Dual receptor NIR-II organic nanoparticles for multimodal imaging guided tumor photothermal therapy

The second near-infrared (NIR-II) fluorescence imaging has attracted continuous attention due to its excellent penetration depth and high spatial resolution. Compared with other fluorophores, NIR-II fluorophores, especially NIR-II organic small molecule fluorophores, are favored because of their controllable structure and good biocompatibility. In this study, we designed and synthesized an S-D-A-D-S type small molecule FEA. However, a new molecule was accidentally obtained in the process of synthesis, which was proved to be a double receptor (A-A) type small molecule, namely S-D-A-A-D-S type organic small molecule FEAA. Compared with FEA molecules, FEAA exhibits superior fluorescence performance and can effectively prevent fluorescence quenching. The fluorescence emission of its nanoparticles (NPs) reaches 1109 nm, extends to about 1400 nm, and has a Stokes shift of up to 472 nm. Subsequently, we realized fluorescence/photoacoustic dual-mode imaging (FI/PAI) of nude mouse liver, and finally effectively ablated 4T1 tumor by photothermal therapy (PTT). In general, FEAA NPs exhibit good fluorescence, photoacoustic, and photothermal effects, and are an excellent multifunctional NIR-II organic small molecule fluorophore. As far as we know, there are few reports on A-A type organic small molecules, most of which are cyanines or D-A-D type structures. Therefore, this study has good exploratory significance and reference value for the discovery of NIR-II fluorophores.

Insight into boron-doped biochar as efficient metal-free catalyst for peroxymonosulfate activation: Important role of -O-B-O- moieties

In recent years, metal-free catalysts for persulfate-mediated oxidation processes have been widely applied to remove contaminants in the aquatic environment. Herein, a simple pyrolysis approach was used to synthesize the boron doped biochars (B@TBCs) derived from boric acid mixed with tea seed shells powders. The obtained B@TBCs exhibited fantastic capability to boost PMS (0.5 mM) activation for 90%∼ removal of oxytetracycline (OTC) within 20 min. Through the correlation analysis and DFT calculations, it was concluded that the apparent rate constant of pollutants removal was greatly related to the -O-B-O- groups on the biochars, which could improve the electron-donating capacity of the biochar. In addition, the degradation process of OTC was pH-dependent because of the changed roles of ROSs under different pH. Finally, according to the DFT calculation, LC-MS and toxicological analysis, the degradation pathways of pollutants and the toxicity changes during the degradation process were obtained. These findings consolidated the theoretical basis for further boosting the catalytic activity of B-doped biochars and expanded the imagination for the modification of other metal-free biochar catalysts for PMS activation.

Poisoning density functional theory with benchmark sets of difficult systems

Large benchmark sets like GMTKN55 [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184] let us analyse the performance of density functional theory over a diverse range of systems and bonding types. However, assessing over a large and diverse set can miss cases where approaches fail badly, and can give a misleading sense of security. To this end we introduce a series of 'poison' benchmark sets, P30-5, P30-10 and P30-20, comprising systems with up to 5, 10 and 20 atoms, respectively. These sets represent the most difficult-to-model systems in GMTKN55. We expect them to be useful in developing new approximations, identifying weak points in existing ones, and to aid in selecting appropriate DFAs for computational studies involving difficult physics, e.g. catalysis.

Linear fractional charge behavior in density functional theory through dielectric tuning of conductor-like polarizable continuum model

A property of exact density functional theory is linear fractional charge behavior as electrons are added or removed from a molecule. Typical density functional approximations (DFAs) exhibit delocalization error, which overstabilizes this fractional charge. Conversely, solvent corrections have been shown to erroneously destabilize this fractional charge. This work will show that an implicit solvent correction with a tuned dielectric can be used as an ad hoc correction to offset the delocalizing character of DFAs and achieve linear fractional charge behavior. While desirable, in principle, we find that this linear charge behavior degrades the vertical ionization energies reported by DFAs. Our results reveal that the localizing character of the solvent correction and the Hartree-Fock (HF) exchange offset each other. This helps explain the decreased ratios of HF exchange to DFA exchange in long-range hybrid tuning studies that use a solvent correction.

UV-Visible Lysine-Glutamate Dimer Excitations in Protein Charge Transfer Spectra: TDDFT Descriptions Using an Optimally Tuned CAM-B3LYP Functional

Recent reports of distinctive UV-vis absorption profiles for monomeric proteins rich in charged amino acids that span 250-800 nm have opened up a new label-free optical spectral window for probing biomolecular structure and interactions. Combined experimental-computational studies have revealed that such broad absorption profiles of these proteins arise from photoexcited charge transfer (CT) transitions in spatially proximal charged amino acids such as lysine (Lys) and glutamate (Glu). Here, using time-dependent density functional theory (TDDFT) with an optimally tuned CAM-B3LYP functional, we refine the computed UV-vis spectra for Lys-Glu dimers within protein folds and quantify the percentage CT character of the constituent transitions. The optimally tuned functionals are derived through a careful analysis of the CAM-B3LYP parameter space for Lys-Glu dimers as a function of amino-acid conformation and side chain separation. Our studies reveal that the tuned Lys-Glu dimer spectrum spans 150-650 nm and possesses 5 specific types of CT excitations with diverse and large spatial charge separation length scales of 2-10 Å. These include inter-/intra-residue peptide backbone to peptide backbone (BB-CT) excitations spanning 160-210 nm, inter-/intra-residue peptide backbone to side chain (BS-CT) excitations spanning 160-260 nm, and side chain to side chain (SS-CT) excitations, which show the broadest absorption range spanning 260-650 nm.

Excited States of One-Electron Oxidized Guanine-Cytosine Base Pair Radicals: A Time Dependent Density Functional Theory Study

One-electron oxidized guanine (G^•+) in DNA generates several short-lived intermediate radicals via proton transfer reactions resulting in the formation of neutral guanine radicals. The identification of these radicals in DNA is of fundamental interest to understand the early stages of DNA damage. Herein, we used time-dependent density functional theory (TD-ωB97XD-PCM/6-31G(3df,p)) to calculate the vertical excitation energies of one-electron oxidized G and G-cytosine (C) base pair in various protonation states: G^•+, G(N1-H)^•, and G(N2-H)^•, as well as G^•+-C, G(N1-H)^•-(H⁺)C, G(N1-H)^•-(N4-H⁺)C), G(N1-H)^•-C, and G(N2-H)^•-C in aqueous phase. The calculated UV-vis spectra of these radicals are in good agreement with the experiment for the G radical species when the calculated values are red-shifted by 40-70 nm. The present calculations show that the lowest energy transitions of proton transfer species (G(N1-H)^•-(H⁺)C, G(N1-H)^•-(N4-H⁺)C, and G(N1-H)^•-C) are substantially red-shifted in comparison to the spectrum of G^•+-C. The calculated spectrum of G(N2-H)^•-C shows intense absorption (high oscillator strength), which matches the strong absorption in the experimental spectra of G(N2-H)^• at 600 nm. The present calculations predict the lowest charge transfer transition of C → G^•+ is π → π* in nature and lies in the UV region (3.4-4.3 eV) with small oscillator strength.

pH Controlled Intersystem Crossing and Singlet Oxygen Generation of 8-Azaadenine in Aqueous Solution

Azabases are intriguing DNA and RNA analogues and have been used as effective antiviral and anticancer medicines. However, photosensitivity of these drugs has also been reported. Here, pH-controlled intersystem crossing (ISC) process of 9H 8-azaadenine (8-AA) in aqueous solution is reported. Broadband transient absorption measurements reveal that the hydrogen atom at N9 position can greatly affect ISC of 8-AA and ISC is more favorable when 8-AA is in its neutral form in aqueous solution. The initial excited ππ* (S₂ ) state evolves through ultrafast internal conversion (IC) (4.2 ps) to the lower-lying nπ* state (S₁ ), which further stands as a door way state for ISC with a time constant of 160 ps. The triplet state has a lifetime of 6.1 μs. On the other hand, deprotonation at N9 position promotes the IC from the ππ* (S₂ ) state to the ground state (S₀ ) and the lifetime of the S₂ state is determined to be 10 ps. The experimental results are further supported by time-dependent density functional theory (TDDFT) calculations. Singlet oxygen generation yield is measured to be 13.8 % for the neutral 8-AA while the deprotonated one exhibit much lower yield (<2 %), implying that this compound could be a potential pH-sensitized photodynamic therapy agent.

Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA

The intrinsic photostability of nucleic acids is intimately related to evolution of life, while its understanding at the molecular and electronic levels remains a challenge for modern science. Among the different decay pathways proposed in the last two decades, the excited-state hydrogen transfer between guanine-cytosine base pairs has been identified as an efficient non-reactive channel to dissipate the excess of energy provided by light absorption. The present work studies the dynamics of such phenomena taking place in a (dG)·(dC) B-DNA homopolymer in water solution using state-of-the-art molecular modelling and simulation methods. A dynamic effect that boosts the photostability of the inter-strand hydrogen atom transfers, inherent to the Watson-Crick base pairing, is unveiled and ascribed to the energy released during the proton transfer step. Our results also reveal a novel mechanism of DNA decay named four proton transfer (FPT), in which two protons of two adjacent G-C base pairs are transferred to form a biradical zwitterionic intermediate. Decay of the latter intermediate to the ground state triggers the transfer of the protons back to the guanine molecules recovering the Watson-Crick structure of the tetramer. This FPT process is activated by the close interaction of a nearby Na+ counterion with the oxygen atoms of the guanine nucleobases and hence represents a photostable channel operative in natural nucleic acids.

Theoretical exploitation of acceptors based on benzobis(thiadiazole) and derivatives for organic NIR-II fluorophores

Small-molecule dyes with fluorescence emission in the second near-infrared (NIR-II) region (1000-1700 nm) have attracted considerable attention in the biomedical and bioimaging fields due to their greater imaging depths, better spatial resolution, and higher signal-to-background ratios. However, currently reported organic NIR-II fluorophores are still limited and there is great demand to develop other novel NIR-II fluorophores besides benzobisthiadiazole (BBT)-based fluorophores. More importantly, there is a lack of an appropriate level of theory capable of providing both efficient and accurate predictions of the electronic structures of organic NIR-II fluorophores. In this work, successful application of time-dependent density functional theory (TDDFT) using optimally-tuned range-separated functionals for calculations of both absorption and fluorescence spectral properties has been demonstrated, compared with the available experimental data. A series of thiadiazole-based acceptors (A) and derivatives based on the D-A-D skeleton are designed coupled with the triphenylamine donor (D). The structure-property relationships for these fluorophores are thus revealed by analyzing their ground (S0) and excited (S1) state geometries, frontier molecular orbitals (HOMO and LUMO), HOMO-LUMO energy gaps, oscillator strengths, hole-electron distributions and fluorescence wavelengths. It is suggested that the existence of a hypervalent structure leading to a much lower LUMO level and accompanying significant hole-electron separation plays a key role in the red-shift of fluorescence emission in the NIR-II region. In addition, the substitution of BBT oligomers and analogues as acceptor cores is an efficient way to achieve both red-shifted fluorescence wavelengths and enhanced oscillator strengths. The present work provides a reliable and efficient theoretical tool for predicting the related electronic and spectral properties of organic fluorophores and future screening out of potential candidates for excellent NIR-II molecular fluorophores.

Rational Design of Molecular Fluorophores for Biological Imaging in the NIR-II Window

A new design for second near-infrared window (NIR-II) molecular fluorophores based on a shielding unit-donor-acceptor-donor-shielding unit (S-D-A-D-S) structure is reported. With 3,4-ethylenedioxy thiophene as the donor and fluorene as the shielding unit, the best performance fluorophores IR-FE and IR-FEP exhibit an emission quantum yield of 31% in toluene and 2.0% in water, respectively, representing the brightest organic dyes in NIR-II region reported so far.

Solvent effects on the excited state characteristics of adenine–thymine base pairs

A systematic analysis of the excited state characteristics of the DNA base pair adenine–thymine in stacked and Watson–Crick hydrogen bonded configurations has been carried out in this study.

Excited state dynamics for hybridized local and charge transfer state fluorescent emitters with aggregation-induced emission in the solid phase: a QM/MM study

Investigation on the excited state dynamics to reveal the AIE and HLCT mechanisms by a QM/MM method.

Challenges in Simulating Light-Induced Processes in DNA

In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.

Using Density Functional Theory To Study Neutral and Ionized Stacked Thymine Dimers

Stacking interactions in thymine dimers are studied with density functional theory. According to our calculations, six dimers of comparable stability can be prepared at low temperature, but dimerization is impossible at room temperature due to the large entropy contribution that accompanies it. Analysis of vibrational anharmonic coupling terms shows that each of the dimers exhibits distinct vibrational dynamics. Properties of electron density in the intermolecular region are used to analyze neutral stacked species and their ionized forms. Bond paths and critical points in the intermolecular region are identified, but a simple relationship between binding energy and total electron density in the intermolecular critical points could not be found due to an uneven electron distribution in the binding region. The reduced density gradient was confirmed to be a useful tool for analysis of weak stacking interactions. Those interactions also affect vertical and adiabatic ionization energies, which are computed to be slightly lower for the dimers compared to the monomer.

Characterization of the excited states of DNA building blocks: a coupled cluster computational study

DNA building blocks consisting of up to four nucleobases are investigated using the EOM-CCSD and CC2-LR methods in two B-DNA-like arrangements of a poly-adenine:poly-thymine (poly-A:poly-T) system. Excitation energies and oscillator strengths are presented and the characteristics of the excited states are discussed. Excited states of single-stranded poly-A systems are highly delocalized, especially the spectroscopically bright states, where delocalization over up to four fragments can be observed. In the case of poly-T systems, the states are somewhat less delocalized, extending to maximally about three fragments. A single A:T Watson-Crick pair has highly localized states, while delocalization over base pairs can be observed for some excited states of the (A)2:(T)2 system, but intrastrand delocalization is more pronounced in this case, as well. As for the characteristics of the simulated UV absorption spectra, a significant decrease of intensity can be observed in the case of single strands with increasing chain length; this is due to the stacking interactions and is in accordance with previous results. On the other hand, the breaking of H-bonds between the two strands does not alter the spectral intensity considerably, it only causes a redshift of the absorption band, thus it is unable to explain the experimentally observed DNA hyperchromism on its own, and stacking interactions need to be considered for the description of this effect as well.