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.

Vibrational reporters have shown significant promise as sensitive probes of local environments in proteins and nucleic acids. The utility of two potential vibrational probes, the cyanate and azide groups in phenyl cyanate and 3-azidopyridine, respectively, has been hindered by accidental Fermi resonance. Anharmonic coupling, between the fundamental –OCN or –N3 asymmetric stretch vibration with a near resonant combination band, results in an extremely broad and complex absorption profile for each of these probes. A total of eight phenyl cyanate and six 3-azidopyridine isotopomers were synthesized and studied. Isotopic editing effectively modulated the accidental Fermi resonance — the absorption profiles of several isotopomers were greatly simplified while others remained complex. The origins of the observed profiles are discussed. Addition of a single neutron to the middle atom of the oscillator converted the absorption profile to essentially a single band resulting from either the cyanate or azide asymmetric stretch vibration.

A crystalline inclusion complex between 1,3,5-benzenetricarboxylic acid (trimesic acid, 1) and pyrene was grown from diethyl ether/ethanol and its structure was determined by X-ray analysis. Trialkyltrimesic acids 4 b ± 4 e were synthesized in seven steps from 1,3,5-trichlorobenzene (5). Trimethyltrimesic acid (4 a) was synthesized in four steps from mesitylene. All five substituted trimesic acids were crystallized to determine their potential as clathrate hosts and to compare their solidstate structures with the parent trimesic acid. The X-ray structures of 4 a ± 4 d were resolved and are reported. A covalent analogue of a trimesic acid dimer (13) was synthesized in seven steps from 2-butylisophthalic acid and its solid-state structure determined.

Nitriles have been shown to be effective vibrational probes of local environments in proteins but have yet to be fully utilized for the study of nucleic acids. The potential utility of 5-cyano-2'-deoxyuridine ( 1) as a probe of local nucleic acid environment was investigated by measuring the dependence of the IR nitrile stretching frequency (nu CN), line shape, and absorbance on solvent and temperature. The nu CN was found to be sensitive to solvent with an observed blue shift of 9.2 cm (-1) in going from THF to water. The dependence of the nitrile IR absorbance band was further investigated in water-THF mixtures. Global line shape analysis, difference FTIR spectroscopy, and singular value decomposition (SVD) were used to show the presence of three distinct local environments around the nitrile group of 1 in these mixtures. A modest blue shift in nu CN was observed upon a hydrogen-bond-mediated heterodimer formation between 2 (a silyl ether analogue of 1) and 2,6-diheptanamido-pyridine ( 3a) in chloroform. The intrinsic temperature dependence of the nu CN was found to be minimal and linear over the temperature range studied. The experimental studies were complemented by density functional theory (DFT) calculations on the dependence of the nitrile stretching frequency on solute-solvent interactions and upon heterodimer formation with model systems.

The historical origins of chemical topology are highlighted and seven open problems in the discipline are defined. The current state of experimental work towards their solutions is reviewed. Open problems discussed include size and tightness limits on molecular knots, synthesis of knots more complex than the trefoil, measurement of the enantiomerization barrier of a topological rubber glove, and syntheses of a polyethylene trefoil knot, a stable open knot with stoppers, and a molecular Whitehead link.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)