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CHAPTER 13: 1D Analysis Workwindow

This chapter describes the details of the 1D Analysis workwindow. All its input fields are explained along with their default settings for the analysis of carbon spectra. (To display all the input fields, select from the Edit menu [Preferences...]. Select the [Full NMRanalyst] and the [Show All Input Fields] switches and click [OK].) Depending on the selected spectrum type, different default settings are provided. For a general description of function and use of a workwindow, see CHAPTER 12: "Using the Workwindows".

The 1D Analysis workwindow provides the user interface to the 1d_analysis program. Its primary use is to read a 1D FID or Bruker or Varian software transformed spectrum and to analyze it. Its output is used as input for the multidimensional spectral analysis and the FindIt, VerifyIt, and AssembleIt generation of molecular structures.

When no acquired 1D spectral data is available, similar information can be generated. A line list of shifts can be converted to NMRanalyst format. A two-dimensional spectrum can be projected on its axes and peak picked. Three-dimensional projections need to be generated by the Varian VNMR or other software to create line lists to be imported into NMRanalyst. This workwindow can also generate generic 1D resonance lists. This generic information allows the complete analysis of multidimensional spectra without requiring experimental 1D spectra.

13.1 Input File

[Generate Generic List]:


[Varian], [Bruker AMX & DMX], [JCAMP-DX], [Import Line List]:

When neither a 1D FID, spectrum, or line list is available, set the Input File Format: option menu (described below) to [Generate Generic List]. The first input field shown above is displayed. Specify the desired distance between resonances in agreement with the mapping information for the analysis of the multidimensional spectrum. If no value is specified, the default value of 4 points is used. When this workwindow is run, the generic 1D line list with the specified line spacing is created.

When experimental 1D information is available, specify the name of the file in the 1D FID, Spectrum, or Line List input field for conversion to NMRanalyst format. Varian VNMR format data files can also be specified in this input field allowing to use VNMR pre-processing (linear prediction, digital filtering, weighting functions, etc.) before the NMRanalyst data analysis. (Key:1 SigDist, SigDistU, FnFID)

The 1d_analysis program can read experimental data in [Varian], [Bruker AMX & DMX], and [JCAMP-DX] format. This option menu sets the expected data format.

Besides FIDs, the [Varian] and [Bruker AMX & DMX] settings allow reading preprocessed spectra in Bruker (called 1r and 1i) and Varian VNMR (called data) files. The Bruker and Varian software can import spectra from different spectrometer vendors and provide data manipulation capabilities (e.g., linear prediction, weighting, filtering). By analyzing preprocessed phase sensitive spectrum files, these facilities can be used before the NMRanalyst data analysis. For Bruker AMX & DMX input files, use the [Load] button in the NMRanalyst window and specify the ?/fid or ?/pdata/?/1r file in the acquired data directory. This calls the bruker2txt script to assemble spectral information from the Bruker acquisition, and if present processing, parameters.

The [JCAMP-DX FID] item specifies an uncompressed JCAMP-DX FID. The jcamp2txt script is used for its parameter and FID conversions. All FID data is included in the specified file. Regular compressions are ineffective for FID data. So it is assumed to be specified uncompressed.

The [Import Line List] item allows converting a table of resonances into NMRanalyst format. The simplest format for the line list is one shift number per line. It is interpreted as a shift in ppm. This format is used to enter carbon resonances. A second column can be specified to indicate the integrals. This format is frequently used for proton information. When several resonances are included in one integral, divide its value through the number of contained resonances for each resonance. Only methyl (or methoxy) group resonances need to be specified by the ratios 3 H, 1.5:1.5 H, 0.75:1.5:0.75 H, or multiples thereof for reliable group recognition. Only the relative size of integrals matters, not their absolute values.

The [Generate Generic List] item allows generating a generic 1D resonance list when no experimental data is available. (Key: DatFmt)

When [Import Line List] or [Generate Generic List] is selected, this input field is displayed and allows specifying the effective relaxation time to be used for all resonances. When not specified, a one Hz linewidth (0.3183 s relaxation time) is assumed. (Key: SetT2)

13.2 Output Files

This input field allows specifying the name of the generated output file containing the numerical description of identified 1D resonances. Information about all detected resonances in the spectrum is stored in this file: chemical shift, integral, transverse relaxation time, and phase for each resonance per line. The detected resonances are numbered in the order of decreasing chemical shift. This file is read and used by the FFT, nD Analysis, Report, and AssembleIt workwindows. If the name of the output file is changed in this input field, it needs to be changed in related workwindows as well. (Key: FnOut)

If a file name is specified, the experimental spectrum, individual simulated resonances, the sum of all simulated resonances ("simulated spectrum"), and the difference between experimental and simulated spectra ("residual spectrum") are stored. These spectra can be plotted using the Graphic workwindow. (Key: FnSpcA)

If a file name is specified, a plot file containing the determined phase, baseline, and error values is created. The file also contains the derived 1D baseline and phase correction functions. (Key: FnParm)

13.3 Spectral Description

In this input field, an identification text for the 1D spectrum can be specified. The specified text appears in the 1D Analysis workwindow output screen and the generated numerical description file. The first 200 characters specified in this Identification Text field are displayed by the computing processes. The text has no effect on the data analysis. (Key: TxSpec)

Enter the observe frequency of the nucleus under consideration. For example, on a 500 MHz spectrometer, the 13C observe frequency is around 125.7 MHz. On a Varian instrument, the observe frequency can be obtained from the VNMR parameter sfrq. (Key: HzPpmF1, HzPpmF1U)

Provide the value of the spectral width, and choose the appropriate unit using the option menu. This is the parameter sw in Varian's VNMR software. (Key: swF1, swF1U)

Specify the frequency of the right-most (low frequency) limit of the acquired 1D spectrum. If a Varian instrument was used to acquire the data, this value can be obtained by subtracting the parameter rfl from the parameter rfp. (Key: spF1, spF1U)

Specify the positive number of phase sensitive points (up to 65536) to be Fourier transformed. If no value is specified, all acquired FID points are used. If a value is specified, the FID is truncated or zero-filled as requested. (Key: nPts)

13.4 Analysis Parameters

The "peak picking" step identifies resonances in the 1D spectrum worth further examination. Only resonances above the specified threshold times the noise level (average distance between adjacent spectral points) are selected for further investigation. The higher the value entered in this input field, the smaller the number of identified resonances. When this threshold is set to a negative value, the single resonance analysis is performed using its absolute value. The normally subsequent resonance cluster optimization is then not performed. (Key: HLimit)

This parameter specifies how much resonance splitting can occur, before each additional splitting is considered a separate resonance. The default value for proton spectra is one and for other spectrum types 1.7 Hertz, or the digital resolution, whichever is higher. (Key: WidthL, WidthLU)

Most NMR baseline distortions result from intensity distortions of the first few FID points. Rather than backward linear prediction, 1d_analysis corrects for distorted FID points in the frequency domain (Dunkel, R. United States Patent 5,218,299). Specify in this input field the number of FID points of which intensities need to be corrected.

Proton spectra typically require one and carbon spectra correction of three FID points. Bruker spectra might show "super smilies" at both spectral edges. They result from digital filtering imperfections. Specifying 99 (or any value above 10) selects a model-free baseline correction. The mentioned values are used by default, when no other value is specified. (Key: BaseN)

This value specifies the frequency range included around a resonance for determining its numerical description. Two neighboring resonances are considered to overlap, if their specified ranges overlap. In this case, both resonances are assigned to the same cluster of overlapping resonances, and the parameter values of all cluster resonances are optimized simultaneously to account for the effects of their mutual overlap. All resonances in a spectrum mutually overlap. Fortunately, effects of resonance overlap decrease rapidly with resonance distance and become negligible. Set this input field to several times the expected width at half-height of the widest resonance of interest. (Key: mSigHz, mSigHzU)

The Min Integral Precision is defined as the integral value of a detected resonance divided by its error value (marginal standard deviation). Noise patterns will typically yield integral precisions around one (i.e., the integral error value is as high as the detected resonance integral). When this input field value is increased, the weaker resonances (which are poorly defined by the data) are removed first. This input parameter should be specified as follows: set the value to 3, and inspect the simulated and residual spectra. If weaker resonances are not detected, decrease this value. If the program reports "too many" resonances, such as impurities or other undesired spectral features, slightly raise the specified value.

Note that only those resonances that have been initially identified in the peak picking step are passed through the filter. If a resonance of interest is not identified initially, then the peak-picking analysis parameters (Peak Picking: Threshold, Min Signal Distance, and Min Cluster Distance) need to be adjusted accordingly. (Key: PInt)

In most 1D spectra, all resonances can be phased to positive absorption using a linear phase function. If that is the case, this option menu should be set to [Positive]. This setting allows negative resonances during the spectral simulation to be eliminated and the phases of three or more resonances in a cluster to be fitted by a linear phase function. Some spectra contain both positive and negative resonances. For example, a DEPT-135 spectrum shows CH and CH3 carbon resonances in positive and CH2 ones in negative absorption. Such a spectrum can be analyzed by selecting the [Pos. & Neg.] (Positive and Negative resonances) setting in this option menu.

Non-Lorentzian resonances can often be fitted as an overlap of Lorentzian component lines with different phase values as selected by the [Random Phase] option. The [Pos. & Neg.] and [Random Phase] settings yield identical results for clusters of one or two resonances. But for three or more resonances per cluster, the [Random Phase] setting continues to determine one phase parameter for each resonance in the cluster, while the [Pos. & Neg.] setting determines a linear phase function for all resonances in the cluster.

For the [Pos. & Neg.] and [Random Phase] options, it is not clear which resonances are supposed to be positive and which ones are supposed to be negative. So the 1d_analysis program phases the spectrum so that the majority of resonances are in positive absorption. The numerical results of the 1D and multidimensional spectral analysis are not affected by this ambiguity, but the y-axis of plotted 1D data might be shown reversed from the desired result. (Key: PseSht)

These two input fields allow limiting the analysis of the 1D spectrum to the specified spectral range. Normally, both input fields are left blank and the first input field defaults to the sum of the Start of Spectrum and Spectral Width input values and the second field to the Start of Spectrum value, corresponding to the analysis of the whole spectrum. Notice, that the low field resonance (corresponding to the higher frequency value) should be entered in the left input field.

If the 1D and 2D spectra of a dataset were acquired with different spectral widths, use these input fields to limit the analysis of the 1D spectrum (and hence the 2D spectrum) to the common spectral range. Another reason for specifying the 1D spectral range is to focus on a particularly challenging spectral area for the optimization of analysis parameters. (Key: FqFrom, FqFromU, FqTo, FqToU)

13.5 General 1D Resonance Analysis

The input fields allow specification and optionally locking of initial parameter values for up to 300 resonances. Resonances with selected [Remove] switch are subtracted from the experimental dataset before the data analysis. This mechanism allows removing solvent and impurities from the spectrum. The 1d_analysis program optimizes the remaining specified resonances.

This switch allows displaying and activating or hiding and deactivating the table of initial parameter estimates. If selected, the specified initial values are used instead of the values generated by the peak-picking algorithm. For the routine analysis of 1D spectra, this button should be deselected. (Key: LFit)

In this table, every line of input fields describes one spectral resonance. Lines with an empty Frequency [ppm] field are ignored. If a frequency value is specified in the Frequency [ppm] field, the corresponding resonance is analyzed starting with the initial values provided in the other input fields of this line. The Integral field defaults to 1, the Relaxation [s] field to 0.31830988 (corresponding to a one Hz linewidth at half-height), and the Phase [rad] field to 0. Each specified resonance can be removed from the spectrum by selecting the corresponding [Remove] switch. (Key: LFreq1, LI1, Relax1, Pse1, LI1L through LFreq300, LI300, Relax300, Pse300, LI300L)

To clear all entries in this 1D resonance table, click the [Clear Table] button at the bottom of the workwindow. The [Undo Clear Table] button is then enabled and can be used to restore the values in the table.

Initially, only 25 lines are displayed in the table. To add more lines, click the [Add Lines to Table] button. This table can contain up to 300 lines.

13.6 Copyright Freely Distributable LIBM

Copyright (C) 2004 by Sun Microsystems, Inc. All rights reserved.

Permission to use, copy, modify, and distribute this software is freely granted, provided that this notice is preserved.

1The NMRanalyst computing processes expect a list of key-value pairs as input. For users of the NMRanalyst graphical interface, the names of the parameters (keys) are irrelevant. However, when working from a command line or integrating NMRanalyst programs in other software, the key names allow setting analysis parameters. For every workwindow interface widget, the corresponding key name is given in parenthesis.



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