The vibrations in the azido-, N3, asymmetric stretching region of 2′-azido-2′-deoxyuridine (N3dU) are examined by two-dimensional infrared spectroscopy. In water and tetrahydrofuran (THF), the spectra display a single sharp diagonal peak that shows solvent sensitivity. The frequency-frequency correlation time in water is 1.5 ps, consistent with H-bond making and breaking dynamics. The 2D IR spectrum is reproduced for N3dU in water based on a model correlation function and known linear response functions. Its large extinction coefficient, vibrational frequency outside the protein and nucleic acid IR absorption, and sensitivity to water dynamics renders -N3 a very useful probe for 2D IR and other nonlinear IR studies: its signal is ca. 100 times that of nitrile.

The synthesis of 2′-azido-5-cyano-2′-deoxyuridine, N3CNdU (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 N3CNdU 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.

COMMUNICATIONS \pectroscop\ (AAS) after di\mlution of known quantities of the zeolites materials i n HF'H,SO, AAS mcasureinents &'ere performed with an Instrumentation Labo-Inc. apparatus uith B nitrous oxide,acetylene flame Scanning electron miiphs (SEM) were obtained by using a Jeol Superprobe 733 instrument. while diffuse reflecrmcc spectroscopy (DRS) was performed on a Varian Cary 5 UVWIS! NIR spectrophotometer at room teniperitture. The diffuse reflectance spectra were recorded against A h;ilon white rellectmce standard in the range 2200 -~200 nm. The computer processing of the spectra consisted of the following steps: 1 ) subtraction of the baseline. 2 ) conversion to wavenumber. and 3) calculation of the Kubelka-Munk ( K M ) function. For ESR spectroscopy. a Bruker ESP300E spectrometer at X-band (ca. 9.5 GHz) was used. Quantitative ESR results were obtained by comparison with Cu(acetylacetonate)..KCI reference samples (spin density : l o i h -10" CU" g-'). The molecular models were generated by the commercial software package HyperchemTM of Autodesk.

The vibrational Stark effect (VSE) has proven to be an effective method for the study of electric fields in proteins via the use of infrared probes. In order to explore the use of VSE in nucleic acids, the Stark spectroscopy of nine structurally diverse nucleosides was investigated. These nucleosides contained nitrile or azide probes in positions that correspond to both the major and minor grooves of DNA. The nitrile probes showed better characteristics and exhibited absorption frequencies over a broad range; i.e., from 2253 cm −1 for 2′-O-cyanoethyl ribonucleosides 8 and 9 to 2102 cm −1 for a 13 C-labeled 5-thiocyanatomethyl-2'-deoxyuridine 3c. The largest Stark tuning rate observed was |Δµ| = 1.1 cm −1 /(MV/cm) for both 5-cyano-2′-deoxyuridine 1 and N2-nitrile-2′-deoxyguanosine 7. The latter is a particularly attractive probe because of its high extinction coefficient (ε = 412 M −1 cm −1 ) and ease of incorporation into oligomers.