Saturday, February 28, 2015

The 15N chemical shift of formamide. Is there an NMR expert in da house?

All I want (for now) is the value of the nitrogen chemical shift of formamide in water, but I found two very different values in Annual Reports on NMR Spectroscopy volume 11B: 263.7 and 267.8 ppm. The reference is nitromethane and for some reason it lists negative chemical shifts (i.e. $-\delta_x = \sigma_x - \sigma_{\mathrm{MeNO_2}}$).

The 263.7 value comes from this paper which reports a chemical shift of 260.0 ppm relative to saturated sodium nitrate which is then converted to the above value by adding the difference in chemical shift between sodium nitrate and nitromethane: 3.7 ppm.

The 267.7 value comes from this paper which reports a chemical shift of 261.6 ppm relative to 1 M nitric acid, which is then converted to the above value by adding the difference in chemical shift between 1 sodium nitrate and nitromethane plus a correction for the difference in bulk magnetic susceptibility ($\Delta\chi$): 4.4 + 1.8 = 6.2 ppm.  This extra correction ($\frac{4}{3}\pi(\chi_{\mathrm{MeNO_2}}-\chi_{\mathrm{H_2O}}$) is done because the experiment was performed with the external magnetic "field parallel to the sample tube".

The question is which value is the correct chemical shift for the nitrogen chemical shift of formamide in water?

Also, how hard would it be to measure it in the gas phase?



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Thursday, February 5, 2015

Open Science - a brief rant

A colleague asked me for feedback on a draft of a viewpoint article on open source and data.  I know at least one of my group members enjoys a good rant so I pasting part of my reply in here and calling it a (free) blog post:

<rant>In my mind there is one aspect in all this that is missing, which is essentially a moral or ethical one. Much of my research (and my salary being at a state run school) is payed for by tax payers.  One of the reasons I publish OA is because I feel the same tax payers have the right to read these papers and use the content  any way they see fit.  The same applies to the code my group produces.

Now, I'm not a zealot.  I actually feel that being open helps my research and career as you also point out, but the ethical principle is still there in the background.  Society is not paying me to to advance my career, society is paying me to advance society.  IMO, that is the real reason funding organizations should insist on Open: it is better for the society - who pays the bills.  All the perceived negatives affect me, the researcher, but it is not about me.

Science funding will not increase unless society sees an advantage in this and this closed, what's-in-it-for-me? attitude among scientists that has led to the reproduceability crisis (which, IMO is a much bigger crisis for long-term science funding than people realize) is incredibly damaging in that regard. </rant>


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Saturday, January 31, 2015

Manuscript submitted to PCCP

The manuscript from my previous post has now been submitted to PCCP (the revised version should appear on arXiv on Monday).  I want to thank the following people for very helpful feedback on the manuscript: Chris Cramer, Mike Gilson, Stefan Grimme, Adrian Jinich, Pedro Silva, and Casper Steinmann.  Putting the draft on Google docs has been very useful.  I am definitely doing that again.

I went with PCCP because

(1) Neither PeerJ nor PLoS ONE accept review papers
(2) The work is not funded, so I can't pay $1000s for open access myself 
(3) The University of Copenhagen pays for open access publishing in RSC journals 
(4) PCCP has an enlightened attitude towards arXiv submission.


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Tuesday, January 20, 2015

New manuscript: Predicting binding free energies in solution

Here is a new manuscript of mine that appeared on arXiv today.  It is a perspective paper, i.e. I mostly summarize what has already been published, and here is the abstract.

AbstractRecent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I summarize some of the many factors that could easily contribute 1-3 kcal/mol errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well-represented by continuum models. While the paper is primarily a synthesis of previously published work there are two new results: the adaptation of Legendre transformed free energies to electronic structure theory and a use of water clusters that maximizes error cancellation in binding free energies computed using explicit solvent molecules. While I focus on binding free energies in aqueous solution the approach also applies (with minor adjustments) to any free energy difference such as conformational free energy differences or activation free energies in any solvent.  

I am very interested in feedback on this paper and I'll wait a while with the submission to incorporate any suggestions.  There are several ways of providing feedback: comments below, comments on PubPeer (which allows for anonymous comments), and comments on Google docs using either the comment or editing tool.



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Saturday, January 17, 2015

What do I want in a learning management system?

I am in a university work group where we discuss recommendations for a new learning management system (LMS). The point of this blogpost is to help me get my thoughts together on this topic.

General philosophy.
1. I would like a barebones open source or easily customizable system where I seamlessly can plug and play different modules such as quizzes, discussion forums, etc.  There could be a default for each, but if I find better options I should be able to use them.

2. I think it is better to encourage the use freely available tools (Google Calendar, Google Docs, Sharelatex, Youtube, Wolfram-Alpha, Reddit, Quora, etc.) that the students will have access to after they graduate. I think the university should offer tutorials, etc. on using these tools directly to students.

3. I think the default for material on the course page should be "viewable by anyone", with an option to change for individual elements.

Things I like/use about the current system (delivered by ITS Learning and called Absalon)
Quiz. I give use reading quizzes extensively.  There are two things about the I really like about the Absalon implementation.  One is that you can label the quiz "obligatory" (it's just a word that appear)s. Students really take this seriously even though there are no explicit penalties for not taking the quiz. Another very useful feature is that I can send email only to students who haven't taken the quiz.

Bulletin board. The bulletin board is very prominently displayed and you can mostly count of students seeing it when they log in.

Planner. Absalon has a rudimentary planner/calendar with links directly to assignments and quizzes.

Mathjax. Very useful for typing equations

Plagiarism detection. Very useful for reports.

Student activity. List of who has logged in when or taken quizzes.

Copy from last year. Of course it's very useful to copy quizzes etc from last years course page.

In-active files/view as student. Files and folders can be made active or inactive where the latter can be viewed only by instructors and TAs.  Very handy for sharing solution sets, etc.  It is pretty easy to see  if a file or folder is inactive, but if I doubt I can choose "view as student".


Things I miss
Quiz.
1. Option to schedule the email to students who haven't taken the quiz at a particular time and date.
2. Option to have the answer to a quiz question revealed immediately after the answer.
3. Some kind of badge system for quizzes, e.g. Genius badge = 10 correct answers in a row, etc.
4. For questions with free text answers: option to see answers from all student on one question at once.
 
Open.  The course page is completely closed to students who are not signed up.  It would be very helpful to give access to other students so they can see what the course is about before they sign up.

SMS or other notification/reminder feature.  Right now every interaction with students is through email, but what good is an email notification about a quiz that is due in two hours if the email is not read.  Actually, iPhone one can mark email contacts as VIP and get notifications when VIP emails arrive, so that might fix it.  Not sure if that works on Android or if students have set up forwarding. Also, next time I teach I'll set up and share a Google calendar for the course, which might help and/or use the remind app.

Integration with social media.  Some way to automatically share announcements, etc. on Twitter, Facebook, Google+, etc.  E.g. with Twitter I am thinking something send directly to their Twitter address, so they get alerted - not some hashtag.

Better discussion forum. I wrote about that here.

Dropbox integration. I spend a lot of time uploading files to the system.  I already keep my course material on dropbox, so it would be great of one could mirror drop-box folders (with some control over what files are visible to the students).

Mobile friendly/app. It is very important to be able access and work on the site with a smartphone or tablet.

In-active files/view as student. More detail is needed on student activity. Who has downloaded what file when?  Create contact lists for groups of students who match certain criteria.  E.g. who has not downloaded the last homework problem yet.  Also overview of single student's activity.

Extract student identifiers to create accounts on other systems.  This is currently amazingly complicated.


Comments and questions very welcome.


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Saturday, January 10, 2015

Blog posts, videos and "other publications" for 2014

Every year I have to fill out several "what have you accomplished last year?" forms. I've just send in one of them. There is a section on "other publications", which, I guess, is intended for non-refereed articles and books. But there are now many other ways to disseminate information so I added:

Blogs
http://molecularmodelingbasics.blogspot.com 69,537 pageviews in 2014
http://proteinsandwavefunctions.blogspot.com 17,964 pageviews in 2014 (group-blog, includes contributions from others)

Web-book
Active Learning: Tools and Tips (https://sites.google.com/site/jhdou363/) 1850 pageviews in 2014

Videos
http://www.youtube.com/user/MolModBasics 45,074 views in 2014

Presentations
http://www.slideshare.net/molmodbasics/ 10,397 views in 2014

Software:
http://propka.org ca 30,000 pageviews in 2014
http://molcalc.org 44,679 pageviews in 2014



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