Structure of 5-methyl-2'-deoxycytidine

Area of Science:

• Crystallography and Molecular Structure
• Organic Chemistry
• Biochemistry

Background:

• Understanding the three-dimensional structure of organic molecules is crucial for predicting their chemical and biological properties.
• Nucleoside analogs are important in medicinal chemistry and molecular biology.
• Detailed structural analysis provides insights into molecular interactions and conformational preferences.

Purpose of the Study:

• To determine the precise crystal structure of the molecule C10H15N3O4.
• To characterize the furanose ring conformation and base orientation.
• To investigate the influence of substituents on molecular geometry and intermolecular interactions.

Main Methods:

• Single-crystal X-ray diffraction was employed to collect diffraction data.
• The crystal structure was solved and refined using standard crystallographic methods.
• Unit cell parameters, space group, and atomic coordinates were determined.

Main Results:

• The compound crystallizes in the orthorhombic system with space group P2(1)2(1)2(1).
• The molecule exhibits a C(2')-endo (2E) furanose ring conformation with an anti base.
• A methyl substituent at the C(5) position reduces the endocyclic bond angle at C(5) by 2.6 degrees.
• The ring oxygen O(4') participates in an intermolecular hydrogen bond.

Conclusions:

• The crystal structure of C10H15N3O4 has been elucidated, revealing specific conformational features.
• The methyl substituent significantly impacts the local geometry of the furanose ring.
• Intermolecular hydrogen bonding involving the ring oxygen plays a role in the crystal packing.