Refer to Paper [Edden and Keeler, JMR, 2003?] for further details of any point. Chapter 1 : File Contents Chapter 2 : Experimental Setup Chapter 3 : Dataset Structure Chapter 4 : Data Processing Chapter 5 : Data Analysis Chapter 1 : File Contents In this folder, there are the following things: Pulse Programs : raee_hmbcg - Figure 1(b) raee_filthmbc - Figure 1(d) raee_hmbc1d - Figure 1(e) Variable Delay List: vdlist [for use with raee_filthmbc] Au programs: raee_jfit - To extract CH couplings from HMBC multiplets in processed spectra. raee_8split - To take the large MBOB-type data file produced by raee_filthmbc and return separate ser files spectra. raee_4split - To take an analogous datset that applies a first-order MBOB filter and return three ser files. raee_fix - A useful macro to manipulate one- dimensional spectra, allowing all the manipulations of the fitting procedure (excise, left-shift, anti-phase coupling, frequency shift). Dataset: errormap - This dataset should be copied into your data directory. It is used to plot the errormap of the fitting procedure. (trialdata) - A simulated dataset that is small enough to download to try the process out. Chapter 2 : Experimental Setup Modelling from Proton Spectrum: It is vital that the correct leftshift corresponds to a whole number of data points in t2 (=n*dw*2). A proton spectrum must be run with identical offset, sweep width etc to the hmbc proton dimension. HMBC Phasing in f1: For correct phasing, set d0 such that (d0 + p2) = (n * in0)/2 where n = 1 (180 degree phase) or 2 (360 degree phase). Delay List: vdlist supplied works for 1J from 125 to 165. Chapter 3 : Dataset structure It may be worth copying the acquire data that is necessary for fitting into a separate dataset so that no other spectra are over written. In general, datasets 118-130 are used during fitting and should be empty (or disposable). The filthmbc dataset is co-added in three different ways to produce the long-range and two one-bond spectra. These will be copied into the three subsequent datasets by raee_split. Chapter 4 : Data Processing Phasing Proton Spectrum: Should be phased to absorption mode. HMBC Spectra: Should be left unphased. Window functions F1 : Any window functions can be used. F2 : If modelling from proton is to be used, currently only exponential windows are supported. The same window must be applied to all 2D spectra and the proton 1D. raee_8split This au program (which will need to be compiled on your machine) will split the bulk dataset up into the three 2D spectra. 1. Ensure the three subsequent datafiles are empty (or expendable). 2. Go to the bulk data file and run raee_nml. 3. xfb the three separate datasets. Any extra processing should be done identically to the three datasets. 4. The data is ready to analyse. Chapter 5 : Data Analysis The program raee_jfit will analyse the HMBC lineshape by Methods 1-3 [see paper]. One-dimensional hmbc spectra can only be analysed by method 1. Output expno 120: Best fit model multiplet. expno 125: HMBC target multiplet. expno 130: Error map. expno [Store No]: Best fit model multiplet. expno [Store No+1]: HMBC target multiplet. Whereas 120, 125 and 130 will be overwritten when the next peak is analysed, the store expnos allow you to keep the spectra. Step-by-step guide Are you using a 1D (1) or 2D (2) hmbc? Model from proton (1) onebond (2) or half-onebond (3)? These three options result in a different chain of Store No? The bestfit model and HMBC multiplet will be copied to this experiment number (and the next). Therefore increment by 2 for every peak analysed. Modelling from Proton: Expno of 1-D proton spectrum: The program needs to be pointed to the 1D spectrum. Leftshift? In seconds, the appropriate leftshift (even multiple of dw). Mark boundaries of region of the HMBC row to be excised, hit return, then save and only then hit OK. The integrate function is used to define the region of the spectrum to be excised. It is important that the region is defined with the middle button and that the intrng file is saved before OK is hit (or the program will crash). Mark boundaries of region of the proton spectrum to be excised, hit return, then save and only then hit OK. The integrate function is used to define the region of the spectrum to be excised. It is important that the region is defined with the middle button and that the intrng file is saved before OK is hit (or the program will crash). Do you want to start with Jtrial as... ? The errormap gives a starting point for the search routine. If you want to start the procedure off in a diferent place, enter the values. Do you want to start with Atrial as... ? The errormap gives a starting point for the search routine. If you want to start the procedure off in a diferent place, enter the values. Modelling from One-Bond or Half One-bond: Expno of first One-Bond spectrum: The program needs to be pointed to the One-bond spectrum. If raee_split was used, then the program will come up with the correct answer. If the one-bond correlations in an un-filtered HMBC are to be used, the HMBC experiment number should be put in. (*) Check n-bond row. Allows manipulation of spectra to check which row the HMBC peak is in. Which row of the HMBC would you like to extract: Enter value. Hit Return or 5 to enter Peak Doctor: Peak Doctor is an extra macro that allows the subtraction of poorly filtered one-bond peaks by adding in some of the same row of the one-bond spectrum. It is only applicable to filtered experiments and is explained further below. Check one-bond row. Allows manipulation of spectra to check which row the one-bond peak is in. Which row of the one-bond correlation would you like to extract: Enter value. Check which one-bond peak is larger\nand hit OK. A dual display allows the user to pick the one-bond peak with the larger intensity. Which One-Bond correlation is larger? green (1) red (2): Enter 1 or 2. Hit Return or 5 to enter Peak Doctor: Peak Doctor applied to the one-bond correlations allows the subtraction of overlapping correlations with a different 1J. It can also be used to reduce noise levels if the intensities of red and green were the same. More below. Measure one-bond coupling constant and hit OK. Allows manipulation of one-bond row to measure 1J. One-bond coupling constant (Hz)? Enter value. Mark boundaries of region to be excised, hit return, then save and only then hit OK. The integrate function is used to define the region of the spectrum to be excised. It is important that the region is defined with the middle button and that the intrng file is saved before OK is hit (or the program will crash). Mark boundaries of region of the one-bond row to be excised, hit return, then save and only then hit OK. The integrate function is used to define the region of the spectrum to be excised. It is important that the region is defined with the middle button and that the intrng file is saved before OK is hit (or the program will crash). (Half One-Bond only : Left- (1) or the right-hand (2) peak of doublet?) If the left-hand portion of the one-bond doublet was excised, type 1, etc. Do you want to start with Jtrial as... ? The errormap gives a starting point for the search routine. If you want to start the procedure off in a diferent place, enter the values. Do you want to start with Atrial as... ? The errormap gives a starting point for the search routine. If you want to start the procedure off in a diferent place, enter the values. Peak Doctor Twiddle to lose one-bond, hit return and Save and return ..and then hit OK. Then hit Cancel and OK on the other windows. The first dataset is the dataset to be doctored, the second the dataset to be added or subtracted. Zoom in on the interesting region and scale the second dataset to the required size, then hit add or diff. If the second dataset shown is no the one you require, the other one-bond press e^ to get to the other one-bond. When the subtraction is satisfactory, hit return and Save and return and then hit OK. Cancel must be hit on the little window (probably behind the larger box that has appeared) BEFORE OK is hit on the bigger window.