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Laccase is an enzyme that plays an important role in fungi, including lignin degradation, stress defense, and formation of fruiting bodies. Auricularia auricula-judae is a white-rot fungus in the Basidiomycota phylum, capable of delignifying wood. In this study, seven genes belonging to the laccase family were identified through de novo sequencing, containing Cu-Oxidase, Cu-Oxidase_2, and Cu-Oxidase_3 domains. Subsequently, the physical characteristics, phylogenetic relationships, protein secondary structure, and tertiary structure of the laccase family (AaLac1–AaLac7) were analyzed. Prediction of N-glycosylation sites identified 2 to 10 sites in the laccase family, with AaLac7 having the highest number of sites at 10. Sequence alignment and analysis of the laccase family showed high consistency in signature sequences. Phylogenetic analysis confirmed the relationship among laccases within the family, with AaLac3–AaLac4 and AaLac5–AaLac6 being closely positioned on the tree, exhibiting high similarity in tertiary structure predictions. This study identified and analyzed laccase family genes in Auricularia auricula-judae using de novo sequencing, offering a simple method for identifying and analyzing the laccase family in organisms with unknown genetic information. [ABSTRACT FROM AUTHOR]

The ultrashort and intense pulses of X-rays produced at X-ray free electron lasers (XFELs) have enabled unique experiments on the atomic level structure and dynamics of matter, with time-resolved studies permitted in the femto- and attosecond regimes. To fully exploit them, it is paramount to obtain a comprehensive understanding of the complex nonlinear interactions that can occur at such extreme X-ray intensities. Herein, we report on the experimental observation of a resonant double-core excitation scheme in N2, where two 1σ core-level electrons are resonantly promoted to unoccupied 1 π g * molecular orbitals by a single few-femtosecond broad-bandwidth XFEL pulse. The production of these neutral two-site double core hole states is evidenced through their characteristic decay channels, which are observed in good agreement with high-level theoretical calculations. Such multi-core excitation schemes, benefiting from the high interaction cross sections and state- and site-selective nature of resonant X-ray interactions, should be generally accessible in XFEL irradiated molecules, and provide interesting opportunities for chemical analysis and for monitoring ultrafast dynamic processes. XFELs can drive multicore-ionization/excitation processes in the fs timescale of typical core-hole lifetimes in molecules. This paper reports experimental evidence of a single XFEL-pulse-driven resonant double-core excitation mechanism, producing a neutral two-site double-core-hole state in the nitrogen molecule. [ABSTRACT FROM AUTHOR]

Recent progress in studies of Rydberg double-well electronic energy states of MeNg (Me = 12-group atom, Ng = noble gas atom) van der Waals (vdW) molecules is presented and analysed. The presentation covers approaches in experimental studies as well as ab initio-calculations of potential energy curves (PECs). The analysis is shown in a broader context of Rydberg states of hetero- and homo-diatomic molecules with PECs possessing complex 'exotic' structure. Laser induced fluorescence (LIF) excitation spectra and dispersed emission spectra employed in the spectroscopical characterization of Rydberg states are presented on the background of the diverse spectroscopic methods for their investigations such as laser vaporization–optical resonance (LV-OR), pump-and-probe methods, and polarization labelling spectroscopy. Important and current state-of-the-art applications of Rydberg states with irregular potentials in photoassociation (PA), vibrational and rotational cooling, molecular clocks, frequency standards, and molecular wave-packet interferometry are highlighted. [ABSTRACT FROM AUTHOR]

Single-molecule magnets (SMMs) are a kind of nanosized magnetic materials that are capable of storing massive bytes of information. Strongly coupling the spin centers in a proper manner is a usual approach to promote the working temperature (or blocking temperature) for SMMs. Electron delocalized radicals have been widely employed to accomplish this job. Here, we show a new manner by using weak but multiple B–Hδ− ⋯ Dy3+ inverse hydrogen bonding (IHB) interactions to control the magnetic couplings in a series of dimeric dysprosiacaborane SMMs. This approach leads to a record high TB100s of 10 K among non-radical bridged dimeric SMMs, which is mainly ascribed to strong ferromagnetic coupling (4.38 cm−1) and the proper alignment of the magnetic principle axes of the adjacent dysprosium(III) ions. In verifying by theoretical calculations, these results demonstrate that IHB interactions can be used to construct strong axial ferromagnetic coupling and enhancing magnetic blocking temperature for SMMs. [ABSTRACT FROM AUTHOR]

During gliotoxin biosynthesis in fungi, the cytochrome P450 GliF enzyme catalyzes an unusual C–N ring-closure step while also an aromatic ring is hydroxylated in the same reaction cycle, which may have relevance to drug synthesis reactions in biotechnology. However, as the details of the reaction mechanism are still controversial, no applications have been developed yet. To resolve the mechanism of gliotoxin biosynthesis and gain insight into the steps leading to ring-closure, we ran a combination of molecular dynamics and density functional theory calculations on the structure and reactivity of P450 GliF and tested a range of possible reaction mechanisms, pathways and models. The calculations show that, rather than hydrogen atom transfer from the substrate to Compound I, an initial proton transfer transition state is followed by a fast electron transfer en route to the radical intermediate, and hence a non-synchronous hydrogen atom abstraction takes place. The radical intermediate then reacts by OH rebound to the aromatic ring to form a biradical in the substrate that, through ring-closure between the radical centers, gives gliotoxin products. Interestingly, the structure and energetics of the reaction mechanisms appear little affected by the addition of polar groups to the model and hence we predict that the reaction can be catalyzed by other P450 isozymes that also bind the same substrate. Alternative pathways, such as a pathway starting with an electrophilic attack on the arene to form an epoxide, are high in energy and are ruled out. [ABSTRACT FROM AUTHOR]

The article discusses the profound impact of advancements in computing and software on theoretical simulations, marking a transformative era in computational chemistry. Focused on theoretical coordination chemistry, it delves into the historical context and underscores the contemporary importance of computational methods. Coordination materials, involving metal atoms surrounded by ligands, are highlighted for their pivotal roles across scientific disciplines. The manipulation of ligands and metal ions within these compounds offers diverse functionalities, from catalytic modifications to enhancing oxygen transport in biological systems. The comprehensive review explores the basics of coordination materials, detailing examples across various categories. Theoretical approaches, including quantum mechanics methods like density functional theory (DFT) and Monte Carlo simulations, are thoroughly examined. The article emphasizes crystallography techniques for Metal-Organic Frameworks (MOFs) and concludes by emphasizing the exponential growth in computing power, making modeling and simulation indispensable in molecular and material research. The development of an integrated computational strategy rooted in DFT is highlighted as a crucial advancement, bridging precision and computational practicality. This holistic approach advances understanding in coordination chemistry and nanostructured materials, paving the way for innovative applications and discoveries. [ABSTRACT FROM AUTHOR]

Model Hamiltonians are regularly derived from first principles to describe correlated matter. However, the standard methods for this contain a number of largely unexplored approximations. For a strongly correlated impurity model system, here we carefully compare a standard downfolding technique with the best possible ground-truth estimates for charge-neutral excited-state energies and wave functions using state-of-the-art first-principles many-body wave function approaches. To this end, we use the vanadocene molecule and analyze all downfolding aspects, including the Hamiltonian form, target basis, double-counting correction, and Coulomb interaction screening models. We find that the choice of target-space basis functions emerges as a key factor for the quality of the downfolded results, while orbital-dependent double-counting corrections diminish the quality. Background screening of the Coulomb interaction matrix elements primarily affects crystal-field excitations. Our benchmark uncovers the relative importance of each downfolding step and offers insights into the potential accuracy of minimal downfolded model Hamiltonians. [ABSTRACT FROM AUTHOR]

Exchange underpins the magnetic properties of quantum matter. In its most basic form, it occurs through the interplay of Pauli's exclusion principle and Coulomb repulsion, being referred to as Coulomb or direct exchange. Pauli's exclusion principle combined with inter-atomic electron hopping additionally leads to kinetic exchange and superexchange. Here we disentangle the different exchange channels in anisotropic Kitaev–Heisenberg context. By quantum chemical computations, we show that anisotropic Coulomb exchange, completely neglected so far in the field, may be as large as (or even larger than) other contributions — kinetic exchange and superexchange. This opens new perspectives onto anisotropic exchange mechanisms and sets the proper conceptual framework for further research on tuning Kitaev–Heisenberg magnetism. Kitaev materials are synonymous with quantum spin liquids, where due to a mix of different exchange interactions, they can house a range of exotic magnetic phenomena. Here, using a quantum chemical computational approach, the authors demonstrate the potentially important role anisotropic Coulomb exchange plays in the magnetic interactions of different Kitaev spin liquid candidate materials. [ABSTRACT FROM AUTHOR]

Photocatalytic CH4 coupling into high-valued C2H6 is highly attractive, whereas the photosynthetic rate, especially under oxygen-free system, is still unsatisfying. Here, we designed the negatively charged metal supported on metal oxide nanosheets to activate the inert C–H bond in CH4 and hence accelerate CH4 coupling performance. As an example, the synthetic Au/ZnO porous nanosheets exhibit the C2H6 photosynthetic rate of 1,121.6 µmol gcat−1 h−1 and the CH4 conversion rate of 2,374.6 µmol gcat−1 h−1 under oxygen-free system, 2 orders of magnitude higher than those of previously reported photocatalysts. By virtue of several in situ spectroscopic techniques, it is established that the generated Auδ− and O− species together polarized the C–H bond, while the Auδ− and O− species jointly stabilized the CH3 intermediates, which favored the coupling of CH3 intermediate to photosynthesize C2H6 instead of overoxidation into COx. Thus, the design of dual active species is beneficial for achieving high-efficient CH4-to-C2H6 photoconversion. [ABSTRACT FROM AUTHOR]

Reaction mechanisms of direct conversion of methane to methanol (DCMM) catalyzed by single vacancy graphene supported single Cu atoms (Cu/C3-Gr and Cu/N3-Gr) were investigated using first principles calculations, taking N2O as the oxidant. The catalytic performance was tuned drastically by replacing three coordinated carbon atoms of active center Cu (Cu/C3-Gr) with three nitrogen atoms (Cu/N3-Gr). For Cu/N3-Gr catalyzing DCMM, a crossing between potential energy profiles of the triplet state and the singlet state occurs after transition state of C–H activation. It makes the reaction energy profile downhill and the free energy barrier of C–H activation is only 0.4 eV. The calculation results indicate that Cu/N3-Gr is likely to be an excellent catalyst for DCMM at room temperature, more superior to Cu/C3-Gr. By modulating micro-coordination environment of single atom Cu, both reactivity and selectivity of DCMM were improved remarkably. [ABSTRACT FROM AUTHOR]

After drawing comparisons between the reaction pathways of cytochrome c oxidase (CcO, Complex 4) and the preceding complex cytochrome bci (Complex 3), both being proton pumping complexes along the electron transport chain, we provide an analysis of the reaction pathways in bacterial ba3 class CcO, comparing spectroscopic results and kinetics observations with results from DFT calculations. For an important arc of the catalytic cycle in CcO, we can trace the energy pathways for the chemical protons and show how these pathways drive proton pumping of the vectorial protons. We then explore the proton loading network above the Fe heme a3-CuB catalytic center, showing how protons are loaded in and then released by combining DFT-based reaction energies with molecular dynamics simulations over states of that cycle. We also propose some additional reaction pathways for the chemical and vector protons based on our recent work with spectroscopic support. [ABSTRACT FROM AUTHOR]

Direct catalytic conversion of methane to liquid oxygenates under mild conditions remains a challenge due to high bond energy of symmetric CH4. Isolated Rh atoms were supported on hydrophobic fluorine modified TS-1 (FTS-1). Single-atom Rh on FTS-1 catalyst was characterized with Ac-HAADF/STEM and CO adsorption FTIR. The aerobic selective conversion of methane to oxygenates was carried out in a fixed bed continuous flow reactor upon co-feeding CO and H2O at 423 K under relative low pressure (42.3 kPa CH4, 21.1 kPa CO, 10.6 kPa O2, 0.476 MPa H2O). Hydrophobic Rh/FTS-1 catalyst exhibits higher activity (151.9 molproducts/(molmetalh)) than the activity (36.4 molproducts/(molmetalh)) over hydrophilic Rh-ZSM-5 (Si/Al = 15) under such reaction conditions. Hydrophobicity of different catalysts were compared by water adsorption test. The catalytic activity of F modified TS-1 supported single-atom Rh (Rh/FTS-1) is higher than that of unmodified Rh/TS-1 which is due to its higher Lewis acidity as shown by pyridine adsorption FTIR and NH3-TPD. [ABSTRACT FROM AUTHOR]

There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.', (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Revealing the origins of kinetic selectivity is one of the premier tasks of applied theoretical organic chemistry, and for many reactions, doing so involves comparing competing transition states. For some reactions, however, a single transition state leads directly to multiple products, in which case non-statistical dynamic effects influence selectivity control. The selectivity of photochemical reactions-where crossing between excited-state and ground-state surfaces occurs near ground-state transition structures that interconvert competing products-also should be controlled by the momentum of the reacting molecules as they return to the ground state in addition to the shape of the potential energy surfaces involved. Now, using machine-learning-assisted non-adiabatic molecular dynamics and multiconfiguration pair-density functional theory, these factors are examined for a classic photochemical reaction-the deazetization of 2,3-diazabicyclo[2.2.2]oct-2-ene-for which we demonstrate that momentum dominates the selectivity for hexadiene versus [2.2.2] bicyclohexane products., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Context: The solvation of metal ions is crucial to understanding relevant properties in physics, chemistry, or biology. Therefore, we present solvation enthalpies and solvation free energies of the ferrous ion in water and ammonia. Our results agree well with the experimental reports for the hydration free energy and hydration enthalpy. We obtained [Formula: see text] kJ mol[Formula: see text] for the hydration free energy and [Formula: see text] kJ mol[Formula: see text] for the hydration enthalpy of ferrous ion in water at room temperature. At ambient temperature, we obtained [Formula: see text] kJ mol[Formula: see text] as the [Formula: see text] ammoniation free energy and [Formula: see text] kJ mol[Formula: see text] for the ammoniation enthalpy. In addition, the free energy of solvation is deeply affected when the temperature increases. This pattern can be attributed to the rise of entropy when the temperature rises. Besides, the temperature does not affect the ammoniation enthalpies and the hydration enthalpy of the [Formula: see text] ion., Method: All the geometry optimizations are performed at the MP2 methods associated with the 6-31++g(d,p) basis set of Pople. solvated phase structures of [Formula: see text] ion in water or in ammonia are performed using the PCM model. The [Formula: see text] program suite was used to perform all the calculations. The program TEMPO was also used to evaluate the temperature sensitivity of the different obtained geometries., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)