2E State Research Articles

First-principles study of geometric and electronic structures, and optical transition energies of Mn4+ impurity ions: K2SiF6 as a prototype

In this study, we present the results of first-principles calculations conducted within the density functional theory to investigate the geometric and electronic structures of the ground 4A2 and excited 2E and 4T2 states, as well as the optical transition energies between these states, in the prototype system of K2SiF6:Mn4+. To achieve this, we employed a comprehensive evaluation of the five representative exchange-correlation functionals, enabling the development of a state-of-art calculation scheme that effectively describes the geometric and electronic structures of the excited 2E and 4T2 states. The calculated excitation, emission and zero-phonon line energies of the optical transitions between the ground 4A2 state and the excited 2E and 4T2 states demonstrate a better agreement with experimental results. However, we observed that the conventional and widely-used approach based on the analysis of the electronic density of states diagrams derived from the ground state calculations failed to accurately evaluate the vertical optical transition energies from the 4A2 ground state to the excited 2E and 4T2 states when compared to experimental data. The calculation technique developed in this study holds the potential for widespread application to other combinations of host materials and impurity ion, which is of great importance for future developments in the field of optical materials.

Dynamic lipid interactions in the plasma membrane Na+,K+-ATPase

The function of ion-transporting Na+,K+-ATPases depends on the surrounding lipid environment in biological membranes. Two established lipid-interaction sites A and B within the transmembrane domain have been observed to induce protein activation and stabilization, respectively. In addition, lipid-mediated inhibition has been assigned to a site C, but with the exact location not experimentally confirmed. Also, possible effects on lipid interactions by disease mutants dwelling in the membrane-protein interface remain relatively uncharacterized. We simulated human Na+,K+-ATPase α1β1FXYD homology models in E1 and E2 states in an asymmetric, multicomponent plasma membrane to determine both wild-type and disease mutant lipid-protein interactions. The simulated wild-type lipid interactions at the established sites A and B were in agreement with experimental results thereby confirming the membrane-protein model system. The less well-characterized, proposed inhibitory site C was dominated by lipids lacking inhibitory properties. Instead, two sites hosting inhibitory lipids were identified at the extracellular side and also a cytoplasmic CHL-binding site that provide putative alternative locations of Na+,K+-ATPase inhibition. Three disease mutations, Leu302Arg, Glu840Arg and Met859Arg resided in the lipid-protein interface and caused drastic changes in the lipid interactions. The simulation results show that lipid interactions to the human Na+,K+-ATPase α1β1FXYD protein in the plasma membrane are highly state-dependent and can be disturbed by disease mutations located in the lipid interface, which can open up for new venues to understand genetic disorders.

Photoluminescence properties and DFT simulations of the Cr ion-implanted (100)-oriented β-Ga2O3 single crystals

Beta-gallium oxide (β-Ga2O3) with tunable optical and electrical properties has great potential in power metal-semiconductor devices. In this work, (100)-oriented β-Ga2O3 single crystals were implanted with 190 keV Cr ions at different fluencies, and their photoluminescence, band structures, and electronic properties have been studied in detail. Our results clearly show that ion implantation-induced lattice damage could be recovered and the implanted Cr ions in (100)-oriented β-Ga2O3 can be activated to produce NIR (R-lines and broadband) emissions after the post-implantation annealing at 900 °C. Temperature-dependent photoluminescence (TDPL) measurements indicate that the increasing temperature could lead to weakness and redshifts of the R-lines emissions centered at about 692 nm, while the broadband emission centered at about 713 nm enhanced because of a higher thermal occupation at the 4T2 state than at the 2E state. Results from Density functional theory (DFT) calculations demonstrate that the Ga atom’s replacements with Cr atoms could occur at the tetrahedral or octahedral sites of the lattices, which allows the Cr atoms to be activated to act as the NIR emission centers.

Thermal Stability Improvement of Cr3+‐Activated Broadband Near‐Infrared Phosphors via State Population Optimization

AbstractTechnological progress has accelerated the researches into broadband near‐infrared (NIR) luminescent materials as next‐generation intelligent NIR light sources; however, poor thermal stability restricts the applications of NIR phosphors. Herein, new insights into Cr3+‐activated NIR phosphors with improved thermal stability are provided. The photoluminescence intensity originating from the 4T2→4A2 broadband emission of CaLu2Al4SiO12:Cr3+(CLAS:Cr) with optimal electron occupation (4T2/2E) increases up to 118% at 475 K compared with that at room temperature, which is the best for Cr3+‐activated broadband NIR phosphor. Accordingly, new ideas for the design of thermally stable phosphors are proposed by optimizing the thermal population between4T2and2E states and electron migration from2E to4T2state. Finally, multifunctional applications of CLAS:Cr in NIR fluorescence intensity ratio thermometry, X‐ray detection, NIR phosphor‐converted light‐emitting diodes, and bio‐imaging are demonstrated.

Structures of the human Wilson disease copper transporter ATP7B

The P-type ATPase ATP7B exports cytosolic copper and plays an essential role in the regulation of cellular copper homeostasis. Mutants of ATP7B cause Wilson disease (WD), an autosomal recessive disorder of copper metabolism. Here, we present cryoelectron microscopy (cryo-EM) structures of human ATP7B in the E1 state in the apo, the putative copper-bound, and the putative cisplatin-bound forms. In ATP7B, the N-terminal sixth metal-binding domain (MBD6) binds at the cytosolic copper entry site of the transmembrane domain (TMD), facilitating the delivery of copper from the MBD6 to the TMD. The sulfur-containing residues in the TMD of ATP7B mark the copper transport pathway. By comparing structures of the E1 state human ATP7B and E2-Pi state frog ATP7B, we propose the ATP-driving copper transport model of ATP7B. These structures not only advance our understanding of the mechanisms of ATP7B-mediated copper export but can also guide the development of therapeutics for the treatment of WD.

Comparison of Performance between Single- and Multiparameter Luminescence Thermometry Methods Based on the Mn5+ Near-Infrared Emission.

Herein, we investigate the performance of single- and multiparametric luminescence thermometry founded on the temperature-dependent spectral features of Ca6BaP4O17:Mn5+ near-infrared emission. The material was prepared by a conventional steady-state synthesis, and its photoluminescence emission was measured from 7500 to 10,000 cm-1 over the 293-373 K temperature range in 5 K increments. The spectra are composed of the emissions from 1E → 3A2 and 3T2 → 3A2 electronic transitions and Stokes and anti-Stokes vibronic sidebands at 320 cm-1 and 800 cm-1 from the maximum of 1E → 3A2 emission. Upon temperature increase, the 3T2 and Stokes bands gained in intensity while the maximum of 1E emission band is redshifted. We introduced the procedure for the linearization and feature scaling of input variables for linear multiparametric regression. Then, we experimentally determined accuracies and precisions of the luminescence thermometry based on luminescence intensity ratios between emissions from the 1E and 3T2 states, between Stokes and anti-Stokes emission sidebands, and at the 1E energy maximum. The multiparametric luminescence thermometry involving the same spectral features showed similar performance, comparable to the best single-parameter thermometry.

Structural and Functional Diversity of Two ATP-Driven Plant Proton Pumps.

Two ATP-dependent proton pumps function in plant cells. Plasma membrane H+-ATPase (PM H+-ATPase) transfers protons from the cytoplasm to the apoplast, while vacuolar H+-ATPase (V-ATPase), located in tonoplasts and other endomembranes, is responsible for proton pumping into the organelle lumen. Both enzymes belong to two different families of proteins and, therefore, differ significantly in their structure and mechanism of action. The plasma membrane H+-ATPase is a member of the P-ATPases that undergo conformational changes, associated with two distinct E1 and E2 states, and autophosphorylation during the catalytic cycle. The vacuolar H+-ATPase represents rotary enzymes functioning as a molecular motor. The plant V-ATPase consists of thirteen different subunits organized into two subcomplexes, the peripheral V1 and the membrane-embedded V0, in which the stator and rotor parts have been distinguished. In contrast, the plant plasma membrane proton pump is a functional single polypeptide chain. However, when the enzyme is active, it transforms into a large twelve-protein complex of six H+-ATPase molecules and six 14-3-3 proteins. Despite these differences, both proton pumps can be regulated by the same mechanisms (such as reversible phosphorylation) and, in some processes, such as cytosolic pH regulation, may act in a coordinated way.

Dissecting movement of the transmembrane segments of non-gastric proton pump mutants with voltage-clamp fluorometry.

The Na+,K+-ATPase (NKA) extrudes 3 Na+ and imports 2 K+ across the plasmalemma of every animal cell. The non-gastric H+,K+- ATPase (ngHKA) exports one H+ and imports one K+ in the apical membrane of several epithelia. Both P-type pumps have ∼65% identity and nearly identical catalytic cycles driven by binding of different ions to two major conformations (E1, high affinity for Na+ or H+ and E2 higher affinity for K+). Recently, we reported the structures of the wild type (WT) ngHKA and its electrogenic mutant K794A and the NKA-like K794S/A797P/W940/R949C (SPWC) mutant, in the K+-occluded E2 state. We also reported SPWC's AMPCP-bound E1 Cryo-EM structure, which is nearly identical to that of the E1(3Na+) NKA. We obtained the WT (Na+ and AlF-ADP) and K794A (Na+ and AMPPCP) structures. While the WT structure was identical to E2P state, the AMPPCP-bound K794A structure with (presumably) 2 Na+ bound has a mixed conformation. The P and N domains as well as cytoplasmic portion of transmembrane segment TM4 shows E1-like conformation, but the A domain, TM1-TM3 and the luminal portion of TM4 took an E2-like conformation. To evaluate displacements of the moving TM segments in all three constructs, we introduced a single Cys residue in the loops between TM1-TM2, TM3-4, or TM5-6, labeled them with tetramethylrhodamine maleimide (TMRM) and evaluated currents and fluorescence changes under voltage clamp fluorometry in Xenopus oocytes. Consistent with the stable E2 state in WT, a TMRM introduced in TM1-TM2 showed minimal voltage dependent changes in fluorescence, while the voltage dependence of the TM1-TM2 fluorescent signals observed with K794A and SPWC mutants were progressively closer to signals observed in NKA. Studies with TMRM introduced at TM3-4 and TM5-6 positions are underway. Funded by NSF MCB-2003251.

Green two-step oxidation for efficient utilization of Huolinhe lignite under the vision of carbon neutrality

To realize carbon neutrality in energy transition process, a two-step oxidation of Huolinhe lignite (HL) with less CO2 emissions is proposed, including pretreatment with H2O2 (PT) or pretreatment with Fenton’s reagent (PTF) and further oxidation in aqueous sodium hypochlorite (ASHC). The results indicate that the insoluble macromolecular moieties in HL are mainly oxidized into alkanedioic acids (ADAs) and non-substituted benzenecarboxylic acids (NSBCAs) and the yield of soluble portion is elevated by PTF from 60.56 % to 74.99 %. The increase in the ADA carbon number indicates that PT and PTF could enhance the oxidation ability of ASHC to break bridged linkages with longer chains. As for NSBCAs, the carboxylic group number (CGN) ranges from 2 to 5 in E1 and 2 to 6 in E2 and E3, respectively. The absence of mellitic acid in E1 states the limited oxidation capacity of ASHC to degrade highly condensed aromatic rings, which could be improved by PT and PTF. Moreover, the highest yield of NSBCAs is achieved at CGN = 2 in E2 and CGN = 4 in E3, implying that PTF is more effective to destruct highly condensed aromatic species in HL. According to the characterizations of coal samples, PT could increase the volatile matter and oxygen contents of HL and create new micropores to corrode HL viaOH attack, which would be enhanced by the introduction of Fe2+ during PTF to break weak covalent bonds, resulting in the preliminary degradation of macromolecular networks in HL. Then, cleavage of strong bonds undergoes easily via the attack of O2− generated from ASHC, leading to the deep decomposition of macromolecular moieties in HL.

Phonon assisted charge transfer in complexes of Zn(II) and Cd(II) with 2-acetylpyridine-aminoguanidine

Metal complexes with some Schiff bases, as one of the most widely used groups of ligands, have a wide field of application. In order to find a material with the required optical properties, it is very important to examine the material characteristics as a function of the type of chelating ligand, metal, and the ions present as coligands. In this paper, the synthesis of two new complexes of 2-acetylpyridine-aminoguanidine (L) with zinc(II) and cadmium(II), viz. [Zn(L)(NCO)2] and [{Cd(L)Cl(μ-NCO)}2] is described. Their structural characterization was provided by using SC-XRD. Spectroscopic characterization of these two new complexes and two previously synthesized complexes - [Zn(L)(NSC)2] and [Cd(L)Cl2] are performed. Their phonon structure was determined based on the IR transmission and Raman spectra. The range of Raman modes with significantly increased intensities was registered (1000-1700 cm−1), the same range for all four samples. Also, the registered photoluminescence and energy transfers were analyzed and three photoluminescence peaks (E1, E2, E3) were determined. It was concluded that phonons with significantly increased intensities participate in transitions from the E1 state to the energy levels in the range from E2 to E3. The strength of the peaks was significantly affected by replacing one [Cl]- with the [NCO]- ligand. The addition of the second [NCO]- ligand increases the photoluminescence over the entire measured range. The analysis performed helps to understand the issues related to the electron-phonon interaction. Also, the perspectives for the application of metal complexes with various ligands are expanding.

Can the E1 state in nitrogenase tell if there is an activation process prior to catalysis?

Model calculations have been performed for the singly reduced ground state of Mo-nitrogenase, usually termed E1. Contradictory conclusions have been reached in two recent experimental studies. In a study based on EPR, it was concluded that there is a bridging hydride in E1, while in an X-ray study it was concluded that there is no hydride in E1. Therefore, the EPR study implies that there is an oxidation of the cofactor going from E0 to E1, the X-ray study implies a reduction. DFT methods have here been used, which have previously been benchmarked on a set of redox enzymes that led to the conclusion that the accuracy is about 3 kcal mol-1 in all cases, even for redox transitions. The methodology should therefore be adequate for resolving the question of the hydride presence in E1. As a comparison, calculations are performed on both Mo- and V-nitrogenase with the same conclusion. The conclusion from the calculations has far reaching consequences for the mechanism of nitrogenase.

Temperature invariant lifetime based luminescent manometer on Mn4+ ions

Lifetime of the 2E state of Mn4+ can be used as an efficient manometric parameter.

The E3 state of FeMoco: one hydride, two hydrides or dihydrogen?

Hydrides are present in the reduced states of the iron-molybdenum cofactor (FeMoco) of Mo nitrogenase and are believed to play a key mechanistic role in the dinitrogen reduction reaction catalyzed by the enzyme. Two hydrides are present in the E4 state according to 1H ENDOR and there is likely a single hydride in the E2 redox state. The 2-hydride E4 state has been experimentally observed to bind N2 and it has been speculated that E3 may bind N2 as well. However, the E3 state has not been directly observed and very little is known about its molecular and electronic structure or reactivity. In recent computational studies, we have explored the energy surfaces of the E2 and E4 by QM/MM modelling, and found that the most stable hydride isomers contain bridging or partially bridging hydrides with an open protonated belt sulfide-bridge. In this work we systematically explore the energy surface of the E3 redox state, comparing single hydride and two-hydride isomers with varying coordination and bridging vs. terminal sulfhydryl groups. We also include a model featuring a triply protonated carbide. The results are only mildly dependent on the QM-region size. The three most stable E3 isomers at the r2SCAN level of theory have in common: an open belt sulfide-bridge (terminal sulfhydryl group on Fe6) and either 2 bridging hydrides (between Fe2 and Fe6), 1 bridging-1-terminal hydride (around Fe2 and Fe6) or a dihydrogen ligand bound at the Fe2 site. Analyzing the functional dependency of the results, we find that functionals previously found to predict accurate structures of spin-coupled Fe/Mo dimers and FeMoco (TPSSh, B97-D3, r2SCAN, and B3LYP*) are in generally good agreement about the stability of these 3 E3 isomers. However, B3LYP*, similar to its parent B3LYP method, predicts a triply protonated carbide isomer as the most stable isomer, an unlikely scenario in view of the lack of experimental evidence for carbide protonation occurring in reduced FeMoco states. Distinguishing further between the 3 hydride isomers is difficult and this flexible coordination nature of hydrides suggests that multiple hydride isomers could be present during experimental conditions. N2 binding was explored and resulted in geometries with 2 bridging hydrides and N2 bound to either Fe2 or Fe6 with a local low-spin state on the Fe. N2 binding is predicted to be mildly endothermic, similar to the E2 state, and it seems unlikely that the E3 state is capable of binding N2.

A Sufficient Condition for Extinction and Stability of a Stochastic SIS Model With Random Perturbation

The system dynamics of the randomly perturbed SIS depend on a certain threshold RS. If RS < 1, the disease is removed from our community, whereas an epidemic will occur if RS > 1. However, what happens when RS = 1? In this paper, we give a solution to this problem. Furthermore, we make some improvements to the free disease equilibrium state E0 when RS < 1. Last, we give some computational simulations to explain our results.

Dynamics of a Hybrid HIV/AIDS Model with Age-Structured, Self-Protection and Media Coverage

Taking into account the effects of the heterogeneity of the population and media coverage on disease transmission, in this paper, a hybrid HIV/AIDS model with age-structure, self-protection awareness and media coverage is formulated, which is made up of five partial differential equations (PDEs) and one ordinary differential equation (ODE). We establish the existence of the solution associated with the hybrid system and prove that the solution is unique, bounded and positive utilizing the semigroup approach. Based on the basic reproduction number R0, the threshold dynamics of this model are rigorously investigated, that is, there always is a unique disease-free steady state E0 and it is globally stable when R0<1, that is, the disease dies out. Further, there exists a unique endemic steady state E* and it is locally stable when R0>1 and some additional technical conditions are met. In addition, the uniform persistence of this hybrid system is demonstrated for R0>1, which means that the disease remains at the endemic level for a long time, which is not discussed in other age-structured infectious disease articles. Numerical simulations are also given to explain the main theoretical results, which suggest that age variability is a non-negligible factor in HIV/AIDS transmission, that is, the moment and scale of HIV/AIDS outbreaks are diverse for people of different ages, and media coverage can encourage people to take steps to avoid potential infection and control the spread of the disease.

QM/MM Study of Partial Dissociation of S2B for the E2 Intermediate of Nitrogenase.

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available for all lifeforms. Previous computational studies have given widely diverging results regarding the reaction mechanism of the enzyme. For example, some recent studies have suggested that one of the μ2-bridging sulfide ligands (S2B) may dissociate from one of the Fe ions when protonated in the doubly reduced and protonated E2 state, whereas other studies indicated that such half-dissociated states are unfavorable. We have examined how the relative energies of 26 structures of the E2 state depend on details of combined quantum mechanical and molecular mechanical (QM/MM) calculations. We show that the selection of the broken-symmetry state, the basis set, relativistic effects, the size of the QM system, relaxation of the surroundings, and the conformations of the bound protons may affect the relative energies of the various structures by up to 12, 22, 9, 20, 37, and 33 kJ/mol, respectively. However, they do not change the preferred type of structures. On the other hand, the choice of the DFT functional strongly affects the preferences. The hybrid B3LYP functional strongly prefers doubly protonation of the central carbide ion, but such a structure is not consistent with experimental EPR data. Other functionals suggest structures with a hydride ion, in agreement with the experiments, and show that the ion bridges between Fe2 and Fe6. Moreover, there are two structures of the same type that are degenerate within 1-5 kJ/mol, in agreement with the observation of two EPR signals. However, the pure generalized gradient approximation (GGA) functional TPSS favors structures with a protonated S2B also bridging Fe2 and Fe6, whereas r2SCAN (meta-GGA) and TPSSh (hybrid) prefer structures with S2B dissociated from Fe2 (but remaining bound to Fe6). The energy difference between the two types of structure is so small (7-18 kJ/mol) that both types need to be considered in future investigations of the mechanism of nitrogenase.

Structural basis of ion uptake in copper-transporting P1B-type ATPases

Copper is essential for living cells, yet toxic at elevated concentrations. Class 1B P-type (P1B-) ATPases are present in all kingdoms of life, facilitating cellular export of transition metals including copper. P-type ATPases follow an alternating access mechanism, with inward-facing E1 and outward-facing E2 conformations. Nevertheless, no structural information on E1 states is available for P1B-ATPases, hampering mechanistic understanding. Here, we present structures that reach 2.7 Å resolution of a copper-specific P1B-ATPase in an E1 conformation, with complementing data and analyses. Our efforts reveal a domain arrangement that generates space for interaction with ion donating chaperones, and suggest a direct Cu+ transfer to the transmembrane core. A methionine serves a key role by assisting the release of the chaperone-bound ion and forming a cargo entry site together with the cysteines of the CPC signature motif. Collectively, the findings provide insights into P1B-mediated transport, likely applicable also to human P1B-members.

The transported cations impose differences in the thermostability of the gastric H,K-ATPase. A kinetic analysis

This work analyses the thermostability of a membrane protein, the gastric H,K-ATPase, by means of a detailed kinetic characterization of its inactivation process, which showed to exhibit first-order kinetics. We observed parallel time courses for the decrease of ATPase activity, the decrease of the autophosphorylation capacity and the loss of tertiary structure at 49 °C. Higher temperatures were required to induce a significant change in secondary structure. The correspondence between the kinetics of Trp fluorescence measured at 49 °C and the decrease of the residual activity after heating at that temperature, proves the irreversibility of the inactivation process. Inactivation proceeds at different rates in E1 or E2 conformations. The K+-induced E2 state exhibits a lower inactivation rate; the specific effect is exerted with a K0.5 similar to that found at 25 °C, providing a further inkling that K+ occlusion by the H,K-ATPase is not really favoured. Increasing [H+] from pH 8 to pH 7, which possibly shifts the protein to E1, produces a subtle destabilizing effect on the H,K-ATPase. We performed a prediction of potential intramolecular interactions and found that the differential stability between E1 and E2 may be mainly explained by the higher number of hydrophobic interactions in the α- and β-subunits of E2 conformation.

Cryo-EM structures of recombinant human sodium-potassium pump determined in three different states

Sodium-Potassium Pump (Na+/K+-ATPase, NKA) is an ion pump that generates an electrochemical gradient of sodium and potassium ions across the plasma membrane by hydrolyzing ATP. During each Post-Albers cycle, NKA exchanges three cytoplasmic sodium ions for two extracellular potassium ions through alternating changes between the E1 and E2 states. Hitherto, several steps remained unknown during the complete working cycle of NKA. Here, we report cryo-electron microscopy (cryo-EM) structures of recombinant human NKA (hNKA) in three distinct states at 2.7–3.2 Å resolution, representing the E1·3Na and E1·3Na·ATP states with cytosolic gates open and the basic E2·[2K] state, respectively. This work provides the insights into the cytoplasmic Na+ entrance pathway and the mechanism of cytoplasmic gate closure coupled with ATP hydrolysis, filling crucial gaps in the structural elucidation of the Post-Albers cycle of NKA.

Dynamics of an HTLV-I infection model with delayed CTLs immune response

This paper deals with a four dimensional mathematical model for Human T-cell leukemia virus type-I (HTLV-I) infection that includes delayed CD8+ cytotoxic T-cells (CTLs) immune response. The proposed system has three biologically feasible steady states, namely disease-free steady state, CTL-inactive steady state and an interior steady state. Our theoretical analysis demonstrates that local and global stability analysis are established by the two critical parameters R0 and R1, basic reproduction numbers due to viral infection and due to CTLs immune response, respectively. The disease-free steady state E0 is globally stable if R0≤1, and the HTLV-I infections are eliminated. The asymptotic-carrier steady state E1 is globally stable if R1≤1<R0, which indicates HTLV-I infection is chronic without persistence of CTLs immune response. The interior steady state E2 is globally asymptotic stable if R1>1, which implies that the HTLV-I infection is choric in persistence of CTLs immune response. Due to immune response delay, our proposed model undergoes a destabilization of the interior steady state leading to Hopf bifurcation and periodic oscillations. We estimate the length of time delay that preserve the stability of period-1 limit cycle. We also derived the direction and stability of Hopf bifurcation around the interior steady state by center manifold theory and normal form method. To determine the robustness of the model, we performed normalized forward sensitivity analysis with reference to R0 and R1. Our proposed model undergoes Hopf bifurcation with respect to the production rate of uninfected CD4+T cells h, removal rate of virus-specific CTLs d4, spontaneous infected CD4+T cell activation d2 and transmissibility coefficient β. Implications of our numerical illustrations to the pathogenesis of HTLV-I infection and the development of HTLV-I related HAM/TSP are explored.