Analysis of Interaction Features of Cyclo[13]carbon with Small Molecules and Formation Mechanism of Its Dimer.

The newly discovered cyclo[13]carbon, the first artificially synthesized odd-numbered carbon ring, is an intriguing carbon isomer that provides a valuable subject for studying low-symmetry carbon materials. In this work, we employed first-principles calculations to explore the geometric structure and electronic properties of cyclo[13]carbon through various techniques such as vibrational mode analysis, bond order analysis, spin density analysis, electron localization analysis, electrostatic potential and van der Waals potential analysis, visualization of weak interactions, and energy decomposition analysis. We investigated the interaction characteristics of cyclo[13]carbon with small molecules and examined its dimer formation mechanism and dynamics features using ab initio molecular dynamics.

Designing Quasi-Intrinsic Photosensitizers with Dual Function of Fluorescence Imaging and Photodynamic Therapy.

Photosensitizers (PSs) with effective two-photon absorption in the therapeutic window are the key to two-photon photodynamic therapy. However, the traditional exogenous PSs usually lead to rejection in the body. Besides, the precise visualization of treatments proposes new demands and challenges for the design of PSs.

Newly Designed Quasi-intrinsic Photosensitizers for Fluorescence Image-Guided Two-Photon Photodynamic Therapy with Type I/II Photoreactions.

In this work, a set of quasi-intrinsic photosensitizers are theoretically proposed based on the 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo[1,2-α]-1,3,5-triazin-4(8H)-one (P), which could pair with the 6-amino-5-nitro-3-(1'-β-d-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z) and keep the essential structural characters of nucleic acid. It is revealed that the ring expansion and electron-donating/electron-withdrawing substitution bring enhanced two-photon absorption and bright photoluminescence of these monomers, thereby facilitating the selective excitation and tumor localization through fluorescence imaging. However, instead of undergoing radiative transition (S → S), the base pairing induced fluorescence quenching and rapid intersystem crossing (S → T) are observed and characterized by the reduced singlet-triplet energy gaps and large spin-orbit coupling values.

Theoretical Insights into the Effect of Different Numbers of Thiophene Groups on Hydrogen Bond Interaction and Excited-State Intramolecular Proton-Transfer Process for Flavonoid Derivatives.

In this study, we systematically explored the impact of varying the number of thiophene groups on the hydrogen bond interaction and excited-state intramolecular proton-transfer (ESIPT) processes in flavonoid derivatives (STF, DTF, and TTF) using the density functional theory and time-dependent density functional theory methods. Initially, a thorough analysis of the optimized geometric structures revealed that the intramolecular hydrogen bond in the S state is enhanced and gradually weakened as the number of thiophene groups increases. To gain a deeper understanding of the hydrogen bond interaction, topological analysis, interaction region indicator scatter plots, and isosurface plots were employed.

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'-β-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'-β-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.

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.

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.

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 ( = -3286.681 cm) and sensitive magnetic responses to the external electric field.

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

N'-(2'-Deoxyguanosin-8-yl)-4-aminobiphenyl (dG) 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 G, 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 G.

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'-β-d-2'-deoxyribofuranosyl)-5-nitro-1-pyridin-2-one (Z), 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2a]-1,3,5-triazin-[8]-4-one (P), 6-amino-9[(1'-β-d-2'-deoxyribofuranosyl)-4-hydroxy-5-(hydroxymethyl)-oxolan-2-yl]-1-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.

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.

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 HAsO and thiourea derivatives and environmental factors influences, aiming to find out the best monomer and optimal preparation conditions for HAsO MIPs.

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

In this work, a set of new potential radiation sensitizers (4-substituted -bases: 4XZ, X = F, Cl, Br, and I) are designed based on the artificial 6-amino-5-nitro-3-(1'--D-2'-deoxyribofuranosyl)-2(1)-pyridone (), which can selectively bind to breast cancer cells. The calculated electron affinities in water solution show that the halogenated -bases are efficient electron acceptors which possess significant electron-withdrawing characters following the order of 4XZ > ≫ . 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.

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'-β-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'-β-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.

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-β-D-2'-deoxyribo-furanosyl)-2 (1H)-pyridone (Z) and paired with its Watson-Crick complement, the purine analog 2-amino-8-(1'-β-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.

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 (HSA) and 2,2'-[1,4-Phenylenebis{(E)-nitrilomethylidyne}] bisphenol (HSPA) with double proton transfer characteristics were synthesized recently (Phys. Chem. Chem.

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.

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.

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.

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.

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.

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.