Structure of the triplet excited state of bromanil from time-resolved resonance Raman spectra and simulation

Time-resolved resonance Raman (TR3) spectroscopy has been used to study the structure of the triplet excited state of bromanil. These experimental results were then simulated using parameters from density functional theoretical (DFT) calculations and wave packet dynamics, in order to understand the structure and mode-specific displacements of the resonant excited state. The transition dipole moments and the energy separation of the T1 and Tn states were obtained from time-dependent DFT calculations. We have demonstrated application of the technique to tetrabromo-p-benzoquinone. From our calculations, the observed T1->Tn absorption spectrum has been assigned to the 3Bg→3Bu transition. The geometry has been optimized for the resonant higher triplet state, Tn, and is found to be in good agreement with the predictions of the wave packet dynamical simulations. Mode-specific displacements of the triplet state geometry have been obtained from simulations and these have been rationalized with respect to the molecular orbital involved. Thus, we have demonstrated that from the simulations of the experimental TR3 spectral data, valuable additional information can be derived on the structure of the transient states that may then be used for elucidation of structure-reactivity correlation in the future

Excited state structure and dynamics of p-benzoquinone and bromanil from time-resolved resonance Raman spectra and simulation

p-Benzoquinone and its halogen substituted derivatives are known to have differing reactivities in the triplet excited state. While bromanil catalyzes the reduction of octaethylporphyrin most efficiently among the halogenated p-benzoquinones, the reaction does not take place in presence of the unsubstituted p-benzoquinone (T. Nakano and Y. Mori, Bull. Chem. Soc. Jpn., 67, 2627 (1994)). Understanding of such differences requires a detailed knowledge of the triplet state structures, normal mode compositions and excited state dynamics. In this paper, we apply a recently presented scheme (M. Puranik, S. Umapathy, J. G. Snijders, and J. Chandrasekhar, J. Chem. Phys., 115, 6106 (2001)) that combines parameters from experiment and computation in a wave packet dynamics simulation to the triplet states of p-benzoquinone and bromanil. The absorption and resonance Raman spectra of both the molecules have been simulated. The normal mode compositions and mode specific excited state displacements have been presented and compared. Time-dependent evolution of the absorption and Raman overlaps for all the observed modes has been discussed in detail. In p-benzoquinone, the initial dynamics is along the C=C stretching and C-H bending modes whereas in bromanil nearly equal displacements are observed along all the stretching coordinates

Solution structures of purine base analogues 6-chloroguanine, 8-azaguanine and allopurinol

<div><p>Analogues of purine bases are highly relevant in the biological context and have been implicated as drug molecules for therapy against a number of diseases. Additionally, these molecules have been implicated to have a role in the prebiotic RNA world. However, experimental data on the structures of these molecules in aqueous solution is lacking. In this work, we report the ultraviolet resonance Raman spectra of 6-chloroguanine, 8-azaguanine and allopurinol, obtained with 260 nm excitation. The reported spectra have been assigned to normal modes computed from density functional theory (B3LYP/6–31G (d,p)) calculations. This work has been useful in identifying the solution-state structures of these molecules at neutral pH. We find that the guanine analogues 6-chloroguanine and 8-azaguanine exist as keto-N9H and keto-N7H tautomers in solution, respectively. On the other hand, the hypoxanthine analogue allopurinol exists as a mixture of keto-N9H and keto-N8H tautomers in solution. We predict that this work would be particularly useful in future vibrational studies where these molecules are present in complexes with their target proteins.</p></div

Isotope effects on the equilibrium of p-benzoquinone and its radical anion: ab initio and DFT studies

The isotope effect on the equilibrium between p-benzoquinone and its radical anion has been quantitatively estimated using Hartree-Fock (3-21G, 6-31G&#8727; and 6-31+G&#8727;&#8727; basis sets) as well as pure and hybrid density functional methods (BP86 and B3LYP with 6-31G&#8727; and 6-31+G&#8727;&#8727; basis sets). Equilibrium constants involving 2H, 13C, 17O and 18O isotopes have been calculated. At all levels, the deuterium isotope effect is substantial, while heavy atom isotope effects are small. The trend remains the same even when the presence of a counterion (Na+) is taken into account explicitly in the calculations. These conclusions differ qualitatively from an earlier experimental study

Structure of the triplet excited state of tetrabromo-p-benzoquinone from time-resolved resonance Raman spectra and ab initio calculations

The triplet excited state of bromanil has been observed using time-resolved resonance Raman spectroscopy. Assignments of the bands have been made by comparison with spectra of the ground state and of benzoquinone as well as its fluorinated and chlorinated analogues. The structure in the triplet excited state has been determined using ab initio calculations. The combined experimental and computed results confirm a greater degree of bond reorganization in the triplet of bromanil compared to benzoquinone or fluoranil

Solution structures of purine base analogues 9-deazaguanine and 9-deazahypoxanthine

<p>Deaza analogues of nucleobases are potential drugs against infectious diseases caused by parasites. A caveat is that apart from binding their target parasite enzymes, they also bind and inhibit enzymes of the host. In order to design derivatives of deaza analogues which specifically bind target enzymes, knowledge of their molecular structure, protonation state, and predominant tautomers at physiological conditions is essential. We have employed resonance Raman spectroscopy at an excitation wavelength of 260 nm, to decipher solution structure of 9-deazaguanine (9DAG) and 9-deazahypoxanthine (9DAH). These are analogues of guanine and hypoxanthine, respectively, and have been exploited to study static complexes of nucleobase binding enzymes. Such enzymes are known to perturb p<i>K</i>_a of their ligands, and thus, we also determined solution structures of these analogues at two, acidic and alkaline, pH. Structure of each possible protonation state and tautomer was computed using density functional theoretical calculations. Species at various pHs were identified based on isotopic shifts in experimental wavenumbers and by comparing these shifts with corresponding computed isotopic shifts. Our results show that at physiological pH, N1 of pyrimidine ring in 9DAG and 9DAH bears a proton. At lower pH, N3 is place of protonation, and at higher pH, deprotonation occurs at N1 position. The proton at N7 of purine ring remains intact even at pH 12.5. We have further compared these results with naturally occurring nucleotides. Our results identify key vibrational modes which can report on hydrogen bonding interactions, protonation and deprotonation in purine rings upon binding to the active site of enzymes.</p

Hypoxanthine guanine phosphoribosyltransferase distorts the purine ring of nucleotide substrates and perturbs the pK_a of bound xanthosine monophosphate

Enzymatic efficiency and structural discrimination of substrates from nonsubstrate analogues are attributed to the precise assembly of binding pockets. Many enzymes have the additional remarkable ability to recognize several substrates. These apparently paradoxical attributes are ascribed to the structural plasticity of proteins. A partially defined active site acquires complementarity upon encountering the substrate and completing the assembly. Human hypoxanthine guanine phosphoribosyltransferase (hHGPRT) catalyzes the phosphoribosylation of guanine and hypoxanthine, while the Plasmodium falciparum HGPRT (PfHGPRT) acts on xanthine as well. Reasons for the observed differences in substrate specificities of the two proteins are not clear. We used ultraviolet resonance Raman spectroscopy to study the complexes of HGPRT with products (IMP, GMP, and XMP), in both organisms, in resonance with the purine nucleobase electronic absorption. This led to selective enhancement of vibrations of the purine ring over those of the sugar–phosphate backbone and protein. Spectra of bound nucleotides show that HGPRT distorts the structure of the nucleotides. The distorted structure resembles that of the deprotonated nucleotide. We find that the two proteins assemble similar active sites for their common substrates. While hHGPRT does not bind XMP, PfHGPRT perturbs the pK_a of bound XMP. The results were compared with the mutant form of hHGPRT that catalyzed xanthine but failed to perturb the pK_a of XMP

Ultrafast Nuclear Dynamics of Photoexcited Guanosine-5′-Monophosphate in Three Singlet States

We report measurement of resonance Raman (RR) spectra of guanosine-5′-monophosphate (GMP), a DNA nucleotide at excitation wavelengths throughout its ππ* absorption band (B_b) in the 210–230 nm range. From these data, we constructed wavelength-dependent Raman intensity excitation profiles (REPs) for all observed modes. These profiles and the absorption spectrum were then modeled using self-consistent simulations based on the time-dependent wave packet propagation formalism. We inferred the initial structural dynamics of GMP immediately after photoexcitation in terms of dimensionless displacements. The simulations also provide linewidth-broadening parameters that in turn report on the time scale of dynamics. We compared deduced structural changes in the purine ring upon photoabsorption into the B_b state with those deduced for the two lowest lying ππ* (L_a and L_b at 280 and 248 nm, respectively) excited states of GMP. We find that excitation to the L_b state lengthens C₆–N₁ and C₂N₃ bonds, which lie along the formation coordinate of various oxidative adducts but B_b excitation does not. We also find that photoabsorption by the B_b state weakens the C₈–N₉ bond and thus might assist imidazole ring opening via cleavage of the same bond. Electronic excitation to different ππ* states of the guanine chromophore results in contrasting structural changes; although absorption by the L_a and L_b states induces expansion of pyrimidine and contraction of imidazole rings, excitation results in overall shrinkage of both the rings. Computed absolute changes in internal coordinates imply that photoexcitation to any of the three singlet states of GMP does not lead directly to the formation of a cation radical of guanine

Mechanism of Discrimination of 8‑Oxoguanosine versus Guanosine by <i>Escherichia coli</i> Fpg

The mutagenic 8-oxoguanosine monophosphate, the predominant product of DNA oxidation, is excised by formamidopyrimidine glycosylase (Fpg) in bacteria. The mechanism of recognition of 8-oxodG, which differs subtly from its normal counterpart, guanosine monophosphate (dG), by <i>Escherichia coli</i> Fpg remains elusive due to the lack of structural data of <i>E. coli</i> Fpg bound to 8-oxodG. Here, we present solution-state structure of 8-oxodG oligomer bound to <i>E. coli</i> E3Q Fpg using UV resonance Raman (UVRR) spectroscopy. The vibrational spectra report on the π-stacking and hydrogen bonding interactions established by 8-oxodG with <i>E. coli</i> E3Q Fpg. Furthermore, we report on the interactions of <i>E. coli</i> E3Q Fpg with the normal, undamaged nucleotide, dG. We show that <i>E. coli</i> Fpg recognizes 8-oxodG and dG through their C2-amino group but only 8-oxodG forms extensive contacts with <i>E. coli</i> Fpg. Our findings provide a basis for mechanism of lesion recognition by <i>E. coli</i> Fpg