Chemaxon Structure Preparation Toolkit

Standardizer’s main purpose is to transform chemical structures into representations that obey your business rules to create a consistent chemical database. You can use it when registering new compounds, or when virtually screening structures. Here are a few highlights of 40 pre-defined standardizer actions:

• Adding or removing explicit Hydrogen atoms
• Neutralizing charged fragments or functional groups
• Recognizing and converting legacy representations of functional groups (like aliases)
• Removing certain fragments (like water and salt counterions)
• 2D cleaning and expanding abbreviated groups
• Unified representation of aromatic rings, tautomers and mesomers

Structure Checker verifies the correctness of molecules. In case it finds an issue, structure checker can fix it automatically or flag it for manual correction. This tool allows you to filter out input errors and incorrect features when registering a new compound. Here are some highlights of 40 checkers:

• Invalid bond length
• Overlapping bonds or atoms
• Molecule charges
• Incorrect chiral flags
• Invalid valences
• OCR errors
• Substructure checker that can be configured to transform a given substructure defined by a SMARTS string

The ability to deal with molecular structures that have identical atomic composition, but different arrangement of bonds or spatial orientation is crucial in the identification, search and property calculation of compounds. Tautomerism, stereoisomerism and resonance are examples of isomerism.

Tautomerization can affect identification, searching and physico-chemical properties of molecules. Stereoisomers have the same physico-chemical properties (e.g.: melting point, solubility), but they differ in pharmacokinetic and pharmacodynamic behavior. Resonance describes the rearrangement of delocalized electrons in the molecule, which results in a set of contributing structures of the original structure.

The Isomer calculator can:

• Generate different tautomer sets useful for searching and tautomer handling
• Calculate tautomer distribution and major tautomer form in water
• Generate tetrahedral and double-bond stereoisomers starting either from a 2D or 3D structure
• Generate resonance structures

Ionization has an essential impact on compound behavior in nearly all protic environments. On top of its application in general and analytical chemistry, relationships to drug pharmacokinetics and pharmacodynamics are well-established. Acidic and basic dissociation constants (pKa) and the microspecies distribution at different pH values are important to quantitatively describe ionization and comprehend physical and biological processes.

The Protonation calculator includes:

• Highly-accurate calculation of pKa values along with pH dependent distribution plots of relevant microspecies in water – pKa documentation
• Calculation of the major microspecies form at a given pH value – Major microspecies documentation
• Isoelectric point calculation

The Toolkit bundles are built to easily integrate with most systems using a range of different APIs including Java, Python, Microservices and .NET.