Bacterial Susceptibility to Ceria Nanoparticles: The Critical Role of Surrounding Molecules.

Investigating the ternary relationship among nanoparticles (NPs), their immediate molecular environment, and test organisms rather than the direct interaction between pristine NPs and test organisms has been thrust into the mainstream of nanotoxicological research. Diverging from previous work that predominantly centered on surrounding molecules affecting the toxicity of NPs by modulating their nanoproperties, this study has unveiled a novel dimension: surrounding molecules altering bacterial susceptibility to NPs, consequently impacting the outcomes of nanobio interaction. The study found that adding nitrate as the surrounding molecules could alter bacterial respiratory pathways, resulting in an enhanced reduction of ceria NPs (nanoceria) on the bacterial surfaces. This, in turn, increased the ion-specific toxicity originating from the release of Ce3+ ions at the nanobio interface. Further transcriptome analysis revealed more mechanistic details underlying the nitrate-induced changes in the bacterial energy metabolism and subsequent toxicity patterns. These findings offer a new perspective for the deconstruction of nanobio interactions and contribute to a more comprehensive understanding of NPs' environmental fate and ecotoxicity.

Computational determination of the S1(Ã1A″) absorption spectra of HONO and DONO using full-dimensional neural network potential energy surfaces.

The Ã1A″ ← X̃1A' absorption spectra of HONO and DONO were simulated by a full six-dimensional quantum mechanical method based on the newly constructed potential energy surfaces for the ground and excited electronic states, which were represented by the neural network method utilizing over 36 000 ab initio energy points calculated at the multireference configuration interaction level with Davidson correction. The absorption spectrum of HONO/DONO comprises a superposition of the spectra from two isomers, namely, trans- and cis-HONO/DONO, due to their coexistence in the ground X̃1A' state. Our calculated spectra of both HONO and DONO were found to be in fairly good agreement with the experiment, including the energy positions and widths of the peaks. The dominant progression was assigned to the N=O stretch mode (20n) associated with trans-HONO/DONO, which can be attributed to the promotion of an electron to the π* orbital of N=O. Specifically, the resonances with higher vibrational quanta were found to be in the domain of the Feshbach-type resonances. The assignments of the spectra and mode specificity therein are discussed.

Impact of Geometric Phase on Dynamics of Complex-Forming Reactions: H + O2 → OH + O.

Reaction dynamics on the ground electronic state might be significantly influenced by conical intersections (CIs) via the geometric phase (GP), as demonstrated for activated reactions (i.e., the H + H2 exchange reaction). However, there have been few investigations of GP effects in complex-forming reactions. Here, we report a full quantum dynamical study of an important reaction in combustion (H + O2 → OH + O), which serves as a proving ground for studying GP effects therein. The results reveal significant differences in reaction probabilities and differential cross sections (DCSs) obtained with and without GP, underscoring its strong impact. However, the GP effects are less pronounced for the reaction integral cross sections, apparently due to the integral of the DCS over the scattering angle. Further analysis indicated that the cross section has roughly the same contributions from the two topologically distinct paths around the CI, namely, the direct and looping paths.

Quantum state-to-state nonadiabatic dynamics of the charge transfer reaction H+ + NO(X2Π) → H + NO+(X1Σ+): Influence of ro-vibrational excitation of NO.

Quantum state-to-state nonadiabatic dynamics of the charge transfer reaction H+ + NO(X2Π, vi = 1, 3, ji = 0, 1) → H + NO+(X1Σ+) has been studied based on the recently constructed diabatic potential energy matrix. It was found that the vibrational excitation of reactant NO inhibits the reactivity, while the rotational excitation of reactant NO has little effect on the reaction probability. These attributes were also observed in the semi-classical trajectory calculations employed in the adiabatic representation. Such an inhibitory effect of the vibrational excitation of reactant NO was owing to lower accessibility of the conical intersection and avoided crossing regions, which are located in the wells with respect to the Π diabat, as evidenced by the analysis of the population of the time-independent wave functions. Calculated vibrational state distributions of the product show that the decrease of the reaction mainly leads to the less formation of low vibrational states (vf < 6), and the product vibrational state distributions are more evenly populated for vi = 1 and 3, suggesting a non-statistical behavior. However, the overall shapes of the product rotational distributions remain unchanged, indicating that the redistribution of energy into the rotation of product NO is sufficient in the charge transfer process between H+ and NO. While the reaction is dominated by the forward and backward scattering in differential cross sections (DCSs), consistent with the complex-forming mechanism, a clear forward bias in the DCSs appears, indicating that the occurrence of the reaction is not sufficiently long to undergo the whole phase space of the interaction configurations.

Quantum Dynamics of Photodissociation: Recent Advances and Challenges.

Recent advances in constructing accurate potential energy surfaces and nonadiabatic couplings from high-level ab initio data have revealed detailed potential landscapes in not only the ground electronic state but also excited ones. They enabled quantitatively accurate characterization of photoexcited reactive systems using quantum mechanical methods. In this Perspective, we survey the recent progress in quantum mechanical studies of adiabatic and nonadiabatic photodissociation dynamics, focusing on initial state control and product energy disposal. These new insights helped to understand quantum effects in small prototypical systems, and the results serve as benchmarks for developing more approximate theoretical methods.

Full-dimensional potential energy surface for the photodissociation of HNCO via its S1 band.

A full-dimensional potential energy surface (PES) for the first excited state S1(1A'') of HNCO has been built up by the neural network method based on more than 36 000 ab initio points, which were calculated at the multireference configuration interaction level with Davidson correction using the augmented correlation consistent polarized valence triple zeta basis set. It was found that two minima, namely, trans and cis isomers of HNCO, and another seven stationary points exist on the S1 PES for the two dissociation pathways: HNCO(S1) → H + NCO/NH + CO. Particularly, a new out-of-plane transition state between the two minima was found in this work, thanks to including all the degree of freedoms for this system. The adiabatic excitation energy of the S1(1A'') ← S0(1A') transition and dissociation energies D0(HNCO → H + NCO) and D0((HNCO →NH(a1Δ) + CO) calculated on the PES are in good agreement with experimental results. In addition, based on the newly constructed S1 PES, the percentage of products H + NCO in the photodissociation of HNCO(S1) was obtained by a quasi-classical trajectory method at the photon wavelengths ranging from 190 to 225 nm, which is in reasonably good agreement with earlier theoretical and experimental results. For the dissociation lifetimes of the trajectories, they were calculated to be less than 5 ps, which is also consistent with experimental observations.

Advanced nanopesticides: Advantage and action mechanisms.

The use of various chemical substances to control pests, diseases, and weeds in the field is a necessary part of the agricultural development process in every country. While the application of pesticides can improve the quality and yield of crops, plant resistance and the harm caused by pesticide residues to the environment and humans have led to the search for greener and safer pesticide formulations to improve the current situation. In recent years, nanopesticides (NPts) have shown great potential in agriculture due to their high efficiency, low toxicity, targeting, resistance, and controlled slow release demonstrated in the experimental stage. Commonly used approaches to prepare NPts include the use of nanoscale metal materials as active ingredients (AI) (ingredients that can play a role in insecticide, sterilization and weeding) or the construction of carriers based on commonly used pesticides to make them stable in nano-sized form. This paper systematically summarizes the advantages and effects of NPts over conventional pesticides, analyzes the formation and functions of NPts in terms of structure, AI, and additives, and describes the mechanism of action of NPts. Despite the feasibility of NPts use, there is not enough comprehensive research on NPts, which must be supplemented by more experiments in terms of biotoxicology and ecological effects to provide strong support for NPts application.

Toward a Unified Analytical Description of Internal Conversion and Intersystem Crossing in the Photodissociation of Thioformaldehyde. I. Diabatic Singlet States.

The photodissociation of thioformaldehyde is an archetypal system for the study of competition between internal conversion and intersystem crossing, which involves its two singlet states (S0 and S1) and two triplet states (T1 and T2). In order to perform accurate dynamic simulations, either quantum or quasi-classical, it is essential to construct an analytical representation for all necessary electronic structure data. In this work, a diabatic potential energy matrix (DPEM), Hd, for the two singlet states (S0 and S1) is reported. The analytical form of DPEM is symmetrized and constructed to reproduce adiabatic energies, energy gradients, and derivative couplings obtained from high-level multireference configuration interaction wave functions. The Hd is fully saturated in the molecular configuration space with a trajectory-guided point sampling approach. This Hd can provide the accurate description of the photodissociation of thioformaldehyde on its singlet states and is also a necessary part for incorporating the spin-orbit couplings into a unified diabatic framework. Preliminary quasi-classical trajectory simulations show that a roaming mechanism also exists in the molecular dissociation channel of thioformaldehyde.

Nonadiabatic quantum dynamics of the charge transfer reaction H+ + NO(X2Π) → H + NO+(X1Σ+).

Nonadiabatic quantum dynamics of the charge transfer (CT) reaction H+ + NO(X2Π) → H + NO+(X1Σ+) is investigated on a new diabatic potential energy matrix (PEM) including the 12A' and 22A' states of HNO+/HON+ at the multireference configuration interaction level with Davidson correction using a large basis set. The diabatization of the two coupled states was achieved by the adiabatic-to-diabatic transformation with a mixing angle and the final diabatic PEM was obtained by fitting each matrix element separately using a three-dimensional cubic spline interpolation including more than 22 000 ab initio points. The reaction was found to be dominated by the resonances supported by the double well associated with HNO+ and HON+ species, manifested by the oscillatory structures in the reaction probabilities and product rotational distributions. The product vibrational states were highly excited due to the large exothermicity of the reaction. Consistent with the complex-forming mechanism, the differential cross sections (DCSs) were found to be dominated by the forward and backward scatterings. A clear forward bias in the vibrational state resolved DCSs suggests that the non-statistical behavior of the reaction mainly comes from the low vibrational states of the product. In addition, the rate constants of the reaction in the temperature range from 50 to 500 K were computed for the first time and found to be in fairly good agreement with the available experimental results at 300 K. In particular, compared to other reactions involving neutral species in this system including N, O, and H atoms, such a CT reaction was found to be much more reactive, which has rate constants more than thirty times larger.

Simulating the HeI photoelectron spectrum of Cl2O with new full-dimensional adiabatic potential energy surfaces of Cl2O(X̃1A1), Cl2O+(X̃2B1), and Cl2O+(C̃2A2) and a three-state diabatic potential energy matrix of Cl2O+(Ã2B2, B̃2A1, and 22A1): a quantum mechanical study.

To interpret the HeI photoelectron spectrum of Cl2O (involving four lowest electronic states of Cl2O+), in this work we first constructed the associated adiabatic full-dimensional potential energy surfaces (PESs) of Cl2O(X̃1A1), Cl2O+(X̃2B1), and Cl2O+(C̃2A2) and a diabatic potential energy matrix (PEM) of Cl2O+(Ã2B2, B̃2A1, and 22A1) using the explicitly correlated internally contracted multi-reference configurational interaction with Davidson correction (MRCI-F12+Q) and neural network methods. Particularly for the Ã2B2, B̃2A1, and 22A1 states of Cl2O+ coupled in terms of conical intersection, their diabatization is achieved by the neural network approach based merely on the associated adiabatic energies. With the help of newly constructed adiabatic PESs and the diabatic PEM, the HeI photoelectron spectrum of Cl2O is further computed quantum mechanically. The calculated photoelectron spectrum is found to be in good accord with experiment. The mode specificity in the HeI photoelectron bands of Cl2O is analyzed in detail.

Nonadiabatic heavy atom tunneling in 1nσ*-mediated photodissociation of thioanisole.

The 1nσ*-mediated photodissociation dynamics of thioanisole is investigated quantum mechanically using a three-dimensional model based on a newly constructed diabatic potential energy matrix. The lifetimes of the low-lying S1(1ππ*) resonances are determined and found to accord well with available experimental data. Specifically, our theoretical results demonstrate that the photodissociation of thioanisole at the low-lying S1(1ππ*) levels takes place via the heavy atom tunneling due to the higher S1/S2 conical intersection and two equivalent out-of-plane saddle points appearing on the dissociation path. The isotopic effect on the lifetimes is found to be pronounced, manifesting the nature of the tunneling process. Moreover, the geometric phase effect around the S1/S2 conical intersection is found to slightly impact the lifetimes due to the weak destructive or constructive interferences in this heavy atom tunneling, which differs significantly from the scenario in the nonadiabatic hydrogen atom tunneling. Importantly, the quantum mechanical treatment is essentially required to accurately describe the 1nσ*-mediated photodissociation dynamics of thioanisole owing to involving quantum tunneling and geometric phase effects near the conical intersection.

Constructing Diabatic Potential Energy Matrices with Neural Networks Based on Adiabatic Energies and Physical Considerations: Toward Quantum Dynamic Accuracy.

A permutation invariant polynomial-neural network (PIP-NN) approach for constructing the global diabatic potential energy matrices (PEMs) of the coupled states of molecules is proposed. Specifically, the diabatization scheme is based merely on the adiabatic energy data of the system, which is ideally a most convenient way due to not requiring additional ab initio calculations for the data of the derivative coupling or any other physical properties of the molecule. Considering the permutation and coupling characteristics of the system, particularly in the presence of conical intersections, some vital treatments for the off-diagonal terms in diabatic PEM are essentially needed. Taking the photodissociation of H2O(X~/B~)/NH3(X~/A~) and nonadiabatic reaction Na(3p) + H2 → NaH(Σ+) + H for example, this PIP-NN method is shown to build up the global diabatic PEMs effectively and accurately. The root-mean-square errors of the adiabatic potential energies in the fitting for three different systems are all small (<10 meV). Further quantum dynamic calculations show that the absorption spectra and product branching ratios in both H2O(X~/B~) and NH3(X~/A~) nonadiabatic photodissociation are well reproduced on the new diabatic PEMs, and the nonadiabatic reaction probability of Na(3p) + H2 → NaH(Σ+) + H obtained on the new diabatic PEMs of the 12A1 and 12B2 states is in reasonably good agreement with previous theoretical result as well, validating this new PIP-NN method.

Geometric Phase Effect in Attosecond Stimulated X-ray Raman Spectroscopy.

Conical intersections (CIs) are diabolical points in the potential energy surfaces generally caused by point-wise degeneracy of different electronic states, and give rise to the geometric phases (GPs) of molecular wave functions. Here we theoretically propose and demonstrate that the transient redistribution of ultrafast electronic coherence in attosecond Raman signal (TRUECARS) spectroscopy is capable of detecting the GP effect in excited state molecules by applying two probe pulses including an attosecond and a femtosecond X-ray pulse. The mechanism is based on a set of symmetry selection rules in the presence of nontrivial GPs. The model of this work can be realized for probing the geometric phase effect in the excited state dynamics of complex molecules with appropriate symmetries, using attosecond light sources such as free-electron X-ray lasers.

Characterization of the lipidomic profile of clam Meretrix petechialis in response to Vibrio parahaemolyticus infection.

Vibrio parahaemolyticus is a devastating pathogen of clam Meretrix petechialis, which brings about huge economic losses in aquaculture breeding industry. In our previous study, we have found that Vibrio infection is closely associated with lipid metabolism of clams. In this study, an untargeted lipidomics approach was used to explore the lipid profiling changes upon Vibrio infection. The results demonstrated that the hepatopancreas of clams was composed of five lipid categories including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids and sterol lipids. And the content of lipid classes altered during Vibrio infection, implying that Vibrio infection altered intracellular lipid homeostasis in clams. Meanwhile, a total of 200 lipid species including 82 up-regulated and 118 down-regulated significantly were identified in response to Vibrio infection, of which ceramide (Cer), phosphatidylcholine (PC) and triglyceride (TG) accounted for the largest proportion. Notably, all Cers showed a significantly decreased trend while nearly all TG species were increased significantly during Vibrio infection, which suggested that Cer and TG could be determined as effective biomarkers. Furthermore, these differentially expressed lipid species were enriched in 20 metabolic pathways and sphingolipid metabolism was one of the most enriched pathways. These results evidenced how the lipid metabolism altered in the process of Vibrio infection and opened a new perspective on the response of marine bivalves to pathogen infection.

Ultrahigh extinction ratio and ultralow insertion loss for polarization beam splitter based on two folded asymmetrical directional couplers with dual-stage etching.

We propose and experimentally demonstrate a polarization beam splitter (PBS) with excellent performance in terms of ultrahigh extinction ratio and ultralow insertion loss. The PBS consists of two dual-stage etched asymmetrical directional couplers, which are cascaded by a bend waveguide to form a folded structure. In the PBS, the fundamental transverse magnetic (T M 0) mode is efficiently cross-coupled to the cross-port, while the fundamental transverse electric (T E 0) mode outputs at the through-port. Thanks to the cascaded structure and dual-stage etching, a silicon-on-insulator-based PBS with ultrahigh extinction ratio and ultralow insertion loss is achieved. The measurement results reveal an extinction ratio beyond 25 dB and an insertion loss less than 0.7 dB within a wide bandwidth of 175 nm for the T E 0 and T M 0 modes.

Defining the Surface Oxygen Threshold That Switches the Interaction Mode of Graphene Oxide with Bacteria.

As antimicrobials, graphene materials (GMs) may have advantages over traditional antibiotics due to their physical mechanisms of action which ensure less chance of development of microbial resistance. However, the fundamental question as to whether the antibacterial mechanism of GMs originates from parallel interaction or perpendicular interaction, or from a combination of these, remains poorly understood. Here, we show both experimentally and theoretically that GMs with high surface oxygen content (SOC) predominantly attach in parallel to the bacterial cell surface when in the suspension phase. The interaction mode shifts to perpendicular interaction when the SOC reaches a threshold of ∼0.3 (the atomic percent of O in the total atoms). Such distinct interaction modes are highly related to the rigidity of GMs. Graphene oxide (GO) with high SOC is very flexible and thus can wrap bacteria while reduced GO (rGO) with lower SOC has higher rigidity and tends to contact bacteria with their edges. Neither mode necessarily kills bacteria. Rather, bactericidal activity depends on the interaction of GMs with surrounding biomolecules. These findings suggest that variation of SOC of GMs is a key factor driving the interaction mode with bacteria, thus helping to understand the different possible physical mechanisms leading to their antibacterial activity.

From marine to freshwater environment: A review of the ecotoxicological effects of microplastics.

Microplastics (MPs) have been widely detected in the world's water, which may pose a significant threat to the ecosystem as a whole and have been a subject of much attention because their presence impacts seas, lakes, rivers, and even the Polar Regions. There have been numerous studies that report direct adverse effects on marine organisms, but only a few have explored their ecological effects on freshwater organisms. In this field, there is still a lack of a systematic overview of the toxic effects and mechanisms of MPs on aquatic organisms, as well as a consistent understanding of the potential ecological consequences. This review describes the fate and impact on marine and freshwater aquatic organisms. Further, we examine the toxicology of MPs in order to uncover the relationship between aquatic organism responses to MPs and ecological disorders. In addition, an overview of the factors that may affect the toxicity effects of MPs on aquatic organisms was presented along with a brief examination of their identification and characterization. MPs were discussed in terms of their physicochemical properties in relation to their toxicological concerns regarding their bioavailability and environmental impact. This paper focuses on the progress of the toxicological studies of MPs on aquatic organisms (bacteria, algae, Daphnia, and fish, etc.) of different trophic levels, and explores its toxic mechanism, such as behavioral alternations, metabolism disorders, immune response, and poses a threat to the composition and stability of the ecosystem. We also review the main factors affecting the toxicity of MPs to aquatic organisms, including direct factors (polymer types, sizes, shapes, surface chemistry, etc.) and indirect factors (persistent organic pollutants, heavy metal ions, additives, and monomer, etc.), and the future research trends of MPs ecotoxicology are also pointed out. The findings of this study will be helpful in guiding future marine and freshwater rubbish studies and management strategies.

Graphene oxide disruption of homeostasis and regeneration processes in freshwater planarian Dugesia japonica via intracellular redox deviation and apoptosis.

The aquatic system is a major sink for engineered nanomaterials released into the environment. Here, we assessed the toxicity of graphene oxide (GO) using the freshwater planarian Dugesia japonica, an invertebrate model that has been widely used for studying the effects of toxins on tissue regeneration and neuronal development. GO not only impaired the growth of normal (homeostatic) worms, but also inhibited the regeneration processes of regenerating (amputated) worms, with LC10 values of 9.86 mg/L and 9.32 mg/L for the 48-h acute toxicity test, respectively. High concentration (200 mg/L) of GO killed all the worms after 3 (regenerating) or 4 (homeostasis) days of exposure. Whole-mount in situ hybridization (WISH) and immunofluorescence analyses suggest GO impaired stem cell proliferation and differentiation, and subsequently caused cell apoptosis and oxidative DNA damage during planarian regeneration. Mechanistic analysis suggests that GO disturbed the antioxidative system (enzymatic and non-enzymatic) and energy metabolism in the planarian at both molecular and genetic levels, thus causing reactive oxygen species (ROS) over accumulation and oxidative damage, including oxidative DNA damage, loss of mitochondrial membrane integrity, lack of energy supply for cell differentiation and proliferation leading to retardance of neuron regeneration. The intrinsic oxidative potential of GO contributes to the GO-induced toxicity in planarians. These data suggest that GO in aquatic systems can cause oxidative stress and neurotoxicity in planarians. Overall, regenerated tissues are more sensitive to GO toxicity than homeostatic ones, suggesting that careful handling and appropriate decisions are needed in the application of GO to achieve healing and tissue regeneration.

Toxicity of ceria nanoparticles to the regeneration of freshwater planarian Dugesia japonica: The role of biotransformation.

Cerium oxide nanoparticles (n-CeO2) have wide applications ranging from industrial to consumer products, which would inevitably lead to their release into the environment. Despite the toxicity of n-CeO2 on aquatic organisms has been largely reported, research on developing organisms is still lacking. In this study, we investigate the toxic effects of n-CeO2 on the stem cells, tissue- and neuro-regeneration, using freshwater planarian Dugesia japonica as a model. Effects of bulk sized (µ-) CeO2 and ionic Ce (Ce3+) were compared with that of n-CeO2 to explore the origin of the toxic effects of n-CeO2. No overt toxicity was observed in µ-CeO2 treatment. n-CeO2 not only impaired the homeostasis of normal planarians, but also inhibited the regeneration processes of regenerated planarians, demonstrated by the inhibited blastema growth, disturbed antioxidant defense system at molecular levels, elevated DNA-damage and decreased stem cell proliferation. Regenerating organisms are more susceptible to n-CeO2 than the normal ones. Ce3+ exhibited significantly higher toxicity than n-CeO2, even though the total Ce uptake is 0.2 % less in Ce3+ than in n-CeO2 treated in planarian. X-ray absorption near edge spectroscopy (XANES) analysis revealed that 12.8 % of n-CeO2 (5.95 mg/kg Ce per planarian) was transformed to Ce3+ after interaction with planarian, suggesting that biotransformation at the nano-bio interface might play an important role in the observed toxicity. Since the biotransformation of n-CeO2 is a slow process, it may cause long-term chronic toxicity to planarians due to the slow while sustained release of toxic Ce3+ ions.

Sodium Benzoate Delays the Development of Drosophila melanogaster Larvae and Alters Commensal Microbiota in Adult Flies.

Sodium benzoate (SB), the sodium salt of benzoic acid, is widely used as a preservative in foods and drinks. The toxicity of SB to the human body attracted people's attention due to the excessive use of preservatives and the increased consumption of processed and fast foods in modern society. The SB can inhibit the growth of bacteria, fungi, and yeast. However, less is known of the effect of SB on host commensal microbial community compositions and their functions. In this study, we investigated the effect of SB on the growth and development of Drosophila melanogaster larvae and whether SB affects the commensal microbial compositions and functions. We also attempted to clarify the interaction between SB, commensal microbiota and host development by detecting the response of commensal microbiota after the intervention. The results show that SB significantly retarded the development of D. melanogaster larvae, shortened the life span, and changed the commensal microbial community. In addition, SB changed the transcription level of endocrine coding genes such as ERR and DmJHAMT. These results indicate that the slow down in D. melanogaster larvae developmental timing and shortened life span of adult flies caused by SB intake may result from the changes in endocrine hormone levels and commensal microbiota. This study provided experimental data that indicate SB could affect host growth and development of D. melanogaster through altering endocrine hormone levels and commensal microbial composition.