High throughput quantum chemistry for molecular design

(View ConStruQt-API Documentation)

ConstruQt Diagram

ConStruQt is our core molecular design tool that underpins all other automation and machine learning technologies that ChemAlive is developing. It is currently available as an API and allows for quick deployment of quantum chemical calculations to enhance your chemistry in the following ways:

  • Transforms list of SMILES molecular designations into state-of-the-art 3D molecular structures in SD format
  • Manages the conformational space of the molecules with a robust shape searching algorithm
  • Generates all reasonable tautomeric forms of the molecule and prioritizes them by energy
  • Generates all stereoisomeric forms of the molecules and differentiates them by energy
  • All molecules are stored in our unique database (Qontext) architecture making the calculations easily augmented and carried through to other processes
  • We currently maintain the largest quantum chemical database known. We are building a contextual data structure commensurate with advanced machine learning algorithms. It is called Qontext.

Try ConStruQt Here!

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All chemical information submitted here will be stored in the ChemAlive database. Users submit at their own risk. All data returned through the ChemAlive engine is for demonstration purposes only and no liability in its use is accepted. Happy computations.

You must accept the Terms and Conditions.

We are happy to test your molecules for you. If you would like, you may use our API (follow documentation link above), or simply email us some SMILES using the form to the left.


  • Please submit up to 25 SMILES
  • We will process your submission with our engine and will return conformations, tautomers and diastereomers in SD format
  • Please provide your contact information so the results can be e-mailed to you (at left)
  • For larger libraries please contact us to build a project at (

ConStruQt Specifications


Most conformations are energetically accessible

Distribution of conformational relative energies (kcal/mol) of over 1.5 million molecules and 35 million conformations at the PM6 semi-empirical level contained in our Qontext database


Classical Force Fields Are Unreliable

The energetic error between universal force field (UFF) relative energies and PM6 derived free-energies (kcal/mol) as a function of PM6 conformational relative energy. Notice the UFF error is upwards of 80% and increases as we move away from equilibrium

Why high throughput quantum chemistry?

  • ConStruQt provides a sea-change in accuracy and scope for molecular modeling
  • Moving away from alchemical rules-based prediction, ConStruQt computes molecular energies and electronic properties from fundamental physics
  • With quantum chemistry you get not just what is possible, but what is probable
  • ConStruQt allows the deployment of these vastly improved metrics at the scale that you are used to using with cheminformatics and classical mechanics force field calculations

The Engine

  • The core ConStruQt computational approach centers around cheminformatics management, classical mechanics initial guess and follow-on semi-empirical quantum chemical calculations for energy assessment
  • Density functional theory calculations can be launched as well.
  • ConStruQt is available as an API to connect to the ChemAlive AWS Supercomputer
  • With Dynamic scalability, ConStruQt can handle up to 5,00 unique molecules per minute per server (depending on size and rotational degrees of freedom)
  • The engine accepts SMILES as input and returns computed 3D data in SD format
  • Whether it be for your chemistry SaaS, on-line catalog or virtual library, the API delivers far more accurate data at unmatched speeds and accuracy.


  • Conformations - Molecular shape is 70% of drug discovery and key to all follow-on calculations at more accurate levels. Legacy methods are unable to accurately predict molecular shape
  • Tautomers - Fundamental to acidity constants and binding affinities, you need to know which tautomer is most stable to understand your structure based determination
  • Diastereomers - Diastereomers can differ sharply in energy. When a set of stereoisomers can result from a reaction, ConstruQt can help you begin to identify which one is present. Follow-on calculations of optical rotation can further elucidate the chemical structure.
  • Micro-states - We can accurately predict protomers using automatic linear regression analysis (coming soon).

The Database

  • The ChemAlive postgreSQL database, Qontext, is built by chemists for chemists
  • The API additionally allows access to the largest repository of quantum chemical data maintained in the ChemAlive database
  • ConStruQt allows direct access to this high quality data by library or single molecule searching
  • Submissions to Qontext will contextualize molecular structure based on the computations requested.