Pyrimidine molecular structure

Nitrogenous base plus sugar moiety are called nucleosides. Ribonucleic acids (RNA) resemble DNA in that nucleoside monophosphates are joined through phosphodiester bonds. RNAs differ in that the sugars are p-D-ribose units and the pyrimidine uracil is found in place of thymine. Molecular structures and nomenclature for nitrogenous bases, nucleosides, and nucleotides are delineated in Table 2.2. 

Just zinc complexes bearing redox-active ligands sometimes display apparently reversible redox processes. Really, in these cases the electron transfer processes are centred on the ligand. This is, for example, the case of [Zn(papm)Cl2] (papm = 2-(phenylazo)pyrimidine), the (distorted) trigonal bipyramidal molecular structure of which is illustrated in Figure 134.194... 

Figure 1. Molecular structures of sulfadimidine (SDM), its 5-hydroxy-4,6-dimethyl-pyrimidine (SOH), its 6-hydroxymethyl-4-...

X-Ray results are available for the molecular structures of nearly all rare pyrimidine constituents of the nucleic acids except for isothiocyto-sine. Thio analogs of uracil exist in the tautomeric form of the 32 type ... 

The 15N chemical shifts as well as the coupling constants Jh.isn in the bases, and related compounds have not been interpreted theoretically. On the other hand, the magnitude of the coupling constants has been predicted from the molecular structure with reasonable accuracy by means of CNDO/2 calculations for pyrimidine, pyridine, or pyra-zole.543 We can expect that a similar prediction of the spin-spin coupling constants may be made for the pyrimidine and purine nucleic acid bases. 

The syn and anti conformations of pyrimidine ribonucleosides have an opposite sign for certain transitions (e.g., the B2u transition) (67B843 69JA831 71JA(93)1600 72JCP2736 72MI3). Such relations are empirical correlations, since the molecular structures are too complicated to allow theoretical calculations of the rotational strengths. A combination of DNMR, CD spectroscopy, and molecular mechanics calculations has been applied to derivatives of indole 77 and thiazoline-2-thione 78 substituted by chiral rotors (Scheme 58). In these molecules the rotor adopts one of the bisected... 

Fig. 9.5 The molecular structures of DNA and RNA components the purine bases adenine and guanine, the pyrimidine bases cytosine, thymine and uracil and the structure of riboso-monophosphates.

Reactions of Cp 2Ti(Me3SiC2SiMe3) (Cp = Cp, Cp ) with triazine afford binuclear chelate complexes. Reactions with pyrazine display varied behavior and trinuclear and tetranuclear complexes are formed. The reaction with pyrimidine gives octanuclear complexes. C-C coupling reactions are observed in these reactions. Some molecular structures of these products have been determined by X-ray diffraction (Scheme 582).1514... 

The dependence of adlayer structure on the molecular structures has been examined in a comparative study of the 3 pyrimidine bases, uracil, thymine and 3-methyl uracil. In situ STM imaging of thymine shows that an adlayer geometry similar to uracil is adopted, with the exception that the adlayer is expanded in one unit cell dimension. An in situ STM image of th5miine chemisorbed on Au(l 11) from 10 mM th5miine and 10 mM HCIO4 is shown in Fig. 7-9A. 

Reid et al. have reported that the reaction of thiadiazolo pyrimidine derivatives with isocyanates, isothiocyanates, and isoselenacyanates, with elimination of acetonitrile and concomitant addition of two molecules of the hetero-cumu-lene, gave the corresponding 7r-sulfuranes 86-93, as shown in Fig. 10 [84]. The molecular structures of 87 (R=Et, Ph) were determined by X-ray crystallographic analysis [85]. 

Figure 9 illustrates better the influence of pH and molecular structure on the adsorption of 5-triazines by clay and organic matter. Maximum adsorption occurred near the pKa of each compound, suggesting that basicity was a significant factor in their adsorbability by particulate matter. Adsorption of other basic molecules by cation exchange adsorbents, including atrazine by a carboxyl resin (118), amitrole by mont-morillonite (84) and organic matter (83), and purines and pyrimidines by montmorillonite (119), exhibit similar responses. 

Vitamin (thiamine, aneurine) has the molecular structure of a pyrimidine and a thiazole ring bridged by a methylene group the molecular weight is 337.3 dal-tons. It contains a quarternary nitrogen atom. The water-soluble, white, crystalline solid is stable in acidic solution but less stable in neutral or alkaline solution. Thiamine is present in high concentrations in yeast, in the pericarp, and germ of cereals. Whole rice and wheat flour are the main sources for this vitamin, but it is present in practically all plant and animal tissues. 

Pyrimidine is an important heterocycle with a variety of biological activities. They are closely related to nucleic acids since they are very mueh alike in stmeture to the pyrimidine bases [93]. Perhaps, because of this straetural similarity, eompounds with such heterocycles in their molecular structure were reported as antitumor, interferon inducer, antiviral, antihypertensive, hypoglyeemie, anticonvulsant, antinociceptive, and anti-inflammatoiy agents [94]. 

Nathan Hammer, a chemistry professor at the University of Mississippi, uses vibrational Raman spectroscopy to help us understand the effects of intermolecular forces on molecular structure and behavior. The vibrational spectrum provides a valuable probe of the electron distribution in the molecules as well. In the spectra shown, for example, a vibrational transition in normal pyrimidine shifts from roughly 1570 cm (where it overlaps with another transition in the spectrum at left) to a clearly distinct peak at over 1580 cm (the spectrum at right) when a water molecule attaches to one of the nitrogen atoms. This upward shift occurs because some electron density transfers from a... 

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