Friday, 28 November 2008

Quantitation of Pharmaceutical Compounds

This is probably something that you weren’t expecting, but I think it’s a fun way to end the week

Monday, 24 November 2008

Intelligent NMR Clipboard

The clipboard is for sure one of the most useful features in any modern Operating System and it is used for short-term data storage and/or data transfer between documents or applications, via copy and paste operations. Any modern application should support clipboard operations and, of course, Mnova is no exception. However, Mnova goes one step further compared to other applications as I will try to show in this post.

Following the same principles as standard Office applications, with Mnova it’s possible to copy any object (e.g. spectra, molecules, etc) into the clipboard and paste it either in Mnova (for example in a different page) or in any other application such as MS Office. The peculiar thing is that once a spectrum has been transferred to the clipboard (via Ctrl+C), it is possible to ‘paste’ it into another spectrum. Two simple examples will illustrate this new feature.

Example #1

You have processed a spectrum and integrated carefully in order to quantify some signals of interest. Next you realize that you also want to integrate a different spectrum but using exactly the same integral regions as those in the first spectrum. There are several ways to do that in Mnova, but a very simple one involves copying the first spectrum into the clipboard and then selecting ‘Paste Integrals’ from the Edit menu. You can paste these integrals either to a single spectrum or to a bunch of selected spectra (or pages).

Example #2

You have customized the graphical properties of a spectrum (e.g. fonts, colors, grid, etc) and you find that you want to rapidly apply the same graphical settings to another spectrum. Once more, this is very easy with the clipboard: copy the first spectrum (Ctrl+C) and then select the target spectrum and issue command ‘Paste NMR Properties’.

Saturday, 22 November 2008

NMR Arithmetics

2D NMR spectra are simply 2D matrices (Note: these matrices can be real, complex or hypercomplex, but for the sake of simplicity, we will consider real matrices only) which can be subject to standard matrix algebra operations. I have presented in previous posts how Indirect and Direct Covariance NMR can be applied by proper matrix algebra. These methods are incorporated in Mnova as a dedicated module which also makes the filtering of spurious resonances possible . In order to show you that Covariance NMR actually involves these matrix operations, you can use Mnova’s powerful Arithmetic module which we have recently completed. This module has been designed in such a way that it operates as a simple spectral calculator. You enter the equation which the program parses and produces the expected result. For example, if we have a HSQC-TOCSY spectrum (A), we can enter the Indirect Covariance formula like this:

Where A corresponds to the real part of the original spectrum and TRANS indicates the transpose operation. This operation will produce the (unnormalized) Covariance NMR spectrum, in this case the 13C-13C correlation spectrum. Of course, in order to better approximate the covariance spectrum to the corresponding standard 2D FT counterpart, it’s necessary to calculate the square-root using, once more, matrix algebra. This is again very simple with our arithmetic module by just adding the square root operation (SQRT) into the equation:

This arithmetic module is not restricted to matrix operations within a single spectrum. We can freely combine as many spectra as we want. For instance, if we have, in the one hand a COSY spectrum and in the other a HSQC spectrum, we can combine both in an analogous way so that the indirect covariance NMR spectrum yields a HSQC-COSY 2D spectrum. More about this in a future post …

Thursday, 20 November 2008

Removal of artifacts in direct Covariance NMR

I have previously blogged about direct Covariance NMR as a technique to increase the digital resolution of the indirect dimension in 2D homonuclear experiments. As is always the case, there is some price to pay: Covariance NMR introduces some unexpected resonances, in special when the number of t1 increments is small making the covariance exhibit poor statistics (JACS, 2006, 128, 15564–15565). Some of these extra resonances are true spurious peaks whilst others correspond to multistep or RCOSY-type correlations (see MRC, 2008, 46, 997-1002)
The picture below shows the regular 2D FFT spectrum of Strychnine:

And this is its standard direct Covariance counterpart where I have highlighted some of the extra resonances.

While some of these additional resonances can be beneficial because they provide kind of TOCSY correlations, others are just pure artifacts which make the analysis of these experiments unreliable (it’s difficult to know in advance whether a peak is a real correlation or just an artifact).
We have recently incorporated into Mnova a new filter which eliminates these artifacts very efficiently. For example, this is the result obtained after automatic filtering of the Covariance NMR spectrum:

It can be observed that extra peaks have been eliminated without giving up the resolution advantage.
All these new processing capabilities will be available in the next version of Mnova (5.3.0, to be released in a few days), although we have a pre-release candidate available to anyone interested. Just contact me and I’ll be happy to send it out.

Monday, 10 November 2008

MestReS: A Virtual NMR Spectrometer

Aircraft pilots use cockpit flight simulators since they are considerably less expensive to operate than actual aircraft and provide an opportunity to practice crisis problem solving without putting real people or aircraft at risk. Following the same principle, MestReS is a virtual NMR simulator package intended to allow students to learn and practice the NMR instrumental techniques while saving rather expensive spectrometer time and avoiding equipment damage due to improper use. MestReS provides real-time simulation of the processes of field locking, shimming and acquisition. Both continuous-wave (Bruker spectrometers) and FT (Varian spectrometers) deuterium channel simulation are included. Most common physical properties (e.g. sweep rate variation, spinning sidebands, etc) can also be simulated. The program provides basic 1D processing and includes the tools needed to effortlessly create 1H and 13C NMR databases from synthetic FID’s

You can download it from the link below:

Download MestReS
at the Mestrelab Research Chemistry Software Product Page

MestReS can emulate locking and shimming effects in real time. Both continuous-wave (Bruker spectrometers) and FT (Varian spectrometers) deuterium channel simulation are included. Emulation of most commonly used shimming coils (Z,Z2..X,Y) is also provided. Most common physical properties are also simulated (sweep rate variation, spinning sidebands, etc) giving to the student a very realistic feeling.

While we offer MestReS as a totally free program, we are not longer developing it further or offering technical support for its use. Nevertheless, should you have any comment on the program, feel free to let me know.

I would particularly like to thank Armando Navarro, of the University of Santiago de Compostela, for his work in developing MestReS and making it available to our user community. It was a pleasure to collaborate with him on this project while I was working at the University

Tuesday, 4 November 2008

EXSYCALC: A free software for NMR analysis of molecular systems undergoing chemical exchange

EXSYCALC is a free program intended for the study by NMR of molecular systems undergoing chemical exchange. It does a quantitative analysis of the experimental intensities of the NMR peaks obtained in EXSY experiments to calculate the magnetization exchange rates k' of the exchange equilibrium (related with the reaction rate constants k ). The program allows the calculation of systems with an arbitrary number of exchange sites, spins, populations and arbitrary longitudinal relaxation rates. The calculations are done according to a full relaxation matrix analysis of the intensities. The range of applicability of the approach used requires that the signal of each different species in the exchange process is conveniently separated from the others in the NMR spectrum (i.e. slow chemical exchange in the chemical shift time scale)

You can download it from this link:

Download EXSYCalc at the Mestrelab Research Chemistry Software Product Page

For the calculation of rate constants, the program requires that the user supplies the experimental amplitudes of certain NMR peaks obtained in two different EXSY experiments, one is an EXSY experiment acquired at a certain mixing time (tm), and the other is an EXSY experiment acquired at 0 or very short mixing time (reference experiment). In the former experiment the mixing time (tm) need to be large enough for the magnetization exchange process to take place. In this experiment the amplitudes (intensities) of those signals in exchange, A(tm), have to be quantified for both diagonal and cross peaks. In the other EXSY experiment, the EXSY reference experiment, no cross peaks due to magnetization exchange should be observed (thermal equilibrium) and the amplitudes of just the diagonal peaks of those signals in exchange, A(0), have to be measured. It is important to mention that both experiments must be acquired and processed under identical conditions, temperature, number of scans etc.

Enjoy it!

Sunday, 2 November 2008

Indirect Covariance NMR – Fast Square Rooting

In my previous post I wrote about Direct Covariance NMR as a powerful processing tool to improve the resolution along the indirect dimension of a 2D homonuclear spectrum. Using a naïve explanation, we can understand this as a resolution transfer from the direct dimension to the indirect one. Mathematically this is done by simply multiplying the transpose of the real part of the spectrum by itself:

Cdirect = (F'.F)^(1/2)

Interestingly, if we have a heteronuclear spectrum, it‘s possible to transfer the correlation information from the indirect dimension to the direct one by simply changing the order in which the multiplication is carried out:

Cindirect = (F.F')^(1/2)

For example, the spectrum below shows the HSQC-TOCSY spectrum of sucrose (left) and its resulting indirect covariance counterpart (right) which contains essentially the same spin-connectivity information as a 13C-13C TOCSY with direct 13C detection (more information here).

The advantage is obvious: Indirect Covariance NMR yields a 13C-13C TOCSY correlation without having to detect the 13C nucleus. In other words, it brings in a sensitivity increase of 8 over a 13C detected experiment. Of course, in indirect covariance NMR spectroscopy, the spectral resolution along both frequency axes is determined by the sampling along the evolution t1 time.
The first time I implemented Indirect Covariance NMR in MestReC, I found that the computational effort required was quite high. The computation of the covariance matrix requires O(N1N2^2/2) floating point operations, whereas the square-root operation based on diagonalization of C requires O(N2^3) floating point operations (see this for more details).
For example, calculation of the indirect covariance NMR spectrum (including square root computation) of the HSQC-TOCSY spectrum showed above (1024x1024 data points) took about 60 seconds in my laptop (Sony VAIO, Intel Core, Duo Processor, 2.40 GHz, 2 GB RAM) in MestReC. The new implementation of Covariance NMR in Mnova is much more efficient and for this particular example, full calculation of the Indirect Covariance spectrum takes less than 3 seconds in the same computer.
The very high performance of Mnova makes Covariance NMR computationally affordable and open to a wide range of routine applications.