Quasi-intrinsic thiobase derivatives as potential targeted photosensitizers in two-photon photodynamic therapy.

In this study, a set of potential quasi-intrinsic photosensitizers for two-photon photodynamic therapy (PDT) are proposed based on the unnatural 2-amino-8-(1'-ß-ᴅ-2'-deoxyribofuranosyl)-imidazo[1,2-ɑ]-1,3,5-triazin-4(8H)-one (P), which is paired with the 6-amino-5-nitro-3-(1'-ß-ᴅ-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z) and can specifically recognize breast and liver cancer cells. Herein, the effects of sulfur substitution and electron-donating/electron-withdrawing groups on the photophysical properties in aqueous solution are systematically investigated. The one- and two-photon absorption spectra evidence that the modifications could result in red-shifted absorption wavelength and large two-photon absorption cross-section, which contributes to selective excitation and provides effective PDT for deep-seated tissues. To ensure the efficient triplet state population, the singlet-triplet energy gaps and spin-orbit coupling constants were examined, which is responsible for a rapid intersystem crossing rate. Furthermore, these thiobase derivatives are characterized by the long-lived T1 state and the large energy gap for radiationless transition to ensure the generation of cytotoxic singlet oxygen.

Effect of GM1 concentration change on plasma membrane: molecular dynamics simulation and analysis.

Ganglioside GM1 is a class of glycolipids predominantly located in the nervous system. Comprising a ceramide anchor and an oligosaccharide chain containing sialic acid, GM1 plays a pivotal role in various cellular processes, including signal transduction, cell adhesion, and membrane organization. Moreover, GM1 has been implicated in the pathogenesis of several neurological disorders, such as Parkinson's disease, Alzheimer's disease, and stroke. In this study, by creating a neural cell model membrane simulation system and employing rigorous molecular models, we utilize a coarse-grained molecular dynamics approach to explore the structural and dynamic characteristics of multi-component neuronal plasma membranes at varying GM1 ganglioside concentrations. The simulation results reveal that as GM1 concentration increases, a greater number of hydrogen bonds form between GM1 molecules, resulting in the formation of larger clusters, which leads to reduced membrane fluidity, increased lipid ordering, decreased membrane thickness and surface area and higher levels of GM1 dissociation. Through a meticulous analysis, while considering GM1's structural attributes, we offer valuable insights into the structural and dynamic traits of the cell membrane. This study provides a robust methodology for exploring membrane characteristics and enhances our comprehension of GM1 molecules, serving as a resource for both experimental and computational researchers in this field.

Simulation for fluorescence detection of O4-methylthymidine with definite photophysical characteristics.

DNA alkylation is caused by long-term exposure of cells to the environmental and endogenous alkylating agents, which can also lead to DNA mutations and therefore trigger some cancers. Since O4-methylthymidine (O4-meT), mismatched with guanine (G), is the most common but not easily repaired alkylated nucleoside, monitoring O4-meT can help to effectively reduce the occurrence of carcinogenesis. In this work, the modified G-analogues are selected as the fluorescence probe to monitor the existence of O4-meT according to its pairing characteristics. The photo-physical properties of considered G-analogues formed by ring expansion or addition of fluorophores were studied in detail. It is found that, compared with natural G, the absorption peaks of these fluorescence analogues are red-shifted (>55 nm) and the luminescence is enhanced by π-conjugation. Especially, the xG has a large Stokes shift (65 nm) with fluorescence insensitive to natural cytosine (C) and retains efficient emission after pairing, while it is sensitive to O4-meT and the quenching phenomenon occurs due to the excited state intermolecular charge transfer. Accordingly, the xG can be used as a fluorescent probe to identify the O4-meT in solution. In addition, the direct use of deoxyguanine fluorescent analogue for monitoring O4-meT was evaluated by the effects of ligating deoxyribose on absorption and fluorescence emission.

External Electric Field Effects on AFM-like Magnetism in Nitroxide-Functionalized C+:C Base Pair.

In this work, we computationally designed a set of nitroxide diradical base pairs (rC+:rC) to propose promising magnetic building blocks for spintronic or magnetic molecular materials. C+:C12 is found to possess a considerably large antiferromagnetic-like (AFM-like) spin-coupling magnitude (J = -3286.681 cm-1) and sensitive magnetic responses to the external electric field. Especially, the presence of the Y direction field that is oriented perpendicular to intermolecular hydrogen bonds has the greatest influence on the magnetic exchange interaction (J being from -2549.578 to -4231.286 cm-1, ΔJY = 1681.708 cm-1), which could be understood by two simultaneously occurring effects. On the one hand, the external electric field in the -Y direction can regulate the charge polarization of negative and positive electrostatic potentials on C12 moiety and further facilitate the spin transport property. On the other hand, with increasing electric field strength on the -Y axis, the spin density on diradical sources diminishes and that on the coupler increases, which can lead to a homogenous spin-density distribution. The achieved understanding provides a new strategy for designing self-assembly magnetic nanomaterials or nanodevices and enhancing the AFM coupling through the assistance of external electric field.

Quasi-intrinsic fluorescent probes for detecting the DNA adduct (ABPdG) based on an excited-state intermolecular charge transfer mechanism.

N'-(2'-Deoxyguanosin-8-yl)-4-aminobiphenyl (ABPdG) is one of the most representative carcinogenic DNA adducts formed by human exposure to 4-aminobiphenyl (4-ABP) during dye production, rubber-manufacturing processes and cigarette smoke. Accordingly, the ultrasensitive detection of ABP-derived adducts in DNA with minimal interference to the native structures becomes key for elucidating carcinogenesis mechanisms and mitigating the risk of cancer. In view of the lack of efficient optical emission in ABPG, we report a theoretical study on the photophysical properties of a set of quasi-intrinsic fluorescent C-analogues, which can form stable W-C base pairs with ABPG. It is found that fluorophore replacement and ring-expansion can bring a red-shifted absorption and bright photoluminescence due to additional π-conjugation. In particular, because the tricyclic cytosine analogue 1,3-diaza-2-oxophenoxazine (tCO) possesses distinct optical properties, it is proposed as a biosensor to identify ABPG. The TDDFT-calculated absorption maximum of tCO is red-shifted by 97 nm in comparison with that of the native C base, which contributes to selective excitation after incorporating into the nucleic acids. Although the fluorescence is insensitive to base pairing with natural guanine, the excited state intermolecular charge transfer (ESICT)-governed "OFF-ON" signal can be observed in the presence and absence of ABPG. Moreover, to evaluate the direct availability of the bright C-analogues with high selectivity for the deoxyguanosine adduct ABPG in DNA, we further investigated thoroughly the effects of its linking to deoxyribose on its absorption and emission, which shows little difference from that of experiment.

Theoretical Simulation on Regulating the Magnetic Coupling Properties of Diradical Artificial Bases.

In this work, we computationally designed a series of diradical molecules with obvious magnetic coupling properties based on newly synthesized artificial bases, 6-amino-3-(1'-ß-d-2'-deoxyribofuranosyl)-5-nitro-1H-pyridin-2-one (Z), 2-amino-8-(1'-ß-d-2'-deoxyribofuranosyl)-imidazo-[1,2a]-1,3,5-triazin-[8H]-4-one (P), 6-amino-9[(1'-ß-d-2'-deoxyribofuranosyl)-4-hydroxy-5-(hydroxymethyl)-oxolan-2-yl]-1H-purin-2-one (B), and found two methods (base pairing and nitro group rotation) of regulating the magnetic magnitude, making them become magnetic switches with promising prospects. On one hand, the modified diradical artificial base P3 possesses an excellent magnetic exchange coupling constant due to its spin density concentration on a unique spin polarization path. Because of the serious mismatch between the singly occupied molecular orbital (SOMO) and the lowest unoccupied molecular orbital (LUMO) of Z-P3 base pairing, the magnetic coupling property of the Z-P3 base pair disappears, which indicates that the base pairing can be used as an effective means to regulate the molecular magnetic coupling properties. On the other hand, the investigation shows that the rotation of the nitro group on Z has an influence on the energy gaps between the closed-shell (CS) singlet and triplet (T) states of the base pairs formed by Z-analogues and thereby the expression of magnetic coupling properties. This work can help to develop the modification strategy of the diradical base and provide theoretical guidance for the design and synthesis of magnetic coupling materials with controllable magnetic coupling properties.

Fluorescent adenine analogues with ESPT characteristic utilized for real-time detecting DNA adduct.

The 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG) is the representative damaged nucleoside that may increase the risk of developing diseases. Accordingly, the selective detection of 8-oxoG in DNA with minimal disturbance to the native structure is important to have an in-depth understanding of the formation mechanism and becomes an attractive tool for genomic research. To identify the DNA adduct in real-time efficiently, a series of quasi-intrinsic optical probes are performed based on the natural adenine, which has preference to form a stable base pair with 8-oxoG in the syn conformation. The calculations revealed that the A-analogues in solution could bring red-shifted absorption spectra and bright photoluminescence arisen from the additional π-conjugation by means of fluorophore modification and the ring expansion. Especially, A1 possesses large Stokes shifts and the highest fluorescence intensity in emission, which is proposed as the biosensor to monitor the optical changes in the presence and absence of the considered 8-oxoG. It is found that the fluorescence is insensitive to base pairing with thymine, while the excited state intermolecular proton transfer (ESPT) induced efficient fluorescence quenching is observed upon pairing with the 8-oxoG. To evaluate the direct usefulness of the bright adenine analogues in biological environment, we further examined the influences of linking deoxyribose on the absorption and emission, which are consistent with the experimental data.

Thiourea derivatives acting as functional monomers of As(Ш) molecular imprinted polymers: A theoretical and experimental study on binding mechanisms.

Thiourea derivatives are expected to be potential monomers of As(Ш) molecular imprinted polymers (MIPs) which are used to specifically recognize As(Ш). However, the specific recognition and binding mechanisms between template and monomers are unclear, which limits the practical applications of MIPs in As(Ш)detection. In this work, density functional theory (DFT) calculations, molecular dynamics (MD) simulations and experimental methods were jointly applied to explore the binding interactions between H3AsO3 and thiourea derivatives and environmental factors influences, aiming to find out the best monomer and optimal preparation conditions for H3AsO3 MIPs. Among five monomer candidates, (2, 6-difluorophenyl) thiourea (FT) was calculated to be the most potential one, while allyl thiourea (AT) was the second choice. Configurations of the most stable binding complexes were found out. The optimal solvent was found to be toluene and the bindings were more favorable at pH 7.5 in aqueous solution. Besides, EGDMA was proved as the best cross-linker with the optimal ratio of template: monomer: cross-linker= 2:3:20. Moreover, the binding interactions were identified to be hydrogen bonds, and the non-covalent nature was revealed. These findings provide references for efficient design and preparation of good-performance H3AsO3 MIPs, which can be used to detect and remove As(Ш) from environment.

Nitro rotation tuned dissociative electron attachment upon targeted radiosensitizer 4-substituted Z bases.

In this work, a set of new potential radiation sensitizers (4-substituted Z-bases: 4XZ, X = F, Cl, Br, and I) are designed based on the artificial 6-amino-5-nitro-3-(1'-ß-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z), which can selectively bind to breast cancer cells. The calculated electron affinities in water solution show that the halogenated Z-bases are efficient electron acceptors which possess significant electron-withdrawing characters following the order of 4XZ > Z ≫ U. To ensure the effective electron attachment induced dissociation, we constructed the energy profiles related to the X-C bond cleavage of neutral and anionic bases. The results show that the X-C bond becomes relatively weak after the electron attachment. In particular, the electron induced dehalogenations of (4BrZ)- and (4IZ)- are low-barrier and exothermic, which support a high radiosensitivity. Furthermore, we characterized the vibrational excitation effect on the dissociative electron attachment, which demonstrates that the charge distribution can be regulated by the rotation-induced structural distortion accompanied by the electron localization on the nitro group. Also examined is the influence of base pairing on the dehalogenation, which is not only conducive to the electron-driven dissociation but is also beneficial to the stabilization of related products. The current study suggests 4BrZ and 4IZ can be regarded as potential targeted radiosensitizers with possible applications in reducing the side effects in radiotherapy.

Photophysical properties of fluorescent nucleobase P-analogues expected to monitor DNA replication.

In this work, we computationally design a series of fluorescent purine analogues based on the 2-amino-8-(1'-ß-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P) to monitor the DNA replication process with merely a minimal perturbation to the natural structure of nucleic acid. The P-modified fluorescent probes present red-shifted absorption spectra and enhanced photoluminescence due to the additional π-conjugation resulting from the fluorophore modification and the ring-expansion. Efficient fluorescence quenching of P-analogues occurs upon pairing with the complementary 6-amino-5-nitro-3-(1'-ß-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z) due to the nonradiative relaxation from the low-lying dark excited state to the ground state of Z moiety. Especially, the P3 and the P7, which have high fluorescence intensity in both gas and liquid phases, are proposed as the sensors for studying conformational switching in the presence and absence of a complementary sequence. Also examined are the influences of hydration and the linking to deoxyribose on absorption and emission processes. Besides, the potential phosphorescence emission of these modified base pairs is taken into account by constructing the relaxed potential energy curves of S0, T1 and S1 states.

Proton Transfer and Nitro Rotation Tuned Photoisomerization of Artificial Base Pair-ZP.

Recently, the successful incorporation of artificial base pairs in genetics has made a significant progress in synthetic biology. The present work reports the proton transfer and photoisomerization of unnatural base pair ZP, which is synthesized from the pyrimidine analog 6-amino-5-nitro-3-(1-ß-D-2'-deoxyribo-furanosyl)-2 (1H)-pyridone (Z) and paired with its Watson-Crick complement, the purine analog 2-amino-8-(1'-ß-D-2'- deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P). To explain the mechanism of proton transfer process, we constructed the relaxed potential energy surfaces (PESs) linking the different tautomers in both gas phase and solution. Our results show that the double proton transfer in the gas phase occurs in a concerted way both in S0 and S1 states, while the stepwise mechanism becomes more favorable in solution. The solvent effect can promote the single proton transfer, which undergoes a lower energy barrier in S1 state due to the strengthened hydrogen bond. In contrast to the excited state ultrafast deactivation process of the natural bases, there is no conical intersection between S0 and S1 states along the proton transfer coordinate to activate the decay mechanism in ZP. Of particular relevance to the photophysical properties, charge-transfer character is obviously related to the nitro rotation in S1 state. We characterized the molecular vibration effect on the electronic properties, which reveals the electronic excitation can be tuned by the rotation-induced structural distortion accompanied with the electron localization on nitro group.

The mechanism of the excited-state proton transfer of Salicylaldehyde azine and 2,2'-[1,4-Phenylenebis{(E)- nitrilomethylidyne}] bisphenol: Via single or double proton transfer.

The Salicylaldehyde azine (H2SA) and 2,2'-[1,4-Phenylenebis{(E)-nitrilomethylidyne}] bisphenol (H2SPA) with double proton transfer characteristics were synthesized recently (Phys. Chem. Chem. Phys., 2018, 20, 23,762). However, the detailed theoretical interpretation of proton transfer (PT) mechanism is inadequate. In the present work, density functional theory (DFT) and time-density functional theory (TDDFT) are employed to study the proton transfer mechanism of H2SA and H2SPA in detail. Bond parameters, infrared (IR) spectra and frontier molecular orbitals (FMOs) calculated by PBE0/TZVP method indicate the strength of hydrogen bond is enhanced in S1 state, which can be visualized by the reduced density gradient (RDG) analysis. The potential energy surfaces (PESs) of H2SA and H2SPA are also constructed. The small barriers indicate that both the single proton transfer and double proton transfer of H2SA and H2SPA are more likely to occur in the S1 state. In addition, the properties of H2SA and H2SPA after chelation with Li+ have also been theoretically characterized. According to the calculated fluorescence spectra of compounds (H2SA-Li+ and H2SPA-Li+), it was found that only the planar structure of H2SA-Li+ can form metallogel, which verified the experimental results.

The novel excited state intramolecular proton transfer broken by intermolecular hydrogen bonds in HOF system.

2-(4-(Dimethylamino)phenyl)-3-hydroxy-6,7-dimethoxy-4Hchromen-4-one (HOF) was synthesized in experiment (Wang et al., Sensor. Actuat. B-Chem. 277 (2018) 484), and its photophysical and photochemical properties was reported. However the corresponding full theoretical interpretation of mechanisms is inadequate. In the present research, the intermolecular hydrogen bond structure of HOF-methanol complex (HOF-2M) was found, and mechanism of alcohols monitoring of HOF was deeply studied using the density functional theory (DFT) and time-dependent density functional theory (TDDFT). The enhancing mechanism of the excited state hydrogen bond is verified by analyzing the hydrogen bond parameters, infrared spectra and frontier molecular orbitals. Importantly, the reduced density gradient visual analysis and topological quantificational analysis confirm that the intramolecular hydrogen bond of HOF is broken by strong intermolecular hydrogen bonds of HOF-2M using the Atoms-In-Molecule theory. The obtained absorption and emission spectra are found to agree well with the experimental results and the complete quenched keto-emission in methanol and ethanol solvents provide a suitable sensing mechanism for detecting alcohols. The reaction path of the excited state intramolecular proton transfer for HOF is explained in detail through the constructed potential energy curves.

Unusual Indirect Nuclear Spin-Spin Exchange Coupling through Solvated Electron.

Solvated electrons have been found to exist in various media which also exhibit more intriguing properties such as superconductivity, nonlinear optical response, and so on. However, how they affect the nuclear spin properties has not been proven. In this work, we present the first detailed study on solvated-electron-triggered indirect nuclear spin-spin J-coupling using density functional theory calculations. Taking 19F as a probe, we verify the presence of unusual J couplings between two distant F atoms in HF-containing anionic clusters. These couplings occur "through solvated electron", rather than through conventional covalent bonds or space. Solvated electron can serve as an additional channel to efficiently realize long-range J-coupling between far separated nuclei because of its dispersivity and Rydberg character. The coupling magnitude strongly depends on the unique distribution of solvated electron and its second-order interaction with solvating HF units. This work provides novel insights into the mediating roles of electrons, possibly opening up potential applications based on weakly bound electrons.

Efficient floating diffuse functions for accurate characterization of the surface-bound excess electrons in water cluster anions.

In this work, the effect of diffuse function types (atom-centered diffuse functions versus floating functions and s-type versus p-type diffuse functions) on the structures and properties of three representative water cluster anions featuring a surface-bound excess electron is studied and we find that an effective combination of such two kinds of diffuse functions can not only reduce the computational cost but also, most importantly, considerably improve the accuracy of results and even avoid incorrect predictions of spectra and the EE shape. Our results indicate that (a) simple augmentation of atom-centered diffuse functions is beneficial for the vertical detachment energy convergence, but it leads to very poor descriptions for the singly occupied molecular orbital (SOMO) and lowest unoccupied molecular orbital (LUMO) distributions of the water cluster anions featuring a surface-bound excess electron and thus a significant ultraviolet spectrum redshift; (b) the ghost-atom-based floating diffuse functions can not only contribute to accurate electronic calculations of the ground state but also avoid poor and even incorrect descriptions of the SOMO and the LUMO induced by excessive augmentation of atom-centered diffuse functions; (c) the floating functions can be realized by ghost atoms and their positions could be determined through an optimization routine along the dipole moment vector direction. In addition, both the s- and p-type floating functions are necessary to supplement in the basis set which are responsible for the ground (s-type character) and excited (p-type character) states of the surface-bound excess electron, respectively. The exponents of the diffuse functions should also be determined to make the diffuse functions cover the main region of the excess electron distribution. Note that excessive augmentation of such diffuse functions is redundant and even can lead to unreasonable LUMO characteristics.

Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions.

Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems.

The Equally Important Role of Adenine Derivatives to That of Pyrimidine Derivatives in Near-0†eV Electron-Induced DNA Lesions.

The role of adenine (A) derivatives in DNA damage is scarcely studied due to the low electron affinity of base A. Experimental studies demonstrate that low-energy electron (LEE) attachment to adenine derivatives complexed with amino acids induces barrier-free proton transfer producing the neutral N7 -hydrogenated adenine radicals rather than conventional anionic species. To explore possible DNA lesions at the A sites under physiological conditions, probable bond ruptures in two models-N7 -hydrogenated 2'-deoxyadenosine-3'-monophosphate (3'-dA(N7H)MPH) and 2'-deoxyadenosine-5'-monophosphate (5'-dA(N7H)MPH), without and with LEE attachment-are studied by DFT. In the neutral cases, DNA backbone breakage and base release resulting from C3' -O3' and N9 -C1' bond ruptures, respectively, by an intramolecular hydrogen-transfer mechanism are impossible due to the ultrahigh activation energies. On LEE attachment, the respective C3' -O3' and N9 -C1' bond ruptures in [3'-dA(N7H)MPH](-) and [5'-dA(N7H)MPH](-) anions via a pathway of intramolecular proton transfer (PT) from the C2' site of 2'-deoxyribose to the C8 atom of the base moiety become effective, and this indicates that substantial DNA backbone breaks and base release can occur at non-3'-end A sites and the 3'-end A site of a single-stranded DNA in the physiological environment, respectively. In particular, compared to the results of previous theoretical studies, not only are the electron affinities of 3'-dA(N7H)MPH and 5'-dA(N7H)MPH comparable to those of hydrogenated pyrimidine derivatives, but also the lowest energy requirements for the C3' -O3' and N9 -glycosidic bond ruptures in [3'-dA(N7H)MPH](-) and [5'-dA(N7H)MPH](-) anions, respectively, are comparable to those for the C3' -O3' and N1 -glycosidic bond cleavages in corresponding anionic hydrogenated pyrimidine derivatives. Thus, it can be concluded that the role of adenine derivatives in single-stranded DNA damage is equally important to that of pyrimidine derivatives in an irradiated cellular environment.

Mechanisms Responsible for High Energy Radiation Induced Damage to Single-Stranded DNA Modified by Radiosensitizing 5-Halogenated Deoxyuridines.

Experimental studies showed that high energy radiation induced base release and DNA backbone breaks mainly occur at the neighboring 5' nucleotide when a single-stranded DNA is modified by radiosensitizing 5-halogenated deoxyuridines. However, no mechanism can be used to interpret these experimental observations. To better understand the radiosensitivity of 5-halogenated deoxyuridines, mechanisms involving hydrogen abstraction by the uracil-5-yl radical from the C2' and C3' positions of an adjacent nucleotide separately followed by the C3'-O3' or N-glycosidic bond rupture and the P-O3' bond breakage are investigated in the DNA sequence 5'-TU(•)-3' employing density functional theory calculations in the present study. It is found that hydrogen abstractions from both positions are comparable with the one from the C2' site slightly more favorable. The N-glycosidic bond cleavage in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is estimated to have the lowest activation free energies, indicating that the adjacent 5' base release dominates electron induced damage to single-stranded DNA incorporated by 5-halogenated deoxyuridines. Relative to the P-O3' bond breakage after the internucleotide C3'-H abstraction, the C3'-O3' bond rupture in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is predicted to have a lower activation free energy, implying that single-stranded DNA backbone breaks are prone to occur at the C3'-O3' bond site. The 5'-TU(•)-3' species has substantial electron affinity and can even capture a hydrated electron, forming the 5'-TU(-)-3' anion. However, the electron induced C3'-O3' bond rupture in 5'-TU(-)-3' anion via a pathway of internucleotide proton abstraction is only minor in both the gas phase and aqueous solution. The present theoretical predictions can interpret rationally experimental observations, thereby demonstrating that the mechanisms proposed here are responsible for high energy radiation induced damage to single-stranded DNA incorporated by radiosensitizing 5-halogenated deoxyuridines. By comparing with previous results, our work proves that the radiosensitizing action of 5-bromo-2-deoxyuridine is not weaker but stronger than its isomer 6-bromo-2-deoxyuridine on the basis of the available data.

Efficient and Substantial DNA Lesions From Near 0 eV Electron-Induced Decay of the O4-Hydrogenated Thymine Nucleotides: A DFT Study.

Possible electron-induced ruptures of C3'-O3', C5'-O5', and N1-C1' bonds in O4-hydrogenated 2'-deoxythymidine-3'-monophosphate (3'-dT(O4H)MPH) and 2'-deoxythymidine-5'-monophosphate (5'-dT(O4H)MPH) are investigated using density functional theory calculations, and efficient pathways are proposed. Electron attachment causes remarkable structural relaxation in the thymine C6 site. A concerted process of intramolecular proton transfer (IPT) from the C2' site of 2'-deoxyribose to the C6 site and the C3'-O3' bond rupture is observed in [3'-dT(O4H)MPH](-). A low activation barrier (9.32 kcal/mol) indicates that this pathway is the most efficient one as compared to other known pathways leading to backbone breaks of a single strand DNA at the non-3'-end thymine, which prevents the N1-C1' bond cleavage in [3'-dT(O4H)MPH](-). However, essentially spontaneous N1-C1' bond cleavage following similar IPT is predicted in [5'-dT(O4H)MPH](-). A moderate activation barrier (13.02 kcal/mol) for the rate-controlling IPT step suggests that base release from the N1-C1' cleavage arises readily at the 3'-end of single strand DNA with the strand ended by a thymine. The C5'-O5' bond has only an insignificant change in the IPT process. Solvent effects are found to increase slightly the energy requirements for either bond ruptures (11.23 kcal/mol (C3'-O3') vs 16.18 kcal/mol (N1-C1')), but not change their relative efficiencies.

Excess electron interaction with radiosensitive 5-bromopyrimidine in aqueous solution: a combined ab initio molecular dynamics and time-dependent wave-packet study.

Radiation-generated secondary electrons can induce resonance processes in a target molecule and fragment it via different pathways. Although the associating electronic resonant states at equilibrium geometry have been well studied for many target molecules in the gas phase, vibrational resonance contributions and the solvent effect are still poorly understood for relevant processes in solution. Taking a radiosensitive drug, 5-bromopyrimidine (5-BrPy), as an example, we here present a combined ab initio molecular dynamics simulation and time-dependent wave packet study with an emphasis on vibrational resonance and solvation effects on excess electron interaction with 5-BrPy in solution. The gaseous results reveal two primary channels for the electron induced C-Br bond cleavage: the highest vibrational resonance on vertical potential energy curve via a tunneling mechanism (e + 5-BrPy → 5-BrPy(*-) →(tunneling) Br(-) + Py(·)), and auto-dissociation along repulsive relaxed potential energy curve (e + 5-BrPy → 5-BrPy(*-) →(relaxation) Br(-) + Py(·)), which account for the two peaks at 0.2 and 0 eV observed in Modelli's experiment. However, a strong solvation effect modifies the mechanism and dynamics of the dissociation of the electron···5-BrPy system. On one hand, the spontaneous dissociation becomes unfavorable due to a barrier on the relaxed free energy surface created by the coupling between the π* and σ* states. Seven vibrational resonances (v = 0-6) are identified for the solution process and only the high-level v = 5, 6 with non-negligible quantum tunneling coefficient can cause the dissociation (e + 5-BrPy →(localization) 5-BrPy(*-) →(tunneling) [Br(δ-)···Py(δ-)] →Br(-) + Py(·)). On the other hand, protonation is also observed at the N sites of the hydrated 5-BrPy anion (e + 5-BrPy →(localization) 5-BrPy(*-) →(relaxation) Prt-5-BrPy), and this inhibits the dissociation along the C-Br bond, suggesting a competing pathway against C-Br bond cleavage. Clearly, this work provides a combination strategy using an ab initio molecular dynamics technique and time-dependent wave packet method to explore the effects of vibrational resonances and solvation on the interaction of radio-generated excess electrons with target biological molecules in complicated solution surroundings.