title: A direct comparison of azide and nitrile vibrational probes.
abstract: The synthesis of 2'-azido-5-cyano-2'-deoxyuridine, N(3)CNdU (1), from trityl-protected 2'-amino-2'-deoxyuridine was accomplished in four steps with a 12.5% overall yield. The IR absorption positions and profiles of the azide and nitrile group of N(3)CNdU were investigated in 14 different solvents and water/DMSO solvent mixtures. The azide probe was superior to the nitrile probe in terms of its extinction coefficient, which is 2-4 times larger. However, the nitrile IR absorbance profile is generally less complicated by accidental Fermi resonance. The IR frequencies of both probes undergo a substantial red shift upon going from water to aprotic solvents such as THF or DMSO. DFT calculations supported the hypothesis that the molecular origin of the higher observed frequency in water is primarily due to hydrogen bonds between the probes and water molecules.
authors.affiliation: Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003, USA.
authors.forename: Xin Sonia
authors.initials: XS
authors.lastname: Gai
authors.forename: Basil A
authors.initials: BA
authors.lastname: Coutifaris
authors.forename: Scott H
authors.initials: SH
authors.lastname: Brewer
authors.forename: Edward E
authors.initials: EE
authors.lastname: Fenlon
mesh_terms: D001386:Azides / Q000737:chemistry*; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry; D004121:Dimethyl Sulfoxide / Q000737:chemistry; D007259:Infrared Rays; D015394:Molecular Structure; D009570:Nitriles / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D017550:Spectroscopy, Fourier Transform Infrared; D014732:Vibration; D014867:Water / Q000737:chemistry
chemical_list: C558969:2'-azido-5-cyano-2'-deoxyuridine; D001386:Azides; D009570:Nitriles; D012997:Solvents; D014867:Water; D003857:Deoxyuridine; D004121:Dimethyl Sulfoxide