Hongmei Zhao

Formation of Guanine-6-sulfonate from 6-Thioguanine and Singlet Oxygen: A Combined Theoretical and Experimental Study

As an end metabolism product of the widely used thiopurine drugs, 6-thioguanine (6-TG) absorbs UVA and produces (1)O2 by photosensitization. This unusual photochemical property triggers a variety of DNA damage, among which the oxidation of 6-TG itself by (1)O2 to the promutagenic product guanine-6-sulfonate (G(SO3)) represents one of the major forms. It has been suspected that there exists an initial intermediate, G(SO), prior to its further oxidation to G(SO2) and G(SO3), but G(SO) has never been observed. Using density functional theory, we have explored the energetics and intermediates of 6-TG and (1)O2. A new mechanism via G(SOOH) → G(SO2) → G(SO4) → G(SO3) has been discovered to be the most feasible energetically, whereas the anticipated G(SO) mechanism is found to encounter an inaccessibly high barrier and thus is prevented. The mechanism through the G(SOOH) and G(SO4) intermediates can be validated further by joint experimental measurements, where the fast rate constant of 4.9 × 10(9) M(-1) s(-1) and the reaction stoichiometry of 0.58 supports this low-barrier new mechanism. In addition to the dominant pathway of G(SOOH) → G(SO2) → G(SO4) → G(SO3), a side pathway with higher barrier, G(SOOH) → G, has also been located, providing a rationalization for the observed product distributions of G(SO2) and G(SO3) as major products and G as minor product. From mechanistic and kinetics points of view, the present findings provide new chemical insights to understand the high phototoxicity of 6-TG in DNA and point to methods of using 6-TG as a sensitive fluorescence probe for the quantitative detection of (1)O2, which holds particular promise for detecting (1)O2 in DNA-related biological surroundings.

Photophysical and Photochemical Properties of 4-Thiouracil: Time-Resolved IR Spectroscopy and DFT Studies

Intensified research interests are posed with the thionucleobase 4-thiouracil (4-TU), due to its important biological function as site-specific photoprobe to detect RNA structures and nucleic acid-nucleic acid contacts. By means of time-resolved IR spectroscopy and density functional theory (DFT) studies, we have examined the unique photophysical and photochemical properties of 4-TU. It is shown that 4-TU absorbs UVA light and results in the triplet formation with a high quantum yield (0.9). Under N2-saturated anaerobic conditions, the reactive triplet undergoes mainly cross-linking, leading to the (5-4)/(6-4) pyrimidine-pyrimidone product. In the presence of O2 under aerobic conditions, the triplet 4-TU acts as an energy donor to produce singlet oxygen (1)O2 by triplet-triplet energy transfer. The highly reactive oxygen species (1)O2 then reacts readily with 4-TU, leading to the products of uracil (U) with a yield of 0.2 and uracil-6-sulfonate (U(SO3)) that is fluorescent at ~390 nm. The product formation pathways and product distribution are well rationalized by the joint B3LYP/6-311+G(d,p) calculations. From dynamics and mechanistic point of views, these results enable a further understanding for 4-TU acting as reactive precursors for photochemical reactions relevant to (1)O2, which has profound implications for photo cross-linking, DNA photodamage, as well as photodynamic therapy studies.

Reaction Mechanisms of a Photo-Induced [1,3] Sigmatropic Rearrangement via a Nonadiabatic Pathway

Time-resolved Fourier transform infrared absorption spectroscopy measurements and B3LYP/cc-pVDZ calculations have been conducted to characterize the reaction dynamics of a remarkable photoinduced 1,3-Cl sigmatropic rearrangement reaction upon 193 or 266 nm excitation of the model systems acryloyl chloride (CH(2)CHCOCl) and crotonyl chloride (CH(3)CHCHCOCl) in solution. The reaction is elucidated to follow nonadiabatic pathways via two rapid ISC processes, S(1) --> T(1) and T(1) --> S(0), and the S(1)/T(1) and T(1)/S(0) surface intersections are found to play significant roles leading to the nonadiabatic pathways. The S(1) --> T(1) --> S(0) reaction pathway involving the key participation of the T(1) state is the most favorable, corresponding to the lowest energy path. It is also suggested that the photoinduced 1,3-Cl migration reaction of RCHCHCOCl (R = H, CH(3)) proceeds through a stepwise mechanism involving radical dissociation-recombination, which is quite different from the generally assumed one-step concerted process for pericyclic reactions.

Adiabatic and nonadiabatic reaction pathways of the O(3P) with propyne.

For the reaction of O((3)P) with propyne, the product channels and mechanisms are investigated both theoretically and experimentally. Theoretically, the CCSD(T)//B3LYP/6-311G(d,p) level of calculations are performed for both the triplet and singlet potential energy surfaces and the minimum energy crossing point between the two surfaces are located with the Newton-Lagrange method. The theoretical calculations show that the reaction occurs dominantly via the O-addition rather than the H-abstraction mechanism. The reaction starts with the O-addition to either of the triple bond carbon atoms forming triplet ketocarbene (3)CH(3)CCHO or (3)CH(3)COCH which can undergo decomposition, H-atom migration or intersystem crossing from which a variety of channels are open, including the adiabatic channels of CH(3)CCO + H (CH(2)CCHO + H), CH(3) + HCCO, CH(2)CH + HCO, CH(2)CO + CH(2), CH(3)CH + CO, and the nonadiabatic channels of C(2)H(4) + CO, C(2)H(2) + H(2) + CO, H(2) + H(2)CCCO. Experimentally, the CO channel is investigated with TR-FTIR emission spectroscopy. A complete detection of the CO product at each vibrationally excited level up to v = 5 is fulfilled, from which the vibrational energy disposal of CO is determined and found to consist with the statistical partition of the singlet C(2)H(4) + CO channel, but not with the triplet CH(3)CH + CO channel. In combination with the present calculation results, it is concluded that CO arises mainly from the singlet methylketene ((1)CH(3)CHCO) dissociation following the intersystem crossing of the triplet ketocarbene adduct ((3)CH(3)CCHO). Fast intersystem crossing via the minimum energy crossing point of the triplet and singlet surfaces is shown to play significant roles resulting into nonadiabatic pathways for this reaction. Moreover, other interesting questions are explored as to the site selectivity of O((3)P) atom being added to which carbon atom of the triple bond and different types of internal H-atom migrations including 1,2-H shift, 3,2-H shift, and 3,1-H shift involved in the reaction.

Photodissociation and photoisomerization dynamics of CH2 = CHCHO in solution

By means of time-resolved Fourier transform infrared absorption spectroscopy, we have investigated the 193 nm photodissociation and photoisomerization dynamics of the prototype molecule of alpha,beta-enones, acrolein (CH(2)=CHCHO) in CH(3)CN solution. The primary photolysis channels and absolute branching ratios are determined. The most probable reaction mechanisms are clarified by control experiments monitoring the product yields varied with the triplet quencher addition. The predominant channel is the 1,3-H migration yielding the rearrangement product CH(3)CH=C=O with a branching ratio of 0.78 and the less important channel is the alpha cleavage of C-H bond yielding radical fragments CH(2)=CHCO+H with a branching ratio of only 0.12. The 1,3-H migration is strongly suggested to correlate with the triplet (3)(pipi*) state rather than the ground S(0) state and the alpha cleavage of C-H bond is more likely to proceed in the singlet S(1) (1)(npi*) state. From the solution experiments we have not only acquired clues clarifying the previous controversial mechanisms, but also explored different photochemistry in solution. Compared to the gas phase photolysis which is dominated by photodissociation channels, the most important channel in solution is the photoisomerization of 1,3-H migration. The reason leading to the different photochemistry in solution is further ascribed to the solvent cage effect.

Physical Quenching in Competition with the Formation of Cyclobutane Pyrimidine Dimers in DNA Photolesion

The potential energy profiles toward formation of cyclobutane pyrimidine dimers CPD and the physical quenching after UV excitation were explored for the dinucleotide thymine dinucleoside monophosphate (TpT) using density functional theory (ωB97XD) and the time-dependent density functional theory (TD-ωB97XD). The ωB97XD functional that includes empirical dispersion correction is shown to be an appropriate method to obtain rational results for the current large reaction system of TpT. Photophysical quenching is shown to be predominant over the photochemical CPD formation. Following the initial excitation to the (1)ππ* state, the underlying dark (1)nπ* state bifurcates the excited population to the prevailing IC to S0 and the small ISC to the long-lived triplet state T1 via T4 ((3)ππ*) state that has negligible energy gap with (1)nπ* state. Even for the reactive T1 state, two physical quenching pathways resulting in the conversion back to ground-state reactant via the T1/S0 crossing points are newly located, which are in strong competition with CPD formation. These results provide rationale for the recently observed nanosecond triplet decay rates in the single-stranded (dT)18 and inefficiency of deleterious CPD formation, which allow for a deeper understanding of DNA photostability.

Mechanism of the Deamination Reaction of Isoguanine: A Theoretical Investigation

Mechanisms of the deamination reactions of isoguanine with H2O, OH(-), and OH(-)/H2O and of protonated isoguanine (isoGH(+)) with H2O have been investigated by theoretical calculations. Eight pathways, paths A-H, have been explored and the thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs energies of activation were calculated for each reaction investigated. Compared with the deamination reaction of isoguanine or protonated isoguanine (isoGH(+)) with water, the deamination reaction of isoguanine with OH(-) shows a lower Gibbs energy of activation at the rate-determining step, indicating that the deamination reaction of isoguanine is favorably to take place for the deprotonated form isoG(-) with water. With the assistance of an extra water, the reaction of isoguanine with OH(-)/H2O, pathways F and H, are found to be the most feasible pathways in aqueous solution due to their lowest Gibbs energy of activation of 174.7 and 172.6 kJ mol(-1), respectively, at the B3LYP/6-311++G(d,p) level of theory.

Capturing the radical ion-pair intermediate in DNA guanine oxidation

The key radical ion-pair transient in DNA guanine oxidation is directly observed at low temperature by time-resolved spectroscopy. Although the radical ion pair has been frequently invoked as a key intermediate in DNA oxidative damage reactions and photoinduced electron transfer processes, the unambiguous detection and characterization of this species remain formidable and unresolved due to its extremely unstable nature and low concentration. We use the strategy that, at cryogenic temperatures, the transient species could be sufficiently stabilized to be detectable spectroscopically. By coupling the two techniques (the cryogenic stabilization and the time-resolved laser flash photolysis spectroscopy) together, we are able to capture the ion-pair transient G+•⋯Cl− in the chlorine radical–initiated DNA guanine (G) oxidation reaction, and provide direct evidence to ascertain the intricate type of addition/charge separation mechanism underlying guanine oxidation. The unique spectral signature of the radical ion-pair G+•⋯Cl− is identified, revealing a markedly intense absorption feature peaking at 570 nm that is distinctive from G+• alone. Moreover, the ion-pair spectrum is found to be highly sensitive to the protonation equilibria within guanine-cytosine base pair (G:C), which splits into two resolved bands at 480 and 610 nm as the acidic proton transfers along the central hydrogen bond from G+• to C. We thus use this exquisite sensitivity to track the intrabase-pair proton transfer dynamics in the double-stranded DNA oligonucleotides, which is of critical importance for the description of the proton-coupled charge transfer mechanisms in DNA.

Theoretical Investigation on the Absence of Spore Photoproduct Analogue at Cytosine‐Thymine Site

As a well known DNA photolesion product, the special UV induced pyrimidine dimmer called spore photoproduct (SP), has aroused strong research interests. The SP formation was reported solely between two adjacent thymidine residues. It remains unclear in pervious experimental observations why there is an absence of the cytosine‐derived SP‐like photoproduct formation at the cytosine containing DNA strand, although the cytosine residue holds great similarity to thymine in terms of molecular structure. From a theoretical perspective, we have explored this issue in this work by means of density functional theory at the B3LYP/6‐311++G(d,p)//B3LYP/6‐31G(d,p) level for the DNA dinucleotide fragment, cytosine phosphate thymine (CpT). Key factors blocking the formation of the SP‐like product between two adjacent cytosine and thymidine residues are revealed. Instead of undergoing photochemical SP reaction, a photophysical deactivation pathway back to the ground state turns out to be favorable for the CpT dinucleotide...

Binding Interactions of Zinc Cationic Porphyrin with Duplex DNA: From B-DNA to Z-DNA

Recognition of unusual left-handed Z-DNA by specific binding of small molecules is crucial for understanding biological functions in which this particular structure participates. Recent investigations indicate that zinc cationic porphyrin (ZnTMPyP4) is promising as a probe for recognizing Z-DNA due to its characteristic chiroptical properties upon binding with Z-DNA. However, binding mechanisms of the ZnTMPyP4/Z-DNA complex remain unclear. By employing time-resolved UV-visible absorption spectroscopy in conjunction with induced circular dichroism (ICD), UV-vis, and fluorescence measurements, we examined the binding interactions of ZnTMPyP4 towards B-DNA and Z-DNA. For the ZnTMPyP4/Z-DNA complex, two coexisting binding modes were identified as the electrostatic interaction between pyridyl groups and phosphate backbones, and the major groove binding by zinc(II) coordinating with the exposed guanine N7. The respective contribution of each mode is assessed, allowing a complete scenario of binding modes revealed for the ZnTMPyP4/Z-DNA. These interaction modes are quite different from those (intercalation and partial intercalation modes) for the ZnTMPyP4/B-DNA complex, thereby resulting in explicit differentiation between B-DNA and Z-DNA. Additionally, the binding interactions of planar TMPyP4 to DNA were also investigated as a comparison. It is shown that without available virtual orbitals to coordinate, TMPyP4 binds with Z-DNA solely in the intercalation mode, as with B-DNA, and the intercalation results in a structural transition from Z-DNA to B-ZNA. These results provide mechanistic insights for understanding ZnTMPyP4 as a probe of recognizing Z-DNA and afford a possible strategy for designing new porphyrin derivatives with available virtual orbitals for the discrimination of B-DNA and Z-DNA.