ACD/PhysChem Suite*

*Formerly ACD/LogD Suite

What's New

Version 11.0 to 12.0

• Amalgamation of PhysChem predictors
  • The individual PhysChem predictor modules for logP, logD, solubility, pK_a, and boiling point have been combined into a single product: ACD/PhysChem Suite, which includes the full capabilities of the individual predictor modules
• Improved user training tools for all ACD/Labs PhysChem databases (all modules)
  • The System Training and Accuracy Extender tools have been refined in version 12 to improve their performance by improving the speed of importing, and reducing calculation times
• Updated QuickReport tool (all modules)
  • The QuickReport tool now has two calculation modes: automatic and manual calculation; eliminating the need to switch between ChemSketch module and Quick Report tool, and allowing the user to see how properties change as the structure is being drawn
• pK_a Module Enhancements
  • Display of relative abundance of ionized species
  • Improved pK_a prediction model

Download a PDF copy of the expanded details on What's New with ACD/PhysChem Suite, or contact your Account Manager or Distributor.

Version 10.0 to 11.0

Among the key new features of ACD/LogD Suite presented below, are:

• A model for prediction of logP
• Enhancements to the pK_a prediction model
• ACD/Quick Report

New Model for LogP Prediction

A generation model for prediction of logP is introduced which combines data for ~12,000 compounds from ACD/Labs' existing internal training set with new experimental data from >13,000 pharmaceutical lead compounds. Changes to the logP model impact logD since it is incorporated in the logD model.

NOTE: Both version 10 and 11 models for logD will be available for use in training and prediction.

Enhancements to pK_a Prediction Model

Version 11 of LogD Suite is further improved due to enhancements to the pK_a model which helps describe the pH dependence of this property. The enhanced pK_a model boasts the addition of >2,000 pharmaceutical lead compounds to the internal database, and over 600 new and revised Hammett equations.

ACD/Quick Report

A PhysChem interface has been developed for version 11 that offers a snapshot of the molecular property profile of individual molecules through customizable, color-coded histograms. Quick Report includes all descriptors available to the user from any ACD/Labs commercial PhysChem product.

Changes to training:

• The availability of both version 10 and 11 models for training, to ease the transition to the new logD model
• The ability to use multiple accuracy extender training files enabling users to combine and extend training across projects, and extend the applicability of training in different modules
• Support for import of SMILES into PhysChem Accuracy Extender

Other improvements to ACD/LogD Suite include:

• Push data directly from Table View to Microsoft Excel at the click of a button
• Addition of 8 descriptors to the PhysChem History which depict the molecular composition of molecules
• Automatically remove explicit hydrogen atoms from structures on import of a file
• Search specific text in both user data and/or notes in database records

Version 9.0 to 10.0

Among the key features of ACD/LogD Suite presented below are:

• Enhancement of pK_a, solubility, and logD algorithms
• Consistent atom numbering between User files and the PhysChem History Window

Enhancement of the algorithms:
Version 10.0 development has addressed limitations of the fragment-breaking algorithm in pK_a, solubility, and logD to allow the solubility profiles and these physical properties to be calculated for larger molecules and more complex structures (such as fused ring-systems). Fragmentation of molecules has now been focused around reaction centers (significant in the calculation of pK_a, upon which solubility and logD values can rely heavily) to minimize the number of fragments generated for a given system.

Atom Numbering Consistency
Manually assigned atom numbering in ACD/ChemSketch, or numbering schemes originating from SDfiles or molfiles, will be retained in the PhysChem History and PhysChem Databases after calculation of all PhysChem values. This functionality is particularly significant for pK_a since calculated values will now be assigned to atoms and reaction centers by means of your own numbering system. This consistency will also extend to data exported for further evaluation or manipulation.

Other improvements specific to the pK_a module include:

More detailed reporting of pK_a calculation to allow facile interpretation of results

• Enhancements to fragment affiliation with pK_a calculation details—improvements have been made to the affiliation (by highlighting) of the calculation details with heteroatoms in certain aromatic systems so that visual association of incremental ΔpK_a values, sigma values, and other calculation details is more complete for a wider range of compounds.
• Reporting of sigma value origin—to give expert users more information about the derivation of ΔpK_a values, the origin of substituent sigma values are reported as experimental or calculated in the Details window, with references to experimental values provided for further investigation.

Ease of use enhancements to pK_a System Training
Enhancements made to pK_a System Training in version 10.0 will benefit users that optimize our pK_a model to increase the accuracy of prediction for novel and proprietary compounds by incorporation of experimental data.

• Flexibility in the application of User databases—you can now choose to simultaneously use fragments from both the user database (pkauser.dat) and the internal calculation database for calculation of pK_a values. The default option to apply fragment increments from the User database first is also available.
• Resize dialog boxes in pK_a system training—the ability to resize the Add pK_a Value and Edit pK_a Value dialog boxes in the Database window will particularly impact users working with very large molecules by giving them a clearer view of the structure and allowing easier identification of dissociating atoms and reaction centers.

Users of ACD/LogD Sol Suite should also review What's New in ACD/Solubility DB for details on expansion of the internal reference database and enhancement of the solubility algorithm to allow for calculation of larger/more complex molecules.

Version 8.0 to 9.0

Among the key new features of ACD/LogD Suite presented below, are:

• Improvements in pK_a prediction that impacts computation of logD and ionic forms.
• Expanded training options with experimental data.
• Greatly improved database handling.

Users of ACD/LogD Sol Suite should also review the What's New document for ACD/Solubility DB for additional details on new solubility algorithm and advanced training options with experimental solubility data.

I. Prediction Modules

Higher accuracy of apparent EXACT pK_a calculation for complex compounds with several ionization centers:

Recent changes in the pK_a calculation methodology has resulted in improved accuracy of pK_a calculations for molecules with 3 or more ionization centers. The improvement is especially notable for compounds with ambiguous dissociation chains and close values of pK_a microconstants for separate ionization centers.

The new unique methodology addresses the challenges of the compounds with close pK_a microconstants, as well as compounds containing a large number of ionization centers where the determination of a clear dissociated sequence might be difficult.

New pK_a algorithm results in the improved accuracy of logD pH profiles and a graph outlining the distribution of ionic forms:

The accurate computation of the ionic forms of a compound in an aqueous solution leads to a more precise prediction of the logD graph, seeing as this curve is based on the abundance and properties of individual ionic forms.

II. Database Modules

New database interface and structure:

To eliminate the need for users to switch between different databases of physicochemical properties, a single unified database is introduced in version 9.0. The new pooled database enhances software training capabilities and simplifies data handling in multi-product installations such as ACD/LogD Suite.

Click image to magnify

The new databasing interface also offers:

• New training management options that allow users to easily include and exclude data in the algorithm training.
   
• Further integration between different ACD/PhysChem desktop programs. In the case of multi-product desktop installation of ACD/PhysChem software (such as ACD/LogD Suite, or any combination of individual PhysChem products), users can easily switch from the new unified database window to any other open ACD/PhysChem program. Open modules are highlighted on the menu bar:

• Augmented template reporting now allows customers to create reports containing data from the Database window, and now customize the reports according to a user-defined template.
   
• Ability to create graphs to visualize the data values present in your database.
   
• Ability to add results from the user's own computational tools to ACD/Labs PhysChem software through adding user-defined properties to ACD/Labs databases.
   
• Ability to add formulas and scripts to the new "calculated fields" to simplify data analysis. This new feature allows users to create new database fields and assign formulas to automatically calculate new values from the values available in other fields of the record. Calculated fields can be used to determine user-defined values, and control records for data presence and quality. Script options include both mathematical and logical operations. Calculated fields can be searched separately or together with other user data.

III. ACD/PhysChem Accuracy Extender

ACD/LogP Accuracy Extender available in the earlier versions has been renamed to ACD/PhysChem Accuracy Extender, and is currently offered in two Modules: LogP and Solubility. New Solubility module expands the capabilities of the algorithm training to include experimental solubility values. New ACD/PhysChem Accuracy Extender also features faster regression calculations and improved interface.

Version 7.0 to 8.0

ACD/LogD Suite underwent significant changes with the introduction of version 8.0, both in the logD module and other incorporated products. Among the most profound new features are the substantial increase in calculation speed, added Assisted Multi-Generation (AMG) capability, and the ability to calculate and review all of the predicted properties at a glance.

Considerably improved speed of calculation:

• The calculations are now seven or more times faster! Numerous programming changes to all of the products, and especially to pK_a predictor, resulted in much shorter calculation times - especially important for batch and AMG predictions.

New AMG capability: multiple properties, multiple compounds, on the desktop:

• For small libraries and other data sets with fewer than 999 structures, you can now import and process SDfiles using the standalone desktop ACD/LogD Suite package. Calculated properties can be exported back to the SDfile, with all of the original SDfile data intact, or reported in accordance with the customizable ACD/ChemSketch templates. You can also review all of the calculation protocols one-by-one through the usual desktop ACD/Labs interface. Essential for library design.
• For ACD/LogD Suite customers, it is now possible to calculate all properties for that compound at once, view them all on the screen (new History Window), and export them to an SDfile.

Support of quaternary ammonium salts.

Customized reports can be printed or saved as ACD/ChemSketch or Adobe PDF files.

Numerous new features and improvements are added to other product modules of ACD/LogD Suite such as calculation of Freely Rotatable Bonds (FRB) in ACD/LogP DB, and enhancements to database formats and search options in ACD/LogP DB and ACD/pK_a DB.

Unsurpassed system training abilities for pK_a predictions are implemented through NEW ACD/pK_a Accuracy Extender, to complement our logP expert customization option (ACD/LogP Accuracy Extender) added in version 7.0. Expert chemists can now add new Hammett equations for their novel chemical classes. These equations are automatically incorporated into algorithms of all ACD/Labs pK_a-dependent products to enhance prediction for all analogs from the new class.

Version 6.0 to 7.0

Consistent with our commitment to continually update and improve our software products according to our user's needs and requirements, we introduced a number of new features to version 7.0 of ACD/LogD software.

The new version allows you to:

• Export the LogD pH profile to ACD/Curve Manager. This new feature allows users to compare predicted curves to the experimental profiles, and to store predicted and experimental data in one structure-searchable database.
• Check and choose Tautomeric forms. Prior to prediction, the user can check the existence of tautomeric forms, and choose which structure to use for prediction. The option can be switched OFF and ON.
• Report your calculations:
  • Send a History file or a User Database record by e-mail from the toolbar menu.
  • Make reports at a click of a button. Select the data to send to the report and use the ACD/ChemSketch reporting tools to create a finished document.

Since ACD/LogD is only available as a part of ACD/LogD Suite, it is worth mentioning a number of new features in other physchem packages that are included into ACD/LogD Suite:

• A new component is added to ACD/LogP DB: ACD/LogP Accuracy Extender. This advanced training capability makes ACD/Labs' LogP and LogD products unsurpassed in both quality and versatility. ACD/LogP Accuracy Extender helps users take full advantage of their own data by extracting fragments and interaction increments from their structures and training the ACD/LogP and LogD software with the available experimental data.

• Avoid mistakes when entering new data into a User Database. You may choose to display a warning if the difference between the entered value and the calculated value is greater than a pre-determined variation set by the user.
• Compare databases, merge them, or find common intersecting records in the User Databases. Track the success of the merging operation with the Merge Information log.
• Search by multiple User Data fields simultaneously. Boolean logic operators such as 'AND' and 'OR', or their combination, allow users to perform advanced searches.
• Highlight the searched substructure. Visually identify the fragments of the molecule that were requested in the original query. Choose the color of display and switch the option on and off.
• Search the database for ALL tautomeric forms. The software checks if the structure is available in different tautomeric forms and suggests the search options.
• Enhanced SDfile import/export. Allows the user to preview the field names in an SDfile during import to allow mapping to the existing fields in the database.