Covalent States Research Articles

Unraveling the evolution of multigap superconductivity in layered Na–B–C films: An additional energy gap induced by the internal B–C layer

Multigap superconductors provide a platform to confirm rich new physics such as time-reversal symmetry breaking, giant paramagnetic response, and hidden criticality. However, an obstacle hindering the experimental validation of these phenomena lies in the lack of superconductors with three or more gaps and critical temperatures higher than the liquid nitrogen temperature. In this work, we predicted NaB2C2 and Na2B3C3 films with high-temperature superconductivity (beyond 90 K) using the fully anisotropic Migdal-Eliashberg theory. The multigap behaviors of Na–B–C films with three and five atomic layers were analyzed in detail, revealing two typical configurations: three-gap (NaB2C2) and four-gap (Na2B3C3) superconductors. Compared with the NaB2C2 film, the additional gap observed in the Na2B3C3 film originates from the in-plane covalent state of the internal B–C layer. This research offers valuable insights into the evolution of multigap superconductivity in layered B–C films.

A trapped covalent intermediate as a key catalytic element in the hydrolysis of a GH3 β-glucosidase: An X-ray crystallographic and biochemical study

Glycoside hydrolases (GHs) are industrially important enzymes that hydrolyze glycosidic bonds in glycoconjugates. In this study, we found a GH3 β-glucosidase (CcBgl3B) from Cellulosimicrobium cellulans sp. 21 was able to selectively hydrolyze the β-1,6-glucosidic bond linked glucose of ginsenosides. X-ray crystallographic studies of the ligand complex ginsenoside-specific β-glucosidase provided a novel finding that support the catalytic mechanism of GH3. The substrate was clearly identified within the catalytic center of wild-type CcBgl3B, revealing that the C1 atom of the glucose was covalently bound to the Oδ1 group of the conserved catalytic nucleophile Asp264 as an enzyme–glycosyl intermediate. The glycosylated Asp264 could be identified by mass spectrometry. Through site-directed mutagenesis studies with Asp264, it was found that the covalent intermediate state formed by Asp264 and the substrate was critical for catalysis. In addition, Glu525 variants (E525A, E525Q and E525D) showed no or marginal activity against pNPβGlc; thus, this residue could supply a proton for the reaction. Overall, our study provides an insight into the catalytic mechanism of the GH3 enzyme CcBgl3B.

Visualizing non-adiabatic quantum dynamics and photo-excitation processes on Excel

We offer two Excel modules that students can use to view the real-time spatial evolution of a diatomic molecule's nuclei when two different potential energy curves governing the nucleus motion spatially cross one another or are coupled by a light field. Module 1 comprises three spreadsheets that can be used to view non-adiabatic nuclear dynamics on two crossing nuclear potential energy curves. These curves cross because there is a value of the spatial coordinate where the two curves have the same energy, which results in a non-zero probability of the probability density crossing from one potential curve to the other. Students can view non-adiabatic nuclear dynamics involving two unbounded nuclear potential curves, pre-dissociation with a bound “ionic state” to an unbound covalent state, and quantum tunneling dynamics between two bounded potential curves. Module 2 comprises two spreadsheets that can be used to view the dynamics of the photo-excitation process, i.e., where the absorption of light leads to transitions between two nuclear potentials. Students can model the light-induced transitions between nuclear potentials when the light is provided by both a continuous wave laser and a pulsed laser. These modules are included as the supplementary material and can be run on any computer that supports Excel.

From covalent transition states in chemistry to noncovalent in biology: from β- to Φ-value analysis of protein folding.

Solving the mechanism of a chemical reaction requires determining the structures of all the ground states on the pathway and the elusive transition states linking them. 2024 is the centenary of Brønsted's landmark paper that introduced the β-value and structure-activity studies as the only experimental means to infer the structures of transition states. It involves making systematic small changes in the covalent structure of the reactants and analysing changes in activation and equilibrium-free energies. Protein engineering was introduced for an analogous procedure, Φ-value analysis, to analyse the noncovalent interactions in proteins central to biological chemistry. The methodology was developed first by analysing noncovalent interactions in transition states in enzyme catalysis. The mature procedure was then applied to study transition states in the pathway of protein folding - 'part (b) of the protein folding problem'. This review describes the development of Φ-value analysis of transition states and compares and contrasts the interpretation of β- and Φ-values and their limitations. Φ-analysis afforded the first description of transition states in protein folding at the level of individual residues. It revealed the nucleation-condensation folding mechanism of protein domains with the transition state as an expanded, distorted native structure, containing little fully formed secondary structure but many weak tertiary interactions. A spectrum of transition states with various degrees of structural polarisation was then uncovered that spanned from nucleation-condensation to the framework mechanism of fully formed secondary structure. Φ-analysis revealed how movement of the expanded transition state on an energy landscape accommodates the transition from framework to nucleation-condensation mechanisms with a malleability of structure as a unifying feature of folding mechanisms. Such movement follows the rubric of analysis of classical covalent chemical mechanisms that began with Brønsted. Φ-values are used to benchmark computer simulation, and Φ and simulation combine to describe folding pathways at atomic resolution.

Theoretical study of inelastic processes in collisions of Y and Y+ with hydrogen atom

ABSTRACT Utilizing a simplified quantum model approach, the low-energy inelastic collision processes between yttrium atoms (ions) and hydrogen atoms have been studied. Rate coefficients corresponding to the mutual neutralization, ion-pair formation, excitation, and de-excitation processes for the above collision systems have been provided in the temperature range of 1000–10 000 K. Three ionic states and 73 covalent states are considered in calculations for the collisions of yttrium atoms with hydrogen atoms, which include six molecular symmetries and 4074 partial inelastic reaction processes. For the collisions of yttrium ions with hydrogen atoms, one ionic state and 116 covalent states are included, which are related to three molecular symmetries and 13 572 partial inelastic collision processes. It is found that the rate coefficients for the mutual neutralization process have a maximum at T = 6000 K, which is an order of magnitude higher than those of other processes. Notably, the positions of optimal windows for the collisions of yttrium atoms and ions with hydrogen atoms are found near electronic binding energy −2 eV (Y) and −4.4 eV (Y+), respectively. The scattering channels located in or near these optimal windows have intermediate-to-large rate coefficients (greater than 10−12 cm3 s−1). The reported data should be useful in the study of non-local thermodynamic equilibrium modelling.

Observation of valence electron-density distribution in covalent bond states by precise X-ray diffraction using synchrotron radiati

Observation of valence electron-density distribution in covalent bond states by precise X-ray diffraction using synchrotron radiati

Mechano-covalent protection of coagulation factor VIII by von Willebrand factor.

von Willebrand factor (VWF) is the protective carrier of procoagulant factor VIII (FVIII) in the shear forces of the circulation, prolonging its half-life and delivering it to the developing thrombus. Using force spectroscopy, VWF-FVIII complex formation is characterized by catch-bond behavior in which force first decelerates then accelerates bond dissociation. Patients with mutations in VWF at the FVIII binding site phenocopies hemophilia A and the most common mutations are of cysteine residues involving multiple disulfide bonds. From differential cysteine alkylation and mass spectrometry experiments, 13 VWF disulfide bonds at the FVIII binding site were found to exist in formed and unformed states, and binding of FVIII results in partial formation of 12 of the VWF bonds. Force spectroscopy studies indicate that the VWF-FVIII bond stiffens in response to force and this feature of the interaction is ablated when VWF disulfide bonds are prevented from forming, resulting in slip-only bond behavior. Exposure of VWF to pathological fluid shear forces exvivo and invivo causes partial cleavage of all 13 disulfide bonds, further supporting their malleable nature. These findings demonstrate that FVIII binding to VWF involves dynamic changes in the covalent states of several VWF disulfides that are required for productive interaction in physiological shear forces.

Dihydropyrene/Cyclophanediene Photoswitching Mechanism Revisited with Spin-Flip Time-Dependent Density Functional Theory: Nature of the Photoisomerization Funnel at Stake!

The complex photoisomerization mechanism of the dihydropyrene (DHP) photochromic system is revisited using spin-flip time-dependent density functional theory (SF-TD-DFT). The photoinduced ring-opening reaction of DHP into its cyclophanediene isomer involves multiple coupled electronic states of different character. A balanced treatment of both static and dynamic electron correlations is required to determine both the photophysical and photochemical paths in this system. The present results provide a refinement of the mechanistic picture provided in a previous complete active space self-consistent field plus second-order perturbation theory (CASPT2//CASSCF) study based on geometry optimizations at the CASSCF level. In particular, the nature of the conical intersection playing the central role of the photochemical funnel is different. While at the CASSCF level, the crossing with the ground state involves a covalent doubly excited state leading to a three-electron/three-center bond conical intersection, SF-TD-DFT predicts a crossing between the ground state and a zwitterionic state. These results are supported by multi-state CASPT2 calculations. This study illustrates the importance of optimizing conical intersections at a sufficiently correlated level of theory to describe a photochemical path involving crossings between covalent and ionic states.

Activity of Metal-Fluorine States upon Delithiation of Disordered Rocksalt Oxyfluorides

The capacity of transition-metal oxides as Li-ion battery cathodes is limited by instabilities that arise when high states of charge are achieved. Oxyfluorides with a disordered rocksalt structure have emerged as attractive alternatives, but the role of F in their electrochemical function, particularly when cationic redox produces high formal oxidation states, remains to be ascertained. Using X-ray absorption spectroscopy, we confirm the existence of Mn–F covalent interactions in Li2MnO2F and Li2Mn2/3Nb1/3O2F. New unoccupied states evolve from hybrid 3d-2p states of both Mn–F and Mn–O bonds when the phases are delithiated, particularly in the presence of Mn(IV). The results challenge the assumption of F as anion whose covalent states with the metal are tapped at very high potentials, providing instead a nuanced picture of redox compensation in oxyfluorides. They suggest the existence of unique knobs of design of battery cathodes by manipulating the covalent interactions between transition metals and two different anions.

Effective hopping between magnetic impurities in silicene

In this work we analyze the effects of the conduction electrons on the hopping function between two magnetic impurities located in the A sublattice in silicene placed in an external electric field. By using the Schrieffer-Wolff transformation we analyze the dependence of the effective hopping on the distance between the magnetic adatoms. By using particle number conservation, the spectrum for different occupation numbers is studied for different values of the Hubbard parameter, the electric field and the inter-impurity distance. We show that for half-filling an ionic to covalent ground state transition and viceversa can be achieved for a specific electric field strength. Finally, we explore the partition function and we study the average energy and average occupation as a function of temperature, obtaining a pattern of Mott plateaus.

Estimation of the on-site Coulomb potential and covalent state in La2CuO4 by muon spin rotation and density functional theory calculations

The on-site Coulomb potential, U, and the covalent state of electronic orbitals play key roles for the Cooper pair symmetry and exotic electromagnetic properties of high-Tc superconducting cuprates. In this paper, we demonstrate a way to determine the value of U and present the whole picture of the covalent state of Cu spins in the mother system of the La-based high-Tc superconducting cuprate, La2CuO4, by combining the muon spin rotation ({\mu}SR) and the density functional theory (DFT) calculation. We reveal local deformations of the CuO6 octahedron followed by changes in Cu-spin distributions caused by the injected muon. Adjusting the DFT and muSR results, U and the minimum charge-transfer energy between the upper Hubbard band and the O 2p band were optimized to be 4.87(4) and 1.24(1) eV, respectively.

Factors determining the band gap of a nanocrystalline multicomponent equimolar transition metal based high entropy oxide (Co,Cu,Mg,Ni,Zn)O

A recently developed transition metal based high entropy oxide (Co,Cu,Mg,Ni,Zn)O (TM-HEO) with phase-pure rocksalt structure has been shown to have potential for a wide range of applications. In this investigation, the optical band gap of the TM-HEO was studied to understand the influence of each cation by synthesising lower combination compounds by systematically eliminating Co, Cu and Zn. Compared to the other cations, Cu played a more significant role in determining the band gap. The obtained band gaps lay in the range of 1.47 to 3.38 eV, making some of the systems relevant for visible light harvesting. Further, to study the variation of the band gap with defect states and crystallite size, the TM-HEO was synthesised using three bottom-up processes. These studies revealed that the band gaps of the TM-HEOs depended on the variation of the covalent nature and oxidation states of the cations.

Low collision energy mutual neutralization reaction of He+ and H−

A Semi-classical Landau-Zener model is employed to theoretically study mutual neutralization in the collisions of 4He+ and H−/D−. The model includes ten covalent states and an ion-pair state of 2Σ+ symmetry for the HeH molecular system. Here the assumption is that only two states are interacting at a given internuclear position. In the diabatic representation, the nuclear dynamics relevant for mutual neutralization is modelled for collision energies below 100 eV. The mutual neutralization reaction cross section and final states distribution are computed and compared with previous theoretical and experimental results.

Experimental characterizations and molecular dynamics simulations of the structures of lead aluminosilicate glasses

Exploring the atomic-level structure of lead aluminosilicate glass is extremely important for improving the performance of the related products such as optical devices and semiconductor packages. In this work, we developed a set of potential parameters for the lead aluminosilicate ternary system. Raman and X-ray photoelectron spectroscopy were used to obtain structural information of the glass, and the results were compared with those of MD simulations to elucidate the structural details of a series of lead aluminosilicate glasses. It is found that both silicon and aluminum assume four-fold coordination and form the backbone of the network structures. At a low PbO content, Pb2+ plays the role of both charge compensators and network modifiers. When the PbO content exceeds 30mol%, some Pb2+ ions will be incorporated into the network that leads to rearranging of the network structures. After entering the glass network, Pb2+ ions first break the Al-O-Si linkages to form the Si-O-Pb and Al-O-Pb bonds. Then the remaining Pb2+ ions preferentially form the Pb-O-Pb bonds. It is found in the Raman spectra and X-ray photoelectron spectra that the number of lead ions in ionic state is decreasing and that in covalent state is increasing with the increase of PbO content, confirming the results from MD simulations. In addition, the network formers first shift to a high degree of polymerization and then gradually depolymerize, which is consistent with the results in MD simulations.

Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase.

β-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At the active site of HypBA1, a cysteine residue (Cys417) coordinates with a Zn2+ atom and functions as the catalytic nucleophile for the anomer-retaining hydrolytic reaction. In this study, the role of Zn2+ ion and cysteine in catalysis as well as the substrate-bound structure were studied based on biochemical and crystallographic approaches. The enzymatic activity of HypBA1 decreased after dialysis in the presence of EDTA and guanidine hydrochloride and was then recovered by the addition of Zn2+. The Michaelis complex structure was determined using a crystal of a mutant at the acid/base catalyst residue (E322Q) soaked in a solution containing the substrate p-nitrophenyl-β-l-arabinofuranoside. To investigate the covalent thioglycosyl enzyme intermediate structure, synthetic inhibitors of l-arabinofuranosyl haloacetamide derivatives with different anomer configurations were used to target the nucleophilic cysteine. In the crystal structure of HypBA1, β-configured l-arabinofuranosylamide formed a covalent link with Cys417, whereas α-configured l-arabinofuranosylamide was linked to a noncatalytic residue Cys415. Mass spectrometric analysis indicated that Cys415 was also reactive with the probe molecule. With the β-configured inhibitor, the arabinofuranoside moiety was correctly positioned at the subsite and the active site integrity was retained to successfully mimic the covalent intermediate state.

Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations.

Covalent inhibitors are assuming central importance in drug discovery projects, especially in this pandemic scenario. Many research groups have focused their attention on inhibiting viral proteases or human proteases such as cathepsin L (hCatL). The inhibition of these critical enzymes may impair viral replication. However, molecular modeling of covalent ligands is challenging since covalent and noncovalent ligand-bound states must be considered in the binding process. In this work, we evaluated the suitability of free energy perturbation (FEP) calculations as a tool for predicting the binding affinity of reversible covalent inhibitors of hCatL. Our strategy relies on the relative free energy calculated for both covalent and noncovalent complexes and the free energy changes have been compared with experimental data for eight nitrile-based inhibitors, including three new inhibitors of hCatL. Our results demonstrate that the covalent complex can be employed to properly rank the inhibitors. Nevertheless, a comparison of the free energy changes in both noncovalent and covalent states is valuable to interpret the effect triggered by the formation of the covalent bond on the interactions played by functional groups distant from the warhead. Overall, FEP can be employed as a powerful predictor tool in developing and understanding the activity of reversible covalent inhibitors.

Covalent states and spin-orbit coupling in electronic and magnetic properties of Ba6Y2Rh2Ti2O17

In $4d$ and $5d$ transition metal compounds, novel properties usually arise from the interplay of electron correlation and spin-orbit interaction based on isolated single-site physics. However, there are also a large number of compounds where the intersite effect plays an important role. Here, we report the electronic and magnetic properties of a hexagonal perovskite ${\mathrm{Ba}}_{6}{\mathrm{Y}}_{2}{\mathrm{Rh}}_{2}{\mathrm{Ti}}_{2}{\mathrm{O}}_{17}$, which is featured with widely spaced ${\mathrm{Rh}}_{2}{\mathrm{O}}_{9}$ spin dimers. Our calculations indicate that ${\mathrm{Ba}}_{6}{\mathrm{Y}}_{2}{\mathrm{Rh}}_{2}{\mathrm{Ti}}_{2}{\mathrm{O}}_{17}$ is a semiconductor with a small band gap of 0.2 eV, which is consistent with the experimental value of 0.16 eV. In particular, the band gap of ${\mathrm{Ba}}_{6}{\mathrm{Y}}_{2}{\mathrm{Rh}}_{2}{\mathrm{Ti}}_{2}{\mathrm{O}}_{17}$ is not due to the ${J}_{\mathrm{eff}}=1/2$ state from isolated single site but due to the joint effect of covalent states and spin-orbit coupling formed by Rh's ${t}_{2g}$ orbitals inside the ${\mathrm{Rh}}_{2}{\mathrm{O}}_{9}$ dimers. Furthermore, we find a giant magnetic anisotropy energy (MAE) of about 20 meV/Rh in ${\mathrm{Ba}}_{6}{\mathrm{Y}}_{2}{\mathrm{Rh}}_{2}{\mathrm{Ti}}_{2}{\mathrm{O}}_{17}$ with the easy axis being the $c$ axis. Model calculations show that the giant MAE is mainly due to first-order perturbation on the doubly degenerate antibonding states of ${e}_{g}^{\ensuremath{\pi}}$ orbitals. Our work not only reveals the interesting electronic and magnetic properties of ${\mathrm{Ba}}_{6}{\mathrm{Y}}_{2}{\mathrm{Rh}}_{2}{\mathrm{Ti}}_{2}{\mathrm{O}}_{17}$ but also could stimulate more studies on the materials with $4d$ and $5d$ spin dimers.

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Metal‐organic compounds, including molecular complexes and coordination polymers, are attractive electrode materials in supercapacitors. Those from the first transition metal series are the most studied due to their rich covalent states, light atom weight, environmental‐friendliness, non‐toxicity and low cost. Wong and co‐workers summarize the supercapacitor performance of these compounds in terms of the types of metal elements and multidentate ligands. image

Supercapacitor electrodes based on metal‐organic compounds from the first transition metal series

AbstractMetal‐organic compounds, including molecular complexes and coordination polymers, have attracted much attention as electrode materials in supercapacitors owing to their large surface area, high porosity, tailorable pore size, controllable structure, good electrochemical reversibility, and abundant active sites. Among the variety of metal‐organic compounds exhibiting desired supercapacitor performances (high specific capacitance, long cycling life, high energy density, and power density), those with metals in the first transition metal series are the most studied due to their rich covalent states, light atom weight, environmental‐friendliness, non‐toxicity, and low cost. In this review, the recent reports on the metal‐organic compounds of the first transition metal series as electrode materials in supercapacitors are summarized and their electrode and device performances are discussed in terms of different metal elements and typical multidentate ligands. Moreover, the current challenges, design strategies, future opportunities and further research directions are also highlighted for metal‐organic compounds in the field of supercapacitors.image

New Insight into the Protein‐based Cofactor of Mycobacterium tuberculosis KatG: Toward Better Understanding an Unusual Catalase Mechanism

Catalase-peroxidases (KatG) has been engineered by nature to exhibit dual functionalism of catalase and peroxidase mechanisms, serving to protect the organisms that carry it against peroxide-dependent oxidative damage. Despite bearing no resemblance to monofunctional (i.e., typical) catalases, KatGs have robust catalase activity due at least in part to a novel covalent linkage between three side chains (by Mycobacterium tuberculosis KatG [MtKatG] numbering, Met-255, Tyr-229, and Trp-107) (MYW). This MYW cofactor redox cycles between its radical (MYW•+) and fully covalent states, enabling KatG to leverage heme intermediates for catalatic O2 production. However, the molecular mechanism by which the adduct is formed and how this unique structure contributes to overall catalytic mechanism of KatG is yet to be explored. Here, optical stopped-flow spectrophotometry, rapid freeze-quench EPR spectroscopy and mutagenesis have been used to investigate the mechanism of MYW adduct formation. We have expressed and purified MtKatG lacking heme and reconstituted with the cofactor after purification. This produces KatG lacking the MYW crosslink, allowing us to monitor its formation upon reaction with peroxides. Under multiple-turnover conditions using H2O2, optical stopped-flow experiments showed an initial appearance of a high-valent ferryl-like (FeIV=O) intermediate instead of the typical FeIII-O2•- -like steady-state intermediate of KatG's catalase activity. Nevertheless, in contrast to catalase-negative canonical heme peroxidases, full catalase H2O2 decomposition did emerge, returning the enzyme to its FeIII state. EPR experiments revealed that an admixture of radical species appeared before MYW cofactor radical intermediate, suggestive of the preferred site of crosslink initiation. In addition to that, KatG variants lacking the MYW adduct (M255I, Y229F and W107F) were also constructed, expressed, purified, and reconstituted with heme. Stopped flow and UV-vis analysis of these variants showed disrupted catalase activities and incomplete catalatic turnover. These observations strongly suggest that, these distal side residues actively participate in intramolecular electron transfer, thereby fulfilling a mechanistic role in KatG catalase mechanism. Our reconstituted KatG proteins may permit investigation of radical transfer reactions leading to formation of KatG's novel MYW cofactor as well as the influence of other protein radical transfer reactions on that process.