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Physical chemistry chemical physics : PCCP
Apr 07, 2011;13 (13): 5926-30.

A direct comparison of azide and nitrile vibrational probes.

Xin Sonia Gai, Basil A Coutifaris, Scott H Brewer, Edward E Fenlon
Author Information
  1. Xin Sonia Gai: Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003, USA.
PMID: 21336362 DOI: 10.1039/c0cp02774j

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.

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Grants

  1. R15 GM093330/NIGMS NIH HHS
  2. R15 GM093330-01/NIGMS NIH HHS
  3. R15GM093330/NIGMS NIH HHS

MeSH Term

Azides
Deoxyuridine
Dimethyl Sulfoxide
Infrared Rays
Molecular Structure
Nitriles
Solvents
Spectroscopy, Fourier Transform Infrared
Vibration
Water

Chemicals

2'-azido-5-cyano-2'-deoxyuridine
Azides
Nitriles
Solvents
Water
Deoxyuridine
Dimethyl Sulfoxide
Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Word Cloud

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