Useful Chemistry

Communicating Chemistry

2009-11-23T14:15:00.001-05:00

In October 2008, I participated in an NSF workshop on eChemistry: New Models for Scholarly Communication in Chemistry. Theresa Velden and Carl Lagoze have now published their reports. Here are the details from their press release:

Public Release of White Paper: The Value of New Scientific Communication Models for Chemistry

Ithaca, NY, November 23, 2009 – The results of a National Science Foundation sponsored workshop in October 2008 are now available in a white paper 'The value of new scientific communication models for Chemistry', publicly accessible at http://hdl.handle.net/1813/14150. An article ʻCommunicating Chemistryʼ,summarizing this white paper, is published in the December issue of Nature Chemistry at http://www.nature.com/nchem/journal/v1/n9/full/nchem.448.html.

This white paper is intended as a starting point for discussion on the possible future of scientific communication in chemistry, the value of new models of scientific communication enabled by web-based technologies, and the necessary future steps to achieve the benefits of those new models. It opens with an overview of publishing reform and e-science initiatives in other disciplines, such as open access, data publishing, and preprint servers. Following this, it reviews the scientific communication system in chemistry, including the established system of journals and databases, and recent web-based innovations and experiments. Next, it analyzes the distinguishing aspects of chemistry that may influence its communication practices and have an impact on the manner in which science communication in chemistry will further evolve.

The white paper concludes with a call for a more comprehensive symposium on this subject. In recognition that the analysis presented in the white paper is yet incomplete, and provides only a starting point for discussion, the proposed international symposium would engage a broad range of participants who would expand on the subjects introduced in the white paper and issue calls for actions and research initiatives. Work on finding funding for this symposium is now in progress.

Members of the chemistry community and other interested parties are encouraged to join in a critical and constructive assessment of the content of the white paper and the issues it addresses. An online forum for this community discussion has been set up at http://groups.google.com/group/echem-white-paper. Other venues for discussion at conferences and workshops are being planned.

CAS curates strychnine m.p. - ChemInfo Class 9

2009-11-20T15:40:00.000-05:00

What is going to distinguish chemistry databases as we move forward in this Web2.0 world?

If I was unsure of it when I started teaching Chemical Information Retrieval 2 months ago, I certainly got my answer yesterday afternoon. Cristian Dumitrescu from CAS contacted me to discuss the problems I had encountered when attempting to use SciFinder to find the melting point of strychnine. He had read my blog post and wanted to make sure he understood the problem. So I had a conference call with him and a CAS colleague and I explained that several m.p. values corresponded to strychnine salts instead of the free base. They agreed to rectify the situation.

Apparently Cristian stays on top of what is being said about CAS products from various sources, including the blogosphere. I think that what will distinguish chemistry databases as we move forward is precisely this type of proactivity and responsiveness.

There are a plethora of databases out there to search for chemical information. Most of them contain surprisingly significant amounts of incorrect data. My students are in the process of demonstrating that with their assignment on finding 5 sources for 5 properties of a chemical of their choice. When they are done in 2 weeks I'll post about that, perhaps doing a top 10 worst data points.

CAS is an example of a commercial database. But the same principle applies to free databases as well.

Consider the glatiramer acetate problem I reported on previously. ChemSpider immediately removed the entry because a random polymer was being incorrectly represented as a physical mixture of amino acids. As far as I know no other free databases have corrected the problem, although contact information for people running various databases was provided by Michael Kuhn and Egon Willighagen on FriendFeed.

I spoke with Cristian about the problem and he said he would look into it. Upon doing a search for glatiramer acetate on SciFinder it appears that there is currently a problem. The text correctly explains that this is a polymer but the empirical formula looks like just a physical mixture of amino acids, with an extra H2O per unit that should not be there after amide formation. But this was minor compared to the problems I reported on previously - for example there were no incorrectly calculated molecular properties, although the images did not represent the structure of the polymer.
This has been a good week for curation. Yesterday Nick successfully completed the evaluation of the stereochemistry of nargenicin and submitted the corrected SMILES to ChemSpider. Tony Williams has already incorporated the fix and now a search for nargenicin on ChemSpider gives just one entry.

Tony has provided several such puzzles for my students and a few are close to resolving the structures. The main problem is that the structures were entered into ChemSpider with at least one undefined stereocenter. Finding the correct structure from the primary literature can be very challenging for structures of this complexity but it certainly puts the chemical information retrieval methods I am teaching my students to good use.

The class itself was short - and covered mainly just details of student assignments - since we won't have much time during the last class on December 3, 2009 for a workshop. Rajarshi Guha and Tony Williams will be my guest lecturers on that day.

Cheminfo Retrieval 8th class

2009-11-17T15:22:00.000-05:00

This is the lecture from the 8th Chemical Information Retrieval class at Drexel University on November 12, 2009. It starts with a demonstration of how to use of ChemSketch and Chemspider to display and manipulate chemical structures, especially those with complicated stereochemistry. Technical issues with using SMILES between the two platforms are addressed, as are optimization of 3D structures and inverting chiral centers. Microsoft Paint is used to process screen captures to images that can be uploaded to Wikispaces. ChemSpider is also used to generate predicted properties. SDBS is used to retrieve NMR and other spectroscopic data.

Mel Reichman's Drug Discovery Talk

2009-11-15T17:26:00.000-05:00

Mel Reichman gave an outstanding presentation at Drexel on November 12, 2009. I think many of our faculty and students benefited from his unique perspective on high throughput drug discovery and the story of Vioxx from both chemistry and intellectual property considerations.

Unfortunately the resolution of the screen was changed during the presentation because the projector was not working properly. As a result some of the screen capture video got de-centered. I'm embedding the slides as well to see all the details.

Mel Reichman, senior investigator and director of the LIMR Chemical Genomics Center at the Lankenau Institute for Medical Research presents at the chemistry department at Drexel University on November 12, 2009. Introduction by Jean-Claude Bradley.

Modern drug discovery by high-throughput screening (HTS) begins with testing hundreds of thousands of compounds in biological assays. The confirmed hit rate for typical HTS is less than 0.5%; therefore, 99.5% of the costs of HTS are for generating null data. Orthogonal convolution of compound libraries (OCL) is 500% more efficient than present HTS practice. The OCL method combines 10 compounds per well. An advantage of this method is that each compound is represented twice in two separately arrayed pools. The potential for the approach to better enable academic centers of excellence to validate medicinally relevant biological targets is discussed.

Mel Reichman on Pool Shark’s Cues for More Efficient Drug Discovery

View more presentations from Jean-Claude Bradley.

Liz Lyon on Open Science at web-scale

2009-11-12T12:43:00.000-05:00

Liz Lyon from UKOLN has just published a JISC report on Open science at web-scale: Optimising participation and predictive potential. This is a very thorough 45 page document that will serve the Open Science community well as a reference for supporting open initiatives. UsefulChem and Open Notebook Science are covered in a balanced way I think.

This report has attempted to draw together and synthesise evidence and opinion associated with data-intensive open science from a wide range of sources. The potential impact of data-intensive open science on research practice and research outcomes, is both substantive and far-reaching. There are implications for funding organisations, for research and information communities and for higher education institutions.

The original specification for the work was highly selective in its choice of areas to study, and this Report addresses only three of these areas in any depth:

* open science including open notebook science : making methodologies, data and results available on the Internet, through transparent working practices
* citizen science including volunteer computing : where volunteers who may not have scientific training, perform or manage research-related tasks such as observation, measurement or computation
* predictive science : data-driven science which enables the forecasting, anticipation or prediction of specific outcomes.

Mel Reichman on Pool Shark’s Cues for More Efficient Drug Discovery

2009-11-11T11:02:00.000-05:00

The Drexel Department of Chemistry Seminar Series presents "Pool Shark’s Cues for More Efficient Drug Discovery" on Thursday, November 12, 2009 at 4:30 p.m. in Disque Hall room 109 (32nd Street between Market and Chestnut Streets). Mel Reichman, senior investigator and director of the LIMR Chemical Genomics Center, the Lankenau Institute for Medical Research, is the guest speaker.

Modern drug discovery by high-throughput screening (HTS) begins with testing hundreds of thousands of compounds in biological assays. The confirmed hit rate for typical HTS is less than 0.5%; therefore, 99.5% of the costs of HTS are for generating null data. Orthogonal convolution of compound libraries (OCL) is 500% more efficient than present HTS practice. The OCL method combines 10 compounds per well. An advantage of this method is that each compound is represented twice in two separately arrayed pools. We will discuss results and the potential for the approach to better enable academic centers of excellence to validate medicinally relevant biological targets.

Sixth Cheminfo Retrieval class: What is the m.p. of strychnine?

2009-11-05T10:06:00.001-05:00

It would seem to be a simple task to find the melting point of a well known alkaloid like strychnine. Our quest to answer that question - and other simple properties - in class using both freely available and commercial databases reveals how treacherous it can be. In the end we don't find an unambiguous answer but we uncover enough information for many applications.

The take home message is that chemists need to be constantly paranoid that their information - whether from their lab or the most prestigious journals - can easily be wrong. Strategies such as finding multiple sources and investigating the experimental details provided in the primary sources are demonstrated to diminish uncertainty. But this is often not easy or quick.

Here is a summary of the lecture:

This is the lecture from the sixth Chemical Information Retrieval class at Drexel University on October 29, 2009. It starts with a review of some of the new questions answered by students from the chemistry publishing FAQ, which covers patent information and accessing electronic journals at Drexel. Tony Williams submitted a puzzle to resolve conflicting structures in ChemSpider, which is too difficult to be a regular assignment. It requires re-analyzing spectroscopic data in papers where stereochemical assignments are determined. An example is paromomycin which has three entries. The regular assignment for the week is then introduced and it involves obtaining 5 different sources each for 5 different properties for a molecule of the student's choosing. To demonstrate how to do the assignment strychnine is chosen as an example. Melting point information is obtained from ChemSpider (ultimately an MSDS sheet), Wikipedia, Wolfram Alpha and in a JACS article via SciFinder. By investigating primary sources several errors are found in SciFinder, where the recorded melting points correspond to salts of the alkaloid. Difficulties in finding primary sources for the melting point from Wikipedia are highlighted. For LD50 information Wikipedia did not even provide proper units (mg instead of mg/kg and no animal or route specified). The importance of ChemSpider predicted values for density and boiling point is demonstrated as a corroborating tool. In the end the reported melting point range of strychnine from the JACS paper did not even overlap with the reference to which it was compared. The exercise is meant to highlight the importance of caution in obtaining values from all available sources. Even the seemingly simple question of determining the melting point of well known alkaloid cannot be answered definitively.

Glatiramer Acetate Cheminformatics Problem and Fifth ChemInfo Retrieval Class

2009-11-04T17:17:00.000-05:00

It started out innocently enough. One of my students picked the multiple sclerosis drug glatiramer acetate for his project in my Chemical Information Retrieval class. This ultimately resulted in the removal of this substance from ChemSpider.

The problem is that this drug is a polymer but it is represented in many places as a simple mixture of acetic acid and 4 amino acids (L-Ala, L-Glu, L-Lys, and L-Tyr). See for example Wikipedia, PubChem and DrugBank.

The SMILES representation is entered as 5 molecules joined by periods:

CC(O)=O.C[C@H](N)C(O)=O.NCCCC[C@H](N)C(O)=O.N[C@@H](CCC(O)=O)C(O)=O.N[C@@H](CC1=CC=C(O)C=C1)C(O)=O

This is probably the source of all subsequent miscalculations - such as a molecular weight of 623.7 (it actually has an average MW one order of magnitude larger), molecular formula C₂₅H₄₅N₅O₁₃, Topological Polar Surface Area of 374, Rotatable Bond Count 13, a 3D structure that is nowhere near reality, etc.

Glatiramer acetate is reported to bind to MHC molecules. If these molecular descriptors are used in any type of QSAR analysis this will just add noise to the models.

ChemSpider does not keep track of polymers, except perhaps for some well defined oligopeptides that can be represented by a single SMILES. Consequently it was removed from the database.

It is difficult to apply common cheminformatics tools to this substance. It might be tempting to try to place it in polypeptide/protein databases such as BioPD. But it does not have a well defined length or composition. In fact it is a random co-polymer so it can not even be represented by a repeating structure, such as one might do for polystyrene.

In order to generate meaningful molecular descriptors for QSAR applications I suppose one strategy would be to generate a collection of SMILES representing the average composition of the drug in terms of ratios of amino acids and molecular weights. Each structure would generate molecular descriptors and 3D structures that are far more realistic than those currently listed. Perhaps it would turn out that only some of these polymer structures interact with MHC molecules. (If this has already been done please forgive the oversight - I didn't research this thoroughly. By the end of the term we should know more from the student's report)

The chronological summary of the lecture is as follows:

The fifth Chemical Information Retrieval class on October 22, 2009 started out with covering the new 3D structure viewer introduced recently at PLoS ONE to provide ideas for students doing a multimedia project this term. The current student answers to the chemistry publishing FAQ are then discussed. The reason for removing glatiramer acetate from ChemSpider is explained and a few databases (Wikipedia, PubChem, DrugBank) are visited that still contain the incorrect SMILES, 3D structure and related properties. An overview of an Open Access site (OAD) suggested by Bill Hooker is provided to suggest additional questions for the FAQ. Examples of questions discussed include primary and secondary sources, peer review, article level metrics (a PLoS ONE article on malaria is used as an example), citation searching, Impact Factors and whether one should use one's real name in the blogosphere. Databases Scirus, Web of Science and PubMed are also reviewed.

Chemistry in Second Life paper in Chemistry Central Journal

2009-10-29T14:53:00.001-04:00

Andrew Lang and I just published a review article on the chemistry content in Second Life:
Andrew SID Lang and Jean-Claude Bradley Chemistry in Second Life, Chemistry Central Journal 2009, 3:14.

Abstract
This review will focus on the current level on chemistry research, education, and visualization possible within the multi-user virtual environment of Second Life. We discuss how Second Life has been used as a platform for the interactive and collaborative visualization of data from molecules and proteins to spectra and experimental data. We then review how these visualizations can be scripted for immersive educational activities and real-life collaborative research. We also discuss the benefits of the social networking affordances of Second Life for both chemists and chemistry students.

This is gratifying on many levels:

1. Andy and I met in Second Life a few years ago and it is fitting that we should finally have a paper highlighting our collaboration and the work of others doing chemistry in Second Life. In fact, our meeting and the resulting projects both inside and outside of Second Life is listed under the networking section of this paper.

2. We found a very appropriate Open Access journal to publish this work. We wanted this review to offer concrete examples of what can be done with chemistry in Second Life and it is loaded with images to illustrate as clearly as possible what these options look like.

Even though it has many educational components we did not want to submit it to a "chemical education" journal. Generally these types of journals require framing the work within a pedagogical theory. We have been through prolonged debates with reviewers around this issue on other papers and did not want to repeat the experience. There is an expectation in some circles that progress in education can only come about when built within the context of testable theories. At least the scope of many educational journals is tied to this viewpoint - and that is absolutely appropriate.

But it is interesting that we have had to rewrite sections of papers - not because the content was incorrect in any way - but because it did not conform to a conceptual format. It makes me realize how much scientific discourse is directed by the expectation of editors and reviewers, when the authors themselves might have preferred to present their content differently.

3. There is lots of useful content that is never published in peer-reviewed publications because it does not fit the mold. The example above fits in the category of describing tools without evaluating them in some quantitative way. So the third point of gratification is that we managed to zip up a number of small developments that might be useful to someone but by themselves were not the right size and shape to publish in the peer-reviewed system. This included the ChemTiles game and the EduFrag project, initiatives that were converted to or from a Second Life format.

Of course, the mechanism of using a review to assemble such content can't be used very often.

In the experimental sciences there are two other types of useful content that are difficult to publish formally: "failed" experiments and lab techniques. I've repeatedly discussed the importance of sharing the results of experiments with disappointing results as a strong motivation behind Open Notebook Science.

But just as important are the details of laboratory techniques - completely separate from the results they provide. In our lab, the measurement of solubility has proven to be far from trivial and we have reported several pitfalls, as well as some techniques which I think could save others much wasted effort.

When I was a graduate student at the University of Ottawa I found a way of visualizing column chromatography that I thought could be helpful to others in speeding up separations. The only mechanism available back in 1992 for wide dissemination of chemical information was peer-reviewed publication so that is what I did (Tet. Lett. 33(50) 7733).

In order to publish using that channel I had to format my communication accordingly. Instead of just reporting on the method (use a quartz column and an insoluble fluorescent agent mixed with silica gel), I had to evaluate the method systematically testing different solvents, stationary phases and specifications. It was a hassle and completely unnecessary to simply share the technique.

If I were doing this today I would just blog about it and record the details in my open notebook as I was experimenting with the technique. There is a good chance that someone else would have given me useful tips as well.

As it turned out, the feedback I did receive was a letter from a chemist who had been using the technique for many years. His use escaped our literature search because it only appeared in the experimental sections and thus did not show up on keyword searches - keep in mind this was before the era of computerized searching - and none of the reviewers knew about it either.

We published a Corrigendum accordingly and that was the full extent of the public scientific discourse. By any standard the new communication tools we have today are far more versatile for quickly and easily communicating this type of information.

4. Once again (here and here), we had no trouble using blog posts and wiki pages as references. The key consideration is: what is the most relevant document to link to. If you are blogging your work it is likely that blog posts will be the only citable option in many cases. In this instance we also wrote the article on a public wiki page, which limited our selection of peer-reviewed journals to those that allowed pre-prints.

I don't know how many journals that don't allow pre-prints would take articles that are based substantially on work that has appeared in public blogs and wikis. Since the article would require re-integration and re-writing of the work there wouldn't be any copyright issues.

Fourth Cheminfo Retrieval class: ChemSpider and Beilstein Databases

2009-10-20T14:53:00.000-04:00

Peggy Dominy, our chemistry librarian at Drexel, was kind enough to teach my third class while I was at NERM. She demonstrated RefWorks - including how to copy and paste the proper formats to Wikispaces - and how to use our ILL (Inter-Library Loan) process.

I'm including a recording of the fourth class on Chemical Information Retrieval on Oct 15, 2009 at Drexel University. It starts with some tips on removing formatting from Wikispaces pages, the Drexel Cisco VPN client for accessing paid subscriptions off campus and how to link to a DOI. The first two assignments for the class are then described. The first involves summarizing each paragraph of an article and an option to use AcaWiki is demonstrated. The second involves filling in an FAQ for publishing in chemistry. FriendFeed is then presented as a resource to help answer questions followed by an extensive overview of available information on ChemSpider, covering SMILES, InChIs, InChIKeys, experimental and predicted properties, linked databases and contributed spectra. Finally a demonstration of Beilstein Crossfire/DiscoveryGate is presented with an emphasis on doing substructure searching.

Interactive 3D Visualisations of Biological Molecules Integrated into the Scholarly Literature

2009-10-19T21:51:00.000-04:00

The embargo has now been lifted on the announcement from PLoS ONE - partially reproduced here:

On October 20th 2009, PLoS ONE will feature an impressive new 3D molecular animation technology on five newly published articles. This represents the start of a new PLoS ONE collection entitled “Structural Biology and Human Health: Medically Relevant Proteins from the SGC” (also known as the ‘Structural Genomics Consortium’).

These peer-reviewed articles, which include some of the research highlights from the SGC, describe new protein structures, including a protein involved in the survival and proliferation of cancer cells, a protein associated with hereditary paraplegia, and a protein involved in degrading foreign compounds and pollutants in the body.

Readers of these enhanced articles will first need to download a free plug-in for their browser but will then be able to click on hyperlinked text within the article to ‘fly’ to the relevant position within the molecule, and to then interact with it at will (by zooming, rotating and exploring). The functionality, whereby the text of an academic article is tightly integrated with an animated and interactive molecular structure, provides an entirely new and enhanced experience with a significant “wow” factor.

The first enhanced articles are available here. I've been trying to evaluate these but I'm having trouble downloading the required plug-in: it is very slow and has just stalled on me. Maybe the problem is on my side so I'm asking the community to give these a spin and report. I am especially curious about the comparison with Jmol. This particular plug-in does not use Java at all from what I can glean from the press release.

Notwithstanding these probably temporary issues I think this is a very exciting development for scientific publication in the life sciences.

NERM 09 session on Chemistry on the Web

2009-10-15T11:24:00.000-04:00

Last week, on October 9, 2009 I presented at the ACS NERM conference. Martin Walker hosted a session on Publishing and Promoting Chemistry in the Internet Age. All of the talks were quite interesting and fit perfectly with the topic:

Martin Walker Chemistry on the Internet
Elizabeth Brown The Chemist's Toolkit for Publishing and Promoting Your Work On the Internet
Antony Williams Navigating the Complex Web of Chemistry Using ChemSpider
Jean-Claude Bradley Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Science

My talk consisted of an overview of Open Notebook Science with some new content on solubility prediction algorithms written by Andrew Lang and a few example of students taking a Chemical Information Retrieval class at Drexel University using research logs on a wiki to flesh out their projects.

Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Science

View more presentations from Jean-Claude Bradley.

Second ChemInfo Retrieval Class

2009-10-06T10:33:00.001-04:00

We had our second class on Chemical Information Retrieval on October 1, 2009 (see screencast here). I spent some time on technical aspects of Wikispaces then introduced topics relating to publishing in chemistry - and science in general. This included primary and secondary/tertiary sources, Open Access, copyright and Web2.0. The associated wiki page is currently just an outline and will get filled with details as students do assignments.

The student projects are coming along nicely. They have been recording the progress of their research on log pages, which I'm finding useful to give feedback. Among the interesting projects being fleshed out are green tea, DMT and trace amine receptors, caffeine, cytochrome C and liposome binding, beer and the psychoactive ingredients in chocolate. I love classes where the instructor learns as much as the students!

If anyone has suggestions for good information sources on these topics please feel free to leave comments.

Chemistry MiniSymposium FA09: Bradley Lab

2009-10-05T19:27:00.001-04:00

Every fall the faculty in the chemistry department at Drexel present the ongoing work in their lab, mainly for the benefit of the new students. The challenge is to fit a meaningful overview in a 15 minute slot. I think this is a useful exercise and it gives me a recording I can use for more general audiences that matches most people's attention span.

My talk was entitled "The synthesis of Anti-Malarial Compounds using the Ugi reaction and Collaboration using Social Software". The NaH oxidation story is a perfect way to introduce the application of Web2.0 tools to current research.

Bradley Lab Research Fall 09 MiniSymposium

View more presentations from Jean-Claude Bradley.

A First General Solubility Model from ONS Challenge Data

2009-09-28T19:33:00.001-04:00

After about a year, the Open Notebook Science Solubility Challenge has resulted in over 680 measurements, with about an additional 100 from the literature. Taking into account averaged repeated measurements, discarding some erroneous results and considering only organic solids (so far all of our liquid solutes have proven to be miscible in our solvents), that leaves us with 244 unique values.

Andrew Lang has created a general model (Model003) to predict solubility based on molecular descriptors of both the solutes and solvents. Previous models, such as Rajarshi Guha's Model002 were built only for selected solvents.

Predictions can be made from this web page by entering the SMILES of the solute and optionally the SMILES, dipole moment and dielectric constant of any solvent (convenient sources for these are Wolfram Alpha and Wikipedia). Boc-glycine with diethyl ether as an optional solvent is shown here.
The prediction service then looks up the relevant molecular descriptors from the CDK and makes predictions for some common solvents and the optional one if requested.

If the name of the solute was entered, the service will also report all of the experimental measurements for that solute from the ONS Challenge with links to the lab notebook pages.

There are a few objectives in making this public.

First, we think that it might provide some ideas about possible good or bad solvents for a given solute. The dataset is certainly not large enough to provide a truly general prediction of solubility in absolute terms. However, comparing relative values might be helpful in many cases. In the example above for boc-glycine, the model predicts that toluene would be the poorest solvent, which matches the order of the experimental values, even if the absolute values are not a close match. DMSO, THF, methanol and ethanol are predicted to be good solvents and this is reflected in the measurements.

Second, we want to make the model and data public so that other researchers with experience in this area can contribute their own models. We have been working with Marcin Wojnars from TunedIT to make it much easier for models to be submitted. Andy has just converted our dataset to ARFF format and it is available here. We should have more to report on this shortly.

By using molecular descriptors from the solvents we should be able to do predictions for solvent mixtures as well. At some point perhaps we can even include temperature.

The current model fits measurement with this type of distribution:
If we are able to build models automatically in real time after the addition of each data point, we should be able to set up automatic solubility measurement requests to minimize the amount of work it takes to improve each model. This is a step in that direction.

Cheminfo Retrieval First Class FA09

2009-09-25T17:06:00.000-04:00

I gave my first lecture yesterday (Sept 24, 2009) for my Chemical Information Retrieval course at Drexel. One of my main objectives for the course is to provide the most current information about how to best find and review chemical information.

To this end, I set up a wiki (http://getcheminfo.wikispaces.com) which should become considerably enriched over the course of the term. I invited students to help contribute useful links to the resource page - and even before I finished giving the first lecture they added several really good ones. I also invite any chemists or librarians to add links to resources we may have missed. Just request to join the wiki to contribute.

The wiki will also be used for students to write a report on a chemical topic making use of cheminfo resources. Right after the lecture I made sure the students joined the wiki and created two pages: one for their report and one for a "research log". The idea is that students will report significant steps in conceptualizing their projects and how they are searching databases. I can then comment directly on their log pages for quick guidance. I suppose anyone with helpful suggestions that I missed could also comment - again just request an account on the wiki.

This class has traditionally required a written report. This term I'm adding a twist: the minimum number of words can be reduced somewhat if students elect to incorporate a multimedia or other creative component. To provide examples of what that might look like I visited Drexel Island on Second Life and demonstrated 3D molecules, interactive NMR spectra and a chemistry museum (from Sandy Adam). There is a lot of chemistry possible on Second Life (see Lang & Bradley) At the end of the tour on the island we visited a wildlife area recently built by Robert Brulle for a project related to environmental science (more on this in a later post). I got a hug from a panda and got sprayed when I tried to pet a skunk - just to give a taste of what kind of fun things can be constructed in a virtual world. Other projects could involve screencasts, Jmol, games, Facebook, etc. As long as it requires students to access chemical information, I am pretty open to ideas. Students will work through their ideas on their log page and the final product will also be available on the wiki. These projects could provide interesting examples for others interested in the topic of chemical information.

At the end of my lecture I provided a brief overview of the NaH oxidation controversy. There really could not be a better example of the importance of staying on top of new communication channels to follow and participate in chemical research. This year the most important of these new tools are probably blogs, wikis and FriendFeed. Next year it might be something else - Google Wave?

Jenna Mancinelli is Sept09 Submeta ONS Award Winner

2009-09-02T12:38:00.000-04:00

Jenna Mancinelli, working under the supervision of Jean-Claude Bradley at Drexel University, is the September 2009 Submeta Open Notebook Science Challenge Award winner. She wins a cash prize from Submeta.

Jenna used both NMR and the sequential precipitation technique to obtain solubility data. See her experiments here:
http://onschallenge.wikispaces.com/list+of+experiments

One more Submeta ONS Award will be made during 2009. Submissions from students in the US and the UK are still welcome.
For more information see:
http://onschallenge.wikispaces.com
http://onschallenge.wikispaces.com/submetaawards08

My talk at ACS FA09 on Social Networking Tools and Teaching Chemistry

2009-08-20T17:06:00.001-04:00

Yesterday (August 19, 2009) I gave my last talk at the American Chemical Society meeting in Washington. I presented on Using social networking tools a la carte for organic chemistry education: Wikis, blogs, Second Life, and more for the Symposium on Using Social Networking Tools to Teach Chemistry, organized by Laura and Henry Pence:

12:05 PM Wikis in chemical education: The best of two worlds
Laura E. Pence
12:25 PM ChemPaths: Learning to meander — an online portal to ChemEd DL resources for intrinsically linked learning
Justin M. Shorb, John W. Moore
12:45 PM ChemEd DL WikiHyperGlossary
Robert E. Belford, J. W. Moore, Daniel Berleant, Michael Bauer, Jon L Holmes, Kyle E. Yancey
1:05 PM Social media: Immersion and its discontents
Elizabeth M. Dorland
1:35 PM Using social networking tools a la carte for organic chemistry education: Wikis, blogs, Second Life, and more
Jean-Claude Bradley, Andrew Lang
1:55 PM SNS, IM, and textng vs. traditional e-mail and voice messaging as a means of facilitating instructor-student contact: Trends and habits of student usage, and techniques to avoid electronic overload (or withdrawal)
Robert B. Gregory
2:15 PM Faculty development, collaborative inquiry, and Web 2.0
Joanne L. Stewart
2:35 PM Are netbooks the next big thing in the chemistry classroom?
Harry E. Pence
2:55 PM Managing laboratory research data using cloud computing as an organizational tool
Harry E. Pence, Jacqueline Bennett

It was a really entertaining symposium. Laura Pence talked about using Wikispaces (the same platform I use) for student projects and emphasized how helpful it is to compare wiki page versions to evaluate each student's contributions. Justin Shorb presented on his work to wikify a chemistry textbook. Despite a broken arm, Bob Belford did a great job in presenting his Wikihyperglossary project. It marks up chemistry terms on web pages, similar to the approach taken by ChemMantis.

Liz Dorland provided a wonderful overview of how Second Life can be used from an educational standpoint, very much complimentary to the content I had on my slides. There is just so much content and so many projects now on that virtual world that it is difficult to appreciate without actually going in and taking a tour but sometimes a good talk can motivate people to give it a closer look.

Robert Gregory's talk was very funny and somewhat shocking: he gave out his cell phone and asked his students to contact him 24/7 - including 2:00 AM when he was sleeping. Joanne Stewart gave an overview of how inorganic teachers kept in contact using various social networking tools and valuable it was for both collaboration and support.

Harry Pence gave two very humorous talks at the end. The most interesting point for me was his collaboration with Jacqueline Bennett, who used Google Spreadsheets to collect experimental results from her students. An example of that work recently appeared in Green Chemistry, 2009, 11, 166 - 168. This is especially relevant for our research - because we also use Google Spreadsheets to aggregate results - but her reaction involves finding the right solvent for mixing an aldehyde and amine and obtaining a pure imine as a precipitate, exactly the same approach for our preparation of Ugi products. Perhaps there is a future collaboration there.

All of the presentations were recorded and I will post a link when available.

Here is the summary of my talk and the recording:

Jean-Claude Bradley describes the use of social networking tools to teach undergraduate organic chemistry. Public free wikis can be used effectively to manage class information as well as serve as a versatile platforms to process student assignments and provide rapid feedback. Examples of using Second Life to deliver quizzes, play games and offer students an environment to create projects involving 3D molecules, spectra and posters are detailed. The continuously evolving role of blogs, podcasting, screencasting and newer faster interactive platforms such as FriendFeed will be outlined. New technologies create the need for new skills to be taught to students - some relating to networking and some involving knowlege of the language to navigate the chemical webspace (such as SMILES and InChI).

Using social networking tools a la carte for organic chemistry education: Wikis, blogs, Second Life, and more

View more presentations from Jean-Claude Bradley.

Spectral Game talk at ACS Fall 09

2009-08-18T10:58:00.000-04:00

Yesterday (August 17, 2009) I gave my talk on the Spectral Game at the Using Technology to Enhance Learning in Organic Chemistry symposium at the American Chemical Society meeting. I was not able to attend the entire symposium but luckily I did catch David Soulby's talk on using Google groups to distribute NMRs for labs that require many students to submit samples. I am a fan of using free and hosted services to simplify workflows of all types.

Also in attendance at the symposium were Liz Dorland and Bob Hanson. It was good to catch up with them. Bob shared a story of how he has been assigning his students tasks in his organic chemistry class which lead to updating Wikipedia. There is so much potential for using the educational infrastructure to create better scientific content for everyone.

My talk on the Spectral Game highlighted the role of openness in teaching and research to create new educational tools, especially for learning NMR. Tony Williams said a few words at the end about ChemSpider, RSC and some upcoming opportunities to publish synthesis articles on ChemSpider.

Spectral Game ACS Fall 09

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My first talk at ACS09 fall meeting on Crowdsourcing Solubility and ONS

2009-08-17T14:10:00.000-04:00

Yesterday (August 16, 2009) I gave my first talk at the ACS meeting in Washington. It was part of an outstanding session on Chemical Text Mining and Public Molecular Databases, organized by Antony Williams and Alex Tropsha.

9:00 AM 1 U.S. EPA computational toxicology programs: Central role of chemical-annotation efforts and molecular databases
Ann M. Richard, Maritja A. Wolf, ClarLynda R. Williams-Devane, Richard Judson
9:25 AM 2 Linking public and commercial chemical data: ChemSpider and SureChem
Nicko Goncharoff
9:50 AM 3 Building an integrated system for chemistry markup and online publishing integrated to online chemistry resources
A J Williams
10:30 AM 4 Turning mining inside out
Colin R Batchelor
10:55 AM 5 Chemreader: A tool for extracting chemical structure information from digital raster images
Jungkap Park, Kazu Saitou, Kerby Shedden, Gus R. Rosania
11:20 AM 6 Exploiting a hidden treasure: Automated chemical entity recognition in Chemisches Zentralblatt
Valentina Eigner-Pitto, Heinz Saller, Peter Loew
1:30 PM 12 Online chemical modeling environment: database
Sergii Novotarskyi, Iurii Sushko, Robert Körner, Anil Kumar Pandey, Igor V. Tetko
1:55 PM 13 Public molecular databases: How can their value be increased by generation of additional data in silico?
Vladimir V. Poroikov, Dmitry Filimonov, Marc C. Nicklaus
2:20 PM 14 Chemical space management of large libraries for new active small molecules selection for prostate cancer treatment
Andrew V. Scorenko, Andrei A. Gakh, Andrey V. Sosnov, Mikhail Yu. Krasavin
2:45 PM 15 Crowdsourcing nonaqueous solubility and synthesis using Open Notebook Science
Jean-Claude Bradley, Khalid Mirza, Rajarshi Guha, Andrew Lang, A. Williams
3:25 PM 16 ChemXSeer: A cyberinfrastructure for environmental chemical kinetics
Karl T. Mueller, William J. Brouwer, C. Lee Giles, Prasenjit Mitra, Carl Lagoze
4:15 PM 18 Reliable reactions and stable structures
Jonathan M Goodman

Many of the presentations highlighted the use of ChemSpider or full collaborations (such as the integration with SureChem patent data). The acquisition of ChemSpider by RSC was repeatedly discussed and this seems to have accelerated such collaborative projects. Colin Batchelor from the RSC provided a great talk on their approach of using ontologies to better leverage the power of chemistry publications. [The presentations were judged and Colin won first prize - I won second, which was pretty cool :) and won me a ticket to the CINF lunch on Tuesday]

I also got to meet Gus Rosania in person for the first time. We had met via the blogsphere a while back over our interests in malaria and Open Notebook Science. Gus was there to share his results from ChemReader, a software package he developed to automatically read chemical structures from images.

I started my presentation by detailing the recent events surrounding the report of the oxidation of secondary alcohols using NaH. The timing of this was perfect because it really showed how useful it can be to immediately share the full data of experiments. This is the type of thing that would have been extremely helpful during the initial reports of Cold Fusion but the tools for sharing in such a detailed way were just not available. Carmen Drahl just wrote an article about this for the August 17, 2009 issue of Chemical & Engineering News (subscriber access).

Crowdsourcing Solubility using Open Notebook Science

View more presentations from Jean-Claude Bradley.

Making the Web Work for Science July 28th 2009

2009-08-14T09:19:00.003-04:00

A panel discussion on bringing digital tools to the world of science with panelists Stephen Friend, Jimmy Wales and John Wilbanks moderated by Tim O'Reilly. This is a pretty general overview of issues revolving around new ways of communicating science.

Making the Web Work for Science - Full from Jordan Mendelson on Vimeo.

NaH and the hydrino controversy

2009-08-07T17:37:00.001-04:00

There has been so much discussion this past week about the use of NaH as an oxidant that I was surprised to see the very same material involved in another chemical controversy. (from Meryn Stol's FriendFeed post).

In this case, BlackLight Power claims to be able to generate energy by dropping the electronic energy of a hydrogen atom to below its ground state, creating hydrinos. One method relies on heating NaH in contact with Raney nickel. In this report, Mills and co-authors appear to provide enough experimental conditions and spectroscopic characterization data to allow others reproduce what they have done.

If you are not a chemist it is difficult to appreciate just how outlandish these claims are. They fly in the face of some extremely well tested theories that form the foundation of what we call chemistry today.

There is an abundance of wacky ideas out there. What makes this case particularly interesting is that that BlackLight Power has $60M in venture capital, intellectual property protection and licensing deals. The company and the standard chemistry model are on a collision course that will play out very soon. Either the company does not deliver or there will be some explaining to do by mainstream academics.

Reading the discussion forum on the technology, it seems like the current situation is in a kind of stalemate. Both detractors and supporters are waiting for others to repeat the experiments. Apparently Mills is remaining secretive until they build their power plant. It does not look like they are sharing the hydrino products they claim to have created.

I think that this is actually a perfect opportunity for Open Science - especially Open Notebook Science. The experiments are more difficult than those that claimed NaH to be an oxidant (which we and Totally Synthetic have investigated). I'm not sure that our lab has the required equipment to maintain the temperatures and conditions but certainly most materials science departments should have it.

And once the putative hydrino products are created they should be stable for sharing with others to analyze. The Mills report cited above even has NMR data for both dihydrino gas and the hydride form (-4.5 ppm). I don't know enough about the NMR of hydrides to know how meaningful that is but certainly it could be investigated further. It sounds like a project that could be tackled for a senior design assignment provided that students had access to the necessary equipment.

The main focus from a commercial angle is the energy generation. But the difficulty there is that failure or success of such experiments can be downplayed by both sides because it is so difficult to reproduce exactly the same conditions. But if only one person makes this new form of matter and is willing to share it, any chemist with access to standard instruments like NMR, IR, etc. will be able to confirm that it exists without ambiguity.

Doing these experiments openly and discussing them can only lead to a resolution. Even if it turns out that the characterization data can be interpreted with our standard model of chemistry that would be satisfying.

Our attempt to reproduce an oxidation by NaH

2009-08-05T16:05:00.000-04:00

Yesterday I was discussing with my students the controversy over the claim that NaH can act as an oxidant for secondary alcohols (Wang, JACS09). There has been a lot of discussion and an attempt to reproduce one of the experiments has appeared on Totally Synthetic.

Khalid Mirza and Marshall Moritz thought it would be worthwhile to see if we can shed any light on the situation. I was also curious to see what the reaction did over time, before quenching.

We had 1-phenylethanol on hand, for which the Wang paper claims a 75% conversion (by GC) to acetophenone. All the details can be found on the notebook page UC243.

The reaction was monitored by taking aliquots of the solution then adding benzene-d6 to lock during NMR acquisition without quenching the reaction. After 19 hours at room temperature there was no change in the spectra, except for loss of the alcoholic proton. Acetophenone would have been easily detected at 7.9 and 2.6 ppm (ChemSpider spectrum)

In a comment on Carbon-Based Curiosities, European Chemist points to a 1965 paper where oxidants on the surface of NaH are likely responsible for oxidative behavior (Lewis JOC). This would certainly explain why some researchers are reporting some oxidation products but with widely divergent yields. For example, Totally Synthetic reported a 15% NMR yield for the conversion of the 4-chloro derivative to the corresponding ketone while Wang isolated the product in 86% yield.

As many have pointed out, this is a very good example of the way Web2.0 tools and community can complement traditional publishing to move science forward.

Daniel Rein is Aug09 Submeta ONS Award Winner

2009-08-03T16:08:00.001-04:00

Daniel Rein, working under the supervision of Jean-Claude Bradley at Drexel University, is the August 2009 Submeta Open Notebook Science Challenge Award winner. He wins a cash prize from Submeta.

Daniel used both NMR and the sequential precipitation technique to obtain solubility data. See his experiments here:
http://onschallenge.wikispaces.com/list+of+experiments

Two more Submeta ONS Awards will be made during 2009. Submissions from students in the US and the UK are still welcome.
For more information see:
http://onschallenge.wikispaces.com
http://onschallenge.wikispaces.com/submetaawards08

Iterating a 5D solubility space

2009-07-29T15:10:00.000-04:00

About three weeks ago I described how we are mapping a 5D solubility space (mixtures of 4 solvents and temperature). Andrew Lang has been re-running his code to populate the DoSol request sheet with the most useful next measurements. After a few iterations of Marshall Moritz doing experiments and combining with any existing data from the literature we now have 76 measurements for the solubility of 4-nitrobenzaldehyde in mixtures of chloroform, acetonitrile, toluene and THF within the temperature range of -25 to 40 C.

We are now working on ways of quantifying how well we have covered the space and how confident we are of specific predictions. At some point we would like to generalize the predictions based on molecular descriptors of the solvents.

The existing dataset can be sliced in some interesting ways. For example, using Mathematica, Andy has created a plot of the solvent combinations giving the highest possible solubilities of 4-nitrobenzaldehyde at a given temperature. At room temperature this corresponds to a mixture of 38% chloroform and 62% acetonitrile (molar ratio). Below 10C, toluene enters the mix to obtain maximum solubility. At no temperature does THF help.