User Guide

Overall:

There are basically two ways to perform the searching with iBond: Searching and Browsing mode (Compound Classification). With the Browsing mode, the result hits will be listed according to the Molecular Formula by default, though which will not be shown on the web pages.

Name searching: all the chemical compounds were named according to the IUPAC nomenclature, which were generated by Chemoffice automatically. However, some of important compounds, such as drugs, natural products, aminoacids, etc. both the scientific and common names can be used for the searching purpose.

Formula Searching: The Hill system was used here for the appearance order of the search hits: the number of carbon atoms in a molecule is indicated first, the number of hydrogen atoms next, and then the number of all other chemical elements subsequently, in alphabetical order of the chemical symbols. When the formula contains no carbon, all the elements, including hydrogen, are listed alphabetically. NOTE: The formula must be inputted according to the Hill system introduced above, otherwise no desired hits will be shown.

Structure Searching: The structure of compound of interest can be drawn or edited with “molecule editor” plugin. Structure searching includes Similarity Search, Substructure search and Wild card character, etc. (Please see examples listed below)

We strongly recommend users to rationally combine the name, formula and Structure searching method together to obtain the desired results.

 Examples:

User can perform similarity and substructure search through the molecule editor. The structure to search can be entered at in form of SMILES or click right button to “Paste MOL or SDF” or draw a molecular substructure directly. Then, user can chose the search type, similarity search or substructure search.

                                                                      

      1. Similarity Search:

        The similarity is defined as following: in order to compare the similarity between molecules computationally, some level of simplification or abstraction is required. The abstraction used in iBonD is molecular fingerprints, which turn the molecules into a sequence of bits that can then be easily compared. Then, the similarity between two molecules (bit codes) is assessed by Tanimoto index, ranging from 0 to 1 (where 1 is the highest similarity), details seeing website: https://docs.chemaxon.com/display/docs/Extended+Connectivity+Fingerprint+ECFP. When “Similarity Search” was chosen as the searching method, users can fill in a “similarity parameter” (0.5 to 1, default value is 1, searching results will be 100 % match the structure drawn in the paint of molecule editor) in the blank box.

      2. Substructure search:

        When “Substructure Search” was chosen as the searching method, the searching result will show all the compounds which contain the structure drawn in the paint of molecule editor.

         

      3. Wild card character:

        The advanced user can use wildcard character function as the searching method, it will provide more parameters to control the accuracy of the searching.

      4. Result Page:

        The reference for the corresponding BDE or pKa will appear when users simply move the mouse pointer on the data without clicking, whereas the fulltext downloading page (if available) will be showed by clicking. The format of the reference is ACS style by default.

      5. Filter Function:

        This function can be utilised to narrow down the number of results obtained from last search, currently user can use pKa range or specific solvent to do so.

      6. Compound Classification:

        Compound Classification lists families of compounds which may be homologues in nature, clicking the individual family bar will give all the bond energy parameters which are shown according to the molecular weight.