Introduction
Electron Distribution
Fischere's original ring numbering system remains the preferred choice due to its historical significance, despite the existence of the Ring Index standard for purine analogs that assigns purine a different designation.
The ring system of purine is formed by the fusion of a pyrimidine and an imidazole ring, sharing carbon atoms at the 4- and 5-positions Pyrimidine is characterized as a π-electron-deficient system due to the competition between its two doubly bonded nitrogen atoms, while imidazole represents a π-electron-excessive system with both doubly and singly bonded nitrogen atoms This interplay results in a unique electron distribution within purine, where the pyrimidine ring contributes to the imidazole's electron pool The partial localization of electrons creates dipoles along the molecule's long and short axes, with purine typically exhibiting major polarization along the long axis However, the presence of strong electron-releasing or -withdrawing groups can alter or reverse this dipole direction Some studies suggest that 9-methyladenine exhibits a major dipole effect along the short axis, a phenomenon also supported by crystallographic evidence in compounds like 1,3,7,9-tetramethyluric acid, while related purines such as theophylline and caffeine maintain long axis major polarization.
7 “The Ring Index,” 2nd ed Am Chem Soc., Washington, D.C., 1960
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Adenine, along with its 9-methyl derivative, exhibits significant polarization along its shorter axis, leading to a broad x-band in the ultraviolet absorption spectrum, specifically in the 230-280 nm range Currently, the individual components of this band cannot be linked to specific dipoles until the orientation of the major dipole in the molecule is established Additionally, some simple purines display a narrower y-band around 220 nm, but this was previously beyond the detection capabilities of standard instruments, resulting in limited data on purine structures.
Structural Features Derived from Spectroscopic Studies 3 C Structural Features Derived from Crystallographic Studies 9 111 Nucleophilic and Electrophilic Substitution
Spectroscopy, including ultraviolet, infrared, and nuclear magnetic resonance, is essential for determining structural configurations in compounds Infrared spectroscopy is particularly effective in identifying functional groups, with extensive reviews on the infrared spectra of heterocycles like purines While ultraviolet absorption spectroscopy is less definitive, it has been utilized to study key aspects of purine structures, such as calculating dissociation constants through pH variations, which reveal proton capture sites Additionally, it helps in understanding tautomerism by comparing spectra of aminopurines with their substituted analogs, confirming that the amino form predominates This has been further validated by infrared and nuclear magnetic resonance studies on compounds like adenosine and guanosine.
11 H Berthod and A Pullman, Compt Rend 257,2738 (1963)
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(1961) gens in adenine gives the corresponding 1- and 3-N-alkyladenines, which on valence considerations can both be depicted in the 6-imino
(2a, 3a) or 6-amino forms (2b, 3b) Physical evidence shows that whereas 1-methyladenine is present as the imino structure (2a,
R = Me)le the absence of an ionizable hydrogen in 3-methyladenine is presumed to indicate the presence of the amino isomer (3b,
The spectra of oxopurines do not reliably indicate which tautomeric modification is present, as they typically exhibit simple forms While differences between the spectra of oxopurines and their methoxyl derivatives may suggest the presence of the oxo form, this evidence is often inconclusive For instance, the spectrum of 6-methoxypurine closely resembles that of 1-methylhypoxanthine, despite their structural differences This similarity can be attributed to the simplicity of their molecular structures, resulting in single peak spectra at the same wavelength The most convincing evidence for the predominance of the oxo form in oxopurines comes from infrared measurements conducted in solid state and deuterium oxide solution.
16 P Brookes and P D Lawley, J Chem SOC 1960,539
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Sec 11 B.] PHYSICOCHEMICAL ASPECTS OF PURINES
Analogous purinethiones and their #-methyl derivatives exhibit more significant spectral differences between tautomeric forms compared to oxopurines Evidence from ultraviolet and infrared studies indicates that the thione form predominates in 2-, 6-, and 8-thiopurines Comparative spectral analysis of oxopurines with their thione and certain seleno derivatives reveals that these heteroatoms are doubly bonded to the ring carbon atom, with their spectral influence varying based on their position in the ring Specifically, replacing the oxygen in a 6-oxopurine with sulfur and then selenium results in a bathochromic shift, while similar substitutions in a 2-oxopurine show no such change These effects may be linked to the formation of an "amidic" system involving adjacent atoms at the 6-position.
-NH-CS- C = , I whereas a t the 2- and 8-positions the adjacent atoms are nitrogen, and a “uridic ” structure, i.e., -NH-CS-N(H)-, exists
Spectral changes linked to pH variation in 2-fluoropurine-6-thione suggest the presence of thiol-thione tautomerism Alkaline solutions exhibit a thione-type spectrum instead of the anticipated anionic form, while acidification leads to a measurable transition to the thiol form spectrum This phenomenon is attributed to the strong negative induction (-I) effect of the 2-fluoro atom, which increases the electronegativity of the sulfur atom compared to the I-nitrogen in acidic conditions.
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In SOC 77, 2569 (1955), it is suggested that abnormal behavior in former compounds may be linked to protonation, which could occur either at a carbon atom or through ring opening and recyclization, both of which are measurable rate reactions While covalent hydration is another possibility, current evidence for its occurrence in purines is limited.
In simple purines, the imidazole ring plays a crucial role in anion formation The similarity between the spectra of the anion of 8-oxopurine and that of 7-methyl-8-oxopurine suggests that dissociation at the nitrogen atom has taken place This conclusion is supported by comparisons of the alkaline spectra of 2- and 8-oxopurines.
The study of 8-aminopurines in neutral solutions reveals a lack of correspondence between the spectra of 0x0 and amino derivatives, suggesting that ionization is likely linked to the five-membered ring structure In contrast, hypoxanthine displays an anionic spectrum similar to that of neutral adenine, indicating that dissociation may lead to the formation of a hydrogen-bonded anion This similarity could imply that adenine also forms a similar internally bonded derivative Research has focused on pinpointing the site of proton loss in hypoxanthine by examining the effects of fluorine atom insertion, with both 2-trifluoromethyl- and 8-trifluoromethylhypoxanthines being analyzed for their acid-strengthening properties.
Research on fluorine-containing derivatives of purines aimed to determine if proximity to the ionization center would significantly reduce the anionic dissociation constant However, both derivatives exhibited similar and inconclusive reductions in value Additionally, studies on the spectra of methylated hypoxanthine derivatives indicated that proton loss occurs equally from both the imidazole and pyrimidine rings Consequently, ionization appears to be influenced by the entire molecular structure rather than being linked to a specific atom.
Di- and trioxopurines can undergo ionization at multiple sites within their molecular structure In xanthine (2,6-dioxopurine), the initial proton loss occurs at the 3-position, a pattern also observed in its 1-methyl, 7-methyl, and 1,7-dimethyl derivatives As the pH increases, the dianion is formed through the deprotonation of the 7-position, followed by the 1-position If the 3-position is substituted, such as in 3-methyl- and 1,3-dimethyl-xanthine, the first proton is lost from the 7-nitrogen Studies on uric acid (2,6,8-trioxopurine) and its derivatives reveal that the imidazole ring has the most easily ionizable hydrogen located at the 8-nitrogen, with the 3- and 1-positions serving as secondary and tertiary ionization sites, respectively.
One observation resulting from this work has been that ionization
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Methylation of xanthine and uric acid derivatives results in similar spectral effects, as the removal of a proton or the addition of a methyl group increases the electron density of the nitrogen atom Although the intensities of the two spectra may differ, they exhibit wavelength changes of comparable magnitude The hypsochromic shift observed between a purine and its 1-methyl derivative parallels that seen when the purine loses a proton at the 1-position Conversely, ionization or alkylation at other nitrogen atoms leads to a bathochromic shift Additionally, fluorescence in guanosine and adenosine solutions at specific pH levels resembles that of neutral solutions of their corresponding methylated nucleosides, indicating correlations between alkylation and ionization sites.
Cation formation via proton addition can occur at various sites within purine and its derivatives, with the pyrimidine ring being a common protonation site While studies suggest that adenine's 6-amino group possesses the most basic nitrogen, this is contradicted by evidence indicating that the pyrimidine ring is often the preferred site for protonation in 6-substituted purines Simple adenine derivatives typically form cations by proton addition at the 1-position, although the 3-position may be favored in certain cases, such as with 2,6-diaminopurine Additionally, a comparison of ionization constants in 2- and 6-methylmercaptopurine reveals that N-1 is the most basic nitrogen, with the cation being stabilized through resonance forms.
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Sec 11 C.] PHYSICOCHEMICAL ASPECTS OF PURINES 9 adenine, protonates in the imidazole ring, with the 7-position being the most likely site Evidence to support this comes from crystallo- graphic studies (Section 11,C)
C STRUCTURAL FEATURES DERIVED FROM CRYSTALLOGRAPHIC
Crystallographic studies of purines, including free bases, salts, and nucleotides, have utilized X-ray diffraction and two-dimensional Fourier techniques to reveal that the ring system is primarily planar, though exocyclic groups may appear in out-of-plane positions Notably, bond lengths can reflect the nature of attached groups, particularly in cases with tautomeric possibilities, despite the lack of direct hydrogen atom localization Additionally, interbase distances within the crystal lattice provide insights into potential hydrogen-bonding sites and protonation locations However, these techniques are limited to solid-state molecular details and do not account for environmental factors like solvent effects.
Adenine hydrochloride and guanine hydrochloride exhibit strong hydrogen bonding within their lattices, which connects neighboring bases, water molecules, and hydrogen halides In adenine, each unit is interconnected with all adjacent units, whereas guanine cations are arranged in sheets with only alternate layers linked This structural pattern is also present in the dihydrated form of guanine hydrochloride.
The positioning of adenine and guanine salts hinders direct hydrogen bond formation between the bases, as their proximity is restricted by the steric effects of the methyl group and the mutual repulsion of the charged cations This phenomenon is exemplified in 9-methyladenine hydrobromide, where hydrogen halides are connected through the 1- and 7-nitrogen atoms, yet interbase bonding remains absent.
%position The steric effect may not in itself be critical, since indirect evidence, obtained from polarized absorption spectra of thin crystals
Research by R F Bryan and K I Tomita (1962) indicates that 9-methyladenine forms intermolecular hydrogen bonds at N-1 and N-7, resulting in vertically stacked base layers Similarly, 9-methylguanine dihydrobromide bonds at the 7-position and amino-group nitrogen with hydrogen bromide molecules, yet lacks interbase bonding In solid-state forms, both adenine and guanine exhibit amino groups instead of imino groups, while guanine predominantly features a double bond character in its carbon-oxygen linkage The adenine cation is protonated at N-1, in contrast to guanine and its 9-substituted derivatives, which carry the proton at N-7 Notably, adenosine-5'-phosphate displays a buckled ring system, attributed to close packing distortion in the lattice between the base and ribose-5'-phosphate.