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+.

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.

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.

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.

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.

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.

Two-Dimensional PC6 with Direct Band Gap and Anisotropic Carrier Mobility.

Graphene and phosphorene are two major types of atomically thin two-dimensional materials under extensive investigation. However, the zero band gap of graphene and the instability of phosphorene greatly restrict their applications. Here, we make first-principle unbiased structure search calculations to identify a new buckled graphene-like PC6 monolayer with a number of desirable functional properties. The PC6 monolayer is a direct-gap semiconductor with a band gap of 0.84 eV, and it has an extremely high intrinsic conductivity with anisotropic character (i.e., its electron mobility is 2.94 × 105 cm2 V-1 s-1 along the armchair direction, whereas the hole mobility reaches 1.64 × 105 cm2 V-1 s-1 along the zigzag direction), which is comparable to that of graphene. On the other hand, PC6 shows a high absorption coefficient (105 cm-1) in a broad band, from 300 to 2000 nm. Additionally, its direct band gap character can remain within a biaxial strain of 5%. All these appealing properties make the predicted PC6 monolayer a promising candidate for applications in electronic and photovoltaic devices.

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.

Strong Electron-Phonon and Band Structure Effects in the Optical Properties of High Pressure Metallic Hydrogen.

The recent claim of having produced metallic hydrogen in the laboratory relies on measurements of optical spectra. Here, we present first-principles calculations of the reflectivity of hydrogen between 400 and 600 GPa in the I4_{1}/amd crystal structure, the one predicted at these pressures, based on both time-dependent density functional and Eliashberg theories, thus, covering the optical properties from the infrared to the ultraviolet regimes. Our results show that atomic hydrogen displays an interband plasmon at around 6 eV that abruptly suppresses the reflectivity, while the large superconducting gap energy yields a sharp decrease of the reflectivity in the infrared region approximately at 120 meV. The experimentally estimated electronic scattering rates in the 0.7-3 eV range are in agreement with our theoretical estimations, which show that the huge electron-phonon interaction of the system dominates the electronic scattering in this energy range. The remarkable features in the optical spectra predicted here encourage extending the optical measurements to the infrared and ultraviolet regions as our results suggest optical measurements can potentially identify high-pressure phases of hydrogen.

Gold as a 6p-Element in Dense Lithium Aurides.

The negative oxidation state of gold (Au) has drawn a great attention due to its unusual valence state that induces exotic properties in its compounds, including ferroelectricity and electronic polarization. Although monatomic anionic gold (Au(-)) has been reported, a higher negative oxidation state of Au has not been observed yet. Here we propose that high pressure becomes a controllable method for preparing high negative oxidation state of Au through its reaction with lithium. First-principles calculations in combination with swarm structural searches disclosed chemical reactions between Au and Li at high pressure, where stable Li-rich aurides with unexpected stoichiometries (e.g., Li4Au and Li5Au) emerge. These compounds exhibit intriguing structural features like Au-centered polyhedrons and a graphene-like Li sublattice, where each Au gains more than one electron donated by Li and acts as a 6p-element. The high negative oxidation state of Au has also been achieved through its reactions with other alkali metals (e.g., Cs) under pressures. Our work provides a useful strategy for achieving diverse Au anions.

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.

Exotic behavior and crystal structures of calcium under pressure.

Experimental studies established that calcium undergoes several counterintuitive transitions under pressure: fcc --> bcc --> simple cubic --> Ca-IV --> Ca-V, and becomes a good superconductor in the simple cubic and higher-pressure phases. Here, using ab initio evolutionary simulations, we explore the behavior of Ca under pressure and find a number of new phases. Our structural sequence differs from the traditional picture for Ca, but is similar to that for Sr. The beta-tin (I4(1)/amd) structure, rather than simple cubic, is predicted to be the theoretical ground state at 0 K and 33-71 GPa. This structure can be represented as a large distortion of the simple cubic structure, just as the higher-pressure phases stable between 71 and 134 GPa. The structure of Ca-V, stable above 134 GPa, is a complex host-guest structure. According to our calculations, the predicted phases are superconductors with Tc increasing under pressure and reaching approximately 20 K at 120 GPa, in good agreement with experiment.

High-pressure crystal structures and superconductivity of Stannane (SnH4).

There is great interest in the exploration of hydrogen-rich compounds upon strong compression where they can become superconductors. Stannane (SnH(4)) has been proposed to be a potential high-temperature superconductor under pressure, but its high-pressure crystal structures, fundamental for the understanding of superconductivity, remain unsolved. Using an ab initio evolutionary algorithm for crystal structure prediction, we propose the existence of two unique high-pressure metallic phases having space groups Ama2 and P6(3)/mmc, which both contain hexagonal layers of Sn atoms and semimolecular (perhydride) H(2) units. Enthalpy calculations reveal that the Ama2 and P6(3)/mmc structures are stable at 96-180 GPa and above 180 GPa, respectively, while below 96 GPa SnH(4) is unstable with respect to elemental decomposition. The application of the Allen-Dynes modified McMillan equation reveals high superconducting temperatures of 15-22 K for the Ama2 phase at 120 GPa and 52-62 K for the P6(3)/mmc phase at 200 GPa.

Spin-flip transitions induced by time-dependent electric fields in surfaces with strong spin-orbit interaction.

We present a comprehensive theoretical investigation of the light absorption rate at a Pb/Ge(111)-ß√3 × âˆš3R30° surface with strong spin-orbit coupling. Our calculations show that electron spin-flip transitions cause as much as 6% of the total light absorption, representing 1 order of magnitude enhancement over Rashba-like systems. Thus, we demonstrate that a substantial part of the light irradiating this nominally nonmagnetic surface is attenuated in spin-flip processes. Remarkably, the spin-flip transition probability is structured in well-defined hot spots within the Brillouin zone, where the electron spin experiences a sudden 90° rotation. This mechanism offers the possibility of an experimental approach to the spin-orbit phenomena by optical means.

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.

Anharmonic stabilization of the high-pressure simple cubic phase of calcium.

The phonon spectrum of the high-pressure simple cubic phase of calcium, in the harmonic approximation, shows imaginary branches that make it mechanically unstable. In this Letter, the phonon spectrum is recalculated by using density-functional theory ab initio methods fully including anharmonic effects up to fourth order at 50 GPa. Considering that the perturbation theory cannot be employed with imaginary harmonic frequencies, a variational procedure based on the Gibbs-Bogoliubov inequality is used to estimate the renormalized phonon frequencies. The results show that strong quantum anharmonic effects make the imaginary phonons become positive even at zero temperature so that the simple cubic phase becomes mechanically stable, as experiments suggest. Moreover, our calculations find a superconducting T(c) in agreement with experiments and predict an anomalous behavior of the specific heat.