Social Media Services and Tools

There are other topics to write about, as promised at the beginning of this series. Being that keeping a blog takes time and soon becomes a boring activity, I have decided to give you links instead of new pages. All the articles in the list below have been written by myself over the last couple of years. I could reorganize them into a more organic and readable form, but the concepts are already clear enough. Manual Corrections Automatic Baseline Correction Automatic Integration Perfect-Looking Integrals Visual Weighting 2D Phase Correction Further Hints for 2D Phase Correction 1D Phase Correction Automatic Phase Correction Non Linear Methods I'll continue the blog when I find something new to say. I thank you all that have been reading me daily during the last month. Yesterday the blog received 84 visits, which was the July record.

My most popular post, in two years of activity, has been the infamous "TopSpin NMR Free Download". That single (short) post has received as many comments as the rest of blog (sob!). People were so prompt to fix their anger in words but nobody was touched by the idea of starting a discussion. Unless you call discussion an exchange of flames. I have learned the lesson, in my own way. This time I have chosen a more explicit title, so nobody can say he arrived here with pure and saint intentions. I myself haven't changed my mind. Year after year, a lot of money is spent to acquire/upgrade NMR instrumentation and software. Attending a conference is not cheap and renting a booth there is really expensive. The number of computers sold keeps increasing year after year. How is it possible that there is so much money in circulation and, at the same time, people cry because they can't pay an NMR program (but could nonetheless find the money to buy a new computer...) ? Our societ...

Take a column of the processed 2D plot (column = indirect dimension). Use a mapping algorithm to identify the transparent regions (not containing peaks). In the following I'll call them the "noisy regions". The idea is to delete these region. Setting all their points to zero would be too drastic and unrealistic. What you do, instead, is to calculate the average value in this region. More exactly, the average of the absolute values. At the end you have a positive number which is a measure of the noise along that column. Repeat for all the columns. At the end you have the values of noise for each column. Noise is higher when there is a big peak (on the diagonal or elsewhere). Noise is low where there's no signal. Annotate the minimum value for this noise, let's call it "min". Now, pick again each column. Divide its "noisy regions" by the value of their own noise, then multiply them by "min". The portions containing true peaks are not a...

Since the beginning of this series of "lessons", the stress has been on 1-D processing. I have shown that 1-D processing can be as tricky and important as 2-D processing. If you are working exclusively with large bio-molecules you may well live with the sensation that there's no NMR with less than 2 dimensions. The NMR field is divided in many rooms and there's not enough communication among them. I have attended several NMR conferences where there was indeed the possibility for the groups, working in distant field, to merge their knowledge for a week. My impression is that every one keeps speaking his own language and keeps doing the same things for decades. NMR is not a unifying technique. The main link between the researcher is not their society, but the factory that builds the instruments. Today I want to write about a couple of processing operations that are specific to 2D. Symmetry is the first example that comes to my mind. In homo-nuclear correlation spectros...

The natural complement to the Multiplet Analyzer is a Report Generator. The former starts from the list of frequencies (the output of peak-picking) and generates a table of chemical shifts and couplings. The Report Generator starts from this table and generates a formatted list, ready to be inserted into a patent or an article; the format is compliant with the rules dictated by the patent office or by the receiving journal, etc.. It's counter-productive, for a software vendor, to explain all this details and intermediate stages. It's more impressive to state that a program can start from the FID and automatically generate the article (and maybe even sending it via email to the editor of the JOC!). If such a monolithic thing really exists, it would be a case of bad design, but the marketing appeal can't be argued. Selling a program is easy. Convincing the customer to use it, that's difficult! We have seen that the multiplet analyzer is limited to first-order signals. We ...

Not all the spectra are second order. Actually, today's marketing insists to generalize that, in our new century, almost all the spectra are first order. Such a generalization makes sense if you process a spectrum (or less) per year, otherwise your destiny is to meet, sooner than you expect, something second-order. It's true that you are allowed to describe your spectrum as a sequence of generic multiplets, avoiding a more detailed analysis. This is tolerated but hasn't become the recommended practice yet. That said, there are certainly a lot of first-order multiplets in our spectra and extracting shifts and J it's an easy but tedious task. Can the computer help us? See for example the following spectrum of 1-pentyne in CDCl3. (The peak at 1.56d is an impurity). There are, from left to right, a triplet of doublets, a triplet, a sextet and another triplet. The manual extraction of parameters is easy. Let's start from the sextet, because it's a curious rarity. It...

The turning point in dynamic NMR was the article "DNMR: the program" by Gerhard Binsch (JACS, March 12, 1969). The article said: if we monitor chemical exchange by the coalescence of two singlets, a large variation of the rate is reflected into a small change of the spectrum. Therefore our estimate will be inaccurate. If, keeping A and B as they are, we simply add a third nucleus C, coupled with both A and B, see what happens: Now a small variation in the rate of exchange is the cause of a large change in the spectrum. Therefore we can estimate the rate (by simulation) with higher accuracy and confidence. 40 years later the lesson has not been learned yet and there's people who prefer to add a methyl group to their compounds to monitor the exchange rate by the coalescence of the singlets. I can understand this choice if the reason is to maximize the intensity of the signals. I suspect, however, that the true reason is a different one. There is an approximate formula from ...

Dynamic NMR includes chemical exchange and internal rotations. They are the same thing, observed via NMR. If the rate of exchange is low, you can start from a non-equilibrium situation and measure the changes of concentration over a period of hours or days. When the rate is higher, you study the situation at equilibrium, either by saturation transfer or by line-shape analysis. The latter is akin to the simulation of spin systems seen so far. There is one more parameter, the exchange rate constant (assumed to be first-order). If you have an exchange among many sites, you can have several different rates, but it's rare. The visible effect of chemical exchange is the broadening of the lines. The effect is dramatic at the coalescence, when two of the corresponding signals of the exchanging species become one. The temperature of coalescence depends on: the exchange rate the difference in Hz The direct consequence is that: a species with n signals can have up to n different temperatures...

A system of 3 different protons has 12 lines. The same system, made of �H nuclei, has 27 lines. Both systems can be described with 3 shifts and 3 coupling constants. That's obvious. Add a common line-width: 7 parameters to describe 27 or 12 lines. There are many other "obvious" relationships that often reduce the degree of freedom of the problem. The group CH3-CH-CH3 contains many more hydrogens, but is described by only 2 or 3 parameters (because of the magnetic equivalence). A para- (or ortho-) di-substituted benzene, if the substituent is the same, is symmetric: all parameters are duplicated. Tin is a mixture of isotopes, 3 of them are magnetically active. If you want to simulate the proton spectrum of a tin compound, you have to declare 3 or 4 systems, but their parameters (shifts, couplings), neglecting the isotope effects, are the same. The above 3 examples can be handled by the software. Summarizing: magnetic equivalence symmetry isotopic mixture The gain in comput...

Now that you know about the three main approaches, where to go from here? If you want to use one of the methods for fitting a spin system (see yesterday's post), the simplest (and single) thing to do is to read the manual of your program. If it's too short, reading it will require a little investment of time. If it doesn't help, it either means that your program is extremely intuitive or that you need a different program. If, instead, the manual is very long, there are two cases: either the program is very powerful and well documented, so there's a lot of things to learn from it, or the program and its manual are a crappy mess. There are a lot of advantages if the same program performs both processing and simulation; it means: less things to learn, a couple of export/import operations are avoided, there are more users (i.e. the program has been more tested), the interface is probably simplified (because they are general-purpose programs targeted at the casual user). The...

When you are able to process an NMR spectrum; when you are also able to simulate the same spectrum (starting from the definition of a spin system); then you are ready to fit the two, one against the other. People tend to skip all the intermediate stages. I would not. If I can't write the single words, I won't be able to write a sentence. Yesterday I said that the simulation of a spin system is a useful exercise to understand a few principles of NMR; now I need to stress that it's also a useful exercise before you move on to the extraction of the NMR parameters by simulation. Once you have the two main ingredients, the experimental spectrum and the synthetic one, there are three main methods to perform the fit; each one has a reason to exist. (1) Manual Adjustment This can work if the spectrum, or portions of it, can be interpreted with first-order rules. Chemical shifts are easy to fit manually, because it's enough to literally drag each multiplet in place. The coupling...

A fortnight ago we saw how to fit a spectrum with a collection of curves. A more evolute approach is to fit the spectrum with a collection of NMR parameters (shifts and Js in the first place). There are two reasons to prefer the latter approach: you introduce logical restrictions into the model, for example you specify that the components of a triplet are in the ratio 1:2:1 you overcome the job of measuring shifts and Js from line positions Simple line fitting to a generic collection of lines remains the best choice for singlets, simple multiplets and when you are not interested at all into the frequencies, but only into the intensities. Simplifying, curve-fitting (the so-called "deconvolution") is more about areas, spin system analysis is more about energies. We have arrived to a large topic from an unusual path. We are in the field of quantum mechanic. It's easy in theory and, in practice, when the nuclei are few. When the number of nuclei in a spin system grows, no com...

All cameras need to be focused before shooting. There are 3 alternatives: manual focus, autofocus and fixed focus. The latter is an economical choice that can't work under all circumstances, it's OK only when the depth of field is large enough. This depth depends on the characteristics of the lens. I can see a similarity in NMR spectroscopy. The phase correction of an high-resolution spectrum is like a lens with a limited depth of field (think to a telescope, if you are more familiar with them; the telescope is an example of a lens with a narrow depth of field). Starting from the optimal correction, a minimal change in the phase correction parameter (movement of the lens, in the parallel example) causes a visible negative effect on the spectrum (clearness of the image). It's not enough to copy the phase correction from a spectrum to the other, you must use either manual or automatic correction or both. Like it or not, you'll become an expert in the field. Weighting is m...

Before the touristic digression, we were slowly coming back to an old topic: Reference Deconvolution. If you are new to this blog, RD it's an alternative technique to weighting. Think at it as "tailored resolution enhancement" or "shimming-after-the-fact". I commented on it in two recent articles: Reference Deconvolution in Theory Reference Deconvolution in Practice

Last Thursday I visited these islands for the first time. Pictures by Maria Luisa.

At the basis of weighting there's the convolution theorem . FT( f � g ) ? FT(f) * FT(g) which can also be written as: FT( f � g ) ? FT(f) ? FT(g) The choice depends, exclusively, on which symbol you use to indicate the convolution operation. If, after reading the linked Wikipedia pages, you feel like being still at the point you had started from, I can propose a simplified approach, based upon Fourier Pairs and practical examples. If, in time domain, you have an exponential decay, after FT you get a Lorentzian curve. The two functions form a Fourier pair. The Gaussian function pairs with itself. A stationary sinusoid pairs with an infinitely narrow line (a nail pointing upwards). It's a curve with no shape and no width (but it has a frequency). Convolution of two curves yields a third curve with the shape of both ancestors and a patrimony (line-widths) equal to the sum of the widths of the ancestors. You can think at the result curve as an empty and opaque envelope with no sh...

Weighting functions are so easy in practice and so (apparently) difficult in theory, that I wonder if we can just ignore the latter and pretend it doesn't exist. It's a matter of language. Instead of moving towards simplification, we keep creating more names, more languages, more ways to measure things. If you have learned NMR from the literature, you'll discover a different language in software, and can't find the vocabulary for the translation. The same happens when you want to write your own article: how you describe your NMR processing? It's the inverse translation. Last but not least, different softwares have different names and units for the weighting functions. Don't be mislead by the names, what matters is the shape of the window function. Ideally, it should be reproduced into your manual. Given that the shape often depends on a user-settable parameter, they can't illustrate all the possible cases. You can, however, ask the program to show the plot o...