Input format for DNMR3

Input File Format for DNMR3

The following tables show the column positions of each piece of data in each line of the input file. Only the plot line is different from the format for the version of DNMR3 published in 1977 as DNMRL

Mutual versus Non-mutual Exchange

Chemically exchanging systems may be divided into Mutual or Non-mutual categories

Concatenated Runs

The data formats below may be repeated, without a blank line between them, to concatenate several runs in one input file. In this way, plots for different multiplets in the spectrum may be calculated
The total number of plots over the concatenated jobs must be <= 20 for them all to be viewed (and plotted) using N3PLOT for Windows

Mutual Exchange Case

Here the two (or three) chemical configurations all have the same set of chemical shifts and coupling constants
The configurations are thus chemically the same, though they may be enantiomers of each other, since these are indistinguishable by normal NMR
The configurations will have therefore equal energies and populations, the equilibrium constant(s) between the configurations will be 1, and all the rate constants, forwards and backwards, will be the same as each other
In going from one configuration to the next, at least two nuclei exchange their roles in the chemical structure
The change in going from one configuration to the next is given as an 'exchange vector'. Suppose structural sites of the (sets of magnetically equivalent) NMR-active nuclei are numbered sequentially in the first configuration. Then for the second configuration a vector can be written in which the indices of the elements represent these same sites, while the values of the elements are the sites in the first configuration from which the occupying nuclei came

If there is a third configuration, its exchange vector relates also to the first configuration, not to the second

Thus, for rotation of a methyl group, the exchange vector for the second configuration is 312 and for the third configuration it is 231

For a two-site exchange in which nucleus 1 retains its role, while nuclei 2 and 3 exchange theirs, the exchange vector is 132

Mutual Exchange Format
Line no.	Left	Right	Justification	Dec. pt.?	Content	Comment
	Column numbers
1	1	3	Right	No	Run no.
1	4	4			No. of nuclei	Total in spin system
1	5	5			No. of configs.	2 or 3 (1 for static system)
1	6	6			1	Flag for mutual exchange
1	7	7			No. of groups	= No. of nuclei, if no mag. equivalence
1	8	8			No. of symm. pairs	Blank if no symm. pairs. 2 for an AA'BB' system (for which No. of groups = 4)
2	1 2 etc.	1 2 etc.			No. of mag. equiv. nuclei in group	Omit line altogether if no mag. equiv. groups, i.e. if No. of groups = No. of nuclei Order groups in decreasing size.
3	1	72	Left		Title text
4	1 11 21 etc.	10 20 30 etc.	Left	Yes!	Chemical shifts in Hz	no. of entries = No. of groups Order as in line 2, otherwise put symm. pairs first, if there are any, two entries for each. If two shifts are for different isotopic species, alter one of them, if necessary, by a large displacement, e.g. 50000 Hz, so that J/d is negligible between them.
5	1 11 etc.	10 20 etc.	Left	Yes!	Coupling constants	J(12) J(13) etc. Couplings from group 1
5b	1 11	10 20	Left	Yes!	More coupling constants	J(23) J(24) if 4 groups. Couplings from group 2. Omit line if only two groups.
5c	1	10	Left	Yes!	Coupling constant	J(34) Omit line if not four groups
6	1	4	Left	No	Exchange vector	See above Omit line if static system
6b	1	3	Left	No	Exchange vector	For third config. Omit line if no third config.
7	1	2	Right	No	No. of rate constants	This is no. of plots for different rate constants, to be generated in this run. Zero for a static system, when one plot will be generated.
7	11	20	Left	Yes!	Left limit of plot, in Hz	Only one plot per rate constant per run allowed. Use concatenated separate runs for different multiplets, or for an overall plot as well. Allow enough space around broad peaks.
7	21	30	Left	Yes!	Right limit of plot, in Hz
7	31	40	Left	Yes!	Horizontal scale, in Hz/cm	Choose a scale such that width of plot is <= 25 cm (Note difference from original version)
7	41	50	Left	Yes!	Vertical plot scale	Height of tallest peak in plot range, as fraction of 25 cm. Maximum value 0.6 (Note difference from original version) Use a small enough value for broadened multiplets, otherwise a misleading shape may be generated
7	51	62	Left		Title for plot region	e.g. 'PA region'. Optional. (Note difference from original version)
8						There is no line 8 for mutual exchange
9	1	10	Left	Yes!	Relaxation time in seconds	T2. This is 1/(π * (peak width at half height)) for a single transition peak not broadened by the exchange. If there is no such peak in the observed spectrum, guess based on spectra of static systems measured under similar conditions
10	1	10	Left	Yes!	Rate constant in s^-1	First rate constant
10a, etc.	1	10	Left	Yes!	Rate constant in s^-1	Second rate constant, etc. Total number of type 10 lines is No. of rate constants given at the beginning of the type 7 line. For a static system, omit type 10 lines altogether.

Non-mutual Exchange Case

Here the two (or three) chemical configurations each has a different set of chemical shifts and coupling constants
The configurations in principle will be chemically distinguishable
However, the configurations may be different isotopomers of the same conformation (or its enantiomer), in which a nucleus of an NMR-active low abundance isotope exchanges with a nucleus of a non-NMR-active isotope of the same element at a different chemical site

In that case, the molecules will be chemically very similar, and other nuclei which do not exchange their roles will keep very similar chemical shifts and possibly some coupling constants between the configurations
This kind of system has much in common with mutual exchange, e.g. equal populations of the configurations and equal rate constants, but in DNMR3 must be dealt with using the non-mutual exchange format
This kind of non-mutual exchange may apply to satellite spectra of compounds where the main spectrum (no low-abundance NMR-active isotope present) is caused by a mutually exchanging system

In the general case, the populations of the configurations will be different, i.e. the equilibrium constant between them is not 1, and the forward and backward rate constants are different
The input to DNMR3 uses forward rate constants only, along with configuration populations, to define these parameters
In the case of a three-site exchange, the forward rate constant for each step is different, so three rate constants are required for each plot. Sets of rate constants replace the single rate constants in the mutual exchange format
No exchange vectors are specified, because the entire set of chemical shifts and coupling constants are repeated for each configuration. A nucleus keeps the same indices in these arrays between configurations, with the changes in the values of the parameters describing the change in its role

Non-mutual Exchange Format
Line no.	Left	Right	Justification	Dec. pt.?	Content	Comment
	Column numbers
1	1	3	Right	No	Run no.
1	4	4			No. of nuclei	Total in spin system
1	5	5			No. of configs.	2 or 3
1	6	6			0	Flag for non-mutual exchange
1	7	7			No. of groups	= No. of nuclei, if no mag. equivalence
1	8	8			No. of symm. pairs	Blank if no symm. pairs. 2 for an AA'BB' system (for which No. of groups = 4)
2	1 2 etc.	1 2 etc.			No. of mag. equiv. nuclei in group	Omit line altogether if no mag. equiv. groups, i.e. if No. of groups = No. of nuclei Order groups in decreasing size.
3	1	72	Left		Title text
4	1 11 21 etc.	10 20 30 etc.	Left	Yes!	Chemical shifts in Hz for configuration 1	no. of entries = No. of groups Order as in line 2, otherwise put symm. pairs first, if there are any, two entries for each. If two shifts are for different isotopic species, alter one of them, if necessary, by a large displacement, e.g. 50000 Hz, so that J/d is negligible between them.
5	1 11 etc.	10 20 etc.	Left	Yes!	Coupling constants for configuration 1	J(12) J(13) etc. Couplings from group 1
5b	1 11	10 20	Left	Yes!	More coupling constants	J(23) J(24) if 4 groups. Couplings from group 2. Omit line if only two groups.
5c	1	10	Left	Yes!	Coupling constant	J(34) Omit line if not four groups
4(ii) and 5(ii)					Shifts and coupling constants for configuration 2	Repeat the set of type 4 and type 5 lines above, for configuration 2
4(iii) and 5(iii)					Shifts and coupling constants for configuration 3	Repeat the set of type 4 and type 5 lines above, for configuration 3, if there is one
6						There is no type 6 line for non-mutual exchange
7	1	2	Right	No	No. of (sets of) rate constants	This is no. of plots for different (sets of) rate constants, to be generated in this run
7	11	20	Left	Yes!	Left limit of plot, in Hz	Only one plot per (set of) rate constant(s) per run allowed. Use concatenated separate runs for different multiplets, or for an overall plot as well. Allow enough space around broad peaks.
7	21	30	Left	Yes!	Right limit of plot, in Hz
7	31	40	Left	Yes!	Horizontal scale, in Hz/cm	Choose a scale such that width of plot is <= 25 cm (Note difference from original version)
7	41	50	Left	Yes!	Vertical plot scale	Height of tallest peak in plot range, as fraction of 25 cm. Maximum value 0.6 (Note difference from original version) Use a small enough value for broadened multiplets, otherwise a misleading shape may be generated
7	51	62	Left		Title for plot region	e.g. 'PA region'. Optional. (Note difference from original version)
8(i)	1	10	Left	Yes!	Relative population of configuration 1, as a fraction of 1	For equal populations in two configurations, this would be 0.5
8(ii)	1	10	Left	Yes!	Relative population of configuration 2
8(iii)	1	10	Left	Yes!	Relative population of configuration 3	Omit line if there are only two configurations
9	1	10	Left	Yes!	Relaxation time in seconds	T2. This is 1/(π * (peak width at half height)) for a single transition peak not broadened by the exchange. If there is no such peak in the observed spectrum, guess based on spectra of static systems measured under similar conditions
10(i)	1	10	Left	Yes!	Rate constant in s^-1	Rate constant for going from config. 1 to config. 2, in first set
10(ii)	1	10	Left	Yes!	Rate constant in s^-1	Rate constant for going from config. 1 to config. 3, in first set. Omit line if there are only two configurations
10(iii)	1	10	Left	Yes!	Rate constant in s^-1	Rate constant for going from config. 2 to config. 3, in first set. Omit line if there are only two configurations
10(i)a, 10(ii)a etc.	1	10	Left	Yes!	Rate constant in s^-1	Repeat the (set of) type 10 lines above, for the second (set of) rate constant(s), if more than one (set) has been requested at the beginning of the type 7 line
10(i)b, 10(i)b etc.						If there are two configurations, the total number of type 10 lines is No. of rate constants given at the beginning of the type 7 line. If there are three configurations, the total number of type 10 lines is three times the number of sets of rate constants