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Spectral Zoo: Combined Spectroscopy Practice Problems for Organic Chemistry
The Spectral Zoo is a freely accessible browser-based application designed to provide spectroscopy practice problems (IR, 1H NMR, and 13C NMR) for organic chemistry students. JSpecView is used to display the spectra interactively so that the user can zoom in to inspect splitting. The website does not require the use of Java, Flash, or plug-ins, so it works well even on tablets.
Importance of spectroscopy for organic chemistry
Spectroscopy is important in the sophomore organic chemistry sequence. Since the Alexander survey was published nearly 20 years ago,1 organic chemistry educators have continued to focus on this topic. Bodner explored differences between sophomore organic chemistry students and more experienced chemists as they solve combined spectral problems.2 Pienta’s recent eye-tracking study documented distinct gaze patterns in sophomore organic students and more experienced students as they answered questions related to 1H NMR spectra.3 Pedagogical approaches used to help organic chemistry students develop their skills solving spectroscopy problems include Shultz’s jigsaw approach4 and Flynn’s tactile strategy using sticky notes.5
Faculty members have devised various ways to introduce spectroscopy in their courses as they guide students in developing relevant skills. Chemistry instructors have described pedagogical approaches such as Kurth’s synthesis spectroscopy road map problems6 and Livengood’s individualized homework problems.7 In laboratory courses, creative approaches have been described that require students to solve combined spectral problems or that facilitate student access to spectra they generate.8–11
Online resources for teaching/learning spectroscopy
Over ten years ago, Debska reviewed the wealth of online resources available for teaching 1H NMR spectroscopy to organic chemistry students.12 While some of the resources are no longer available online,13,14 alternative online books, tutorials, and other resources have been developed in their absence. Reusch and Spinney have each contributed substantial modules on spectroscopy to the LibreTexts library.15,16 Wong has developed an interactive tutorial on 1H NMR spectroscopy.17 Other valuable information about spectroscopy is available at sites developed by Starkey,18 Lancashire,19 and the Royal Society of Chemistry.20
Enabling students’ transition from spectroscopy learners to chemists who are adept at solving spectral problems would be facilitated by exposing students to a larger number of combined spectral problems. Instructors make use of the several key websites that provide spectral data ranging from images of spectra,21 to JCAMP-DX IR spectra displayed in a viewer,22 and even to files that can be processed to generate spectra.23,24 Chalk’s recently developed Open Spectral Database is a resource designed to facilitate sharing and searching spectral data, providing spectra in several formats including JCAMP-DX.25,26
Several other websites serve as resources directed at students, providing them with combined spectroscopy problems on which to practice. The most familiar of these is Merlic’s WebSpectra, which uses gif images of spectra combined with cgi scripts to allow users to expand spectral regions of interest.27,28 Graham’s more recently reported collection which focuses on 2D NMR also uses static images of spectra.29,30 Vosegaard’s iSpec is a browser-based game to provide students with spectroscopy practice using images of spectra.31,32 Agnello’s study convincingly demonstrates that the UlgSpectra application was helpful for student learning.33 Unfortunately, the Java application was difficult for students to install, required a VPN for students to access the spectra, and took students 1-2 hours to learn to use. A subset of the spectra is available for use at other institutions, but the need to download and install a Java application remains a technological barrier for many students. Several other collections are available but have not been described in journal articles.34–39
Online resources for teaching/learning spectroscopy
The Spectral Zoo is a web-based application that provides practice problems designed to help organic chemistry students solve combined spectroscopy problems.40 The website is freely accessible with a web browser (https://tinyurl.com/speczoo) and does not require the installation of special software, browser plug-ins, or even Java. The current iteration of the Spectral Zoo uses JSpecView41,42 to display spectra interactively, so that the user can zoom into signals or determine frequency/chemical shift by placement of the cursor. This approach differs from most of the other collections available online, which display static images. There are 74 unknowns in this set, with IR and 1H NMR available for all of the compounds. For thirteen of the unknowns, the 13C NMR is also available. Because the site is intended for student practice rather than being a homework assignment submitted for grading, the answers are available by clicking a button.
Using the Spectral Zoo
The website is designed to be user friendly and require no instructions other than the one presented when the page is first loaded, as shown in Figure 1.
Figure 1. Spectral Zoo Opening Display
Once the user has selected an unknown, the display changes, providing links to the spectra and the structure for that unknown, as seen in Figure 2.
Figure 2. Spectral Zoo display after an unknown has been selected.
Figure 3 shows the application displaying the IR spectrum for unknown 7 in the JSpecView applet. The slider to the right of the spectrum allows the user to modify the vertical scale for the spectrum. The slider at the top of the spectrum allows the user to zoom in or out for the spectrum’s x-axis. It is also possible to zoom in by clicking and dragging with the mouse. Several other convenient features offered by JSpecView can be accessed by right clicking on the spectrum.
Figure 3. IR spectrum for Unknown 7 in Spectral Zoo.
Proton NMR spectra are slightly more complex, as the user typically needs to expand regions of the spectrum to inspect splitting. With the JSpecView applet this zooming process is intuitive for users. Another complexity associated with 1H NMR spectra is integration. The JSpecView applet provides an interface that allows the user to normalize the integrals based on a specific signal selected by the user. Figure 4 displays a zoomed section of interest of the 1H NMR spectrum for Unknown 7. Also shown in this figure is the popup panel allowing the user to configure the integrals. Although the integration interface is intended to be intuitive, there is a video tutorial demonstrating its use which was developed by a Centre College student.43
Figure 4. Proton NMR spectrum of Unknown 7 while normalizing integrals.
Figure 5 shows the popup window displaying the structure for Unknown 7, which is accessed by clicking the “Show structure” button at the bottom of the screen (See Figures 2 and 3). The Jsmol applet is used to display the structure, which means the structure may be rotated for inspection by the user.
Figure 5. Structure of Unknown 7
Student response
Students at Centre College and other institutions have been using the Spectral Zoo since 2002. Site statistics have been captured since June 2012. Unfortunately there is an 18-month gap in the data from July 2016 through the end of 2017 even though the site remained active during that time period. For the approximately five years of site statistics, there have been over 74,000 page views. This large number of page views suggests that most visitors to the site are not students in the author’s classes, which typically have 17-25 students in a given section. Since the site provides answers, these users are visiting the site because they perceive it to be useful rather than it being a requirement for a course assignment. Most visitors are from North America and have been directed to the site through a link in the Sapling Learning homework system. Site statistics for the past three weeks suggest that the visitors from Sapling Learning represent 73% of visitors during this time period.
With Centre College IRB approval, pre- and post-surveys were administered to Centre College students during the 2012-13 academic year. The surveys were based on the New Traditions pre- and post-surveys for introductory chemistry.44–46 Questions on the post-survey ask students to respond about the relative impact different course activities and assignments had on their learning. Additional items were added asking about the Spectral Zoo and how the website influenced student learning in the class. Thirty-two students responded to the post survey from two classes (total of 34 students) taught in separate semesters, giving a survey response rate of 94%. Responses to the Likert-scale question about how the Spectral Zoo influenced their learning were very favorable, with 87.5% (28 students) indicating that the Spectral Zoo had a positive impact on their learning for the course. The distribution of responses is displayed graphically in Figure 6.
Figure 6. Distribution of student responses about Spectral Zoo effect on learning.
Most of the students (29 students, 90.6%) responded to the open-ended question, with most of the comments being positive in nature (23 students, 71.9%) Three students reported that they did not use the Spectral Zoo on their own. Two students (6.3%) expressed frustration about technical aspects of the site and one said the site was not helpful. The 2014 switch to JSpecView for display of spectra addressed student concerns about integration, as JSpecView provides integrals that can be normalized to provide numerical values. Representative student comments are provided in Table 1.
Table 1. Representative student comments about Spectral Zoo |
|||
|
Type of comment |
Topic of comment |
Percentage of comments |
Representative student comment |
|
Positive |
Useful practice |
53.1% |
“It helped to provide a place to practice and learn from my mistakes when using NMR, IR, and interpreting data.” |
|
Positive |
Helpful |
18.7% |
“It helped greatly learning how to do spectroscopy questions.” |
|
Neutral |
Didn’t use |
9.4% |
“Not very much. I rarely used it.” |
|
Negative |
Technology |
6.3% |
“Spectral Zoo confused me at times because there was no clear integration. I would get halfway through a problem & then get frustrated or give up because I didn’t feel like I had sufficient info to find the structure.” |
Conclusions
For sixteen years students have been accessing the Spectral Zoo to gain practice analyzing spectra and solving combined spectroscopy problems. Development of the site has continued, keeping pace with changes in web technology. That development will continue into the foreseeable future. Comments from Centre College students about the site have been positive. Robust traffic to the site from visitors who are not on the Centre College campus suggests that many individuals have found this site helpful through the years.
Technical details
The first version of the Spectral Zoo, which was based on JavaScript, was described in a presentation at the 2002 Biennial Conference on Chemical Education.47 The site used MDL’s Chemscape Chime plugin for the Netscape web browser to display JCAMP spectra interactively.48 Unfortunately MDL had stopped development for Chime around 1998.49 Further, the Chime plug-in did not have native support for integrals important for 1H NMR spectra. Thus, the Spectral Zoo was updated to use a Java-based spectral viewer able to display integrals in proton NMR around 2006.10 The next major update to the site was to implement a database (PHP/MySQL) to contain the information about the unknowns instead of having those details in JavaScript.50 Around 2014 when security issues related to Java began to increase, the Spectral Zoo transitioned to using the JavaScript version of JSpecView which had by then been incorporated into Jmol/JSmol.51,52
The IR and NMR spectra in the Spectral Zoo are in JCAMP-DX format.53 Infrared spectra for the unknowns were obtained from the National Institute of Standards and Technology in JCAMP format.22 1H and 13C NMR spectra were obtained from the Pacific Lutheran FID archive23 and were processed with NUTS software from Acorn NMR, exported in the JCAMP-DX format.54 Spectra are displayed using the JavaScript version of JSpecView applet41,42 which has been incorporated into the Jmol/JSmol applet.55 Structures are displayed using JSmol. The database uses MySQL with PHP as an interface. The only client-side scripting is JavaScript. The author would be happy to share her code with other instructors interested in developing their own instance of this application. Alternatively, instructors are encouraged to refer their students to the site at Centre College.
Acknowledgments
I thank Pacific Lutheran University FTNMR FID Archive for sharing NMR data which were used in the development of the Spectral Zoo. I am particularly grateful to Robert Lancashire and Robert Hanson for helpful discussions over the years as I upgraded the site. I would like to thank Ian Kaster, who developed the Java applet used for many years to display spectra on the site and who encouraged me to convert the hard-coded JavaScript to a database format. Thanks also to Alexander Williams, who developed the YouTube video demonstrating the use of the JSpecView integration panel.
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Comments
Mass Spec data
Hi Jennifer,
Very interesting database- do you plan to add mass spec data?
Also, just a comment (more for me than anything)- this type of practicum (leaning more toward IR/Raman) would be a great inorganic resource as well.
Jason
mass spec data
Thanks for your suggestion, Jason,
I'm not aware of a source of mass spec data in JCAMP format that's freely available. But maybe there's one out there and I've missed it? I must admit I did not search extensively. We don't spend much time teaching organic students to interpret mass spectra, and I mostly developed this resource as a tool to help my organic students.
Jennifer
I think the NIST Chemistry
I think the NIST Chemistry Webbook mass spec data is available in JCAMP format.
NIST webbbook
NIST is the source of most of the IR spectra in my database, so I should have thought to look there for the mass spec as well. Thanks for this suggestion, Kristen. Perhaps the next big upgrade to the site will be to include mass spectra for as many unknowns as possible.
Crowd source extra help for problems?
Hi Jennifer,
Looks like a great resource! Of course as I started to dig into this, I started to wonder where students might need extra help. For example, a link to a descrption on how to fully take advantage of the NMR integration. I was not able to quickly figure out how to integrate individual peaks, and I wonder if you give your students a demonstration on how to use the interface. Maybe an embedded or linked YouTube video would suffice?
Since this is set up for students to be able to check their own work, they can see the correct answer, but not how that answer fits the data. I wonder if there would be a way to crowd source answer explanations or spectral interpretation for the problems (maybe that could be a student project or class project or splitting it up between some interested faculty members as 74 problems is quite a database). I also wonder if there are some hints that could be provided with a few other buttons.
Ehren
extra help
Thanks for the suggestions, Ehren! I usually introduce the application in class, so students have an opportunity to observe my interactions with the interface. A few students every year express frustration about their uncertainty in interpreting the integrals. Students really appreciate other video tutorials I have developed, so embedding or linking a video to explain the integration interface would probably be well received.
I remember that Robert Lancashire developed a nice system to display correlations between structures and spectra. See his 2007 article in Chemistry Central Journal. I never investigated how difficult it would be to incorporate something like that, so I am not sure how challenging it would be. If folks are interested in helping with that task, I would definitely be interested in talking to potential new collaborators!
Spectra and Group Theory
Hi Jennifer and other CCE devotees,
although I retired 4 years ago I still maintain an Office at UWI and helped out with a few Computer assisted Labs this year on the use of JSmol (now including JSpecView) for showing IR and Raman spectra and how Group Theory could be used to predict the presence or absence of peaks for various vibrational modes. Some examples are available at http://wwwchem.uwimona.edu.jm/spectra/jsmol/demos/ Look for DCE (dichloroethenes), ClMethanes (includes some deuterated samples as well). Note that IR and Raman spectra can be simulated for "simple" molecules using WebMO.net and the output Gaussian zip file can be read by JSmol directly.
JSpecView and vibrational spectra
Hi, Robert,
Thanks for the link to your nice page with vibrational spectra and corresponding animated vibrations. I think there's some overlap between a couple of your examples and substances in my database. So maybe I'll figure out how to modify the PHP scripts to provide a link to structure/spectral correlations when I discover that those also exist.
Looking at the documentation for JSpecView and JCAMP-DX it sounds like they should be able to handle spectra like HSQC that Brian Esselman has his students generating and interpreting. Do you have any advice for me with as I contemplate working with nD NMR spectra in JSpecView?
ChemSpider Spectral Games
Hi Ehren and Jennifer,
I know Jean Claude Bradley and others had set up a spectral game for curating spectra uploaded to chemspider,
https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-1-9
But I don't think it is being maintained, and the domain (http://spectralgame.com/) has been taken over by some commercial advertiser.
Pubchem has also added a section on Spectra (section 4)
https://pubchem.ncbi.nlm.nih.gov/compound/2244#section=Mass-Spectrometry
Cheers,
Bob
JCB's Spectral Game
Hi, Bob,
I remember Jean Claude's spectral game and how challenging some of those spectra were to assign! It's disappointing to see that the domain name has been grabbed by someone who wants to sell it for 500 bucks. I wish one of us in the chemistry community had thought to adopt the domain before that had happened.
Thanks to the link for the PubChem section on mass spectrometry. It looks like there are an abundance of sources of mass spectra that I could rely on to incorporate mass spectra in the application. What subdisciplines of chemistry regularly teach students to interpret mass spectra?
-Jennifer
Spectral usage
To address your question about mass spectra... At UW, we are pretty fortunate in our available resources and most of our experiments include students analyzing a varity of spectral data generated from their own samples (IR, GC-MS, 1H-NMR, 13C-NMR with APT, and HSQC). I think expanding the types of spectra involved for each sample would make the Spectral Zoo a lot more rich and allow for its use at a broader range of institutions.
APT and HSQC
Thanks for the details about the different kinds of spectra you have students analyze at UW, Brian. It looks like NMRDB will simulate HSQC spectra. (Unfortunately I do not see APT available at NMBDB.) Do you think simulated spectra would be reasonable to include if I decide to expand the database to incorporate other spectral types? Or maybe you can point me to a source of HSQC spectra? I am assuming that JSpecView would be able to display HSQC but I haven't previously used it for those.
I have no idea where to get
I have no idea where to get HSQC data. Most of the spectra we use with our students come from two methods
1) Inauthentic data compiled from the Aldrich Spectral Viewer (1H-NMR and 13C-NMR) with IR and MS from SDBS.
2) Authentic data that we collect ourselves on our instruments. Only with the authentic data do we have access to HSQC and 13C-NMR APT.
Knowing nothing about your software can you take authentic fid data from an NMR output and use it?
FID data
As far as I know, all the spectra in my collection were acquired rather than simulated. In the past (~20 years ago) when I had FIDs I had to process them and then export them into the JCAMP format so that Chime could import them. JSpecView imports everything that Chime could handle. I do not know whether JSpecView will process the FIDs and convert them into spectra because that’s not a feature that I have previously used. I am aware that most NMR and IR spectrometers will export data in the JCAMP format that makes it easy to share data between instruments from different manufacturers. Perhaps you could check to see if your spectrometer could export the data in JCAMP format. If that’s not a possibility, I could probably figure out how to process the FIDs so that JSpecView can read and display them. Sadly, I have two more weeks of classes. So it will be awhile before I have time to think about this interesting new task.
Nice Article
Hi Jennifer,
I remember the first version of the Spectral Zoo back in 2002 or 2003 using the Chemscape Chime plugin and Netscape browser. It seems like this new verson is a lot better. Your students should love this. Oh, If this type of technology had been around when I was a student.
Chemscape Chime
Thanks for your kind words, Sylvester. I remember how disappointed I was when I learned that Chemscape Chime was no longer being developed. That meant we had no chance of getting integrals from the JCAMP data. Then Bob Hanson came along and figured out how to add the integrals to the jcamp data so Chime would show them. The spectral display with JSpecView is definitely an improvement over Chemscape Chime. We owe a lot to Robert Lancashire and Bob Hanson for developing the technology to do these cool things without Java or any plugins!
-Jennifer
More spectra, student annotations, and assignments
The strengths of this web-based resource are obvious. Students can access it from anywhere, can practice determining structures using two types of complimentary data, and can find out whether or not their structural determinations are correct. The ability to zoom in on signals is great and allows the user to display peaks nicely and observe coupling. The integrations are clear and obvious. I’m sure with a little bit of time spent, most users would get pretty comfortable with the interface. There are three areas of growth for the Spectral Zoo that would make it much more useful to students at other institutions and provide a deeper/more transferable learning experience. (I make these statements without regard to the practicality and ease of coding.)
As mentioned, it would be great for each molecule to have 13C-NMR (with or without APT) in addition to 1H-NMR. The increase in the 13C-NMR incorporation would broaden the utility of the Spectral Zoo for students taking courses where 13C-NMR is used. Selfishly, I’d love to be able to send my students here and have them see 13C-NMR and mass spectra for each molecule as they are included in my courses. Based upon the responses here, I think a lot of people would be enthused by an expansion of the types of spectra available.
It isn’t clear that when students use this interface or any other currently created that they would be labeling signals with part structures or making tentative assignments in the same manner they would on paper. The ability to annotate as a student works through the spectrum would be excellent. Until people become experts at this type of analysis, they need to make a lot of annotations to reduce their cognitive load and allow them to hold onto all the pieces of information. Our best students tend to do this, while our weaker students attempt to simply arrive at a solution. It isn’t clear that any online tool does this smoothly, but we should as a community be thinking about how to get students to routinely annotate their spectra in an online space. The ability to label signals with part structures or make notes about the integrations would help a lot.
This type of solving spectra is really only the first level task that many instructors expect of their students. Assigning the spectra is the next level task. Once the student identifies the molecule, it would be fantastic for them to be able to attempt the assignments of each signal in the 1H-NMR/13C-NMR and key functional group signals in the IR. The assigning of the signals ensures that the student is getting the correct structure with the correct reasoning. Perhaps a later, more advanced phase of this tool could have a way for students to label the structure with the signals, as well.
More spectra and annotations
I am interested in adding additional spectra and am happy about the sources of mass spectra that I’ve learned about in this discussion. The discussion also helped me find more C-13 spectra that were not available 20 years ago when I started this project. I am looking forward to incorporating MS and C-13 NMR for as many compounds as possible.
Your ideas about providing students with the ability to annotate the spectra sound interesting. I agree that approach would be valuable for student learning. At the moment I have not envisioned what kind of programming might be appropriate to accomplish such a task. But I will be thinking about it and chatting with my computer science colleagues to try to sort through the issue. I also realize there are plenty of folks participating in the conference who have more training in programming than I do. Perhaps one or more of them will chime in with ideas about how to approach this task....
I am starting to wonder if
I am starting to wonder if some of this could be incorporated into OpenOChem, which is the paper we will be discussing next week. We already have a system for students to draw in proposed structures and can be graded. In relation to my suggestion about student feedback, we could have common mistakes already figured out and can be included for feedback on wrong answers and they could try again.
I was also playing with rdkit to find functional groups in molecules. That could be used as part of the answer evaluation. If for example a student misinterpreted a molecule to have carbonyl instead of a C=C, we could determine that from the structure and provide feedback that says something like- you should check to see if the IR spectrum has a peak at ~1700 or closer to ~1600. I think rdkit would also allow us to determine if there were specific alkyl chains. If a student put in an ethyl into a molecule, but there was no triplet/quartet in the NMR that could be part of feedback. This is part of the algorithmic thinking we do in solving problems, so it could be programmed (if we want to convice Carl!).
good ideas
Ehren, thansk for your very useful suggestions. I look forward to continuing these discussions about how to help organic chemistry students learn!
Learning spectroscopy
The learning that precedes deducing a structure from the formula and spectral data is very significant. I think that we think students have a much deeper understanding of structure than they actually do. From my BestChoice data students have difficulty deducing, for example, the number of hydrogen or carbon environments in a given structure or even deducing which methyl groups or methylene groups in a given alkane structure are equivalent. Web-based activities certatinly can serve the purpose of encouraging students to do this kind of analysis, including working out double bond equivalents from formulae, using that to deduce which functional groups could be present, subtracting the elements of their partial structure from the formula etc etc.
I have dabbled in this as a support for spectroscopy lessons for first year University and high school students. The BestChoice authoring tool allows me to combine structures and spectra and questions (and annotations in one IR activity) and feedback. I can see for example that they are good at telling me which functional group should have an OH stretch in their IR but not so good at telling me which functional groups have a C=O stretch in their IR. A couple of links are given below. Be aware that the integrated one was written yonks ago. The spectra are just images which likely need tidying. There are more activities at www.bestchoice.net.nz under Spectroscopy in the menu.
Functional groups from IR absorptions
Integrated spectroscopy (IR and NMR)
Spectrocopy Software
I used to teach basic IR, MS, and H-NMR to sophomore organic students. Some may be skeptical about them learning the abstract parts of these methods but if pushed a bit, they can do better than one might think. I wrote CAI programs for them as well which helped a lot. They were old DOS programs using CGA technology; they will not run on newer Windows systems. (a lot of C is now in digital heaven). Somewhere I have the EGA version of NMR because I never was able to get anyone to publish it. I doubt if it will run on Windows either. I was able to add some commercial videos to it which helped solidify learning somewhat. My IR checkers game was published in The Chemical Educator. It used spectra made public on the Nation Bureau of Standards website. I do not remember seeing any MS or NMR spectra then.
Best Wishes
<Richard>
resources for teaching spectroscopy
Richard,
I remember your IR checkers article! My students appreciate games that can combine friendly competition with learning. It takes a lot of time and energy to develop the games, but the enthusiasm generated in students makes them valuable. I wish I could see the programs and videos that you developed for DOS. Constantly improving computer resources mean instructors have to continually reinvent our teaching tools. I guess I need to up my game and pay more attention to mass spec. I agree with you that students rise to the challenges we as instructors present to them.
Jennifer
BestChoice
Sheila, I didn't realize that BestChoice had spectroscopy lessons! I associate your wonderful resource with first year college students, and I forget that first year students sometimes study organic chemistry. I look forward to exploring your spectroscopy resources in BestChoice, especially your combinations of structures and spectra with annotations.
Tools and function
Hi Jennifer,
I am a big proponent of exposing students to authentic data. I think that having a library or, as you call it, a zoo, of spectra that can be manipulated by students is excellent. I have a few comments about the current tools and some suggestions of added function.
I agree with one of the previous commenters that a tutorial or guide on the tools available to manipulate/interact with the spectra would be beneficial. While your students seem to manage with the use fine, you report that most of the traffic is coming from outside of your student body. Outside viewers will not have the benefit of watching firsthand the use of the interface and it would be unfortunate if they were losing out on the full utility of the spectral zoo.
I was wondering if there was a way to display Hz as you mouse-over the signals as it currently displayed in ppm and intensity. It is great that this Hz information can be found under peaks with additional break down of the difference between close peaks. However, the difference is only applied based on proximity and can be convoluted with complex coupling or overlapping signals. Displaying Hz upon hovering over the peak may help key in students that this information greatly helps in solving structures. This would also help students to readily compare distance between peaks that are not immediately adjacent in complex systems without having to orient the table output to the spectra.
Related to the table outputs, it would be helpful if the labels found in the tables (peak 1, 2, 3,…) were somehow displayed on the spectra. I noticed that if I changed the view on the window the table did not adjust in real time. However, when the zoom was changed the table would update to the new active window (though the threshold would reset for peak picking). While the chemical shift could be used to reorient the window to the table, a second confidence check would be great. Labeling would make translating table outputs easier.
I really appreciate that the structure answers are presented with a 3D model that is rotatable. This is great for reinforcing structure while students interpret the molecular connectivity with spectral data. While clicking though the structures I notice however, that there were structures that were not drawn in the low energy conformation or had incorrect connectivity. Often, for convenience, instructors depict non optimized structure with 2D drawings. With the 3D representations there is the opportunity to improve student understanding of geometry with accurate depictions of the low energy structures. Additionally, there were a handful of structures that lacked pi bonds but it was implied by the geometry and chemical formula and confirmed by spectral data (structure 76, 183). The high achieving students may be able to interpret what the correct structure is meant to be but there may be a few students that are left with a misconception of structure and bonding.
tools and function
Hi, Aubrey,
I hear you that site users would benefit from a tutorial to help guide them as they learn to manipulate the spectra in their browsers. I will be working on a resource of that type over the summer. Your suggestions about the JSpecView interface sound interesting. I use that applet as a resource but my programming skills are not up to the task of programming such an intense app. I'll share your suggestions with Robert Lancashire and Bob Hanson in case they might be interested in incorporating some of those ideas.
Thanks for the observation that some of the 3D models don't show double bonds appropriately. When I originally set up the Spectral Zoo, Chemscape Chime was the plug-in used to display both structures and spectra. Back in the day, Chemscape Chime didn't have a mechanism to show double bonds. Later Jmol eventually added the ability to display double bonds. Apparently I didn't catch all of the double bond-containing compounds and update the .mol or .pdb files to explicitly show the double bonds. I'll go hunt down those other compounds to fix their structures. Adding 2D structures in addition to the 3D versions is a nice idea that I may include as well.