Vibrational analysis and molecular force field of hypoxanthine as determined from ultraviolet resonance Raman spectra of native and deuterated species

Uličný, Jozef; Ghomi, Mahmoud; Tomkova, A.; Miškovský, Pavol; Turpin, Pierre‐Yves; Chinsky, L.

doi:10.1007/bf00208865

Cited by 14 publications

(9 citation statements)

References 23 publications

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“…p* for this compound. 24,25 The other occupied molecular orbitals of HYP (tautomers I and II) can be assigned to r and p and when appropriate, to a specific combination of atomic lone pairs.…”

Section: Equilibrium Structures and Hartree2fock Molecular Orbitalsmentioning

confidence: 99%

Theoretical study of valance photoelectron spectra of hypoxanthine, xanthine, and caffeine using direct symmetry‐adapted cluster/configuration interaction methodology

Farrokhpour

Fathi

2011

J Comput Chem

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UV photoelectron spectra of hypoxanthine, xanthine, and caffeine, up to 20 eV, were calculated and compared with the experimental spectra reported in literature. The calculations were performed using a novel version of the quantum mechanical symmetry-adapted cluster/configuration interaction (SAC-CI) method termed, direct SAC-CI. The Duning/Huzinaga valance double-zeta D95+(d,p) Gaussian basis set was also employed with this method. The ionization energies and intensities were calculated, and the corresponding spectral bands were assigned. Natural bonding orbital (NBO) calculations were employed for better spectral band assignment. The calculated ionization energies and intensities reasonably produced the experimental photoelectron spectra.

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Section: Equilibrium Structures and Hartree2fock Molecular Orbitalsmentioning

confidence: 99%

Theoretical study of valance photoelectron spectra of hypoxanthine, xanthine, and caffeine using direct symmetry‐adapted cluster/configuration interaction methodology

Farrokhpour

Fathi

2011

J Comput Chem

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“…While the neutral forms of these bases and nucleotides have been investigated by a range of experimental and computational studies, 5,6,[8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] the protonated and deprotonated forms which are directly relevant to enzymatic processes are not well characterized, a fact noted by Shugar and co-workers as well. 21 In the following, we have made comprehensive assignments of the spectra of the neutral, protonated, and deprotonated species by deuterium labeling of labile hydrogen atoms.…”

Section: Introductionmentioning

confidence: 99%

Structures, Ionization Equilibria, and Tautomerism of 6-Oxopurines in Solution

2009

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6-Oxopurine and its analogues form an important class of biological molecules that include nucleobases and their precursors and are substrates of a wide range of enzymes. Solution structures of purines have been debated in the literature because of the many possible tautomers and protonation states in which they can exist in solution. Substitutions on the pyrimidine and imidazole rings alter tautomerization and protonation equilibria, and as a consequence, the solution compositions and structures of closely related analogues can be significantly different. We have obtained resonance Raman spectra of 6-oxopurines: hypoxanthine, xanthine, their riboside phosphates, guanine monophosphate in the protonated and deprotonated forms with UV excitation at 260 nm. The species present in solution under different pH conditions were identified by isotopic labeling with deuterium as well as by comparison with extensive density functional theoretical calculations. At physiological pH, while N7H and N9H tautomeric forms of hypoxanthine exist in equilibrium, in xanthine, the additional carbonyl group at C2 shifts the equilibrium in favor of the N7H tautomer. The corresponding nucleotide of xanthine, xanthosine monophosphate, on the other hand, is in the anionic form (pK(a) 5.5). We find that Raman spectra show systematic shifts with change in the protonation state and substitution on the ring. In general, deprotonation of the neutral molecule is marked by a downshift in the observed Raman wavenumbers, and protonation is accompanied by an upshift.

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“…29,32 The sensitivity of these modes to ribose conformation is not unexpected as normal mode calculations of hypoxanthine, 9-methylinosine, and inosine have shown that the nature of the N 9 substituent can dramatically affect the frequency of modes with significant N 9 vibrational motions. 24,25 Vibrational motions of the phosphate backbone have been shown to be strongly indicative of DNA…”

Section: Poly (Ri) Ribosyl Ring Conformationmentioning

confidence: 99%

“…Earlier uv resonance Raman studies investigating hypoxanthine and inosine only used 281 and 257 nm as excitation wavelengths, and therefore the relative enhancement of the important carbonyl and ribose modes at shorter excitation wavelengths was not observed. 24,25 Figure 2 depicts spectra of IMP obtained with 210 and 250 nm excitation. The most intense band in the 250 nm excited spectrum, the 1469 cm Ϫ1 mode, results from coupled C 2 AN 3 bond stretching and N 1 H bending motions 24 and is not enhanced with 210 nm excitation ( Figure 3).…”

Section: Spectral Characterization Of Inosinementioning

confidence: 99%

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A UV resonance Raman investigation of poly(rI): Evidence for cation-dependent structural perturbations

1998

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Poly(rI) stabilized by either Na+ or K+ was investigated using uv resonance Raman (UVRR) spectroscopy. Raman excitation profiles of inosine 5′‐monophosphate demonstrated the 250 nm excitation selectively enhances base stacking interactions, while ribose and carbonyl stretching vibrations are preferentially enhanced with 210 nm excitation. These wavelengths were used to examine the structure of poly(rI) in the presence of either K+ or Na+ as a function of temperature. UVRR studies revealed that the K+ stabilized form is more thermally stable, yielding a Tm of ∼ 47°C compared to a Tm of ∼ 30°C for the Na+ stabilized form. We observed that both the ribosyl conformation and the coordination of the carbonyl groups depend on the nature of the cation. The C6O stretching frequency indicates that Na+ coordinates much more strongly to the carbonyl groups than K+ (1672 cm−1 Na+ vs 1684 cm−1 K+ at 4°C). Conformationally sensitive modes of the phosphate backbone and the ribosyl ring indicate that Na+ stabilized poly(rI) predominantly exists in a C3′‐endo ribose conformation, whereas K+ stabilized poly(rI) adopts a C2′‐endo conformation possibly as a consequence of the larger ionic radius of the K+ ion. © 1998 John Wiley & Sons, Inc. Biopoly 46: 475–487, 1998

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Vibrational analysis and molecular force field of hypoxanthine as determined from ultraviolet resonance Raman spectra of native and deuterated species

Cited by 14 publications

References 23 publications

Theoretical study of valance photoelectron spectra of hypoxanthine, xanthine, and caffeine using direct symmetry‐adapted cluster/configuration interaction methodology

Theoretical study of valance photoelectron spectra of hypoxanthine, xanthine, and caffeine using direct symmetry‐adapted cluster/configuration interaction methodology

Structures, Ionization Equilibria, and Tautomerism of 6-Oxopurines in Solution

A UV resonance Raman investigation of poly(rI): Evidence for cation-dependent structural perturbations

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