Open the list of Families available in the database and select one. Then, if there is any Type available, another list will appear. Once a particular Type is selected, all the Groups belonging to it will appear.
Example of family: Terpenoids
Example of type: Triterpenoids
Example of group: Oleananes
You can also enter the complete molecular formula by adding a number after each atomic symbol or the atomic symbols only followed by an asterisk in each of its sections
Write the common or semi-systematic name in the appropriate section. You can also write it with asterisks (*) or question marks (?) in any part of the name. An asterisk represents any number of characters, while the question mark only one.
You can fill in or leave blank as many sections as desired
Draw the structure and substructure you wish to find in the MOLECULE EDITOR.
To speed up the generation of structures an upper palette with associations already defined is available. Press any of them and then click on the inside of the editor.
In the left palette there is a mark to indicate the stereochemistry and the atomic symbols. This is initially continuous; if you wish to indicate a striped one draw initially a continuous one and after click on it. It will change alternately from one type to another
The atomic symbols represented on the programme are the most frequent. X is a catch-all category. It initially represents a hydrogen, but if you wish to change it by any other symbol, you can specify so in its dialog box.
The search can be restricted to one family, type or group of natural products.
It is possible to search by chemical shift specifying the type of carbon.
Search tolerance is by default 1; but a different one can be established for each of the introduced carbons.
To introduce additional shifts, press the button "new shift" and another empty line will appear. A new one will come out when the previous has been completed. This can be repeated as many times as chemical shifts you wish to introduce.
Additionally, the search can be restricted, if you know the type of problem compound, by specifying its family, type or group.
With this search, you will find those compounds with a maximum number of shifts similar to those searched by the specified tolerance. For example, you could add 20 chemical shifts and obtain compounds which have 12 shifts in common with those established in the search.
All the compounds found in the search will be sorted by the similarity of their shifts with those introduced in the search.
Carbon type:CH, Shift:75, Tolerance:3
Carbon type:CH2, Shift:101, Tolerance:4
Carbon type:CH3, Shift:26, Tolerance:1
You could find compounds with a CH at 72 ppm and a CH3 at 25 ppm and without CH2 between 97-105 ppm
It is possible to search compounds by the number they have of different types of Carbon (C, CH, CH2, CH3). In the search, you can also establish the number of carbons connected to Oxigens and Nitrogens, together with the number of heteroatoms.
A specific number for each type of atom or an interval can also be specified, as it has a bar system with two markers to establish the interval in a quick and easy way.
The search is very easy to configure. You only need to press the "Configure" button. A new window will appear. Insert the number of bars to define the type of atoms to be searched and another window will come up. This one is to establish the carbon type and the heteroatoms by which the search has to be carried out. This option can be established only for the skeleton of the compound or for the whole structure of the compound.The available atom types are:
SKELETON: C*, CH*, CH2*, CH3*, C-O*, CH-O*, CH2-O* y CH3-O*
WHOLE STRUCTURE: C, CH, CH2, CH3, C-O, CH-O, CH2-O, CH3-O, Br, Cl, F, H, I, N, O, P and S
Atom type: C* Interval: 0-5
Atom type: CH* Interval: 4-4
When you press the "search" button in any search, a new page with the search history comes into view. Each search will be defined in a line and will be sorted in a correlative way. In each of them, the search number is specified, together with the number of compounds found and the criterion followed. There is a dialog box for its deletion and another one for its activation in order to carry out further Boolean searches with "OR" or "AND".Those structures found in each search can be consulted by pressing the button "see".
When you press the button "View" in the history screen, the compound structures obtained from the searches are displayed. Under each of the structures you will see two links to access the properties of the compound and to represent its SPECTRUM graphically.
On the top of the window you can find the following buttons:
Help: Access this help system
Analysis tool: Access a visual analysis tool.
Refine Search: Go back to the last search page.
"δ(ppm)in table": Shows a table with the data of the chemical shifts of the selected compound carbons.
"δ(ppm) in structures": Shows the chemical shifts over every carbon atom in the structure.
MENU BUTTONS:
: Shows the SMILES of structure
CLR: deletes the editor
NEW: Creation of a new molecule may be started only after clicking this button
DEL: Deletes the selected element.
123: To mark an atom press the 123 button and then the atom
D-R: deletes functional groups - choose this option and then click on the bond connecting the group with the main skeleton.
QRY: button (if enabled in the param tag) allows easy specification of atomic queries for substructure searches:
To specify several types of atoms in any position.
To specify the type of connections, if they comprise of a ring.
This way the searches are harnessed considerably
+/-: Atomic charges may be changed by this button. Editor enables modification of charges only in "reasonable" cases
UDO: Undo last editing step.
JME: Shows the author and version of applet.
FORMS:
These buttons allow to create forms standard already defined
BONDS:
These buttonss allow to choose the different types of connections that form the substructure
ATOMS:
These buttons represent the different atoms that can be chosen to create the substructure.
They are the types of atom more common in organic chemistry, but if you need some that is not in the list and knows its SMILES can create pressing it in control "X". Only you must introduce the SMILES in the text area
