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Small Molecule Drugs Crystal Structure Prediction


Small-molecule compounds with high activity/strong selectivity need to possess druggability before they may eventually become commercially marketed drugs. Among these pharmaceutical properties, crystal structure has become one of the indispensable part in the research process. The medicinal crystal structure is essential in the development of drugs. Alfa Chemistry has developed a diversity of calculation tools to assist in predicting and discovering the crystal structure. We perform accurate crystal structure prediction to predict the possible crystal structure through calculation based on a given two-dimensional structure.

Significance of Crystal Structure Prediction

Polymorphism is a phenomenon that the same substance has two or more spatial arrangements and unit cell parameters, which can form multiple crystal structures. It has been found that different crystal structure of the same drug may have significant differences in appearance, solubility, melting point, dissolution, and bioavailability, which affects the stability, bioavailability and efficacy of the drug. Crystal structure prediction of small molecule drugs therefore plays a crucial role in improving the bioactivity in the new drugs.

Predicting the crystal structure of an energetic compound.Figure 1. Predicting the crystal structure of an energetic compound. (Wang, C.; et al. 2021)

Crystal Structure Prediction Process

  • Input small molecule
  • Crystal structure search
  • Structure pool establishment
  • Energy filter
  • Clustering and optimization
  • Energy landscape
  • Free energy calculation

Application of Our Crystal Structure Prediction

  • Guide a more targeted experimental screening and reduce unnecessary experimental trials
  • Significantly accelerate the crystal form selection and confirm the dominant solid phase
  • Reduce the risk associated with the application of solid forms
  • Improve the quality and success rate of subsequent drug development

Our Services

Alfa Chemistry provides drug crystal structure prediction services based on computational chemistry and artificial intelligence methods, and offers brand-new solutions for crystal structure research.

1. Our fast, efficient, and high-precision crystal structure prediction services can identify the most stable crystal structure of small molecules, and deliver thermodynamic stability ranking of different structures at a limited temperature (0 K-400 K).

2. Our technology integrates the core technology of crystal structure search algorithm, XForce Field, quantum dynamics calculation and crystal free energy calculation, to achieve high-precision prediction of the relative thermodynamic stability of different crystal structures.

Alfa Chemistry's Advantages

  • At Alfa Chemistry, massive cloud computing resources are available to complete crystal structure screening more efficiently and accurately.
  • We can determine their stabilities with accuracy and efficiency at a faster speed. Our crystal structure prediction of conventional small molecule drugs can be completed within 2 to 3 weeks.
  • Our technologies are also applicable to more complex molecular systems including complex isomers of multiple flexible rings, different salt types, co-crystals, hydrates, solvation, etc.

Our small molecule drugs crystal structure prediction services remarkably reduce the cost, promote further experiments, and accelerate the process of drug design for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!


  • Wang, C.; et al. Crystal Structure Prediction of 2,4,6,8,10,12-Hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) by a Tailor-Made OPLS-AA Force Field. Crystal Growth & Design. 2021.

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