Pyrene, structure

The only purine-aromatic complex crystal structure published thus far is the tetramethyluric acid-pyrene structure (6). The orientation of the molecules in this complex is shown below in VIII. 

A further development was the fusion of 2 methyl anthraquinone with caustic alkali, when water was eliminated, and the dyestuff Indanthren Golden Orange G (C.I. vat orange 9), (21), containing the characteristic pyrene structure, (20), was the resultant product. 

Surface heterogeneity may be inferred from emission studies such as those studies by de Schrijver and co-workers on P and on R adsorbed on clay minerals [197,198]. In the case of adsorbed pyrene and its derivatives, there is considerable evidence for surface mobility (on clays, metal oxides, sulfides), as from the work of Thomas [199], de Mayo and co-workers [200], Singer [201] and Stahlberg et al. [202]. There has also been evidence for ground-state bimolecular association of adsorbed pyrene [66,203]. The sensitivity of pyrene to the polarity of its environment allows its use as a probe of surface polarity [204,205]. Pyrene or ofter emitters may be used as probes to study the structure of an adsorbate film, as in the case of Triton X-100 on silica [206], sodium dodecyl sulfate at the alumina surface [207] and hexadecyltrimethylammonium chloride adsorbed onto silver electrodes from water and dimethylformamide [208]. In all cases progressive structural changes were concluded to occur with increasing surfactant adsorption. 

Benzo[a]pyrene, a molecule with five, fused, hexagonal rings, is among the most carcinogenic of the polycyclic aromatic hydrocarbons (PAHs). Such biological activity may be related to the electronic structure of benzo[a]pyrene and its metabolites. Ionization energies of these molecules therefore have been investigated with photoelectron spectroscopy [28]. 

FIGURE 2.6 The procarcinogen benzo[a]pyrene oriented in the CYPlAl active site (stereo view) via n- n stacking between aromatic rings on the substrate and those of the complementary amino acid side chains, such that 7,8-epoxidation can occur. The substrate is shown with pale lines in the upper structures. The position of metabolism is indicated by an arrow in the lower structure (after Lewis 1996). 

Some examples of different types of hydrocarbons are given in Figure 9.1. Nonaromatic compounds without ring structure are termed aliphatic, whereas those with a ring structure (e.g., cyclohexane) are termed alicyclic. Aromatic hydrocarbons often consist of several fused rings, as in the case of benzo[a]pyrene. 

The structures of some PAHs of environmental interest are given in Figure 9.1. Naphthalene is a widely distributed compound consisting of only two fused benzene rings. It is produced commercially for incorporation into mothballs. Many of the compounds with marked genotoxicity contain 3-7 fused aromatic rings. Benzo[a] pyrene is the most closely studied of them, and will be used as an example in the following account. 

Emission spectra at these points are shown in Figure 8.2d. The band shapes were independent of the excitation intensity from 0.1 to 2.0 nJ pulse . The spectrum of the anthracene crystal with vibronic structures is ascribed to the fluorescence originating from the free exdton in the crystalline phase [1, 2], while the broad emission spectra of the pyrene microcrystal centered at 470 nm and that of the perylene microcrystal centered at 605 nm are, respectively, ascribed to the self-trapped exciton in the crystalline phase of pyrene and that of the a-type perylene crystal. These spectra clearly show that the femtosecond NIR pulse can produce excited singlet states in these microcrystals. 

Molecular structure of a self-immolative AB6 dendron with aminomethyl-pyrene reporter units and a Boc protecting group as a trigger. 

Fig. 1 Chemical structures of pyrene conjugated at the 5 -end (5 -Py) and the 2 sugar position of uridine (PyU), and phenothiazine conjugated at the 5 -end of ODN (5 -Ptz)...

DNA and RNA quantification, SNP typing, hybridization, and structural alteration have been widely carried out by modified oligonucleotides possessing pyrene derivatives [104-113]. As is known, pyrene-1-carboxaldehyde fluorescence is considerably dependent on solvent polarity [114], being strong in methanol but insignificant in nonpolar solvents [115]. Owing to this property, Tanaka and collaborators developed a pyrenecarboxamide-tethered modified DNA base, PyU 46, and applied it to SNP discrimination in DNA [116-120],... 

Ren RXF, Chaudhuri NC, Paris PL, Rumney S IV, Kool ET (1996) Naphthalene, phenan-threne, and pyrene as DNA base analogues synthesis, structure, and fluorescence in DNA. J Am Chem Soc 118 7671-7678... 

Different aromatic hydrocarbons (naphthalene, pyrene and some others) can form excimers, and these reactions are accompanying by an appearance of the second emission band shifted to the red-edge of the spectrum. Pyrene in cyclohexane (CH) at small concentrations 10-5-10-4 M has structured vibronic emission band near 430 nm. With the growth of concentration, the second smooth fluorescence band appears near 480 nm, and the intensity of this band increases with the pyrene concentration. At high pyrene concentration of 10 2 M, this band belonging to excimers dominates in the spectrum. After the act of emission, excimers disintegrate into two molecules as the ground state of such complex is unstable. 

Figure 2. 7-Methylbenz[a]anthracene and benzo[a]pyrene indicating those regions defined as bay regions and the structures of the corresponding bay region dihydrodiol epoxides.

The reaction of metabolically generated polycyclic aromatic diol epoxides with DNA Ua vivo is believed to be an important and critical event in chemical carcinogenesis Cl,2). In recent years, much attention has been devoted to studies of diol epoxide-nucleic acid interactions in aqueous model systems. The most widely studied reactive intermediate is benzo(a)pyrene-7,8-diol-9,10-epoxide (BaPDE), which is the ultimate biologically active metabolite of the well known and ubiquitous environmental pollutant benzo(a)pyrene. There are four different stereoisomers of BaPDE (Figure 1) which are characterized by differences in biological activities, and reactivities with DNA (2-4). In this review, emphasis is placed on studies of reaction mechanisms of BPDE and related compounds with DNA, and the structures of the adducts formed. 

The pyrene-like aromatic chromophore of BaPDE is characterized by a prominent and characteristic absorption spectrum in the A 310-360 nm spectral region, and a fluorescence emission in the X 370-460 nm range. These properties are sensitive to the local microenvironment of the pyrenyl chromophore, and spectroscopic techniques are thus useful in studies of the structures of the DNA adducts and in monitoring the reaction pathways of BaPDE and its hydrolysis products in DNA solutions. 

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