NMR data coding for LSD may initially seem awkward to beginners. The following paragraphs are intended to help them. A useful documentation source may be found in the examples in the Data folder. A data file for LSD is a text file that contains commands, each being followed by one or more parameters. The most useful commands will be first introduced, but a thorough command set description is given in the Data file structure paragraph. A text-type user interface may seem old-fashioned, but it is sometimes easier to modify a text than to navigate though menus and sub-menus whose function is not always totally explicit.
The first step in the elucidation of an unknown molecular structure is to find its elemental formula and to determine the status of all non-hydrogen atoms. The status consists of an index, a chemical symbol, a hybridization state (sp2 or sp3) and a number of attached hydrogen atoms. Defining the status of all atoms is a strong constraint for the user. The status of heteroatoms is not always easy to define, mainly when more than one of their type is present. Even for carbon atoms, the chemical shift value is not sufficient to non-ambiguously deduce the hydridization state. More than a single data set must then be written and tested. More flexibility to status definition will be given in the near future, but for the moment the user has to cope with the present capabilities of LSD.
Atom indexing may be arbitrary.
A recommended procedure is the indexing of carbons from 1 in decreasing
order of their 13C chemical shift value.
Heteroatoms recieve the following numbers as indexes.
Carbon indexes are then reported in the 1D projections around the
2D HMQC and HMBC spectra.
The command that defines an atom status is MULT
.
Uppercase letters need to be uppercase.
MULT
is followed by the atom index, 2 or 3 for
the hydridization state (sp2 or sp3) and
the multiplicity (number of bound hydrogen atoms).
The command MULT 1 C 2 0
says that atom 1 is a
quaternary (0
) sp2 (2
) carbon (C
).
The data file contains as many MULT
lines as non-hydrogen
atoms in the molecule.
The following step is indexing the hydrogen atoms.
Again, the indexes may be given arbitrarily, but it is handy to
give the same index to the proton and to the carbon atom attached to it.
The HMQC spectrum matches carbon and proton indexation schemes.
Two inequivalent hydrogen atoms within a methylene group get the same index.
The hydrogen indexes are then copied in the projections around the 2D
COSY and HMBC spectra.
A correlation in a 2D spectrum is characterized by the type of spectrum,
the index of the atom in dimension 1 (carbon index in HMQC and HMBC spectra),
and the index of the atom in dimension 2 (always a hydrogen atom index).
The command HMQC 4 4
indicates that carbon 4 and hydrogen 4
are bound together.
Commands HMBC
and COSY
are coded in the same way.
Any easily deduced bond must be given to LSD through a BOND
command.
It takes the indexes of the bound atoms as parameters.
If carbon 1 is that of a keto group and if there is an sp2 oxygen 22,
the command BOND 1 22
establishes the bond between atoms 1 and 22.
Unless specified, the order of the commands within a data file has no importance.
All command files must have EXIT
as the last command.
Apart from purely NMR derived commands, other commands are needed for
execution control.
One should prefer to group them at the beginning of the data file.
The most useful one is DISP 1
.
It makes LSD produce solutions in a format suitable for molecular drawing
by the outlsd program.
In a data file, one first finds DISP 1
, then MULT
,
HMQC
, COSY
, HMBC
,
BOND
and EXIT
commands.
This is the skeleton for basic LSD data files.
A less trivial part in the writing of LSD data files is the definition
of atom properties and of the associated lists.
An atom property (PROP
command) indicates for an atom
or for all atoms in a list the exact number of neighbors (1 or more) that must
be members of another atom list.
The number 0 means "all".
A given atom may have only one single property statement.
For example, the chemical shift of carbon atoms indexed 8, 9 and 10 is about
15 ppm.
The hydrogen atoms indexed 8, 9 and 10 are those of methyl groups
appearing at about 1 ppm as singlets.
Carbons 8, 9 and 10 are most probably bound only to quaternary carbons.
You need to build two lists in order to code this constraint with LSD.
The first list contains the atoms 8, 9 and 10 while the second one contains
all the quaternary carbons.
An atom list is described by its index and its content.
The content is either explicitely defined (giving the index
of all atoms within the list) or using atom status.
It is also possible to combine lists according to the operations defined
in the set theory.
Back to the example, LIST L1 8 9 10
defines list 1 and puts atoms
8, 9 and 10 in it.
QUAT L2
defines list 2 and puts all quaternary carbons in it.
Once L1 and L2 are defined, the constraint on atoms 8, 9 and 10
is coded by the PROP L1 0 L2
command.
It could have also been possible to write PROP L1 1 L2
, because
a methyl group carbon always has a single neighbor.
List and property definition commands are treated in the order
they are written in the data file.
Changing the order can change the meaning.
A common temptation for beginners is spectra over-interpretation, meaning that non-significant information is introduced. Inconsistent or wrong data leads LSD to fail, producing a message that indicates which is the deepest analysis level reached (the much hated "max stack level: " message). Introducing nJ COSY or HMBC correlations with n greater than 3 also leads LSD to fail. In order to avoid this unpleasant situation, the weakest COSY and HMBC correlations should be first written as comments, by putting a semicolon at the beginning of the corresponding commands. If the number of found solutions is too big, it's time to remove semicolons to impose more property or correlation constraints to the problem.
This brief overview of LSD commands will allow users to be more confident with the writing of data files. However, reading of Data file structure is a mandatory step in the learning of the LSD command language.
myprompt$ cp Data/pinene .
myprompt$ lsd pinene
where
myprompt$
is the prompt given by the computer.
LSD writes that 1 solution is found.
A file pinene.sol is created, containing atom connectivity information.
A coordinate file pinene.coo can be then generated:
myprompt$ outlsd 6 < pinene.sol > pinene.coo
The outlsd program creates 2D coordinates from connectivities.
The result is viewed using a Postscript® previewer.
Postscript drawings are first produced with:
myprompt$ genpos < pinene.coo > pinene.ps
and displayed on screen using:
myprompt$ xpsview pinene.ps
if xpsview is the currently available Postscript display program.
Remark: The file extensions .sol .coo .mol are not imposed but
it is good practice to use always the same conventions.
myprompt$ solve pinene
does the whole job in one shot: structure resolution, creation and display of the
structure drawings.
It is generally not a good idea to proceed this way with a new data set.
However, this can be done once the data set
runs from the command line without any error
(see From data to structures).
wish
command
installed in order to run M_EDIT
(version 8.0 or later).
myprompt$ m_edit
launches m_edit.
The File menu allows to read and save files, and to exit from
the program.
The View menu is used to navigate forward and backward
through a set of structures within a file.
The supported file formats are .coo (the LSD-specific format)
and .mol.
Using m_edit is very intuitive: atoms are moved using the left mouse button.
There is no multiple selection mechanism available yet, sorry.
myprompt$ chklsd < pinene
If generic atoms X, Y or Z are used (see VALE
)
the molecular mass is correct only if comments
(see Data file structure) like:
;MASS X 19
are provided. In this example X stands for fluorine.
A command is always typed on a single line and
is made of a command mnemonic, generally followed by 1 to 4 parameters.
All parts of a command are separated by spaces.
Commands are case-sensitive.
The very last command in a data file must be EXIT
.
All command mnemonics are made of 4 alphanumeric characters.
Some of them end with space characters (^
), such as CH^^
.
Mnemonics are followed by parameters, separated by blanks.
The parameter types are described using
the following symbols:
C N O X Y Z
only.
S1
.
EXIT
command (the only one without any parameter).
MULT
I A I I: defines atom status.
C N O X Y Z
. X
, Y
and Z
is defined using the VALE
command.
MULT 1 C 2 0
.
Atom 1 is a quaternary (0
) sp2 (2
) carbon (C
).
VALE
A I: sets valence, if not already set.
VALE X 1
. This defines the valence of an halogen atom X.
BOND
I I: bond
HMQC
I I: heteronuclear correlation through 1 bond
HMQC 4 4
. Carbon 4 and hydrogen 4 are bound together.
COSY
I I: three bond COSY correlation
HMBC
V I: heteronuclear correlation through 2 or 3 bonds
HMBC (4 5) 8
. Carbon 4 or 5 correlates with hydrogen atom 8.
LIST
Ln S: defines a list of atoms
LIST L1 4 6 14
: The list L1 contains the atoms 4, 6 and 14.
PROP
B I Ln: environment of atoms
PROP L1 0 L2
. Each atom in L1 has all its neighbors in L2.
EXIT
: end of data file
CARB
: carbon atoms.
HETE
: non-carbon atoms.
SP3
: atoms with only single bonds (SP3^
, with a trailing space).
SP2
: atoms with exactly one double bond.
FULL
: the full atom list.
QUAT
: atoms bound to 0 hydrogen atom.
CH
: atoms bound to 1 hydrogen atom (CH^^
, with 2 trailing spaces).
CH2
: atoms bound to 2 hydrogen atoms.
CH3
: atoms bound to 3 hydrogen atoms.
CARB L5
. L5 is the list of all carbon atoms of the molecule.
GREQ
: atoms whose reference is greater than or egal to P2.
LEEQ
: atoms whose reference is smaller than or egal to P2.
GRTH
: atoms whose reference is strictly greater than P2.
GREQ
: atoms whose reference is strictly smaller than P2.
GREQ L1 10
. L1 is the list of all atom references from 10, 10 included.
UNIO
: P3 is the union of P1 and P2.
INTE
: P3 is the intersection of P1 and P2.
DIFF
: P3 contains the atoms in P1 not belonging to P2.
UNIO L1 10 L2
. L2 contains the atoms in L1 and 10.
ENTR
I: lists atoms state before problem solving.
HIST
I: lists the resolution path of the solutions
DISP
I: output format
VERB
I: verbosity
PART
I: output of uncomplete solutions
STEP
I: single step operation
VERB 2
.
The user is prompted for the action to be taken.
WORK
I: search solutions
MLEV
I: stop analysis at step number P1
DUPL
I: elimination of duplicate solutions
SUBS
I: substructure validation
SSTR
Sn A V V: sub-atom status
2
(sp2) or 3
(sp3)
or (2 3)
(both).
SSTR S1 C (2 3) (0 1 2)
. Atom 1 of the substructure is a carbon,
either sp2 or sp3, with possibly 0, 1 or 2 hydrogen atoms.
LINK
Sn Sn : bond within the substructure.
LINK S1 S2
. Sub-atoms 1 and 2 are chemically bound.
ASGN
Sn I : assignment of a sub-atom.
ASGN S3 5
. Sub-atom 3 is identified as being atom 5.
DISP 1
.
myprompt$ outlsd 7 < pinene.sol > pinene.mol
Depending on n, the result contains
myprompt$ genpos < pinene.coo > pinene.ps
The resulting file can be opened by Postscript previewers or be sent to Postscript printers.