Normal coordinate calculations are carried out for all the in‐plane modes of octaethylporphyrinato‐Ni (II) and its meso‐deuterated and 15N substituted derivatives. With 37 constants of a modified Urey–Bradley force field and a structural model with D4h symmetry, 59 resonance Raman lines (A1g+B1g +A2g+B2g) and 38 infrared bands (Eu) of these three molecules are assigned. The vibrational modes of the Raman active species are represented in terms of the Cartesian atomic displacement vectors. Based on the present results, some important resonance Raman lines of hemoproteins are interpreted. The so‐called ’’oxidation state maker’’ (Band IV) is due to an in‐phase breathing‐like mode of four pyrrole rings although being somewhat deformed by the large contribution of the Cα–N symmetric stretching term. The spin state sensitive Raman lines, namely, Band I and III, are associated mainly with methine bridge (Cα–Cm) stretching modes. Two prominent anomalously‐polarized Raman lines of hemoproteins around 1580 and 1300...

Resonance Raman spectra of octaethylporphyrinato‐Ni(II) and meso‐deuterated and 15N substituted derivatives. II. A normal coordinate analysis

A Raman microprobe has been used to measure the surface-enhanced Raman spectra of adenine, guanine, cytosine and thymine. Comparison of the SERS spectrum with solution spectra shows that some line positions are not influenced by the adsorption process while others show large shifts. In the SERS spectrum new lines, not visible in the solution spectrum, appear while some lines visible in the solution spectrum are not enhanced to a detectable level and are therefore not seen in SERS. The relative intensities are changed owing to an apparently vibration-dependent enhancement factor. A line-broadening effect occurs for most lines except carbonyl stretching vibrations in cytosine and thymine. All SERS spectra show increased contributions of bending vibrations and side-chain groups. In particular, amino group vibrations in adenine and cytosine are clearly visible. Comparison of the shape and intensity of the carbonyl stretching vibrations in cytosine, thymine and guanine show important differences. It is hypothesized that these differences indicate differences in the orientation of these groups with respect to the surface.

/pdf/surface-enhanced-raman-spectroscopy-of-dna-bases-22yxwwsq2d.pdf

Surface-enhanced Raman spectroscopy of DNA bases

Quaternary structures and low frequency molecular vibrations of haems of deoxy and oxyhaemoglobin studied by resonance Raman scattering

Since Watson and Crick's historical papers on the structure and function of DNA based on Rosalind Franklin's and Maurice Wilkin's X-ray diffraction patterns tremendous scientific curiosity has been aroused by the unique and dynamic structure of the molecule of life. A-DNA and B-DNA represent different conformations of the DNA molecule, which is stabilised by hydrogen interactions between base pairs, stacking interactions between neighboring bases and long-range intra- and inter-backbone forces. This review highlights the contribution Fourier transform infrared (FTIR) spectroscopy has made to the understanding of DNA conformation in relation to hydration and its potential role in clinical diagnostics. The review will first begin by elucidating the main forms of DNA conformation found in nature and the general structures of the A, B and Z forms. This is followed by a detailed critique on infrared spectroscopy applied to DNA conformation highlighting pivotal studies on isolated DNA, polynucleotides, nucleoprotein and nucleohistone complexes. A discussion on the potential of diagnosing cancer using FTIR spectroscopy based on the detection of DNA bands in cells and tissues will ensue, highlighting the recent studies investigating the conformation of DNA in hydrated and dehydrated cells. The method of hydration as a way to facilitate DNA conformational band assignment will be discussed and the conformational change to the A-form upon dehydration will be used to explain the reason for the apparent lack of FTIR DNA signals observed in fixed or air-dried cells and tissues. The advantages of investigating B-DNA in the hydrated state, as opposed to A-DNA in the dehydrated state, are exemplified in a series of studies that show: (1) improved quantification of DNA in cells; (2) improved discrimination and reproducibility of FTIR spectra recorded of cells progressing through the cell cycle; (3) insights into the biological significance of A-DNA as evidenced by an interesting study on bacteria, which can survive desiccation and at the same time undergo the B–A–B transition. Finally, the importance of preserving the B-DNA conformation for the diagnosis of cancer is put forward as way to improve the sensitivity of this powerful technique.

/pdf/the-importance-of-hydration-and-dna-conformation-in-oiqrux6kuk.pdf

The importance of hydration and DNA conformation in interpreting infrared spectra of cells and tissues.

High resolution resonance Raman spectra of octaethylporphyrinato‐Ni(II) [Ni (OEP)], its meso‐deuterated and 15N substituted derivatives were measured. With excitation near the O–1 transition, about 90 nonfundamental modes and previously unrecognized fundamental modes were observed for each derivative. The analysis of the nonfundamental Raman lines allowed the determination of all the fundamental frequencies in the A1g, B1g, A2g, and B2g species of D4h symmetry. Experimental classification of depolarized Raman lines to the B1g and B2g species was worked out. Combinations of B1g and B2g modes give rise to anomalously‐polarized Raman lines while combinations of B1g modes and of B2g modes give rise to polarized lines. The Raman lines of the B1g species of Ni(OEP) with D4h symmetry are correlated with those in the Ag species of H2(OEP) with D2h symmetry while the B2g species of D4h is correlated with the B1g species of D2h. The experimental frequencies of fundamental modes thus determined satisfied the product...

Resonance Raman spectra of octaethylporphyrinato‐Ni(II) and meso‐deuterated and 15N substituted derivatives. I. Observation and assignments of nonfundamental Raman lines

J.S. Ard

Papers

Vibrational spectra of nucleic acid constituents—II: Planar vibrations of cytosine

Planar valence force constants and assignments for pyrimidine derivatives

A valence force field for nickel porphin and copper porphin