Solid State Structural Elucidation and Confirmation

The determination or confirmation of solid state molecular structure for a chemical entity can be performed with a combination of analytical techniques. Some of these techniques are mass spectrometry, NMR spectroscopy, infrared spectroscopy, elemental analysis, and single crystal X-ray diffraction. SSCI is able to combine any or all of these techniques to address complex structural problems. As an example, mass spectrometry and NMR spectroscopy are discussed in more detail below.

Mass Spectrometry

Mass spectrometry (MS) is the preferred technique to determine molecular weight and fragmentation data to support the structure elucidation. The use of LC-MS enables one to collect structural data for many components in a complex mixture. Impurities observed using the LC procedure can be further characterized using mass spectrometry. The LC-MS data can be collected using different ionization techniques depending upon the nature of the sample. SSCI can perform LC-MS, LC-MS/MS, and LC-MS/MS/MS analyses using a linear ion trap instrument. The mass spectrometry data can be used for both quantitative and qualitative purposes.

NMR Spectroscopy

High resolution 1D and 2D NMR spectroscopy can be used to determine the atomic connectivity and structural conformation of molecules in solution. Both 1H and 13C NMR spectroscopy provide detailed information about molecules. Various 2D proton NMR correlation experiments such and COSY, TOCSY, and NOESY enable one to determine the relative locations of protons or the conformation of a molecule in solution. Additional 2D proton-carbon NMR correlation experiments such and HMQC, HSQC, and HMBC can be used to connect the carbon backbone of complex molecules. These NMR techniques are used to determine the assignments of all resonances for a molecule, and knowledge of the relative position of each nucleus permits the determination of the molecular conformation in solution. SSCI can perform variable temperature, multinuclear, and gradient selected NMR analyses. Quantitative and qualitative data can be obtained using NMR spectroscopy.

Single Crystal X-ray Diffraction

Single crystal X-ray diffraction analysis is used to determine the dimensions of the unit cell and atomic coordinates. This information can be used to:

  • Confirm the chemical structure of an API,
  • Unambiguously determine the absolute configuration of all stereocenters in a molecule,
  • Determine if the crystalline phase is a neat phase (pure API) or if it is a multi-component crystal such as a hydrate or solvate,
  • Determine the stoichiometric ratio of components for salts, cocrystals, hydrates, and solvates,
  • Uniquely identify forms and unravel the form landscape of polymorphic compounds.

If single crystals can be grown of sufficient size and quality, the crystal structure can be determined. SSCI uses an in-house Rigaku SuperNova diffractometer, equipped with a copper anode microfocus sealed X-ray tube and a Dectris Pilatus3 R 200K hybrid pixel array detector. Crystal structures can be obtained on crystals that are on the order of 100 microns in size. Absolute configuration is determined routinely on molecules that contain elements no heavier than oxygen. Supra-molecular aspects of the crystal structure such as hydrogen bonding are noted and discussed where applicable. Ambient temperature is the default used for data collection on routine crystals. More challenging crystals can be analyzed at subambient temperatures as low as 100 K when necessary. The calculated powder X-ray pattern is generated from the determined crystal structure to be used as a reference XRPD pattern for that particular form. This pattern can also be compared to the as-received powder material XRPD to assess the purity of the bulk material and confirm its form.