ACD/I-Lab

Basic PhysChem Properties Module Facts

The module performs a quick check on several useful properties characterizing the compound of interest in general. The results cover physicochemical properties (e.g. index of refraction, surface tension, etc.), Lipinski-type properties (MW, TPSA, numbers of hydrogen bond donors and acceptors, etc.) as well as Mass Spec related calculations for various possible molecular ions (22 calculated values are provided in total for each structure).

1: Tree View

A list presenting all available ACD/I-Lab modules. Use the "+/-" nodes to expand/collapse corresponding sections of the list.

2: Structure Pane

The Structure Pane displays a 2-D representation of the molecule used for calculation along with the five buttons representing the most common chemical structure manipulation actions. Click here to see detailed explanation of the possibilities that these tools provide for a user.

3: Results Pane

As its name implies this pane displays the values predicted by a corresponding module as well as the results of any supporting calculations. Please return to the main browser window displaying the ACD/I-Lab interface and hover with mouse pointer over any objects (text, tables, graphs, buttons, etc.) in this area to see hints with further descriptions and explanations.

Structure Pane with structure manipulation buttons

Examples of color maps (top) and substructure highlights (bottom)

• Opens current molecule in the ChemSketch window for editing.
• Allows to search and display the structure from the Dictionary with >36,000 available names for >8,900 chemical substances.
• Opens a file containing a molecular structure. ACD/I-Lab supports all versions of MDL *.mol files, as well as ISIS Draw *.skc, ChemDraw *.cdx, ACD/ChemSketch *.sk2 formats.
• Pastes an input structure from the clipboard to the Structure Pane. Also, if you are pasting a SMILES string from the clipboard, you can save a step by clicking directly on this button to display the 2-D structure.
• Type or paste SMILES notation string in this field. The string will automatically be converted to 2-D structure.

NOTE: Calculations are performed automatically after any change to the the input structure.

In some of the modules additional information can be provided within the Structure Pane in the form of color-coded maps and sub-structure highlights (see Illustration for examples). The fragmental contribution maps illustrate the role of individual atoms and fragments in case of the property of interest in a color-coded manner: red color indicates a positive contribution to the final predicted value whereas green color means the atom/fragment has a negative coefficient in the regression equation. Yellow substructure highlights usually accompany the knowledge based "expert-like" models in which the reasoning for distinguishing that particular part of the structure is provided in the Results pane.

• Module View

  The default view of the program which is always automatically loaded after logging in. It provides access to all of the predictive, naming, and database modules available within ACD/I-Lab 2.0.

• History View

  The History View enables the user to browse through the list of actions performed in the recent past. Each compound structure, submitted to ACD/I-Lab 2.0 by the user, or looked-up in its internal databases is stored here, and corresponding results (module predictions, generated names, database entry info, etc.), once originally obtained, can be reviewed later without additional charges. The limit for the entries kept in the ACD/I-Lab 2.0 history is two weeks time or 1000 records per user, whichever runs out first.

• Settings

  Provides the means to customize several basic options and settings, e.g., perform a password change, select the decimal separator, turn hints on or off, etc.

• Help

  Opens a pop-up window containing dedicated context help for the currently selected module or program view (e.g., History View). A typical help provides a brief explanation of the program window panes visible within particular module/view together with their main functions, and a compilation of the most relevant facts associated with the module/view in question. The latter content varies depending on the type of the description subject and can contain information about model development (training/validation set sizes, etc.), validation statistics, limitations, etc. General help pages on module independent topics (e.g., How to...?) can also be accessed via this pop-up window.

• Buy Credits

  Provides a quick and convenient way for an account holder himself to replenish credits used to pay for the ACD/I-Lab 2.0 usage (i.e., eliminating the need to contact ACD/Labs sales department, and all consequent procedures). Currently the only accepted payment method is via PayPal^TM.

• How to submit a compound structure to ACD/I-Lab 2.0?

  ACD/I-Lab 2.0 provides a variety of tools for the structural information input. The easiest way is to look-up the compound name in the internal Dictionary. The user can also switch to an external chemical structure drawing program to compose a compound structure from scratch and then copy/paste it. Alternatively he can use a built-in Structure Editor application. ACD/I-Lab 2.0 accepts SMILES strings and the most popular molecular structure file formats as well. All of the aforementioned functions are invoked by using dedicated buttons in the Structure Pane. Please have a look at a corresponding tab in this help window for more information on this topic.

• How to purchase credits for additional calculations?

  Buy Credits link in the top toolbar provides the easiest and fastest way to prolong your usage of ACD/I-Lab 2.0 by purchasing preset credit packages via PayPal^TM. Please contact sales@acdlabs.com if you have further questions or wish to discuss other options, e.g., a smaller/larger package, a site license, or similar.

• How to change my account password?
  1. Click on Your <Username> in the top right corner of the ACD/I-Lab window to open a menu containing Your account configuration options
  2. Click on the change password link
  3. In appropriate dialog boxes provide Your existing password, enter and confirm a new one, and press OK

• How to turn hints on or off?

  Hints are enabled by default, however there is a dedicated check-box to turn them off, or re-activate them after doing so. It is located in the Settings pop-up window accessible from the Top Toolbar

• How to turn the reminder about applicable charges upon module switch or compound input change on or off?

  This reminder is activated by default at the beginning and can be disabled at any time it is displayed by clicking on an appropriate check-box. There is also a dedicated check-box to turn it back on at any point in the future. It is located in the Settings pop-up window accessible from the Top Toolbar

• How to share the results I have obtained with my colleagues?

  There is a dedicated Download Report button within each of the modules in ACD/I-Lab 2.0. However, please do not forget, that ACD/I-Lab 2.0 is a web based application and an internet browser is used as a primary means of accessing it, which automatically enables the user to select and grab almost any text and pictures directly from the screen by simply using mouse pointer and right-click context menu or Ctrl+C command.

1: Inorganic compounds

Properties will NOT be calculated for inorganic compounds. Inorganic compound – a compound with no carbon atoms in it.

2: Metalo-organic compounds

Properties will NOT be calculated for metallo-organic compounds. Metallo-organic compound – a compound with a covalent bond between metal and non-metal atoms. All elements are considered metals except: H, B, C, N, O, F, Si, P, S, Cl, Ge, Ar, Se, Br, Te, I, Sn, Sb, Bi.

The following are examples of compounds that will be treated as metallo-organic (no properties will be calculated for them):

NOTE:
Salts , e.g. sodium acetate, will be calculated if it is drawn in the ionic form as shown below.

3: Salts, hydrates and mixtures

3.1 Salts

For all of the modules salts are converted into the neutral form (where possible) before any calculation. The rationale is that in the absolute majority of the properties calculated by the corresponding software products happens in buffer conditions, i.e. it doesn’t matter whether compound is administered as free acid/base or salt – it will have the same proportion of ionized and unionized forms, which depends solely on ionization properties of free acid/base and pH of the environment.

The following compounds will produce the same predictions as they are converted to the “free” ethyl diamine first.

3.2 Hydrates

Water molecules are removed from non-covalent hydrates before any prediction.

3.3 Mixtures

For mixtures, only the biggest organic component of the mixture will be used for the prediction.

This includes salts with organic counter ions, as shown below.

NOTE: For a mixture, each compound is checked separately to see if it is inorganic or metallo-organic.

4: Stereoisomers

Stereoisomer centers of any kind (R/S, D/L, cis/trans, etc.) are NOT considered in the predictions. All stereoisomers will produce the same prediction.

5: Proteins

Properties will be calculated for proteins and polypeptides. However we recommend that the MW not surpass 2000 Daltons. Since the internal training libraries do contain only some small proteins and polypeptides, any conformational effects will NOT be taken into account.

6: Polymers

Properties will be calculated for polymers when they are represented in a conventional form as any other organic compound. However, since the internal training libraries do not contain any polymers, we recommend treating such predictions with caution as they are highly likely to be unreliable due to excessive extrapolation.

Polymer structures drawn using brackets to indicate repeating motifs will NOT be recognized as polymers and the brackets will be omitted when pasting such molecules into the program.

7: High Molecular Weight Compounds

Properties will be calculated for high MW compounds. We recommend that the MW not surpass 2000 Daltons (even more conservative threshold would be 1500 Daltons) as conformational and supramolecular effects will NOT be taken into account. Calculation time will increase with larger compounds.