Category Archives: nmr

Open Notebook NMR: Commercial re-use of data?

Posted on October 23, 2007 by pm286

Antony Williams of Chemspider has offered to participate in our Open Notebook NMR experiment. Now this offer has been joined by ACDLabs – I am not sure of the formal relation between the companies but they have clear common interests. … Continue reading →

Posted in nmr, open issues, open notebook science | 8 Comments

Open Notebook NMR – interesting outlier(s)

Posted on October 23, 2007 by pm286

Here is an interesting outlier which caught me out, until Christoph explained it. Here are two spectra. They are both from the same source: (There are 3 peaks – note the disagreement) Also 3 peaks. Here is the metadata for … Continue reading →

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Open Notebook NMR – Outliers

Posted on October 23, 2007 by pm286

Egon asks: Egon Willighagen Says: October 23rd, 2007 at 4:00 pm eWhere in which wiki can I find the outliers? That would allows people to indicate problems, and possible annotate existing publications with ratings (”this article has a incorrectly assigned … Continue reading →

Posted in data, nmr, open notebook science | Leave a comment

Open Notebook NMR : the act of discovery

Posted on October 23, 2007 by pm286

Things are happening so fast on the Open Notebook NMR project that we need to take stock. Here’s today’s developments: Nick Day is working round the clock to manage the data and create the plots. He has a thesis to … Continue reading →

Posted in data, nmr, open notebook science | 1 Comment

Open Notebook NMR – Henry's improved protocol

Posted on October 22, 2007 by pm286

When we first started this (nearly a month ago). Henry suggested a protocol for calculating the chemical shifts. Nick tooled up for this and had to overcome several technical problems on job submission, etc. (A typical example – the order … Continue reading →

Posted in chemistry, nmr, open notebook science | 3 Comments

Open Notebook NMR: Anticipated errors

Posted on October 22, 2007 by pm286

Nick and I sat down this morning and thought about what possible errors might arise in the “data” or “experimental” axis and also on the “predicted” axis. Some of these may overlap with Antony’s suggestions but they are independent. An … Continue reading →

Posted in chemistry, data, nmr, open notebook science | Leave a comment

Open Notebook NMR – cont

Posted on October 22, 2007 by pm286

We are now close to releasing the first results of the calculations – at present 300+ molecules. We think that really major foul-ups have been superseded (i.e. when all the Gaussian files failed to run because of a missing blank … Continue reading →

Posted in data, nmr, open notebook science | 1 Comment

Experiment and Calculation in WWMM-NMR. Open Notebook Science

Posted on October 22, 2007 by pm286

Antony guessed the graph – regular readers will recognise the context of previous posts. We are starting an Open Notebook project to determine whether theoretical calculations and experimental observations agree – or rather within what limits. (Earlier this year I … Continue reading →

Posted in nmr, open notebook science, XML | 3 Comments

Open NMR

Posted on October 13, 2007 by pm286

As I have already blogged (WWMM calculation of spectra) we are hoping to provide Jean-Claude Bradley and others an Open service to calculate NMR spectra from structure. This  needs a lot of software components and a lot of glueware. With … Continue reading →

Posted in blueobelisk, nmr, open issues, open notebook science, programming for scientists, theses | 6 Comments

Posting spectra

Posted on October 11, 2007 by pm286

Jean-Claude Bradley Says: October 11th, 2007 at 1:32 pm e http://www.chemspider.com/spectra.aspx and for example benzaldehyde: http://www.chemspider.com/Chemical-Structure.235.html I think a lot of the errors in the literature are due to poor quality spectra and improper referencing. It is really useful to … Continue reading →

Posted in nmr, open notebook science | 3 Comments