Identification of Riluzole derivatives as novel calmodulin inhibitors with neuroprotective activity by a joint synthesis, biosensor, and computational guided strategy.

The development of new molecules for the treatment of calmodulin related cardiovascular or neurodegenerative diseases is an interesting goal. In this work, we introduce a novel strategy with four main steps: (1) chemical synthesis of target molecules, (2) Förster Resonance Energy Transfer (FRET) biosensor development and in vitro biological assay of new derivatives, (3) Cheminformatics models development and in vivo activity prediction, and (4) Docking studies. This strategy is illustrated with a case study. Firstly, a series of 4-substituted Riluzole derivatives 1-3 were synthetized through a strategy that involves the construction of the 4-bromoriluzole framework and its further functionalization via palladium catalysis or organolithium chemistry. Next, a FRET biosensor for monitoring Ca2+-dependent CaM-ligands interactions has been developed and used for the in vitro assay of Riluzole derivatives. In particular, the best inhibition (80%) was observed for 4-methoxyphenylriluzole 2b. Besides, we trained and validated a new Networks Invariant, Information Fusion, Perturbation Theory, and Machine Learning (NIFPTML) model for predicting probability profiles of in vivo biological activity parameters in different regions of the brain. Next, we used this model to predict the in vivo activity of the compounds experimentally studied in vitro. Last, docking study conducted on Riluzole and its derivatives has provided valuable insights into their binding conformations with the target protein, involving calmodulin and the SK4 channel. This new combined strategy may be useful to reduce assay costs (animals, materials, time, and human resources) in the drug discovery process of calmodulin inhibitors.

MLe-KCNQ2: An Artificial Intelligence Model for the Prognosis of Missense KCNQ2 Gene Variants.

Despite the increasing availability of genomic data and enhanced data analysis procedures, predicting the severity of associated diseases remains elusive in the absence of clinical descriptors. To address this challenge, we have focused on the KV7.2 voltage-gated potassium channel gene (KCNQ2), known for its link to developmental delays and various epilepsies, including self-limited benign familial neonatal epilepsy and epileptic encephalopathy. Genome-wide tools often exhibit a tendency to overestimate deleterious mutations, frequently overlooking tolerated variants, and lack the capacity to discriminate variant severity. This study introduces a novel approach by evaluating multiple machine learning (ML) protocols and descriptors. The combination of genomic information with a novel Variant Frequency Index (VFI) builds a robust foundation for constructing reliable gene-specific ML models. The ensemble model, MLe-KCNQ2, formed through logistic regression, support vector machine, random forest and gradient boosting algorithms, achieves specificity and sensitivity values surpassing 0.95 (AUC-ROC > 0.98). The ensemble MLe-KCNQ2 model also categorizes pathogenic mutations as benign or severe, with an area under the receiver operating characteristic curve (AUC-ROC) above 0.67. This study not only presents a transferable methodology for accurately classifying KCNQ2 missense variants, but also provides valuable insights for clinical counseling and aids in the determination of variant severity. The research context emphasizes the necessity of precise variant classification, especially for genes like KCNQ2, contributing to the broader understanding of gene-specific challenges in the field of genomic research. The MLe-KCNQ2 model stands as a promising tool for enhancing clinical decision making and prognosis in the realm of KCNQ2-related pathologies.

A Janus CrSSe monolayer with interesting ferromagnetism.

The search for intrinsic half-metallic ferromagnetic (FM) monolayers with a high Curie temperature (TC), considerable magnetic anisotropy energy (MAE), and multiferroic coupling is key for the development of ultra-compact spintronics. Here, we have identified a new stable FM Janus monolayer, the tetrahedral CrSSe, through first-principles structural search calculations, which not only exhibits very interesting magnetoelectric properties with a high TC of 790 K, a large MAE of 0.622 meV per Cr, and robust half-metallicity, but also shows obvious ferroelasticity with a modest energy barrier of 0.31 eV per atom. Additionally, there appears to be interesting multiferroic coupling between in-plane magnetization and ferroelasticity. Furthermore, by replacing the Se/S atoms in the CrSSe monolayer with S/Se atoms, we obtained two new half-metallic FM CrS2 and CrSe2 monolayers, which also exhibit excellent magnetoelectric properties. Therefore, our findings provide a pathway to design novel multiferroic materials and enrich the understanding of 2D transition metal chalcogenides.

Emergent superconductivity in TaO3 at high pressures.

Tantalum (Ta) is an interesting transition metal that exhibits superconductivity in its elemental states. Additionally, several Ta chalcogenides (S and Se) have also demonstrated superconducting properties. In this work, we propose the existence of five high-pressure metallic Ta-O compounds (e.g., TaO3, TaO2, TaO, Ta2O, and Ta3O), composed of polyhedra centered on Ta/O atoms. These compounds exhibit distinct characteristics compared to the well-known semiconducting Ta2O5. One particularly interesting finding is that TaO3 shows an estimated superconducting transition temperature (Tc) of 3.87 K at 200 GPa. This superconductivity is primarily driven by the coupling between the low-frequency phonons derived from Ta and the O 2p and Ta 5d electrons. Remarkably, its dynamically stabilized pressure can be as low as 50 GPa, resulting in an enhanced electron-phonon coupling and a higher Tc of up to 9.02 K. When compared to the superconductivity of isomorphic TaX3 (X = O, S, and Se) compounds, the highest Tc in TaO3 is associated with the highest NEF and phonon vibrational frequency. These characteristics arise from the strong electronegativity and small atomic mass of the O atom. Consequently, our findings offer valuable insights into the intrinsic physical mechanisms of high-pressure behaviors in Ta-O compounds.

Molecular dynamics simulations of the calmodulin-induced α-helix in the SK2 calcium-gated potassium ion channel.

The family of small-conductance Ca2+-activated potassium ion channels (SK channels) is composed of four members (SK1, SK2, SK3, and SK4) involved in neuron-firing regulation. The gating of these channels depends on the intracellular Ca2+ concentration, and their sensitivity to this ion is provided by calmodulin (CaM). This protein binds to a specific region in SK channels known as the calmodulin-binding domain (CaMBD), an event which is essential for their gating. While CaMBDs are typically disordered in the absence of CaM, the SK2 channel subtype displays a small prefolded α-helical region in its CaMBD even if CaM is not present. This small helix is known to turn into a full α-helix upon CaM binding, although the molecular-level details for this conversion are not fully understood yet. In this work, we offer new insights on this physiologically relevant process by means of enhanced sampling, atomistic Hamiltonian replica exchange molecular dynamics simulations, providing a more detailed understanding of CaM binding to this target. Our results show that CaM is necessary for inducing a full α-helix along the SK2 CaMBD through hydrophobic interactions with V426 and L427. However, it is also necessary that W431 does not compete for these interactions; the role of the small prefolded α-helix in the SK2 CaMBD would be to stabilize W431 so that this is the case. In conclusion, our findings provide further insight into a key interaction between CaM and SK channels that is important for channel sensitivity to Ca2+.

Intrinsic Ferromagnetism in 2D Fe2H with a High Curie Temperature.

The rational design of ferromagnetic materials is crucial for the development of spintronic devices. Using first-principles structural search calculations, we have identified 73 two-dimensional transition metal hydrides. Some of them show interesting magnetic properties, even when combined with the characteristics of the electrides. In particular, the P3̅m1 Fe2H monolayer is stabilized in a 1T-MoS2-type structure with a local magnetic moment of 3 µB per Fe atom, whose robust ferromagnetism is attributed to the exchange interaction between neighboring Fe atoms within and between sublayers, leading to a remarkably high Curie temperature of 340 K. On the other hand, it has a large magnetic anisotropic energy and spin-polarization ratio. Interestingly, the above room-temperature ferromagnetism of the Fe2H monolayer is well preserved within a biaxial strain of 5%. The structure and electron property of surface-functionalized Fe2H are also explored. All of these interesting properties make the Fe2H monolayer an attractive candidate for spintronic nanodevices.

Superconducting Li10Se electride under pressure.

Achieving a compound with interesting multiple coexisting states, such as electride, metallicity, and superconductivity, is of great interest in basic research and practical application. Pressure has become an effective way to realize high-temperature superconductivity in hydrides, whereas most electrides are semiconducting or insulating at high pressure. Here, we have applied swarm-intelligence structural search to identify a hitherto unknown C2/m Li10Se electride that is superconducting at high pressure. More interestingly, Li10Se is estimated to exhibit the highest Tc value of 16 K at 50 GPa, which is the lowest pressure among Li-based chalcogen electrides. This superconducting transition is dominated by Se-related low frequency vibration modes. The increasing electronic occupation of the Se 4d orbital and the decreasing amount of interstitial anion electrons with pressure heighten their coupling with low-frequency phonons, which is responsible for the enhancement of the Tc value. The finding of Li-based chalcogen superconducting electrides provides a reference for the realization of other superconducting electrides at lower pressures.

Do calmodulin binding IQ motifs have built-in capping domains?

Most calmodulin (CaM) targets are α-helices. It is not clear if CaM induces the adoption of an α-helix configuration to its targets or if those targets are selected as they spontaneously adopt an α-helical conformation. Other than an α-helix propensity, there is a great variety of CaM targets with little more in common. One exception to this rule is the IQ site that can be recognized in a number of targets, such as those ion channels belonging to the KCNQ family. Although there is negligible sequence similarity between the IQ motif and the docking site on SK2 channels, both adopt a similar three-dimensional disposition. The isolated SK2 target presents a pre-folded core region that becomes fully α-helical upon binding to CaM. The existence of this pre-folded state suggests the occurrence of capping within CaM targets. In this review, we examine the capping properties within the residues flanking this core domain, and relate known IQ motifs and capping.

Wide Band Gap P3S Monolayer with Anisotropic and Ultrahigh Carrier Mobility.

Phosphorene has offered an additional advantage for developing new optoelectronic devices due to its anisotropic and high carrier mobility. However, its instability in air causes a rapid degradation of the performance of the device. Thus, improving the stability of phosphorene while maintaining its original properties has become the key to the development of high-performance electronic devices. Herein, we propose that the formation of two-dimensional (2D) P-rich P-S compounds could achieve this goal. First-principles swarm-structural searches revealed two previously unkonwn P3S and P2S monolayers. The P3S monolayer, consisting of n-bicyclo-P6 units along the armchair direction, exhibits anisotropic and wide band gap characteristics. Interestingly, its carrier mobility reaches 1.11 × 104 cm2 V-1 s-1 and is much higher than in phosphorene. Its electronic band gap and optical absorption coefficients in the ultraviolet region reach 2.71 eV and 105 cm-1, respectively. Additionally, the P3S monolayer has a high structural stability and resistance to air oxidation.

Anisotropic and High-Mobility C3S Monolayer as a Photocatalyst for Water Splitting.

Taking into account the high conductivity and stability of carbon materials, such as graphene, and the strong polar covalent bonding character of main-group compounds, we explore potential 2D materials in the C-S binary system through first-principles structure search calculations. Herein, a hitherto unknown semiconducting C3S monolayer is identified, consisting of well-known n-biphenyl and S atom linked benzenes, exhibiting an obvious direction-dependent atomic arrangement. Thus, it exhibits anisotropic mechanical properties and carrier mobility. Its electron mobility reaches 2.14 × 104 cm2 V-1 s-1 in the b direction, along which n-biphenyl units are arranged, and is much higher than that in the well-used MoS2 monolayer and black phosphorus. Meanwhile, the C3S monolayer has high optical absorption coefficients (105 cm-1), high thermal and dynamical stabilities, and a moderate ability to split water. All these desirable properties make the C3S monolayer a promising candidate for applications in novel optoelectronic devices.

An epilepsy-causing mutation leads to co-translational misfolding of the Kv7.2 channel.

BACKGROUND: The amino acid sequence of proteins generally carries all the necessary information for acquisition of native conformations, but the vectorial nature of translation can additionally determine the folding outcome. Such consideration is particularly relevant in human diseases associated to inherited mutations leading to structural instability, aggregation, and degradation. Mutations in the KCNQ2 gene associated with human epilepsy have been suggested to cause misfolding of the encoded Kv7.2 channel. Although the effect on folding of mutations in some domains has been studied, little is known of the way pathogenic variants located in the calcium responsive domain (CRD) affect folding. Here, we explore how a Kv7.2 mutation (W344R) located in helix A of the CRD and associated with hereditary epilepsy interferes with channel function. RESULTS: We report that the epilepsy W344R mutation within the IQ motif of CRD decreases channel function, but contrary to other mutations at this site, it does not impair the interaction with Calmodulin (CaM) in vitro, as monitored by multiple in vitro binding assays. We find negligible impact of the mutation on the structure of the complex by molecular dynamic computations. In silico studies revealed two orientations of the side chain, which are differentially populated by WT and W344R variants. Binding to CaM is impaired when the mutated protein is produced in cellulo but not in vitro, suggesting that this mutation impedes proper folding during translation within the cell by forcing the nascent chain to follow a folding route that leads to a non-native configuration, and thereby generating non-functional ion channels that fail to traffic to proper neuronal compartments. CONCLUSIONS: Our data suggest that the key pathogenic mechanism of Kv7.2 W344R mutation involves the failure to adopt a configuration that can be recognized by CaM in vivo but not in vitro.

Ba with Unusual Oxidation States in Ba Chalcogenides under Pressure.

The preparation of compounds with novel atomic oxidation states and emergent properties is of fundamental interest in chemistry. As s-block elements, alkali-earth metals invariably show a +2 formal oxidation state at normal conditions, and among them, barium (Ba) presents the strongest chemical reactivity. Herein, we propose that novel valence states of Ba can be achieved in pressure-induced chalcogenides, where it also shows a feature of 5d-elements. First-principles swarm-intelligence structural search calculations identify three novel stoichiometric compounds: BaCh4 (Ch = O, S) containing Ba2+, Ba3Ch2 (Ch = S, Se, Te) with Ba+ and Ba2+, and Ba2Ch (Ch = Se, Te) with Ba+ cations. The pressure-induced drop of the Ba 5d level relative to Ba 6s is responsible for this unusual oxidation state. These compounds display captivating structural characters, such as Ba-centered polyhedra and chain-shaped Ch units. More interestingly still, the interaction between two Ba+ ions ensures their structural stability.

Anomalous High-Temperature Superconductivity in YH6.

Pressure-stabilized hydrides are a new rapidly growing class of high-temperature superconductors, which is believed to be described within the conventional phonon-mediated mechanism of coupling. Here, the synthesis of one of the best-known high-TC superconductors-yttrium hexahydride I m 3 ¯ m -YH6 is reported, which displays a superconducting transition at ≈224 K at 166 GPa. The extrapolated upper critical magnetic field Bc2 (0) of YH6 is surprisingly high: 116-158 T, which is 2-2.5 times larger than the calculated value. A pronounced shift of TC in yttrium deuteride YD6 with the isotope coefficient 0.4 supports the phonon-assisted superconductivity. Current-voltage measurements show that the critical current IC and its density JC may exceed 1.75 A and 3500 A mm-2 at 4 K, respectively, which is higher than that of the commercial superconductors, such as NbTi and YBCO. The results of superconducting density functional theory (SCDFT) and anharmonic calculations, together with anomalously high critical magnetic field, suggest notable departures of the superconducting properties from the conventional Migdal-Eliashberg and Bardeen-Cooper-Schrieffer theories, and presence of an additional mechanism of superconductivity.

Semiconducting MnB5monolayer as a potential photovoltaic material.

Exploring new two-dimensional (2D) materials is of great significance for both basic research and practical applications. Although boron can form various 3D and 2D allotropes due to its ease of forming multi-center bonds, the coexistence of honeycomb and kagome boron structures has never been observed in any 2D material yet. In this article we apply first-principle swarm structural searches to predict the existence of a stable MnB5structure, consisting of a sandwich of honeycomb and kagome borophenes. More interestingly, a MnB5nanosheet is a semiconductor with a band gap of 1.07 eV and a high optical absorption in a broad band, which satisfies the requirements of a very good photovoltaic material. Upon moderate strain, MnB5undergoes a conversion from an indirect to a direct band gap semiconductor. The power conversion efficiency of a heterostructure solar cell made of MnB5is up to 18%. The MnB5nanosheet shows a robust dynamical and thermal stability, stemming from the presence of intra- and interlayer multi-center σ and π bonds. These characteristics make MnB5a promising photovoltaic material.

Weyl fermions, Fermi arcs, and minority-spin carriers in ferromagnetic CoS2.

Magnetic Weyl semimetals are a newly discovered class of topological materials that may serve as a platform for exotic phenomena, such as axion insulators or the quantum anomalous Hall effect. Here, we use angle-resolved photoelectron spectroscopy and ab initio calculations to discover Weyl cones in CoS2, a ferromagnet with pyrite structure that has been long studied as a candidate for half-metallicity, which makes it an attractive material for spintronic devices. We directly observe the topological Fermi arc surface states that link the Weyl nodes, which will influence the performance of CoS2 as a spin injector by modifying its spin polarization at interfaces. In addition, we directly observe a minority-spin bulk electron pocket in the corner of the Brillouin zone, which proves that CoS2 cannot be a true half-metal.

Achieving high hydrogen evolution reaction activity of a Mo2C monolayer.

Two-dimensional Mo2C materials (1T and 2H phases) have emerged as promising electrocatalysts for the hydrogen evolution reaction (HER) due to their low cost, inherent metallicity, and high stability. Unfortunately, the catalytic activity of Mo2C is lower than that of Pt, and it needs to be substantially improved for practical applications. It is necessary and urgent to consider the effect of synergetic interactions among defects, functions, and strain on the HER activity. In this study, the geometric structures, electronic properties, and the HER activity of the Mo2C monolayer, with vacancy defects (i.e. Mo and C), oxygen functionalization, and strain, are studied by using first-principles calculations. According to our results, the combination of Mo vacancies, which can be obtained under C-rich conditions, and oxygen functionalization is the most effective way to improve the HER activity of 1T- and 2H-Mo2C. Considering the abundant active sites and optimal Gibbs free energy of hydrogen adsorption, the 1T phase we obtained shows excellent HER activity even at high H coverage and improves the utilization of active sites, for which the HER activity is comparable to that of Pt. This can be attributed to the fact that oxygen atoms gain more electrons from Mo2C, which weakens the strength of the O-H bond. Our work provides not only an opportunity to better understand the catalytic mechanism, but also a guide to achieving high HER activity of a Mo2C monolayer.

The Subchalcogenides Ir2In8Q (Q = S, Se, Te): Dirac Semimetal Candidates with Re-entrant Structural Modulation.

Subchalcogenides are uncommon compounds where the metal atoms are in unusually low formal oxidation states. They bridge the gap between intermetallics and semiconductors and can have unexpected structures and properties because of the exotic nature of their chemical bonding as they contain both metal-metal and metal-main group (e.g., halide, chalcogenide) interactions. Finding new members of this class of materials presents synthetic challenges as attempts to make them often result in phase separation into binary compounds. We overcome this difficulty by utilizing indium as a metal flux to synthesize large (millimeter scale) single crystals of novel subchalcogenide materials. Herein, we report two new compounds Ir2In8Q (Q = Se, Te) and compare their structural and electrical properties to the previously reported Ir2In8S analogue. Ir2In8Se and Ir2In8Te crystallize in the P42/mnm space group and are isostructural to Ir2In8S, but also have commensurately modulated (with q vectors q = 1/6a* + 1/6b* and q = 1/10a* + 1/10b* for Ir2In8Se and Ir2In8Te, respectively) low-temperature phase transitions, where the chalcogenide anions in the channels experience a distortion in the form of In-Q bond alternation along the ab plane. Both compounds display re-entrant structural behavior, where the supercells appear on cooling but revert to the original subcell below 100 K, suggesting competing structural and electronic interactions dictate the overall structure. Notably, these materials are topological semimetal candidates with symmetry-protected Dirac crossings near the Fermi level and exhibit high electron mobilities (∼1500 cm2 V-1 s-1 at 1.8 K) and moderate carrier concentrations (∼1020 cm-3) from charge transport measurements. This work highlights metal flux as a synthetic route to high quality single crystals of novel intermetallic subchalcogenides with Dirac semimetal behavior.

A New Three-Dimensional Subsulfide Ir2In8S with Dirac Semimetal Behavior.

Dirac and Weyl semimetals host exotic quasiparticles with unconventional transport properties, such as high magnetoresistance and carrier mobility. Recent years have witnessed a huge number of newly predicted topological semimetals from existing databases; however, experimental verification often lags behind such predictions. Common reasons are synthetic difficulties or the stability of predicted phases. Here, we report the synthesis of the type-II Dirac semimetal Ir2In8S, an air-stable compound with a new structure type. This material has two Dirac crossings in its electronic structure along the Γ-Z direction of the Brillouin zone. We further show that Ir2In8S has a high electron carrier mobility of ∼10 000 cm2/(V s) at 1.8 K and a large, nonsaturating transverse magnetoresistance of ∼6000% at 3.34 K in a 14 T applied field. Shubnikov de-Haas oscillations reveal several small Fermi pockets and the possibility of a nontrivial Berry phase. With its facile crystal growth, novel structure type, and striking electronic structure, Ir2In8S introduces a new material system to study topological semimetals and enable advances in the field of topological materials.

Predicted Pressure-Induced Superconducting Transition in Electride Li_{6}P.

Electrides are unique compounds where most of the electrons reside at interstitial regions of the crystal behaving as anions, which strongly determines its physical properties. Interestingly, the magnitude and distribution of interstitial electrons can be effectively modified either by modulating its chemical composition or external conditions (e.g., pressure). Most of the electrides under high pressure are nonmetallic, and superconducting electrides are very rare. Here we report that a pressure-induced stable Li_{6}P electride, identified by first-principles swarm structure calculations, becomes a superconductor with a predicted superconducting transition temperature T_{c} of 39.3 K, which is the highest among the already known electrides. The interstitial electrons in Li_{6}P, with dumbbell-like connected electride states, play a dominant role in the superconducting transition. Other Li-rich phosphides, Li_{5}P, Li_{11}P_{2}, Li_{15}P_{2}, and Li_{8}P, are also predicted to be superconducting electrides, but with a lower T_{c}. Superconductivity in all these compounds can be attributed to a combination of a weak electronegativity of phosphorus (P) with a strong electropositivity of lithium (Li), and opens up the interest to explore high-temperature superconductivity in similar binary compounds.

Phonon Collapse and Second-Order Phase Transition in Thermoelectric SnSe.

Since 2014 the layered semiconductor SnSe in the high-temperature Cmcm phase is known to be the most efficient intrinsic thermoelectric material. Making use of first-principles calculations we show that its vibrational and thermal transport properties are determined by huge nonperturbative anharmonic effects. We show that the transition from the Cmcm phase to the low-symmetry Pnma is a second-order phase transition driven by the collapse of a zone border phonon, whose frequency vanishes at the transition temperature. Our calculations show that the spectral function of the in-plane vibrational modes are strongly anomalous with shoulders and double-peak structures. We calculate the lattice thermal conductivity obtaining good agreement with experiments only when nonperturbative anharmonic scattering is included. Our results suggest that the good thermoelectric efficiency of SnSe is strongly affected by the nonperturbative anharmonicity.