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.

Dynamics of C(3P) + OH(X 2Π) reaction on the new global HCO(X2A') potential energy surface.

A precise analytical potential energy surface (PES) of HCO(X2A') is fitted from a great quantity of ab initio energy points computed with the multi-reference configuration interaction method and aug-cc-pV(Q/5)Z basis sets. The whole energy points extrapolated to the complete basis set limit are fitted by the many-body expansion formula. The calculated topographic characteristics are analyzed and compared with the existing work to prove the precision of the present HCO(X2A') PES. By utilizing the time-dependent wave packet and quasi-classical trajectory methods, the reaction probabilities, integral cross sections, and rate constants are computed. The results are compared in detail with the former results carried out on the other PES. Moreover, the provided information on stereodynamics leads to an in-depth understanding of the role of collision energy in product distribution.

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.

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.

A new global analytical ab initio potential energy surface for the dynamics of the C+(2P) + SH(X2Π) reaction.

The global potential energy surface (PES) of HCS+(X1Σ+) is constructed using many-body expansion (MBE) methodology. The obtained analytical function is found by fitting the 7907 ab initio energy points computed at the Davidson-corrected multi-reference configuration interaction level with the aug-cc-pV(5+d)Z basis set. The final root mean square error is 0.0419 eV, and the maximum deviation is 0.2039 eV, showing that the analytical formula agrees well with the energy points. The topological features are calculated and discussed based upon the analytical PES of HCS+(X1Σ+). The reaction probability, integral cross sections and other details of the C+(2P) + SH(X2Π) → H(2S) + CS+(X2Σ+) reaction are investigated using the quasi-classical trajectory and time-dependent quantum wave packet methods.

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.

ZnCdO2 monolayer - A complex 2D structure of ZnO and CdO monolayers for photocatalytic water splitting driven by visible-light.

ZnO monolayer possesses band structure matching the conditions of water splitting for hydrogen generation but cannot well response to the visible light, while CdO one, contrariwise, have obvious optical absorption in the visible light range but no satisfactory band edges for the water splitting to produce hydrogen. Here, we predict a two-dimensional ZnCdO2 structure comprising of ZnO and CdO ones to achieve their strengths. The band structures, optical properties, carrier mobility, and the strain engineering for ZnCdO2, ZnO and CdO monolayers are investigated by using the first-principles hybridization functional calculations. The results demonstrate that the two-dimensional ZnCdO2 structure is a promising candidate for water splitting to produce hydrogen. All the structures show a direct band energy gap and the character remains unchanged under the considered biaxial strains. All the conduction band minimums are suitable for water splitting reaction even under the -4% to +4% strain. Moreover, the valence band maximum of ZnCdO2 monolayer matches the conditions of the water-splitting reaction under the -2% to +4% strain. Interestingly, the unsatisfactory valence band maximum of CdO monolayer can be overcome by strain larger than +2%. As expected, the enhanced optical absorption in the visible light range is observed for the ZnCdO2 monolayer. Additionally, the mobilities of the hole and the electron are significantly different for the three monolayers, implying that the low recombination ratio of the photogenerated carrier pairs is available, which is also beneficial for the photocatalytic performance. Therefore, ZnCdO2 monolayer and CdO monolayer (with tensile strain larger than 2%) is a promising candidate for the water splitting to produce hydrogen under the irradiation of the solar light.

Accurate global potential energy surface for SiH2 +(X2A1) and quantum dynamics of related reaction H(2S) + SiH+(X1Σ+).

With the many-body expansion method, an accurate global potential energy surface (PES) is constructed for SiH2 +(X2A1) by mapping 4762 ab initio energy points calculated on the multireference configuration interaction level including Davidson corrections with aug-cc-pV6Z Dunning's basis set. The dissociation energies and equilibrium geometries of SiH+(X1Σ+) and H2(X1Σg +) agree well with the experimental results. The topographical characteristics of all stationary points for the SiH2 +(X2A1) PES are discussed in detail and compared with other theoretical and experimental results. In order to verify the validity and usability of the present PES, the dynamics calculations based on the Chebyshev quantum wave packet method are performed for the H(S2)+SiH+(X1Σ+)→Si+(P2)+H2(X1Σg +) reaction. The probabilities, the total integral cross sections, and the rate constants are computed, and the analogies with the corresponding ones of reaction H(S2) + CH+(X1Σ+)→C+(P2) + H2(X1Σg +) are also made. The reasonable dynamical behavior throughout the entire configuration space indicates that the PES is suitable for relevant dynamics investigations and serves as a building block for constructing the PES of larger molecular systems containing Si+/H.

Photocatalytic hydrogen production from water splitting with N-doped ß-Ga2O3 and visible light.

Based on the first principles calculations, the feasibility of the photocatalytic hydrogen production from water splitting driven by N-doped ß-Ga2O3 in the visible light is investigated. The formation energy and dynamics properties are used to examine the stability of the doped structures. The absolute positions of the band energy edges are obtained and compared to the redox potentials of the hydrogen production reaction. Moreover, we calculate the carrier lifetime and mobility for both electron and hole of all the considered structures. The optical absorption is also calculated for each structure. The results show that the 5.00 at.% N-doped ß-Ga2O3 has the satisfactory band energy edges, obvious difference of mobilities between electron and hole, and significant enhancement of absorption in visible light range, indicating it is a promising photocatalytic material to catalyze hydrogen production from water splitting under the irradiation of the visible light.

Accurate potential energy surface of H2S+(X 2 A″) via extrapolation to the complete basis set limit and its use in dynamics study of S + ( D 2 ) + H 2 ( X 1 Σ g + ) reaction.

The single-sheeted potential energy surface (PES) of H 2 S + ( X 2 A ' ' ) is developed based on the ab initio energies calculated by the multi-reference configuration interaction method including the Davidson correction. All the ab initio energies are first calculated using aug-cc-pVQdZ and aug-cc-pV5dZ basis sets, which are then extrapolated to the complete basis set (CBS) limit. A switching function is developed to model the transition of S + D 2 to S + S 4 . The many-body expansion formalism is employed to obtain the H 2 S + ( X 2 A ' ' ) PES by fitting such CBS energies and the root-mean square derivation is 0.0367 eV. The topographical features of the present PES are examined in detail, which are well consistent with previous studies. The quasiclassical trajectory method is subsequently utilized to study the S + D 2 + H 2 ( X 1 Σ g + ) → S H + ( X 3 Σ - ) + H ( S 2 ) reaction. The capture time, integral cross sections, and rovibrational distributions are calculated. By examining the capture time, it can be concluded that the title reaction is mainly controlled by the indirect mechanism for lower collision energies, while the direct and indirect mechanisms coexist and the latter plays a dominant role for higher collision energies.

Globally accurate potential energy surface for the ground-state HCS(X2A') and its use in reaction dynamics.

A globally accurate many-body expansion potential energy surface is reported for HCS(X2A') by fitting a wealth of accurate ab initio energies calculated at the multireference configuration interaction level using aug-cc-pVQZ and aug-cc-pV5Z basis sets via extrapolation to the complete basis set limit. The topographical features of the present potential energy surface are examined in detail and is in good agreement with the raw ab initio results, as well as other theoretical results available in literatures. By utilizing the potential energy surface of HCS(X2A'), the dynamic studies of the C(3P) + SH(X2Π) → H(2S) + CS(X1∑+) reaction has been carried out using quasi-classical trajectory method.

State-to-State Quantum Dynamics of Reactions O((3)P) + HD (v = 0-1, j = 0) → OH+D and OD+H: Reaction Mechanism and Vibrational Excitation.

Time-dependent quantum wave packet dynamics calculations have been performed in order to characterize the dynamics and mechanism of O((3)P) + HD (v = 0-1, j = 0) → OH+D and OD+H reactive collisions using the adiabatic potential energy surface by Rogers et al. [J. Phys. Chem. A 2000, 104, 2308] Special attention has been paid to the calculations and discussion of the state resolved integral and differential cross sections and the product state distributions. In addition, the intramolecular isotopic branching ratio has been determined. The results revealed that the OD + H is the favored product channel and the product OH has the same quantum number v as the reactant HD. For low collision energy, the product angular distributions concentrate in the backward region being consistent with a rebounding mechanism. In the case of higher collision energy, the stripping collisions with larger impact parameters tend to produce sideways and forward scatterings, especially for the HD vibrationally excited state. The cross section and intramolecular isotopic branching ratio are in agreement with the previous theoretical results. A cartoon depiction collision model is built and works well for our calculation results.

Quantum reaction dynamics of the C(1D)+H2(D2)→CH(D)+H(D) on a new potential energy surface.

The gas-phase reaction dynamics for the C((1)D) + H2(D2) → CH(D) + H(D) is investigated on a new ab initio potential energy surface (PES). The initial state-specified integral cross section and rate constant are obtained using the Chebyshev real wave packet method; the low-lying vibrational energy levels are also calculated on this new PES using Lanczos algorithm. The vibrational energy levels agree well with the experimental data and are superior to Bussery-Honvault-Honvault-Launay [B. Bussery-Honvault, P. Honvault, and J.-M. Launay, J. Chem. Phys. 115, 10701 (2001)] surfaces' results. The reaction probabilities display oscillatory structure due to the numerous long-lived resonances supported by the deep potential well. The rate constants show nearly temperature independence at the range of 100 K-350 K.