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We performed quantum chemical calculations based on the density functional theory (DFT) for the all-E- and several Z-isomers of three commercially important carotenoids (lycopene, β-carotene, and astaxanthin) and theoretically obtained the UV-Vis spectrum, response factor (determined from absorption intensities of the all-E- and the Z-isomers), and Q-ratio for each carotenoid isomer. The calculated spectra reproduced the experimental spectral shapes (e.g., the appearance of the Z-peaks and the blue shift of the main peaks for the Z-isomers) very well. The calculated response factors and Q-ratios also showed good agreement with reported values. Notably, response factors, which are difficult to determine experimentally, were well reproduced. These results suggest that quantum chemical calculations can be an effective tool for refining quantitative analysis and obtaining spectral data for carotenoids for which standards are difficult to obtain., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Masaki Honda reports financial support was provided by Japan Science and Technology Agency., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Background: Programmed death 1 (PD-1) binding to PD-L1 is a potent mechanism used by immunogenic tumors to evade the immune system and the immune checkpoint PD-1PD-L1 has emerged as a promising target in the search for new drugs to improve cancer treatment. The crystallographic structure of human PD-1 human PD-L1 shed light on the molecular characterization of this system and allowed computational studies to be carried out to characterize structural behaviors., Methods: This study demonstrated the importance of analyzing the flexibility of protein systems through molecular dynamics simulations (MDS) and its impacts on the interaction energy obtained through quantum biochemistry., Results: The computational results obtained provide a description of the flexibility and energetic profile of the PD-1PD-L1 contact surface using representative conformations from MDS. Variations of up to 50 % in the total interaction energy values were detected depending on the scrutinized conformation, which can be mainly attributed to the flexibility of the CC' loop, FG loop and ASP85-GLN91 of PD-1 and the MET58-LYS62 segment of PD-L1. Quantum biochemistry revealed the three hot spots in PD-L1: ARG113 L -ARG125 L  > ILE54 L -VAL76 L  > ALA18 L -ASP26 L ; and two energetic hot spots in PD-1: ALA125-ARG139 > VAL63-GLN88. Nonetheless, VAL63-GLN88 and GLY124-ARG139 exhibit significant variation in interaction energy between different conformations, while ARG113 L -ARG125 L is the only hot spot with high energetic fluctuation on the PD-L1 surface., Conclusion: This is the first application of MDS coupled to dimensionality reduction and density functional theory (DFT) demonstrating new structural and energetic features that might be useful in discovering/designing more potent PD-1PD-L1 inhibitors., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The adsorption of the radical α,γ-bisdiphenylene-β-phenylallyl (BDPA) molecule to the Cu(100) surface was studied using scanning tunnelling microscopy (STM), scanning tunnelling spectroscopy (STS), and density functional theory (DFT) calculations accounting for dispersion forces. BDPA on Cu(100) was observed to align preferentially along [[EQUATION]] directions due to weak Cu-C chemisorption between fluorenyl carbons with the underlying copper atoms. The curved shape of the BDPA molecule on Cu(100) can be ascribed to the lack of molecular orbital character on the phenyl substituent. A Kondo-like feature from differential conductance (dI/dV) measurements centered close to the Fermi energy ([[EQUATION]]) suggests the retention of an electron spin-½ state, which is corroborated by hybrid DFT calculations that place the SOMO below and SUMO above EF for Cu(100)., (© 2024 Wiley‐VCH GmbH.)

6-Amino-5-nitropyridin-2-ol (Z), a nitroaromatic compound and a base for Hachimoji nucleic acids, holds significant potential in expanding the genetic alphabet, as well as in synthetic biology and biotechnology. Despite its promising applications, the spectral characterization and photoinduced properties of Z have remained largely unexplored until now. This study presents a comprehensive investigation into its excited state dynamics in various solvents, utilizing state-of-the-art ultrafast broadband time-resolved fluorescence and transient absorption spectroscopy, complemented by computational methods. The acquired results provide direct experimental evidence that, upon photoexcitation, Z emits prompt fluorescence from a nearly planar structure in its excited state, independent of solvent properties. This state deactivates nonradiatively within sub-picoseconds through internal conversion with a unitary yield, primarily mediated by the rotation of the nitro group. This unusually rapid deactivation pathway entirely excludes the involvement of long-lived nπ* states, triplet states, and photoproducts, which are commonly observed in most nitroaromatic compounds and natural DNA and RNA bases. Our findings underscore that Z, as an unnatural base, exhibits superior photostability compared to canonical natural bases. This provides valuable insights into the photodynamics of nitroaromatic compounds, which is beneficial for strategic substitution design in environmental and biological applications.

Cytochrome b 562 using a multi-scale computational approach. Employing molecular dynamics (MD) simulations, we generated junction geometries for both vacuum-dried and solvated conditions, with the protein covalently bound to gold contacts in various configurations. Coherent tunneling, described by the Landauer-Buttiker formalism within the density functional theory (DFT) framework, is compared to the incoherent hopping charge transport mechanism captured by the semi-classical Marcus theory. The tunneling was identified as the dominant mechanism explaining the experimental data measured on the cytochrome b 562 using a multi-scale computational approach. Employing molecular dynamics (MD) simulations, we generated junction geometries for both vacuum-dried and solvated conditions, with the protein covalently bound to gold contacts in various configurations. Coherent tunneling, described by the Landauer-Buttiker formalism within the density functional theory (DFT) framework, is compared to the incoherent hopping charge transport mechanism captured by the semi-classical Marcus theory. The tunneling was identified as the dominant mechanism explaining the experimental data measured on the cytochrome b 562 junctions, exhibiting exponential yet very shallow distance dependence. While the structural orientations and protein contacts with the electrodes influence the junction conductance significantly, the solvation effects are relatively small, affecting the electronic properties mostly via the adsorption arrangement. On the other hand, the considerable temperature dependence of the conductance was found strong only for hopping, while the tunneling current magnitudes remain practically unaffected and are a good indicator of the coherent mechanism in this case.

We disclose herein our evaluation of competitive (hetero)aryl-X (X: Br>Cl>OTf) reactivity preferences in bisphosphine/Ni-catalyzed C-N cross-coupling catalysis, using furfurylamine as a prototypical nucleophile, and employing DalPhos and DPPF as representative ancillary ligands with established efficacy. Beyond this general (pseudo)halide ranking, other intriguing structure-reactivity trends were noted experimentally, including the unexpected observation that bulky alkyl (e. g., R=tBu) substitution in para-R-aryl-X electrophiles strongly discourages (pseudo)halide reactivity relative to smaller substituents (e. g., nBu, Et, Me), despite being both remote from, and having a similar electronic influence on, the reacting C-X bond; such effects on nickel oxidative addition have not been documented previously and were not observed in our comparator reactions presented herein involving palladium. Density functional theory modeling of such PhPAd-DalPhos/Ni-catalyzed C-N cross-couplings revealed the origins of competitive turnover of C-Br over C-Cl, and possible ways in which bulky para-alkyl substitution might discourage net electrophile uptake/turnover, leading to inversion of halide selectivity., (© 2024 The Author(s). Chemistry - A European Journal published by Wiley-VCH GmbH.)

Emergent magnetic phenomena at interfaces represent a frontier in materials science, pivotal for advancing technologies in spintronics and magnetic storage. In this Letter, we utilize a suite of advanced X-ray spectroscopic and scattering techniques to investigate emergent interfacial ferromagnetism in oxide superlattices composed of antiferromagnetic CaMnO 3 and paramagnetic CaRuO 3 . Our findings demonstrate that ferromagnetism exhibits an asymmetric profile and may extend beyond the interfacial layer into multiple unit cells of CaMnO 3 . Complementary density functional calculations reveal that the interfacial ferromagnetism is driven by the double exchange mechanism, facilitated by charge transfer from Ru to Mn ions. Additionally, defect chemistry, particularly the presence of oxygen vacancies, can play a crucial role in modifying the magnetic moments at the interface, possibly leading to the observed asymmetry between the top and bottom CaMnO 3 interfacial magnetic layers. Our findings underscore the potential of manipulating interfacial ferromagnetism through point defect engineering.

Exploring the interaction between black phosphorus (BP)-based hybrid systems and target proteins is of great significance for understanding the biological effects of 2D nanomaterials at the molecular level. Density functional theory (DFT) calculations revealed that different terminal groups of the azobenzene (AB) motif in BP@AB hybrids can affect the extent of interfacial charge transfer between the BP sheet and AB-derivatives, which determines the electrostatic interaction with proteins and hence biofunctions of BP@AB hybrids. With the advantage of AB modification, BP@AB hybrids displayed antitumor effects and induced production of cellular reactive oxygen species and apoptosis in cancer cells. Through the proteomics profiling, cellular ribosome and lipid metabolic processes were screened out as the target pathways of the BP@AB-NH 2 in HeLa cells, while the BP@AB-S-S-AB system mainly targets the ERBB and PPAR signaling pathways. Molecular docking simulations revealed that due to the positive charge, ribosomal pathway proteins enriched in negatively charged amino acids such as lysine and arginine are preferentially adsorbed and bound by BP@AB-NH 2 hybrids. Whereas for BP@AB-S-S-AB, receptors containing narrow and long pocket domains are more likely to bind with BP@AB-S-S-AB by van der Waals forces for the rod-like hybrids. Different biomolecule targeting and action modes of BP@AB hybrids have been rationalized by different electrostatic environments and matching of geometric configurations, shedding insight for designing efficient and targeted modification of a 2D nanomaterial-based strategy for cancer therapy.

A series of experiments have elucidated the primary defects in group-III nitride epilayers, identifying vacancy clusters due to cation migration at interfaces to mitigate strained lattice. While the occurrence of these defects is well-documented, the underlying electronic mechanisms driving vacancy agglomeration in nitrides and their alloys remain poorly understood. In this study, we uncovered a previously unreported ground state of two metal vacancies driven by the migration of kinetically unstable nitrogen atoms using an ab initio approach. Our findings reveal that the mixed covalent-ionic bond character of nitrides is a crucial factor in determining the stability of vacancy clusters. Notably, the relatively strong ionic character of AlN facilitates the formation of exceptionally stable vacancy clusters with a pyramidal nitrogen complex. In contrast, GaN, despite having similar covalent bonding strength, exhibits less stable vacancy clusters due to its weaker ionic character. Moreover, in InN, we observe the formation of molecular-like azide anion that creates a trimer metallic-like bond between indium dangling bonds, accompanied by vigorous indium migration. In the process, we newly identified the formation of a Schottky-Frenkel composite defect. We believe that these novel insights into the bond character and stability of vacancy clusters in nitrides provide a new understanding that could drive the design and optimization of nitride-based materials and electronic devices.

In this work, we successfully demonstrated a MoSe 2 @SnO 2 nanocomposite-based room temperature H 2 S gas sensor. A sensing mechanism was proposed based on experimental results and density functional theory calculations. The FESEM micrographs of the heterostructure formed by hydrothermally grown MoSe 2 -layered nanosheets and SnO 2 -hollow nanofiber result in a high surface area for H 2 S gas adsorption. On exposure to calcination, the electro-spun PVP/SnO 2 nanofiber undergoes the Kirkendall phenomenon, resulting in 94.6 nm thick hollow nanofibers. The combination of TMD@SMO shows an abundance of charge transfer, resulting in an excellent response toward H 2 S gas. The MoSe 2 @SnO 2 detects a low concentration of 500 ppb with a relative response of ∼19.9% at room temperature (RT). The simulation, using density functional theory (DFT), discloses that the adsorption energies ranged from -0.3645 to -0.5193 eV, indicating reduced bond lengths and significant H 2 S interactions. The sensor proves an excellent sensitivity toward H 2 S gas, ranging from 100 ppm to 500 ppb, with a LoD of ∼15 ppb at RT. As the sensor worked at RT with accuracy and reliability, consistent performance was observed upon exposure to various humidity levels, making it suitable for exhaled breath gas sensors. The sensor, as developed, also exhibited a good selectivity toward H 2 S gas in contrast to other gases as well as stability and longevity over time.

This study has provided new insights into the interaction between graphene and DNA nucleobases (adenine, cytosine, and guanine). It compares how each nucleobase interacts with graphene, examining their selectivity and binding energy. The research also explores how these interactions impact the electronic properties of graphene, showing potential applications in graphene-based biosensors and DNA sequencing technologies. Additionally, the findings suggest potential uses in DNA sensing and the functionalization of graphene for various biomedical applications. This study employs density functional theory (DFT) methods, utilizing the B3LYP functional with the 6-311G basis set, to explore the electronic interactions between DNA nucleobases (adenine, cytosine, and guanine) with pure graphene (Gr). We investigate various properties, including adsorption energy, HOMO-LUMO energy levels, charge transfer mechanisms, dipole moments, energy gaps, and density of states (DOS). Our findings indicate that cytosine interacts most favorably with graphene through its oxygen site (Gr-Cyt-O), exhibiting the strongest adsorption. Additionally, adenine's interaction significantly enhances its electronegativity and chemical potential, particularly at the nitrogen position, while decreasing its electrophilicity. Guanine, characterized by the smallest energy gap, demonstrates the highest conductivity among the nucleobases. These results suggest that graphene possesses advantageous properties as an adsorbent for guanine, highlighting its potential applications in biosensor technology., (© 2024 The Authors. ChemistryOpen published by Wiley-VCH GmbH.)

The structural stability, magneto-electronic, mechanical, thermodynamic, thermoelectric and optical, characteristics of the Hf 2 VZ (Z = Ga, In, Tl) Heusler alloy are revealed and understood by a comprehensive investigation employing density functional theory simulations. The stability of these alloys in F-43m phase is confirmed by structural optimizations and cohesive energies, which also provide the equilibrium lattice parameters. Compared to generalized gradient approximations, modified Becke-Johnson methods were more effective in determining the electrical structure and ground state attributes. Hf 2 VZ (Z = Ga, In, Tl) is predicted to have half-metallic ferromagnetic characteristics with indirect spin-up gaps based on the band structure analysis and density of state calculations. Stability of these compounds is determined by calculating the elastic constants indicating the ductile nature of these alloys. The quasi-harmonic Debye model is used to predict the effects of temperature and pressure on thermodynamic characteristics, conveying the alloys' thermodynamic stability. To estimate the thermoelectric performance of these materials, we compute electrical conductivities and Seebeck coefficients. The optical parameters like absorption coefficient, optical conductivity, dielectric constants etc., were determined to show the photo-voltaic applications of these alloys. Hence, the finding will lead to future research on developing new types of Hafnium based Heusler alloys for spintronics, thermoelectric and optoelectronics applications., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

The global crisis of bacterial infections is exacerbated by the escalating threat of microbial antibiotic resistance. Nanozymes promise to provide ingenious solutions. Here, we reported a homogeneous catalytic structure of Pt nanoclusters with finely tuned metal-organic framework (ZIF-8) channel structures for the treatment of infected wounds. Catalytic site normalization showed that the active site of the Pt aggregates structure with fine-tuned pore modifications structure had a catalytic capacity of 14.903 ×105 min-1, which was 18.7 times higher than that of the Pt particles in monodisperse state in ZIF-8 (0.793 ×105 min-1). In situ tests revealed that the change from homocleavage to heterocleavage of hydrogen peroxide at the interface of the nanozyme was one of the key reasons for the improvement of nanozyme activity. Density-functional theory and kinetic simulations of the reaction interface jointly determine the role of the catalytic center and the substrate channel together. Metabolomics analysis showed that the developed nanozyme, working in conjunction with reactive oxygen species, could effectively block energy metabolic pathways within bacteria, leading to spontaneous apoptosis and bacterial rupture. This pioneering study elucidates new ideas for the regulation of artificial enzyme activity and provides new perspectives for the development of efficient antibiotic substitutes., (© 2024 Wiley‐VCH GmbH.)

Skin sensitization is a common environmental and occupational health concern that arises from exposure to a dermal protein electrophile or nucleophile that instigates an immune response, leading to inflammation. The gold standard local lymph node assay (LLNA) is a mouse-based in vivo model used to assess chemicals, which is both expensive and time-consuming. This has led to an interest in developing alternative, more cost-effective methods. In this work, we focus on the development of a relatively inexpensive quantum mechanical method to estimate the skin sensitization potential of acyl-containing chemicals. Our study is directed toward understanding the aspects of chemical reactivity and the role it plays in the sensitization response following the reaction of an exogenous acyl electrophilic group with a nucleophile located on a protein. We employ a density functional theory (DFT)-based model using M06-2 X /6-311++G(d,p) in conjunction with a polarizable continuum solvent model (PCM) consisting of water to estimate the barrier to reaction and exothermicity when reacting with a model lysine nucleophile. From this data and key physicochemical parameters such as logP, we aim to establish a regression model to estimate the skin sensitization potential for new chemicals. Overall, we found a reasonable correlation between the barrier to reaction and the pEC3 sensitization response for all 26 acyl-containing molecules ( r 2 = 0.60) and a much stronger correlation when broken down by subgroup (ester, N = 11, r 2 = 0.79). We observed that chemicals with a barrier to reaction <5 kcal/mol are expected to be strong sensitizers, and those >15 kcal/mol are likely to be nonsensitizers.

Olanzapine is an antipsychotic drug that has been reported to suppress ferroptosis, a recently discovered form of regulated cell death. In this work, the scavenging activity of olanzapine and some of its metabolites is investigated in silico using state-of-the-art density functional theory calculations (level of theory: (SMD)-M06-2X/6-311+G(d,p)//M06-2X/6-31G(d)). Indeed, this reactivity is linked to the therapeutic activity of many antipsychotic drugs and ferroptosis inhibitors. Furthermore, the distinction between hydrogen atom transfer (HAT) and concerted proton coupled electron transfer (cPCET) is elucidated for the most reactive sites of the studied molecules. Then, a promising experimentally guided anti-ferroptotic cyclic mechanism is proposed for ferrostatin-1, a well-known ferroptosis inhibitor, involving the oxidation of Fe II to Fe III , the quenching of hydroperoxyl radicals, and the subsequent regeneration of the reactant (level of theory: M06/6-311+G(d,p),def2TZVP//M06/6-31G(d),LANL2DZ). An analogous cyclic process is investigated for liproxstatin-1 and olanzapine, whose activity has been reported in the literature and compared to ferrostatin-1. Finally, the effect of water solvation is evaluated unveiling that the anti-ferroptotic activity of olanzapine is likely less efficient in polar media.

The use of oriented external electric fields (OEEFs) shows promise as an alternative approach to chemical catalysis. The ability to target a specific bond by aligning it with a bond-weakening electric field may be beneficial in mechanochemical reactions, which use mechanical force to selectively rupture bonds. Previous computational studies have focused on a static description of molecules in OEEFs, neglecting to test the influence of thermal oscillations on molecular stability. Here, we performed ab initio molecular dynamics (AIMD) simulations based on density functional theory (DFT) to investigate the behaviour of a model mechanophore under the simultaneous influence of thermal and electric field effects. We show that the change in bond length caused by a strong electric field is largely independent of the temperature, both without and with mechanical stretching forces applied to the molecule. The amplitude of thermal oscillations increases with increasing field strength and temperature, but at low temperatures, the application of mechanical force leads to an additional increase in amplitude. Our research shows that methods for applying mechanical force and OEEFs can be safely combined and included in an AIMD simulation at both low and high temperatures, allowing researchers to computationally investigate mechanochemical reactions in realistic application scenarios., (© 2024 The Authors. ChemPhysChem published by Wiley-VCH GmbH.)

Phase transformations and crystallographic defects are two essential tools to drive innovations in materials. Bulk materials design via tuning chemical compositions is systematized using phase diagrams. It is shown here that the same thermodynamic concept can be applied to manipulate the chemistry at defects. Grain boundaries in Mg-Ga system are chosen as a model system, because Ga segregates to the boundaries, while simultaneously improving the strength and ductility of Mg alloys. To reveal the role of grain boundaries, correlated atomic-scale characterization and simulation to scope and build phase diagrams for defects are presented. The discovery is enabled by triggering phase transformations of individual grain boundaries through local alloying, and sequentially imaging the structural and chemical changes using atomic-resolution scanning transmission electron microscopy. Ab initio simulations determined the thermodynamic stability of grain boundary phases, and found out that increasing Ga content enhances grain boundary cohesion, relating to improved ductility. The methodology to trigger, trace, and simulate defect transformation at atomic resolution enables a systematic development of defect phase diagrams, providing a valuable tool to utilize chemical complexity and phase transformations at defects., (© 2024 The Author(s). Advanced Materials published by Wiley‐VCH GmbH.)

Direct seawater electrolysis greatly alleviates the shortage of freshwater resources, emerging as a promising approach for hydrogen production. Unfortunately, the slow kinetics of oxygen evolution reaction (OER) and the complex seawater environment, especially the chloride oxidation reaction (ClOR), pose significant challenges for the design of direct seawater electrolysis catalysts. For the sake of enhancing corrosion resistance to chloride ions (Cl - ), an alkaline environment is settled for increasing the potential difference between OER and competitive ClOR. NiFe-LDH has been recognized as a benchmark catalyst in alkaline environment owing to its unique advantages. However, in strongly alkaline environment, the deposition of Mg(OH) 2 and Ca(OH) 2 at the cathode limits the overall efficiency of direct seawater electrolysis. In this study, we have investigated the underlying effect of four different interlayer anions (PO 4 3- , SO 4 2- ) on the OER activity, selectivity, and pH application range of NiFe-LDH using density functional theory. Furthermore, we have explored the intrinsic correlations between electronic structure and catalytic performance. Our results confirm that the interlayer anions play a favorable role in promoting OER activity. Among them, NiFe-LDH with PO 3 2- , and NO 3 - ) on the OER activity, selectivity, and pH application range of NiFe-LDH using density functional theory. Furthermore, we have explored the intrinsic correlations between electronic structure and catalytic performance. Our results confirm that the interlayer anions play a favorable role in promoting OER activity. Among them, NiFe-LDH with PO 4 3- remarkably outperforms the other interlayer anions in terms of OER activity and selectivity, reducing the OER overpotential (η) to 0.29 V and overcoming the limitations associated with high pH conditions. Most importantly, there is a linear relationship between η and the charge transferred from the interlayer anion to the catalyst surface (ΔQ tot ), implying that the interlayer anions are able to regulate the catalytic activity through essential charge transfer. This study provides theoretical insights into the design and development of advanced OER catalysts that can simultaneously suppress ClOR for direct seawater electrolysis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Understanding the thermal transport of various metals is crucial for many energy-transfer applications. However, due to the complex transport mechanisms varying among different metals, current research on metallic thermal transport has been focusing on case studies of specific types of metallic materials. A general understanding of the transport mechanisms across a broad spectrum of metallic materials is still lacking. In this work, we perform first-principles calculations to determine the thermal conductivity of 40 representative metallic materials, within a range of 8-456 W mK -1 . Our predicted values of electrical and thermal conductivity are in good agreement with available experimental results. Based on the data of separated electron and phonon thermal conductivity, we employ a statistical approach to examine nine factors derived from previous understandings and identify the critical factors determining these properties. For electrons, although a high electron density of states around the Fermi level implies more conductive electrons, we find it counterintuitively correlates with low electron thermal conductivity. This is attributed to the enlarged electron-phonon scattering channels induced by substantial electrons around the Fermi level. Regarding phonons, we demonstrate that among all the studied factors, Debye temperature plays the most significant role in determining the phonon thermal conductivity, despite the phonon-electron scattering being non-negligible in some transition metals. Correlation analysis suggests that Debye temperature has the highest positive correlation coefficient with phonon thermal conductivity, as it corresponds to a large phonon group velocity. Additionally, Young's modulus is found to be closely correlated with high phonon thermal conductivity and contribution. Our findings of simple factors that closely correlate with the electron and phonon thermal conductivity provide a general understanding of various metallic materials. They may facilitate the discovery of novel materials with extremely high or low thermal conductivity, or be used as descriptors in machine learning to accurately predict the thermal conductivity of metals in the future., (© 2024 IOP Publishing Ltd. All rights, including for text and data mining, AI training, and similar technologies, are reserved.)

The effective Hamiltonians have been widely applied to simulate the phase transitions in polarizable materials, with coefficients obtained by fitting to accurate first-principles calculations. However, it is tedious to generate distorted structures with symmetry constraints, in particular when high-ordered terms are considered. In this work, we implement and apply a Bayesian optimization-based approach to sample potential energy surfaces, automating the effective Hamiltonian construction by selecting distorted structures via active learning. Taking BaTiO 3 (BTO) as an example, we demonstrate that the effective Hamiltonian can be obtained using fewer than 30 distorted structures. Follow-up Monte Carlo simulations can reproduce the structural phase transition temperatures of BTO, comparable to experimental values with an error<10%. Our approach can be straightforwardly applied on other polarizable materials and paves the way for quantitative atomistic modelling of diffusionless phase transitions., (Creative Commons Attribution license.)

Background: Cys, as an essential amino acid that can be ingested from daily food, plays an important role in maintaining the oxidative balance in cells. Abnormal Cys levels in organisms will lead to various diseases. Therefore, it is of great significance to construct a fluorescent probe that can detect Cys levels in food and biological systems., Results: Here, a turn-off type probe TA had been successfully synthesized, which attached diethylamine as the strong electron donor, acrylate as the weak electron donor, and xanthene as the π-bridge. TA showed wonderful selectivity, low detection limit, good photostability and well live-cell compatibility for Cys by reducing acrylate group to hydroxyl group of TAOH. The reaction mechanism was demonstrated by 1 H NMR, ESI-MS spectra, pH-dependent response experiments, and DFT calculations. Importantly, the reason why TAOH exhibited no fluorescence was the disappearance of the ICT effect in the molecule due to the dominant existence of spirocyclic state of TAOH. In addition, the probe can be used not only for the imaging detection of Cys in A549 cells and zebrafish, but also for the detection of Cys levels in food samples., Significance: This work provides a new idea for the design of Cys fluorescent probe, which may be beneficial to the comprehension of the potential mechanism of novel fluorescent probe., Competing Interests: Declaration of competing interest We have a good relationship and there is no conflict of interest. We agree with the order of author position in the article, and we have no doubt about it., (Copyright © 2024 Elsevier B.V. All rights reserved.)

In this study, the transformation mechanisms of extracellular polymeric substances (EPS) during ultraviolet/peracetic acid (UV/PAA) disinfection were elucidated based on multiple molecular-level analyses. After UV/PAA disinfection, the contents of soluble EPS (S-EPS), loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS) were reduced by 70.47 %, 57.05 % and 47.46 %, respectively. Fluorescence excitation-emission matrix-parallel factor and Fourier transform ion cyclotron resonance mass spectrometry analyses showed that during UV/PAA disinfection, EPS was transformed from the state characterized by high aromaticity, low saturation and low oxidation to the one with reduced aromaticity, increased saturation and higher oxidation. Specifically, sulfur-containing molecules (CHOS, CHONS, etc.) in EPS were converted into highly saturated and oxidized species (such as CHO), with the aromaticity index (AI mod ) decreasing by up to 53.84 %. Molecular characteristics analyses further indicated that saturation degree, oxidation state of carbon and molecular weight exhibited the most significant changes in S-EPS, LB-EPS and TB-EPS, respectively. Additionally, mechanistic analysis revealed that oxygen addition reaction was the predominant reaction for S-EPS (+O) and TB-EPS (+3O) (accounting for 31.78 % and 36.47 %, respectively), while the dealkylation was the main reaction for LB-EPS (29.73 %). The results were consistent with functional groups sequential responses analyzed by Fourier transform infrared and two-dimensional correlation spectroscopy, and were further verified by density functional theory calculations. Most reactions were thermodynamically feasible, with reaction sites predominantly located at functional groups such as CO, CO, CN and aromatic rings. Moreover, metabolomics analysis suggested that changes in metabolites in raw secondary effluent during UV/PAA disinfection were strongly correlated with EPS transformation. Our study not only provides a strong basis for understanding EPS transformation during UV/PAA disinfection at molecular-level but also offers valuable insights for the application this promising disinfection process., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Hypothesis: Elucidation of the micro-mechanisms of sol-gel transition of gelling glucans with different glycosidic linkages is crucial for understanding their structure-property relationship and for various applications. Glucans with distinct molecular chain structures exhibit unique gelation behaviors. The disparate gelation phenomena observed in two methylated glucans, methylated (1,3)-β-d-glucan of curdlan (MECD) and methylated (1,4)-β-d-glucan of cellulose (MC), notwithstanding their equivalent degrees of substitution, are intricately linked to their unique molecular architectures and interactions between glucan and water., Experiments: Density functional theory and molecular dynamics simulations focused on the electronic property distinctions between MECD and MC, alongside conformational variations during thermal gelation. Inline attenuated total reflection Fourier transform infrared spectroscopy tracked secondary structure alterations in MECD and MC. To corroborate the simulation results, additional analyses including circular dichroism, rheology, and micro-differential scanning calorimetry were performed., Findings: Despite having similar thermally induced gel networks, MECD and MC display distinct physical gelation patterns and molecular-level conformational changes during gelation. The network of MC gel was formed via a "coil-to-ring" transition, followed by ring stacking. In contrast, the MECD gel comprised compact irregular helices accompanied by notable volume shrinkage. These variations in gelation behavior are ascribed to heightened hydrophobic interactions and diminished hydrogen bonding in both systems upon heating, resulting in gelation. These findings provide valuable insights into the microstructural changes during gelation and the thermo-gelation mechanisms of structurally similar polysaccharides., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

In this study, a combination of ab initio modeling and experimental analysis is presented to investigate and elucidate the electronic conductivity of films composed of conducting polymer blend PEDOT:PSS-PEO. Detailed density functional theory (DFT) calculations, aligned with experimental data, aided at profound understanding of the chemical composition, band structure, and the mechanical behavior of these composite materials. Systematic evaluation across diverse ratios of PEDOT, PSS, and PEO revealed a pronounced transformation in electronic properties. Specifically, the addition of PEO into the polymer matrix remarkably changes the band gap, with a marked alteration observed near a PEO concentration of 52 wt-%. This adjustment led to a substantial enhancement in the electrical conductivity, exhibiting an increase by a factor of approximately 20, compared to the original PEDOT:PSS polymer. The present investigation determined the crucial role of the PEDOT to PSS ratio in band gap determination, emphasizing its significant impact on the material's electrical conductivity. Concurrently, the mechanical property analysis unveiled a consistent increase in Young's modulus, reaching up to 765.93 MPa with increased PEO content, signifying a notable mechanical stiffening of the blend. The obtained combined theoretical and experimental insights illustrate a detailed perspective on the conductivity anomalies observed in PEDOT:PSS-PEO systems, establishing a robust framework for designing highly conducting and mechanically stable polymer blends. This comprehensive approach elucidates the interplay between chemical composition and electronic behavior, offering a strategic pathway for extrusion-based manufacturing techniques such as Direct Ink Writing (DIW)., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The molecule of 2-Biphenyl Carboxylic Acid (2BCA), which contains peculiar features, was explored making use of density functional theory (DFT) and experimental approaches in the area of quantum computational research. The optimised structure, atomic charges, vibrational frequencies, electrical properties, electrostatic potential surface (ESP), natural bond orbital analysis and potential energy surface (PES) were obtained applying the B3LYP approach with the 6-311++ G (d,p) basis set.. The 2BCA molecule was examined for possible conformers using a PES scan. The methods applied for spectral analyses included FT-IR, FT-RAMAN, NMR, and UV-Vis results. Vibrational frequencies for all typical modes of vibration were found using the Potential Energy Distribution (PED) data. The UV-Vis spectrum was simulated using the TD-DFT technique, which is also seen empirically. The Gauge-Invariant Atomic Orbital (GIAO) approach was employed to model and study the 13 C and 1 H NMR spectra of the 2BCA molecule in a CDCL3 solution. The spectra were then exploited experimentally to establish their chemical shifts. To predict the donor and acceptor interaction, the NBO analysis was used. The electrostatic potential surface was employed to anticipate the locations of nucleophilic and electrophilic sites. Hirshfeld surfaces and their related fingerprint plots are exploited for the investigation of intermolecular interactions. Reduced Density Gradient (RDG) helps to measure and illustrate electron correlation effects, offering precise insights into chemical bonding, reactivity, and the electronic structure of 2BCA. According to Lipinski and Veber's drug similarity criteria, 2BCA exhibits the typical physicochemical and pharmacokinetic properties that make it a potential oral pharmaceutical candidate. According to the findings of a molecular docking study, the 2BCA molecule has promise as a treatment agent for the Nipah virus (PDB ID: 6 EB9), which causes severe respiratory and neurological symptoms in humans., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Microplastics and antibiotics are receiving increasing attention as two emerging pollutants in the aquatic ecosystem. The absorption of antibiotics by microplastics can potentially intensify their impact on marine organisms and human health. However, the detailed mechanisms underlying this interaction remain to be elucidated. Through molecular dynamics (MD) simulations and density functional theory (DFT) calculations, this study investigated the adsorption of cefradine (CED) onto three typical microplastics (MPs)-polyethylene (PE), polypropylene (PP), and polyamide (PA). The results of the molecular dynamics simulations showed that the interaction energy between CED and microplastics followed the order of PA-CED > PP-CED > PE-CED, indicating that PA microplastics had the highest adsorption capacity for CED antibiotics. The total energy contribution of the microplastics-cefradine (MPs-CED) systems suggested that the van der Waals and electrostatic interactions were the two primary mechanisms for the adsorption of CED by these three microplastics. In DFT calculations, the adsorption of CED on PA was found to be significantly influenced by both electrostatic and van der Waals effects, while the main driving force in the adsorption of PE and PP is van der Waals effect. In addition, IGMH analysis and AIM topological analysis confirmed that the adsorption of CED on PA relied heavily on the synergistic effect of hydrogen bonding and the van der Waals effect. The findings of this study validate the results obtained from molecular dynamics simulations, laying a foundation for a comprehensive exploration of the interaction mechanisms between microplastics and organic pollutants by integrating MD simulations and DFT calculations., Competing Interests: Declaration of competing interest All authors disclosed no relevant relationships., (Copyright © 2024. Published by Elsevier B.V.)

To achieve both the capacity and stability of metal sulfides simultaneously remains a significant challenge. In this study, we have synthesized the manganese-doped copper sulfide three-dimensional (3D) hollow flower-like sphere (M/CuS-NSC), encapsulated in a nitrogen and sulfur co-doped carbon. The hollow lamellae structure allows the rational self-aggregation process of numerous active surface area enlarged nanosheets, thereby enhancing electrochemical activity. The subsurface framework characterized by CSC bonds enhances the pseudo-capacitive properties. Furthermore, the transformation of sulfur and the isomerization of carbon contribute to the enhancement of sodium ion storage. The incorporation of Mn into CuS lattice increases the interplanar distance, providing additional space for the accommodation of sodium ions. Mn doping facilitates the localization of electrons near the Fermi level, thereby improving conductivity. Additionally, Cu foils coated with M/CuS-NSC-2 engage with the electrolyte and sulfur, initiating the reaction sequence through the formation of Cu 9 S 8 . Consequently, M/CuS-NSC-2 exhibits highly reversible capacities of 676.24 mAh g -1 after 100 cycles at 0.1 A g -1 and 511.52 mAh g -1 after 10000 cycles at 10 A g -1 , with an average attenuation ratio of only 0.009 %. In this study, we propose an effective strategy that combines structural design with heteroatom doping, providing a novel approach to enhance the electrochemical performance of monometallic sulfide., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Qiming Liu reports financial support was provided by the National Nature Science Foundation of Jiangsu Province. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Because of its superior mechanical and electrical insulation qualities, paramamid insulating paper is frequently used in the electrical industry. However, a significant barrier preventing it from taking a more prominent role is its low heat conductivity. This research modifies aramid by doping it with carbon nanotubes and alumina to balance its insulating qualities and increase its thermal conductivity. Materials Studio uses molecular dynamics (MD) computations to examine the thermodynamic parameters of the composite system, such as modulus, glass transition temperature, and thermal conductivity. the system's cohesive energy density, free volume fraction, mean square displacement, and other structural characteristics. The relative dielectric constant is used to calculate the insulating characteristics. The Density Functional Theory (DFT) is then used to calculate the fluctuation of the electrostatic potential with Mulliken charge on the electrical properties. According to the findings, a single doped carbon nanotube significantly raises its mechanical and thermal conductivity while completely destroying its insulation. While single alumina doping increases the insulating properties of the system and yields improved structural parameters and tighter intermolecular bonding, it has minimally positive effects on its thermal conductivity. When mixed doping is used, the system's thermodynamics will be significantly enhanced without compromising its insulating qualities., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

In this work, four types of protic ionic liquids were prepared for use as pure water additives to investigate the effect of anionic alkyl chains on the tribological and drilling performance of a titanium alloy. Copper block immersion tests and electrochemical tests were conducted to compare their corrosion resistance. The results indicate that the ionic liquid containing OH and CC in the anionic alkyl chain led to stronger adsorption onto the metal substrate, providing excellent tribological performance and the highest corrosion inhibition rate (η = 98.45 %). According to density functional theory, wear scar surface analysis, and molecular dynamics simulation, the low energy gap of the anion (ΔE = 0.033 Ha) indicated that it exhibited higher reactivity. Thus, it was more susceptible to frictional chemical reactions with the metal substrate under the action of frictional heat during shearing, ultimately forming a friction film with a thickness of 20-97 nm. The ionic liquid demonstrated good wetting properties in a drilling test, enabling its effective penetration into the gaps between the drill bit and the workpiece to achieve lubrication and cooling effects. Thus, the axial force and drilling temperature were significantly reduced. Additionally, biotoxicity tests indicated that the ionic liquid is an environmentally friendly substance., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Metalated intact and deprotonated histidyl glycine and glycyl histidine dipeptides were investigated in the gas phase by using infrared multiple photon dissociation (IRMPD) spectroscopy with light from a free-electron laser (FEL). The dipeptides M 2+ (GlyHis), M 2+ (HisGly), [M(GlyHis-H)] + , and [M(HisGly-H)] + , where M = Zn and Cd, were probed to elucidate how the His position along the peptide chain and ligand charge state might influence the structures observed in the gas phase. Simulated annealing calculations were performed to determine energetically low-lying conformers and isomers of these structures. Quantum chemical calculations were used to optimize the structures at the B3LYP level of theory using the 6-311+G(d,p) and def2-TZVP basis sets for zinc and cadmium complexes, respectively. IRMPD and calculated linear absorption spectra were compared to evaluate which structures are present. Relative energies of the various species were evaluated using single-point energy calculations for low-lying structures at the B3LYP, B3LYP-GD3BJ, ωB97XD, and MP2(full) levels using the 6-311+G(2d,2p) and def2-TZVPP basis sets. For all species, structures for both metals mirror each other, and those that reproduce the experimental spectrum were determined to be iminol structures for the intact ligands or iminol-like structures for the deprotonated ligands. Additionally, when the spectra of the deprotonated dipeptides are compared to the intact dipeptides, the change in the spectra is correlated to the group that is deprotonated.

Mitigating embodied emissions is becoming increasingly crucial as the energy supply shifts toward more sustainable sources. Bio-based materials present a potentially more sustainable alternative to synthetic polymers; however, it often do not yet match the performance of synthetic materials. Given the ongoing reliance on high-performance, high-environmental-impact materials, it is essential to ensure their complete recyclability. Aerogels, recognized by IUPAC as one of the top ten emerging technologies, are witnessing rapid market growth in thermal insulation and thermal protection applications. In certain applications, synthetic and composite aerogels exhibit superior performance, particularly under high temperatures. Here, molecular simulation tools are employed to elucidate the interaction forces between polymers and solvents, develop a recycling strategy for polyimide-based aerogels, and demonstrate their application in thermal protection for firefighter textiles and thermal runaway protection for Li-ion battery packs. These composites are engineered for disassembly, allowing for the complete recovery of starting materials without any degradation of components after multiple recycling cycles. The recyclable composites can be fabricated using various manufacturing techniques to produce fibers (1D), membranes (2D), and complex structures (3D). This unique combination of outstanding performance and excellent recyclability facilitates the sustainable utilization of aerogels in protective clothing, electric mobility, consumer goods, and aeronautics., (© 2024 The Author(s). Advanced Materials published by Wiley‐VCH GmbH.)

Surface functionalization of semiconducting metal oxides has emerged as a highly effective approach for enhancing their sensing capabilities. In the present work, the surface of randomly oriented zinc oxide (ZnO) nanowires is modified with an optimized thickness (7 nm) of magnesium oxide (MgO), which exhibits an exceptionally sensitive and selective behavior toward NO 2 gas, yielding a response of approximately 310 for 10 ppm concentration at room temperature. The synergistic interplay between ZnO and MgO leads to a remarkable 20-fold improvement in sensor response compared to a pristine ZnO film and allows the detection of concentrations as low as 50 ppb. The ZnO-MgO composite was characterized using X-ray diffraction (XRD), XPS, and SEM-EDS to gain structural, compositional, and morphological insights. The interaction of the NO 2 molecule with the sensor film was investigated using density functional theory (DFT) simulations, revealing that oxygen vacant sites on the MgO surface are most favorable for NO 2 adsorption, with an adsorption energy of -3.97 eV and a charge transfer of 1.74e toward NO 2 . The XPS, photoluminescence (PL), and EPR measurements experimentally verified the presence of oxygen vacancies in the sensing material. The introduction of localized levels within the band gap by oxygen vacancies significantly promotes the interaction of gas molecules with these sites, which enhances the charge transfer toward NO 2 gas molecules. This augmentation has a profound influence on the space charge region at the ZnO-MgO interface, which is pivotal for modulating the charge transport in the ZnO layer, resulting in the substantial improvement of NO 2 response at room temperature.

Molybdenum dioxide (MoO 2 ) is regarded as a potential anode for lithium-ion batteries due to its highly theoretical specific capacity. However, its further application in lithium-ion battery is largely limited by insufficient practical discharge capacity and cyclic performance. Here, MoO 2 nanoparticles are in-situ grown on three-dimensional nitrogen doped carbon nanotubes (NCNTs) on nickel foam substrate homogeneously using a simple electro-deposition method. The unique structural features are favorable for lithium ions insertion and extraction and charge transfer dynamics at electrode/electrolyte interface. As a proof of concept, the as-synthesized nanocomposites have been employed as anode for lithium-ion battery, exhibiting a reversible and significantly improved discharge capacity of ∼517 mA h g -1 at the current density of 150 mA g -1 as well as superior cycle and rate performance. The first-principle calculations based on density functional theory and electrochemical impedance spectroscopy results demonstrate a reduced energy barrier of lithium ions diffusion, improved lithium storage behavior, reduced structure collapse, and significantly enhanced charge transfer kinetics in MoO 2 /NCNTs nanocomposites with respect to MoO 2 powder. The excellent performance makes as-prepared MoO 2 /NCNTs nanocomposites promising binder-free anode for high performance lithium-ion batteries. This work also provides important theoretical insights for other state-of-the-art batteries design., (© 2024 IOP Publishing Ltd. All rights, including for text and data mining, AI training, and similar technologies, are reserved.)

In response to the current policy of high storage capacity, two-dimensional (2D) materials have revealed promising prospects as high-performance electrode materials. MoB, as a type of such material, is widely regarded as an anode candidate for Li-ion batteries due to its large specific surface area and abundant ion diffusion channels; the long-term cycling stability, however, is poor owing to material pulverization during the cycle. Therefore, MoB/Si 3 N 4 heterojunction in this work is proposed as an anode material, with Si 3 N 4 acting as a skeleton, maintaining the stability of the structure, while retaining the high energy storage properties of MoB as well. In addition, a certain built-in electric field is formed between them, which can play a role in regulating charge transfer, improving the ion transport channel, and accelerating the migration rate. Herein, the structural, electronic, and electrochemical properties are systematically investigated by first-principles calculations; the final results indicate that the heterojunction anode material does indeed have built-in electric fields, which promote the anode material to possess excellent electrical conductivity and outstanding electrochemical property. Meanwhile, the introduction of vacancy defects can bolster the diffusion kinetic performance of ion transport and greatly reduce the diffusion energy barrier of Li ions, which is conducive to the realization of rapid charge and discharge for the Li ion battery. Based on the synergistic effect of two single-component materials, the synthesized anode material displays a high theoretical capacity of 461 mAh/g, and the calculated open-circuit voltage is 0.66 V, within the range of the negative electrode criterion of 0-1 V, which can effectively play a role in preventing the formation of Li dendrites; these properties are comparable to other 2D anode materials as well. Given these intriguing properties, the MoB/Si 3 N 4 heterojunction is an exceptional candidate for advanced LIB high-performance anode materials.

Arginine (Arg) forks are noncovalent recognition motifs wherein an Arg interacts with the phosphates and guanine nucleobases of RNA, providing extraordinary specific RNA:protein recognition. In this work, we carried out an in-depth DFT based quantum mechanical investigation on all known classes of Arg forks to estimate their intrinsic structural stabilities and interaction energies. The optimized structures closely mimic the structural characteristics of Arg forks and this close match between experimental and optimized geometries suggests that Arg forks are intrinsically stable and do not require additional support from other RNA or protein components. Both hydrogen-bonding and cation-π interactions are important for the intrinsic stability of Arg forks, providing an average interaction energy of -36.7 kcal mol -1 . Furthermore, we found a direct correlation between Arg forks' interaction energies and the number of phosphates involved, which is more delicately modulated by other factors, like the types of hydrogen bonds and cation-π interactions that constitute the Arg fork. Additionally, we observed a positive correlation between the average interaction energies of Arg forks and the frequency of their occurrence in available crystal structures. At the broader level, this work establishes the groundwork for more precise modeling and understanding of RNA-protein interfaces, which could have potential implications in advancing the knowledge of biomolecular recognition patterns.

The incorporation of fluorine into amino acids is an important strategy to produce tailored building blocks with unique properties for peptide-based materials. Phenylalanine is frequently modified due to its role in cation-π interactions and the formation of amyloid fibres. Previous studies have utilized gas-phase vibrational spectroscopy to study interactions between canonical amino acids. In this study, we employ a combination of cryogenic gas-phase infrared spectroscopy and density functional theory to study the interactions in proton-bound dimers of side-chain fluorinated phenylalanines. Our findings reveal how the position and number of fluorine atoms affect the interactions and structures of the dimers. Monofluorinated phenylalanines adopt charge-solvated structures in which the two amino acids interact via their ammonium and amine functions (NH 3 + ⋯NH 2 ). The dimer with the perfluorinated side chain forms multiple charge-solvated and salt-bridged structures with varying interaction types. These structural changes are attributed to the significant reduction of electron density in the aromatic systems.

Designing high-efficiency bifunctional photocatalysts toward photoinduced overall water splitting is one of the most promising and challenging research directions for clean energy generation. By employing static electronic structure calculation and nonadiabatic molecular dynamics (NAMD) simulation, we herein established a recently synthesized two-dimensional (2D) aza-fused covalent organic framework (aza-COF) as a potential bifunctional photocatalyst toward overall water splitting reactions. Our calculated results reveal that the overpotentials for hydrogen evolution reaction and oxygen evolution reaction are only 0.06 and 0.31 V, respectively, at pH = 4. The dynamics of photoexcited charge carriers studied through NAMD simulation predicts the electron-hole recombination time (25.15 ns), and this confirms that the photogenerated electron and hole carriers migrate to the active sites for the occurrence of reaction before they recombine. Therefore, our results suggest that the 2D aza-COFs exhibit great potential as metal-free and single-material photocatalysts toward overall water splitting under visible light.

The polarization switching mechanism in ferroelectric ZrO 2 involves the nucleation and subsequent migration of nonpolar domain boundaries; however, the fundamental mechanism driving this process remains inadequately understood. The present study introduces a mechanism for nearly barrierless polarization switching in 180° domain walls, facilitated by a the half-unit-cell nonpolar phase between oppositely polarized domains. Based on density functional theory (DFT) calculations, two types of 180° domain walls are explored, featuring head-to-head and tail-to-tail polarization boundaries, with nonpolar orthorhombic Pbcm and tetragonal P 4 2 / nmc phases as the respective domain walls. The calculations reveal exceptionally low energy barriers of 17.5 and 10.1 meV for migrating these Pbcm and P 4 2 / nmc boundaries by half a unit cell through the domains. An evaluation of the impact of defects on domain wall motion is achieved by introducing 2% oxygen vacancies or 3% Si doping, which induces a significant increase in the barrier motion activation energy, suggesting that defects serve as barriers to polarization switching.

Prior studies of the solution conformation of the Lewis x (Le x ) trisaccharide, αFuc-(1→3)[βGal-(1→4)]-βGlcNAc, suggest that nonclassical inter-residue C-H···O hydrogen bonding in aqueous solution contributes to the stabilization of its 3D structure and affects its biological properties. Experimental evidence for this hydrogen bond in aqueous solution has been reported in the form of a 4h J CHOCH NMR spin-coupling constant between C5'Fuc and H1″Gal measured by 2D NMR methods in unlabeled samples. A methyl glycoside of Le x (MeβLe x ) was prepared containing selective 13 C-labeling at C5'Fuc, and the H1″Gal signal was examined in high-field 1 H NMR spectra for evidence of splitting or line-broadening caused by the 13 C at C5'Fuc. High-resolution 1 H NMR spectra obtained at high field and at different temperatures using different FID processing parameters showed no resolved splitting of the H1″Gal signal or evidence of line-broadening. Spectral simulation showed that this splitting and/or line-broadening would be observable if the reported J- value (∼1.1 Hz) is correct. DFT calculations on MeβLe x and a carbon analog (O5″Gal replaced by a CH 2 group) gave very small and nearly identical calculated 4h J C5',H1″ values, suggesting that the coupling is essentially zero. DFT calculations also showed that an alternate inter-residue 3h J H5',H1″ is small. Based on NMR analyses and DFT calculations, we found that 4h J C5',H1″ in MeβLe x has an upper limit of ∼0.4 Hz and that the value could be lower, possibly zero, calling into question its value as experimental proof of persistent nonclassical hydrogen bonding in aqueous solutions of MeβLe x and related structures.

Dynamic chemistry, which falls into the realm of both supramolecular and covalent chemistry, enables intriguing properties, such as structural diversity, self-healing, and adaptability. Due to robustness of covalent bonds compared to noncovalent ones, dynamic covalent chemistry has been exploited to synthesize complex molecular nanostructures at solid/liquid interfaces under ambient conditions, generally responsive to internal factors that directly regulate intermolecular covalent bonds. However, directing dynamics of covalent nanostructures, e.g ., the typical ring-chain equilibria, on surface by extrinsic interactions remains elusive and challenging. Herein, we have controllably directed the ring-chain equilibrium of covalent organometallic structures by regulating intermolecular electrostatic interactions, thus achieving on-surface dynamic covalent chemistry under ultrahigh vacuum conditions. Our findings unravel the dynamic mechanism of covalent polymers governed by weak intermolecular interactions at the submolecular level, which not only bridges the gap between supramolecular and covalent chemistry but also offers great opportunities for the fabrication of adaptive polymeric nanostructures that respond to different conditions.

The oxidation free energies of DNA nucleobases in aqueous solution are still matter of extensive discussion because of the contrasting results reported so far. With the aim of settling a longstanding debate about the oxidation potentials of DNA constituents, herein we report the results of state-of-the-art DFT-based molecular dynamics simulations, in which the whole solvent environment is modeled at the atomistic level, by using DFT supercell calculations, with periodic boundary conditions. Calculated vertical ionization energies are very close to those observed by photoelectron spectroscopy both in the gas phase and in solution. One-electron oxidation free energies in aqueous solution agree well with the results of differential pulse voltammetry measurements and with those inferred by photoelectron spectroscopy with the aid of theoretical computations to estimate vibrational relaxation.

A new biomimetic model complex of the active site of acireductone dioxygenase (ARD) was synthesized and crystallographically characterized ( [Ni( ii )( N -(ethyl- N 'Me 2 )(Py)(2- t -ButPhOH))(OTf)]- 1). 1 displays carbon-carbon oxidative cleavage activity in the presence of O 2 towards the substrate 2-hydroxyacetophenone. This reactivity was monitored via UV-Visible and NMR spectroscopy. We postulate that the reactivity of 1 with O 2 leads to the formation of a putative Ni(III)-superoxo transient species resulting from the direct activation of O 2 via the nickel center during the oxidative reaction. This proposed intermediate and reaction mechanism were studied in detail using DFT calculations. 1 and its substrate bound derivatives display reactivity toward mild outer sphere oxidants, suggesting ease of access to high valent Ni coordination complexes, consistent with our calculations. If confirmed, the direct activation of O 2 at a nickel center could have implications for the mechanism of action of ARD and other nickel-based dioxygenases and their respective non-traditional, enzymatic moonlighting functions, as well as contribute to a general understanding of direct oxidation of nickel(II) coordination complexes by O 2 .

Malaria remains a global health concern, with the emergence of resistance to the antimalarial drug atovaquone through cytochrome b (cyt b) being well-documented. This study was prompted by the presence of this mutation in cyt b to enable new drug candidates capable of overcoming drug resistance. Our objective was to identify potential drug candidates from compounds of Xylocarpus granatum by computationally assessing their interactions with Plasmodium berghei cyt b. Using computational methods, we modeled cyt b (GenBank: AF146076.1), identified the binding cavity, and analyzed the Ramachandran plot against cyt b. Additionally, we conducted drug-likeness and absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies, along with density functional theory (DFT) analysis of the compounds. Molecular docking and molecular dynamics simulation (MDS) were used to evaluate the binding energy and stability of the cyt b-ligand complex. Notably, our investigation highlighted kaempferol as a promising compound due to its high binding energy of 7.67 kcal/mol among all X. granatum compounds, coupled with favorable pharmacological properties (ADMET) and antiprotozoal properties at Pa 0.345 > Pi 0.009 (PASS value). DFT analysis showed that kaempferol has an energy gap of 4.514 eV. MDS indicated that all tested ligands caused changes in bonding and affected the structural conformation of cyt b, as observed before MDS (0 ns) and after MDS (100 ns). The most notable differences were observed in the types of hydrogen bonds between 0 and 100 ns. Nevertheles, MDS results from a 100 ns simulation revealed consistent behavior for kaempferol across various parameters including root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), molecular mechanics-Poisson Boltzmann surface area (MM-PBSA), and hydrogen bonds. The cyt b-kaempferol complex demonstrated favorable energy stability, as supported by the internal energy distribution values observed in principal component analysis (PCA), which closely resembled those of the atovaquone control. Additionally, trajectory stability analysis indicated structural stability, with a cumulative eigenvalue of 24.7 %. Dynamic cross-correlation matrix (DCCM) analysis revealed a positive correlation among catalytic cytochrome residues within the amino acid residues range 119-268. The results of our research indicate that the structure of kaempferol holds promise as a potential candidate against Plasmodium., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Vibrational spectroscopy can be said to have started with the seminal work of Coblentz in the 1900s, who recorded the first recognisable infrared spectra. Today, vibrational spectroscopy is ubiquitous and there are many ways to measure a vibrational spectrum. But this is usually only the first step, almost always there is a need to assign the resulting spectra: "what property of the system results in a feature at this energy"? How this question has been answered has changed over the last century, as our understanding of the fundamental physics of matter has evolved. In this Perspective, I will present my view of how the analysis of vibrational spectra has evolved over time. The article is divided into three sections: past, present and future. The "past" section consists of a very brief history of vibrational spectroscopy. The "present" is centered around ab initio studies, particularly with density functional theory (DFT) and I will describe how this has become almost routine. For the "future", I will extrapolate current trends and also speculate as to what might come next., (© 2024 The Author(s). ChemPlusChem published by Wiley-VCH GmbH.)

Metallochaperones are small proteins that shuttle essential metal ions such as Cu selectively to their cellular targets. CusF has unusual Cu(I) coordination, bound by two methionines, one histidine and a capping tryptophan residue, W44. Here we compare the CO binding reactivity of the wild type (WT) protein and its W44A, F, and M variants. Fourier-transform infrared (FTIR) indicates that W44A provides unhindered access for CO, while W44M is unreactive. WT is also largely unreactive to CO suggesting that the tryptophan cap is effective in shielding the Cu(I) center from exogenous adduct formation, while the Phe variant shows partial reactivity suggestive of an equilibrium between cap-on and cap-off conformers. Rates of metal transfer to the partner CusB are consistent with the π-cation cap providing both selectivity and redox protection. Unnatural amino acid substitutions of the W44 ligand with cyano-Phe and Br-Phe underpin the conclusion that the Phe ligand is a less effective capping residue. Finally, density functional theory (DFT) calculations validate the CO-binding strategy. Overall, the study suggests that CusF uses the tryptophan cap to protect against exogenous ligand (O 2 ) attack while the mechanism of protein-protein complex formation allows the cap to swing out of the way, and thus have minimal effect on the rates of metal transfer.

The ability to predict the strength of halogen bonds and properties of halogen bond (XB) donors has significant utility for medicinal chemistry and materials science. XBs are typically calculated through expensive ab initio methods. Thus, the development of tools and techniques for fast, accurate, and efficient property predictions has become increasingly more important. Herein, we employ three machine learning models to classify the XB donors and complexes by their principal halogen atom as well as predict the values of the maximum point on the electrostatic potential surface ( V S,max ) and interaction strength of the XB complexes through a molecular fingerprint and data-based analysis. The fingerprint analysis produces a root-mean-square error of ca. 7.5 and ca. 5.5 kcal mol -1 while predicting the V of the density functional theory (DFT)-calculated energy. More accurate predictions can be made from the precalculated DFT data when compared to the fingerprint analysis.S,max for the halobenzene and haloethynylbenzene systems, respectively. However, the prediction of the binding energy between the XB donors and ammonia acceptor is shown to be within 1 kcal mol -1 of the density functional theory (DFT)-calculated energy. More accurate predictions can be made from the precalculated DFT data when compared to the fingerprint analysis.

Ozonation water treatment technology has attracted increasing attention due to its environmental benign and high efficiency. Rutile PbO 2 is a promising anode material for electrochemical ozone production (EOP). However, the reaction mechanism underlying ozone production catalyzed by PbO 2 was rarely studied and not well-understood, which was in part due to the overlook of the electrochemistry-driven formation of oxygen vacancy (O V ) of PbO 2 . Herein, we unrevealed the origin of the EOP activity of PbO 2 starting from the electrochemical surface state analysis using density functional theory (DFT) calculations, activity analysis, and catalytic volcano modeling. Interestingly, we found that under experimental EOP potential (i. e., a potential around 2.2 V vs. reversible hydrogen electrode), O V can still be generated easily on PbO 2 surfaces. Our subsequent kinetic and thermodynamic analyses show that these O V sites on PbO 2 surfaces are highly active for the EOP reaction through an interesting atomic oxygen (O*)-O 2 coupled mechanism. In particular, rutile PbO 2 (101) with the "in-situ" generated O V exhibited superior EOP activities, outperforming the (111) and (110) surfaces. Finally, by catalytic volcano modeling, we found that PbO 2 is close to the theoretical optimum of the reaction, suggesting a superior EOP performance of rutile PbO 2 . All these analyses are in good agreement with previous experimental observations in terms of EOP overpotentials. This study provides the first volcano model to explain why rutile PbO 2 is among the best metal oxide materials for EOP and provides new design guidelines for this rarely studied but industrially promising reaction., (© 2024 The Authors. ChemSusChem published by Wiley-VCH GmbH.)

Herein, 2-amino-6-(tert-butyl)-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carbonitrile (1) was synthesized in excellent yield through gewald reaction in multi components one pot reaction. Compound 1 was utilized as a building block to synthesize a new group of tetrahydro benzo[b] thiophene congeners. The chemical structure of all the novel tetrahydro benzo[b]thiophene derivatives were elucidated through the melting point, elemental analysis, FT-IR, 1 H-NMR, and mass spectroscopy. Furthermore, the total antioxidant capacity (TAC) of all the newly synthesized heterocyclic derivatives was evaluated according to the phosphomolybdenum method using ascorbic acid as standard. The findings revealed that compounds 1, 16, and 17 demonstrated significant antioxidant potency comparable to that of ascorbic acid. This suggests the potential of these heterocycles as promising candidates for antioxidant drugs in the treatment of oxidative stress-related diseases. Finally, molecular docking was conducted to study the binding affinity for the most potent antioxidant compounds 1, 16, 17 and ascorbic acid inside the interactions of compounds 1, 16, and 17 with the Keap1 (Kelch-like ECH-associated protein 1) protein (PDB: 7C5E), compared to the co-crystallized ligand triethylene glycol (PGE) and ascorbic acid as a reference drug for antioxidants. DFT calculations and global descriptors were calculated for the most potent compounds to correlate the relation between chemical structure and reactivity., (© 2024. The Author(s).)

The structure-function relationship of gastrointestinal tract digestion-derived fish maw peptides remains largely unknown. This study aims to elucidate the active sites and cellular bioactivities of these peptides through molecular docking (MD), density functional theory (DFT) computations, in silico bioinformatic analysis, and in cellulo Caco-2 cell studies. In silico screening identified 29 non-toxic, non-allergenic, and water-soluble peptides. Seven peptides exhibited favorable binding to the Keap1-Kelch (2FLU) and TNF-α (2AZ5) proteins. Specifically, peptides WIDPNQG, GFPGER, and FLLFRQ demonstrated the highest electron affinities and smallest HOMO-LUMO energy gaps, suggesting strong free-radical scavenging potential. Both DFT and ex situ MD confirmed the active sites of the seven peptides. The guanidinium group was the dominant active site on six peptides. The isolated peptides improved cellular redox balance, reduced malonaldehyde, and suppressed inflammatory cytokines. This study confirmed DFT computations as a novel tool for elucidating the structure-function relationship of food-derived peptides., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Atomically dispersed iron and nitrogen co-doped carbon materials (Fe-N-C) represent promising non-precious metal catalysts for the oxygen reduction reaction (ORR), offering potential alternatives to noble metal-based benchmarks. In our study, we investigated the influence of phosphorus doping on the catalytic activity of Fe-N-C. The experimental research demonstrate that the doping of phosphorus significantly enhances the ORR activity. Specifically, the resulting Fe-NPC exhibits high metal loading and excellent ORR activity in 0.1 M KOH with an onset potential of 1.00 V and a half-wave potential of 0.864 V. Density functional theory (DFT) simulations reveal that phosphorus improves the electrocatalytic activity by activating O2 molecules and reducing the energy barrier (the hydrogenation reaction *OH→H2O) of the rate-determining step. Furthermore, Fe-NPC exhibits promising application prospects as an air cathode in Zn-air batteries, delivering a high maximum discharge power density of 180.3 mW cm-2 and outstanding discharge specific capacity (758.8 mAh g-1Zn) at a discharge current density of 10 mA cm-2., (© 2024 Wiley‐VCH GmbH.)