SpecSurf XS Illustrated Guide
SpecSurf XS is our new, easy-to-use, web browser client for accessing
SpecInfo. SpecSurf XS is a Java applet and can be used for accessing SpecInfo
on the Internet as well as an inhouse installation. You can search and
display C-NMR, H-NMR, Hetero-NMR, IR and mass spectra together with structures
and additional information. NMR shifts for the most important nuclei can
be predicted by using two different algorithms.
SpecSurf XS can be regarded as a Web page inside your browser. Therefore
a click on your browser's "Back" icon will bring you back to the Login
Page. Please do not use the browser's ”Reload” icon. In case of performance
problems, start from the Login Page and "reload" SpecSurf XS.
You can run SpecSurf XS in its own window by using the Float/All menu
option. The Float menu also allows the display of all other objects in
separate windows.
Spectrum Search
Search Result
Select
Databases
Structure
and Substructure Search
Structure Editor
Search
for Name, Formula, MW Ranges...
NMR Shift Prediction
and Estimation
Spectrum Search
13C-NMR, Hetero-NMR and mass spectra can be searched using shift information
or peak lists, 1H-NMR and IR spectra as full spectra. Shift or peak lists
can also be entered manually by choosing Edit/Peaklist....
To import a spectrum, go to File/Import/JCAMP. Please use only JCAMP-DX
files for import. JCAMP-DX is a standard exchange format which is supported
by most instrument software. If the import of some of your experimental
spectra in JCAMP-DX format is not possible, please feel free to supply
us with an example file so that we can adjust our import routine. Future
releases of SpecSurf will contain direct import of native Instrument formats.
Please contact Chemical Concepts for a list of these formats.
A new window will appear which offers you the opportunity to either
type in the location and the name of the file. You can also choose “Browse”
to select a file to be imported. After the selection of the file, please
click on “Import”.
When the import is completed, please close the window.
In addition to JCAMP-DX files peaklists can be imported as x,y table:
no text is allowed, remove header and footer lines.
only x,y pairs are allowed (not x, y1, y2,..) but each line can contain more than one pair (see example below).
the x and y values must be separated by comma (,), semicolon (;), tabs or space.
After the import of the peaktable please select the method and click
on "O.K.".
The Peaklist Editor allows you to type in a peaklist. Please
enter the multiplicities with a character (s, d, t, q). If you do not enter
this information, the intensity is automatically set to 1 and the multiplicity
to u (unknown).
To start the spectrum similarity search, choose Search/Spectrum.
Search Result
The upper spectrum is your query spectrum, the lower one the first hit.
The hitlist gives you an overview of the retrieved hits.
Floated Hitlist with resized columns
It is possible that a compound appears in more than one hitlist entry,
like the entries 5 and 6 above. In this case, spectra of the compound were
measured in two different solvents. The difference in the measurement conditions
leads to different spectra, and further different quality factors.
Select Databases
As a default, all libraries are preselected.
A search on all spectral libraries can result in multiple hit entries
for one compound, if, for example, it is present in IR, NMR as well
as in MS databases. If you are just interested in one spectroscopic method,
you can filter the hits by preselecting the databases you are interested
in (Settings/Databases/Searches) by Shift + click or Ctrl + click.
The databases of SpecInfo on the Internet are listed below. More detailed
information is displayed by double-clicking on an entry. In total, there
are more than 660,000 spectra available.
Other features of this window:
-Maximum Number of Hits
You can change the maximum number of hits which are retrieved from
SpecInfo. If you increase the number of hits retrieved (default 20 hits),
the retrieval time will also increase.
-Minimum Hit Quality
You can define a minimum hit quality between 0 and 1000 where zero
indicates “No similarity” and 1000 represents an “Exact Match” for
the item searched. The default value of 800 is recommended.
Your changes are immediately active. You can either keep the window
open or click on the Close button to return to the main window.
Structure and Substructure Search
To import a structure, select File/Import/MDL/Molfile. To draw a structure,
open the structure editor in Edit/Structure.
The imported structure is displayed in the query field. If you want
to make changes just open the structure editor, the query structure is
automatically transferred. Another way to open the structure editor is
by double clicking on the query structure.
You can search for an identical structure or a substructure.
To perform a substructure search, please indicate the position of a substitution
by a question mark ("?"). Multiple question marks and multiple substructures
are allowed for a substructure search. If the structure contains
no question mark, an exact match search is performed.
Structure Editor
The default drawing mode ( 
compass) offers the easiest way to draw a structure:
Press the left mouse button and move the pointer to a compass dot to
create a new bond or a chain by dragging the pointer outside the compass
ring.
Moving the pointer on an atom or bond activates it.
Activate a bond and click on it to change the bond order or type a number
between 3 and 9 to change the respective bond into a 3- to 9-membered ring.
Activate a bond and type u(p) or d(own).
A click inside of a six-membered ring makes it aromatic, or vice versa
.
Activate an atom and change the type by typing the element symbol (ie."n"
for nitrogen). Add charges stepwise by typing "+" or "-". Typing "1" or
"2" generates a new bond. Add rings by typing "3 ... 9" when an atom
is activated.
For all other functions, please refer to the online help.
Some Drawing conventions:
Unlike all other atoms, hydrogen atoms do not need to be drawn explicitly.
SpecInfo uses aromatic bonds for six-membered rings, as found in benzene
or naphthalene.
When you draw alternating single and double bonds, they will be automatically
transformed into an aromatic ring.
Please do not use charges in non-ionic compounds. Nitro groups must be
drawn using pentavalent nitrogen.
Five- membered hetereocycles, like thiophene, are drawn with two double
bonds.
Detailed information and further examples
for the drawing conventions.
Search for Name, Formula, MW Ranges ...
Choose Search/Note Fields... and select a property. After entering the
query string, please click on Start to initiate the search.
Query string conventions:
Compound name: Enter a name or part of a name with asterisks
(*) as wild cards.
MW: Enter the molecular weight range, e.g. 120 to 121. Please
do not use any other characters instead of "to".
Formula: Type the formula in the order C, H, hetero-atoms with
no spaces (atom symbols are case sensitive). Additional elements can be
specifically excluded by entering a zero as element count. An asterisk
can be used for further elements. E.g. C3H6*0 will find the exact formula
C3H6 without any other elements whereas C3H6*0-2 will find the formula
including all combinations of zero, one or two additional elements.
Searches for Compound Name, MW and Formula are not currently possible
on the Hummel IR collection "Defined Polymers".
NMR Shift Prediction and Estimation
The structure used for a prediction can either be drawn with the structure
editor (Edit/Structure) or imported as a Molfile (File/Import/MDL/Molfile).
Choose Predict/Database based/ and select a nucleus for a database based
prediction
or select Predict/Rule based/ for a rule based estimation.
Atoms are assigned to their NMR shifts.
Move the mouse pointer over a shift or an atom to get highlighted aassignment
information. The numerical ppm value is displayed below the spectrum.
Back to
Spectrum Search
Search Result
Select
Databases
Structure
and Substructure Search
Structure Editor
Search
for Name, Formula, MW Ranges...
NMR Shift Prediction
and Estimation
