Simulations of Excitonic Couplings in Spinach Light-Harvesting Complex II Using a More Realistic Model in the Presence of Photosystem II Core.

In this study, we employed a method for evaluating dynamic exciton couplings by using atomic transition density moments and molecular dynamics (MD) coordinates. We then applied this computational approach to investigate protein-regulated exciton couplings in spinach light-harvesting complex II (LHCII). Our findings, based on a more realistic all-atom computational model in the presence of the photosystem II (PSII) core and minor antennas, reveal distinct coupling strength patterns for the monomers in LHCII.

Quantum Mechanics/Molecular Mechanics Studies on the Excited-State Relaxation Mechanisms of Cytidine Analogues: 2'-Deoxy-5-Methylcytidine and 2'-Deoxy-5-Hydroxymethylcytidine in Aqueous Solution.

We have used the high-level QM(CASPT2//CASSCF)/MM method to investigate the excited-state properties and decay pathways of two important cytidine analogues, i.e., 2'-deoxy-5-methylcytidine (5mdCyd) and 2'-deoxy-5-hydroxymethylcytidine (5hmdCyd), in aqueous solution.

Dual-Additive Synergistic Complementation Electrolyte Engineering with "Job-Sharing" Modulation Mechanism for Long-Lifespan Zn-Iodine Batteries.

The large-scale practical application of Zn-iodine batteries (ZIBs) with environmental benignity and cost-effectiveness is hindered by the challenges of poor reversibility of Zn anode and serious polyiodide shuttling. Herein, a dual-additive synergistic complementation electrolyte engineering method is proposed to promote Zn transport, enhance Zn deposition reversibility, and improve iodine conversion kinetics by introducing lactulose and caffeine into 1 M ZnSO. It is revealed that lactulose can reduce the desolvation barrier by substituting the coordinated water of Zn ions and increase the Zn transference number by hydrogen bond-assisted SO/HO-locking.

Apatinib regulates the glycolysis of vascular endothelial cells through PI3K/AKT/PFKFB3 pathway in hepatocellular carcinoma.

Background: Hepatocellular carcinoma (HCC) is a prevalent and aggressive malignancy in the Chinese population; the severe vascularization by the tumor makes it difficult to cure. The high incidence and poor survival rates of this disease indicate the search for new therapeutic alternatives. Apatinib became a drug of choice because it inhibits tyrosine kinase activity, mainly through an effect on vascular endothelial growth factor receptor-2, thereby preventing tumor angiogenesis.

Quantum mechanics/molecular mechanics studies on mechanistic photophysics of epigenetic C5-halogenated DNA nucleosides: 2'-deoxy-5-chlorocytidine and 2'-deoxy-5-bromocytidine in aqueous solution.

In this work, we have employed the high-level QM(CASPT2//CASSCF)/MM method to study the photophysical mechanisms of two important metabolized DNA/RNA nucleoside byproducts, , 2'-deoxy-5-chlorocytidine (5CldCyd) and 2'-deoxy-5-bromocytidine (5BrdCyd), in aqueous solution. On the basis of our optimized minimum-energy structures, conical intersections, and crossing points, as well as the computed associated excited-state relaxation pathways involving the different internal conversion (IC) and intersystem crossing (ISC) processes in and between the S, T, T, and S states, we have suggested the feasible excited-state relaxation mechanisms of these two important epigenetic halogenated DNA nucleosides. The initially populated spectroscopic bright ππ* state in the Franck-Condon (FC) region is the S state both for 5CldCyd and 5BrdCyd under 295 nm irradiation.

Unidirectional Photoisomerization of the Green Fluorescent Protein Chromophore in a Reversibly Photoswitchable Fluorescent Protein rsKiiro: Insights from Quantum Mechanics/Molecular Mechanics Simulations.

In this study, a quantum mechanics/molecular mechanics (QM/MM) framework combined with the CASPT2//CASSCF approach was used to investigate the excited-state decay and isomerization of the rsKiiro green fluorescent protein (GFP) from its neutral "OFF" trans state. Upon irradiation at 400 nm, the trans conformation is initially excited to the bright S state. A rapid decay of the excited state then occurs and ultimately leads the molecule to the ground state.

Excited-State Decay and Photolysis of -Nitrophenol before Proton Transfer. I: A Theoretical Investigation in the Microsolvated Atmospheric Environment.

As a potential source of the hydroxyl (OH) radical and nitrous acid (HONO), photolysis of -nitrophenol (ONP) is of significant interest in both experimental and theoretical studies. In the atmospheric environment, the number of water molecules surrounding ONP changes with the humidity of the air, leading to an anisotropic chemical environment. This may have an impact on the photodynamics of ONP and provide a mechanism that differs from previously reported ones in the gas phase or in solution.

Excited-State Decay and Photolysis of -Nitrophenol after Proton Transfer. II: A Theoretical Investigation in the Microsolvated Atmospheric Environment.

Changes in atmospheric humidity affect the number of water molecules surrounding -nitrophenol (ONP), creating an anisotropic chemical environment. It, in turn, influences the photodynamic behaviors of ONP, differing from those observed in the gas phase and in solution. Recently, we explored the excited-state decay and the generation of the hydroxyl (OH) radical before proton transfer of ONP in the microsolvated environment using the MS-CASPT2//CASSCF approach.

Construction of Highly Accurate Machine Learning Potential Energy Surfaces for Excited-State Dynamics Simulations Based on Low-Level Data Sets.

Machine learning is capable of effectively predicting the potential energies of molecules in the presence of high-quality data sets. Its application in the construction of ground- and excited-state potential energy surfaces is attractive to accelerate nonadiabatic molecular dynamics simulations of photochemical reactions. Because of the huge computational cost of excited-state electronic structure calculations, the construction of a high-quality data set becomes a bottleneck.

[Spatio-temporal Evolution of Drought and Its Impact on Key Resources in the Important Ecological Functional Area: A Case Study in the Yellow River Basin].

This study explored the characteristics of spatial and temporal changes in drought in the Yellow River Basin from 2001 to 2020 based on TVPDI, surface runoff, vegetation net primary productivity, and grain yield data. Further, the effects of drought on water resources, grain resources, and vegetation resources were also analyzed using data spatialization methods, slope trend analysis, and Pearson correlation analysis. The results showed that:① The spatial distribution of drought in the Yellow River basin was stepped from southeast to northwest, and 60.

Multi-fidelity machine learning for predicting bandgaps of nonlinear optical crystals.

Nonlinear optical (NLO) materials are of great importance in modern optics and industry because of their intrinsic capability of wavelength conversion. Bandgap is a key property of NLO crystals. In recent years, machine learning (ML) has become a powerful tool to predict the bandgaps of compounds before synthesis.

Comparative molecular dynamics simulations provided insights into the mechanisms of cold-adaption of alginate lyases from the PL7 family.

Alginate is an important polysaccharide that is abundant in the marine environments, including the Polar Regions, and bacterial alginate lyases play key roles in its degradation. Many reported alginate lyases show characteristics of cold-adapted enzymes, including relatively low temperature optimum of activities (T) and low thermal stabilities. However, the cold-adaption mechanisms of alginate lyases remain unclear.

Annotation of 2,507 genomes.

(baker's yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Currently, a huge number of genome sequences are available at the public domain. However, these genomes are distributed at different websites and a large number of them are released without annotation information.

Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains.

Introduction: Marine microorganisms are essential in marine ecosystems and have always been of interest. Currently, most marine microbial communities are studied at the bulk scale (millimeters to centimeters), and the composition, function and underlying assembly mechanism of microbial communities at the microscale (sub-100 micrometers) are unclear.

Methods: The microbial communities on microsand grains (40-100 µm,  = 150) from marine sediment were investigated and compared with those on macrosand grains (400-1000 µm,  = 60) and bulk sediments ( = 5) using amplicon sequencing technology.

Enrichment Pretreatment Expands the Microbial Diversity Cultivated from Marine Sediments.

The majority of the microbial diversity in nature has not been recovered through cultivation. Enrichment is a classical technique widely used in the selective cultivation of specific taxa. Whether enrichment is suitable for cultivation studies that aim to recover large numbers of species remains little explored.

Quantum mechanics/molecular mechanics studies on the excited-state decay mechanisms of cytidine aza-analogues: 5-azacytidine and 2'-deoxy-5-azacytidine in aqueous solution.

The excited state properties and deactivation pathways of two DNA methylation inhibitors, , 5-azacytidine (5ACyd) and 2'-deoxy-5-azacytidine (5AdCyd) in aqueous solution, are comprehensively explored with the QM(CASPT2//CASSCF)/MM protocol. We systematically map the feasible decay mechanisms based on the obtained excited-state decay paths involving all the identified minimum-energy structures, conical intersections, and crossing points driving the different internal conversion (IC) and intersystem crossing (ISC) routes in and between the ππ*, nπ*, ππ*, nπ*, and S states. Unlike the nπ* state below the ππ* state in 5ACyd, deoxyribose group substitution at the N1 position leads to the ππ* state becoming the S state in 5AdCyd.

Improved Interfacial Ion Migration and Deposition through the Chain-Liquid Synergistic Effect by a Carboxylated Hydrogel Electrolyte for Stable Zinc Metal Anodes.

The large-scale applicability of Zn-metal anodes is severely impeded by the issues such as the dendrite growth, complicated hydrogen evolution, and uncontrollable passivation reaction. Herein, a negatively charged carboxylated double-network hydrogel electrolyte (Gelatin/Sodium alginate-acetate, denoted as Gel/SA-acetate) has been developed to stabilize the interfacial electrochemistry, which restructures a type of Zn ion solvent sheath optimized via a chain-liquid synergistic effect. New hydrogen bonds are reconstructed with water molecules by the zincophilic functional groups, and directional migration of hydrated Zn ions is therefore induced.

Understanding the Excited-State Relaxation Mechanisms of Xanthophyll Lutein by Multi-configurational Electronic Structure Calculations.

The contradictory behaviors in light harvesting and non-photochemical quenching make xanthophyll lutein the most attractive functional molecule in photosynthesis. Despite several theoretical simulations on the spectral properties and excited-state dynamics, the atomic-level photophysical mechanisms need to be further studied and established, especially for an accurate description of geometric and electronic structures of conical intersections for the lowest several electronic states of lutein. In the present work, semiempirical OM2/MRCI and multi-configurational restricted active space self-consistent field methods were performed to optimize the minima and conical intersections in and between the 1Ag, 2Ag, 1Bu, and 1Bu states.

Mechanistic photophysics of tellurium-substituted cytosine: Electronic structure calculations and nonadiabatic dynamics simulations.

Previously, the MS-CASPT2 method was performed to study the static and qualitative photophysics of tellurium-substituted cytosine (TeC). To get quantitative information, we used our recently developed QTMF-FSSH dynamics method to simulate the excited-state decay of TeC. The CASSCF method was adopted to reduce the calculation costs, which was confirmed to provide reliable structures and energies as those of MS-CASPT2.

Phosphorus-Mediated Local Charge Distribution of N-Configuration Adsorption Sites with Enhanced Zincophilicity and Hydrophilicity for High-Energy-Density Zn-Ion Hybrid Supercapacitors.

Tailor-made carbonaceous-based cathodes with zincophilicity and hydrophilicity are highly desirable for Zn-ion storage applications, but it remains a great challenge to achieve both advantages in the synthesis. In this work, a template electrospinning strategy is developed to synthesize nitrogen and phosphorous co-doped hollow porous carbon nanofibers (N, P-HPCNFs), which deliver a high capacity of 230.7 mAh g at 0.

Quantum mechanics/molecular mechanics studies on mechanistic photophysics of cytosine aza-analogues: 2,4-diamino-1,3,5-triazine and 2-amino-1,3,5-triazine in aqueous solution.

The excited-state properties and photophysics of cytosine aza-analogues, , 2,4-diamino-1,3,5-triazine (2,4-DT) and 2-amino-1,3,5-triazine (2-AT) in solution have been systematically explored using the QM(MS-CASPT2//CASSCF)/MM approach. The excited-state nonradiative relaxation mechanisms for the initially photoexcited S(ππ*) state decay back to the S state are proposed in terms of the present computed minima, surface crossings (conical intersections and singlet-triplet crossings), and excited-state decay paths in the S, S, T, T, and S states. Upon photoexcitation to the bright S(ππ*) state, 2,4-DT quickly relaxes to its S minimum and then overcomes a small energy barrier of 5.

Photoinduced boron atom insertion of benzocyclobutene forming an unprecedented fused boron heterocyclic radical.

Two novel boron heterocyclic radicals, an addition bicyclo[4.2.1]octa-1,3,5-trien-1-yl-borane radical (A) and an insertion 7-1-borolo[1,2-]borinine radical (B), were synthesized, and characterized in the reaction of atomic boron with benzocyclobutene.