC/MS. Those individuals or small groups then convene to report to the entire group, updating them of the advancements and observations they have made.  The project culminates with an off-campus presentation to members of an environmentally-centered organization that would benefit from the students’ data set and interpretations.  In the fall of 2003, students in this course presented their findings to staff biologists and conservation managers at the US Fish and Wildlife Service’s John Heinz National Wildlife Refuge Center at Tinicum Marsh, PA.   

Assessment of Implementation and Future Directions

During the past two years of development and implementation of GC-MS into our chemistry and biochemistry courses, we have assessed these changes through use of questionnaires and surveys.  Modeled after Deckert et al.(1), questions are posed to gauge how effective our approach is at encouraging creativity and independence. We are also interested in whether students have a better appreciation of what working in a team environment requires.  Faculty observations have also been critical in the assessment process.  We have witnessed that students are better prepared and are much more engaged in the inquiry laboratories as compared to the conventional, ‘cookbook’ laboratories used before.  Lastly, an external reviewer monitored our progress throughout the past two years and was helpful in suggesting redesign of some aspects of the guided-inquiry laboratories.  Further refinement to promote even more learning and impartment of skills will be made through subsequent offerings of these courses.

The incorporation of inquiry-based problem solving in the laboratory has transformed our upper level majors courses into more interactive and enthusiastic environments, benefiting both students and faculty.  Though we have highlighted the changes made to courses, we must also mention the tremendous changes that the acquisition of the GC-MS has made for both faculty and student research. Research using the instrument has not been restricted to the principal investigators of this project.  Rather, many of faculty members have expanded their research interests with the arrival of the GC-MS.  Lastly, we admit that learning new GC-MS hardware and software can be daunting and initially much time is needed to become comfortable with the instrument.  However, the benefits quickly overshadow the initial time and effort investments, both in our teaching laboratories as well as with research projects

Acknowledgements
Partial support for this work was provided by the National Science Foundation's Course, Curriculum, and Laboratory Improvement program (DUE 0126468).  We wish to thank Prof. Julio dePaulo of Haverford College for his helpful insights and advice through his role as external reviewer on this project.   

Literature Cited  

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2. Poon, T.; Mundy, B.P.; McIntyre, J.; Woods, L.; Favaloro, Jr., F.G.; Goudreau, C.A. J. Chem. Ed. 1997, 74, 1218-1219.

 3.  Galipo, R. C.; Canhoto, A. J.; Walla, M. D.; Morgan, S. L. J. Chem. Ed. 1999, 76, 245-248.

 4. Canfield, T. J.; Dwyer, F. J.; Fairchild, J. F.; Haverland, P. S.; Ingersoll, C. G.;

Kemble, N. I.; Mount, D. R. LaPoint, R. W.; Burton, G. A.; Swift, M. C. J. Great Lakes Res. 1996, 22, 565-583.

 5.  Chapman, P. M. Sci. Total Environ. 1990, 97/98, 515-825.