The catalytic mechanism of a 𝐶𝑎+2-dependent family 92 α- mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease a- mannosidosis, has been investigated using quantum mechanics/molecular mechanics and metadynamics methods. Computational efforts show that the enzyme follows a conformational itinerary of 0S2/B2,5 → [B2,5]‡ → 1𝑆5, and the 𝐶𝑎+2 ion serves a dual purpose, as it not only distorts the sugar ring but also plays a crucial role in orchestrating the arrangement of catalytic residues. This orchestration, in turn, contributes to the facilitation of 0S2 conformers for the ensuing reaction. This mechanistic insight is well-aligned with the experimental predictions of the catalytic pathway, and the computed energies are of the same order of magnitude as the experimental estimations. Hence, our results extend the mechanistic understanding of glycosidases.

In this computational work it is shown that hydrogen clusters doped with ions, formed by molecules in the first excited rotational state (ortho-H₂), are more stable and tend to have larger coordination numbers than clusters composed by molecules in the ground rotational state (para-H₂).

Abstract

Interactions between molecular hydrogen and ions are of interest in cluster science, astrochemistry and hydrogen storage. In dynamical simulations, H₂ molecules are usually modelled as point particles, an approximation that can fail for anisotropic interactions. Here, we apply an adiabatic separation of the H₂ rotational motion to build effective pseudoatom-ion potentials and in turn study the properties of (H₂) _n Na⁺/Cl⁻ clusters. These interaction potentials are based on high-level ab initio calculations and Improved Lennard-Jones parametrizations, while the subsequent dynamics has been performed by quantum Monte Carlo calculations. By comparisons with simulations explicitly describing the molecular rotations, it is concluded that the present adiabatic model is very adequate. Interestingly, we find differences in the cluster stabilities and coordination shells depending on the spin isomer considered (para- or ortho-H₂), especially for the anionic clusters.

A methodical approach to investigate Ni@C CO₂ methanation catalysts obtained by thermal decomposition of nickel MOFs using hard X-rays is established and applied. The procedure involves high-energy-resolution X-ray absorption near-edge structure spectroscopy and X-ray emission spectroscopy in combination with ab initio FEFF calculations.

Abstract

A new approach for the characterization of CO₂ methanation catalysts prepared by thermal decomposition of a nickel MOF by hard X-ray photon-in/photon-out spectroscopy in form of high energy resolution fluorescence detected X-ray absorption near edge structure spectroscopy (HERFD-XANES) and valence-to-core X-ray emission (VtC-XES) is presented. In contrast to conventional X-ray absorption spectroscopy, the increased resolution of both methods allows a more precise phase determination of the final catalyst, which is influenced by the conditions during MOF decomposition.

MS-CASPT2//CASSCF calculations reveal detailed mechanisms for the photoisomerization of boron compounds, showing that the steric hindrance influences their photoisomerization activity.

Abstract

Boron compound BOMes₂ containing an internal B−O bond undergoes highly efficient photoisomerization, followed by sequential structural transformations, resulting in a rare eight-membered B, O-heterocycle (S. Wang, et al. Org. Lett. 2019, 21, 5285–5289). In this work, the detailed reaction mechanisms of such a unique carbonyl-supported tetracoordinate boron system in the first excited singlet (S₁) state and the ground (S₀) state were investigated by using the complete active space self-consistent field and its second-order perturbation (MS-CASPT2//CASSCF) method combined with time-dependent density functional theory (TD-DFT). Moreover, an imine-substituted tetracoordinated organic boron system (BNMes₂) was selected for comparative study to explore the intrinsic reasons for the difference in reactivity between the two types of compounds. Steric factor was found to influence the photoisomerization activity of BNMes₂ and BOMes₂. These results rationalize the experimental observations and can provide helpful insights into understanding the excited-state dynamics of heteroatom-doped tetracoordinate organoboron compounds, which facilitates the rational design of boron-based materials with superior photoresponsive performances.

Surfactants significantly influence the air-water interfacial properties, yet their connection with the surfactant molecular structure remains unclear. Combining simulations and experiments to explore the molecular arrangement of SDS and DTAB surfactants at the air-water interface reveals noteworthy findings, which offer valuable insights into the influence of surfactants on the macroscopic behaviour of aqueous foams and foaming solutions, particularly the foamability and foam stability.

Abstract

Surfactants are used to control the macroscopic properties of the air-water interface. However, the link between the surfactant molecular structure and the macroscopic properties remains unclear. Using sum-frequency generation spectroscopy and molecular dynamics simulations, two ionic surfactants (dodecyl trimethylammonium bromide, DTAB, and sodium dodecyl sulphate, SDS) with the same carbon chain lengths and charge magnitude (but different signs) of head groups interact and reorient interfacial water molecules differently. DTAB forms a thicker but sparser interfacial layer than SDS. It is due to the deep penetration into the adsorption zone of Br⁻ counterions compared to smaller Na⁺ ones, and also due to the flip-flop orientation of water molecules. SDS alters two distinctive interfacial water layers into a layer where H⁺ points to the air, forming strong hydrogen bonding with the sulphate headgroup. In contrast, only weaker dipole-dipole interactions with the DTAB headgroup are formed as they reorient water molecules with H⁺ point down to the aqueous phase. Hence, with more molecules adsorbed at the interface, SDS builds up a higher interfacial pressure than DTAB, producing lower surface tension and higher foam stability at a similar bulk concentration. Our findings offer improved knowledge for understanding various processes in the industry and nature.

B−N co-doped biphenylene is proposed as a promising metal-free cathode catalyst for Li−O₂ batteries, based on density functional theory calculations. Specially, the modeling results reveal that strengthening the Li−O bond reduces the overpotential during the discharge process, and that a moderate adsorption energy of *Li₂O₂ facilitates the charge process.

Abstract

Lithium-oxygen batteries (LOBs) meet the growing demand for long-distance transportation over electric vehicles but face challenges because of the lack of high-performance cathode catalysts. Herein, using density functional theory calculations, we report a unique graphene allotrope, biphenylene, of which the doping structures exhibit great potential as metal-free catalysts for LOBs. Our modeling results demonstrate that the biphenylene nanosheets retain metallic properties after B doping, N doping, or B−N co-doping. Compared with the pristine biphenylene, the catalytic activity of the doped biphenylene is greatly improved due to charge redistributions. Notably, the overpotentials of the B−N co-doped biphenylene are as low as 0.19 and 0.18 V for the discharge and charge processes, respectively. Based on the electronic structure and bonding analysis, we identify two factors, i. e., Li−O bond strength and *Li₂O₂ adsorption energy, that can influence the Li−O₂ electrochemical reactions. This study not only proposes a promising cathode catalyst but also provides insights into optimizing cathode catalysts for LOBs.

The formation and properties of oxygen vacancies on thin NiO_x films were investigated in situ at elevated temperatures and high oxygen pressures. Due to charge redistribution and altered bond lengths of the atoms surrounding the oxygen vacancies, they appear as distinct spectral features in O1s and O K-edge spectra, clearly distinguishable from all other peaks.

Abstract

NiO_x films on Si(111) were put in contact with oxygen at elevated temperatures. During heating and cooling in oxygen atmosphere Near Ambient Pressure (NAP)-XPS and -XAS and work function (WF) measurements reveal the creation and replenishing of oxygen vacancies in dependence of temperature. Oxygen vacancies manifest themselves as a distinct O1s feature at 528.9 eV on the low binding energy side of the main NiO peak as well as by a distinct deviation of the Ni2p_3/2 spectral features from the typical NiO spectra. DFT calculations reveal that the presence of oxygen vacancies leads to a charge redistribution and altered bond lengths of the atoms surrounding the vacancies causing the observed spectral changes. Furthermore, we observed that a broadening of the lowest energy peak in the O K-edge spectra can be attributed to oxygen vacancies. In the presence of oxygen vacancies, the WF is lowered by 0.1 eV.

In the context of the Fenton-like reaction involving cerium oxide, cubic CeO₂ primarily facilitate the decomposition of H₂O₂ into reactive oxygen species, resulting in significant damage to lung adenocarcinoma cells. In contrast, rod-like CeO₂ predominantly engage in the complexation of H₂O₂, leading to the formation of peroxides, thereby demonstrating a pronounced capability of organic dye degradation.

Abstract

As an exceptional Fenton-like reagent, cerium oxide (CeO₂) finds applications in biomedical science and organic pollutants treatment. The Fenton-like reaction catalyzed by CeO₂ typically encompasses two distinct processes: one resembling the classical Fenton reaction, wherein cerium (Ce³⁺) triggers the decomposition of hydrogen peroxide (H₂O₂) to yield reactive oxygen species (ROS), and the other involves the complexation of H₂O₂ on the Ce³⁺ surface, leading to the formation of peroxides. However, the influence of diverse CeO₂ morphologies on these two reaction pathways has not been comprehensively explored. In this study, CeO₂ exhibiting three typical morphologies, rods, cubes, and spheres, were prepared. The generation of ROS and peroxides was evaluated using the 3,3,5,5-tetramethylbenzidine (TMB) oxidation reaction and the reduction current of H₂O₂, respectively. Moreover, the impacts of pH variations and CeO₂/H₂O₂ concentrations on the production and conversion of these two reaction products were investigated. To corroborate the distinctions between the resultant products and their applicability, apoptosis assays and acid orange 7 (AO7) degradation analyses were performed. Notably, CeO₂ rods exhibited the highest proportion of Ce³⁺, predominantly engaging in complexation with H₂O₂ to foster peroxide formation, thereby facilitating the robust degradation of AO7. However, the generated peroxides appeared to occupy Ce³⁺ sites, thereby impeding the H₂O₂ decomposition process. Conversely, Ce³⁺ species on the surface of CeO₂ cubes were primarily involved in H₂O₂ decomposition, leading to heightened ROS production, and thus showcasing substantial potential for damaging A549 tumor cells. It is worth noting that the ability of these Ce³⁺ species to form peroxides through complexation with H₂O₂ was comparatively reduced. In summation, this study sheds light on the intricate interplay between distinct CeO₂ morphologies and their divergent impacts on Fenton-like reactions. These findings expand our comprehension of the influences on its reactivity of CeO₂ morphologies and open new insights for applications in diverse domains, from organic dye degradation to tumor therapy.

A systematic noncovalent interaction study of thiazole-2-ylidene derivatives with five different proton donor molecules. This computational investigation will contribute towards designing of an efficient catalyst for synthetic chemists and drug designing for medicinal chemistry.

Abstract

The importance of noncovalent interaction has gained attention in various domains covering drug and novel catalyst design. The present study mainly characterizes the role of hydrogen bond (H-bond) and other intermolecular interactions in different (1 : 1) complex analogues formed between the N-aryl-thiazol-2-ylidene (YR) and five proton donor (HX) molecules. The analysis of the singlet-triplet energy gap ( ) confirmed the stability of the singlet state for this class of N-aryl-thiazol-2-ylidenes than the triplet state. The interaction energy values of the YR-HX complexes follow the order: YR-NH₃<YR-HCN<YR-H₂O<YR-MeOH<YR-HF. In addition, substituting the H-atom of the N−H bond with bulky groups (−R) leads to an increase in the interaction energy of the YR-HX complexes. Hence, it was found that the replacement of N-atom in N-heterocyclic carbene (NHC) by S-atom forming N-aryl-thiazol-2-ylidene results in comparable intermolecular interactions with proton donor molecules similar to imidazole-2-ylidene (NHC). The current study enlightened the role of noncovalent interactions in carbene complexes with proton donor molecules. We hope that our work on carbene chemistry will pave the way for its application in the designing and synthesis of efficient catalysts.

The manufacture of alkenyl halides on a larger scale often result in the formation of a mixture of isomers each having individual significant applications while their separation from each other is a strenuous task. Since most of the conventional distillation techniques are known to be intricate, energy consuming and expensive, the quest for an alternative strategy is still continuing. In this context, recently reported trianglimine macrocycle - a new class of intrinsically porous material, is promising in discerning cis isomer from a mixture of cis and trans dichloroethene. In this work, an attempt has been made to apprehend the host-guest inclusion phenomenon accountable for the selectivity of cis over the trans isomers of 1,2-dihaloethene (F, Cl and Br) using molecular dynamics simulation and DFT calculations at ω-B97xd/6-311G+(d,p) level of theory. Our results show that trianglimine can stabilise the cis isomers of the dihaloethenes inside its cavity forming complexes with high interaction energies and the rationale behind the recyclability of the host molecule has been clarified. The outcomes of the calculations bring out the potential utility of this new host architecture to produce highly pure value added chemicals in industries.